Bioinformatics and Computational Biology
Bioinformatics and Computational Biology
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date | PubMedLink |
|---|---|---|---|---|---|---|
| Computational biology for visualization of brain structure. | Toga AW | Anatomy and embryology | 16177906 | Anat Embryol (Berl) | 2005 Dec | https://www.ncbi.nlm.nih.gov/pubmed/16177906 |
| Assessing the application of Ka/Ks ratio test to alternatively spliced exons. | Xing Y, Lee C | Bioinformatics (Oxford, England) | 16091412 | Bioinformatics | 2005 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/16091412 |
| Gender effects on cortical thickness and the influence of scaling. | Luders E, Narr KL, Thompson PM, Rex DE, Woods RP, Deluca H, Jancke L, Toga AW | Human brain mapping | 16124013 | Hum Brain Mapp | 2006 Apr | https://www.ncbi.nlm.nih.gov/pubmed/16124013 |
| Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. | Xing Y, Lee C | Proceedings of the National Academy of Sciences of the United States of America | 16157889 | Proc Natl Acad Sci U S A | 2005 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/16157889 |
| Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. | Alekseyenko AV, Kim N, Lee CJ | RNA (New York, N.Y.) | 17369312 | RNA | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17369312 |
| Direct cortical mapping via solving partial differential equations on implicit surfaces. | Shi Y, Thompson PM, Dinov I, Osher S, Toga AW | Medical image analysis | 17379568 | Med Image Anal | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17379568 |
| Genetic algorithms for finite mixture model based voxel classification in neuroimaging. | Tohka J, Krestyannikov E, Dinov ID, Graham AM, Shattuck DW, Ruotsalainen U, Toga AW | IEEE transactions on medical imaging | 17518064 | IEEE Trans Med Imaging | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17518064 |
| Brain atlases of normal and diseased populations. | Toga AW, Thompson PM | International review of neurobiology | 16387199 | Int Rev Neurobiol | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16387199 |
| Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. | Alekseyenko AV, Lee CJ | Bioinformatics (Oxford, England) | 17234640 | Bioinformatics | 2007 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/17234640 |
| Mean diffusivity: a biomarker for CSF-related disease and genetic liability effects in schizophrenia. | Narr KL, Hageman N, Woods RP, Hamilton LS, Clark K, Phillips O, Shattuck DW, Asarnow RF, Toga AW, Nuechterlein KH | Psychiatry research | 19081707 | Psychiatry Res | 2009 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/19081707 |
| Computer simulations of isolated conductors in electrostatic equilibrium. | Chang HH | Physical review. E, Statistical, nonlinear, and soft matter physics | 19113234 | Phys Rev E Stat Nonlin Soft Matter Phys | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19113234 |
| Online resource for validation of brain segmentation methods. | Shattuck DW, Prasad G, Mirza M, Narr KL, Toga AW | NeuroImage | 19073267 | Neuroimage | 2009 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/19073267 |
| Elucidating a magnetic resonance imaging-based neuroanatomic biomarker for psychosis: classification analysis using probabilistic brain atlas and machine learning algorithms. | Sun D, van Erp TG, Thompson PM, Bearden CE, Daley M, Kushan L, Hardt ME, Nuechterlein KH, Toga AW, Cannon TD | Biological psychiatry | 19729150 | Biol Psychiatry | 2009 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/19729150 |
| Localization of deformations within the amygdala in individuals with psychopathy. | Yang Y, Raine A, Narr KL, Colletti P, Toga AW | Archives of general psychiatry | 19736355 | Arch Gen Psychiatry | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19736355 |
| Identifying heritable brain phenotypes in an extended pedigree of vervet monkeys. | Fears SC, Melega WP, Service SK, Lee C, Chen K, Tu Z, Jorgensen MJ, Fairbanks LA, Cantor RM, Freimer NB, Woods RP | The Journal of neuroscience : the official journal of the Society for Neuroscience | 19261882 | J Neurosci | 2009 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/19261882 |
| The underlying anatomical correlates of long-term meditation: larger hippocampal and frontal volumes of gray matter. | Luders E, Toga AW, Lepore N, Gaser C | NeuroImage | 19280691 | Neuroimage | 2009 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/19280691 |
| Fiber tractography reveals disruption of temporal lobe white matter tracts in schizophrenia. | Phillips OR, Nuechterlein KH, Clark KA, Hamilton LS, Asarnow RF, Hageman NS, Toga AW, Narr KL | Schizophrenia research | 19028423 | Schizophr Res | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19028423 |
| Next generation sequence analysis and computational genomics using graphical pipeline workflows. | Torri F, Dinov ID, Zamanyan A, Hobel S, Genco A, Petrosyan P, Clark AP, Liu Z, Eggert P, Pierce J, Knowles JA, Ames J, Kesselman C, Toga AW, Potkin SG, Vawter MP, Macciardi F | Genes | 23139896 | Genes (Basel) | 2012 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/23139896 |
| Obstetric complications and risk for conversion to psychosis among individuals at high clinical risk. | Mittal VA, Willhite R, Daley M, Bearden CE, Niendam T, Ellman LM, Cannon TD | Early intervention in psychiatry | 22640387 | Early Interv Psychiatry | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22640387 |
| The structure of the corpus callosum in obsessive compulsive disorder. | Di Paola M, Luders E, Rubino IA, Siracusano A, Manfredi G, Girardi P, Martinotti G, Thompson PM, Chou YY, Toga AW, Caltagirone C, Spalletta G | European psychiatry : the journal of the Association of European Psychiatrists | 23078960 | Eur Psychiatry | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23078960 |
| Modeling diffusion-weighted MRI as a spatially variant gaussian mixture: application to image denoising. | Gonzalez JE, Thompson PM, Zhao A, Tu Z | Medical physics | 21859036 | Med Phys | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21859036 |
| Robust brain extraction across datasets and comparison with publicly available methods. | Iglesias JE, Liu CY, Thompson PM, Tu Z | IEEE transactions on medical imaging | 21880566 | IEEE Trans Med Imaging | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21880566 |
| Integrated, Multidisciplinary and Technology-Enhanced Science Education: The Next Frontier. | Dinov ID | Journal of online learning and teaching | 21552453 | J Online Learn Teach | 2008 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21552453 |
| Mapping corticocortical structural integrity in schizophrenia and effects of genetic liability. | Phillips OR, Nuechterlein KH, Asarnow RF, Clark KA, Cabeen R, Yang Y, Woods RP, Toga AW, Narr KL | Biological psychiatry | 21571255 | Biol Psychiatry | 2011 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/21571255 |
| fMRI of syntactic processing in typically developing children: structural correlates in the inferior frontal gyrus. | Nuñez SC, Dapretto M, Katzir T, Starr A, Bramen J, Kan E, Bookheimer S, Sowell ER | Developmental cognitive neuroscience | 21743820 | Dev Cogn Neurosci | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21743820 |
| Cortical and hippocampal atrophy in patients with autosomal dominant familial Alzheimer's disease. | Apostolova LG, Hwang KS, Medina LD, Green AE, Braskie MN, Dutton RA, Lai J, Geschwind DH, Cummings JL, Thompson PM, Ringman JM | Dementia and geriatric cognitive disorders | 21952501 | Dement Geriatr Cogn Disord | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21952501 |
| Anatomic brain asymmetry in vervet monkeys. | Fears SC, Scheibel K, Abaryan Z, Lee C, Service SK, Jorgensen MJ, Fairbanks LA, Cantor RM, Freimer NB, Woods RP | PloS one | 22205941 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22205941 |
| Enhanced brain connectivity in long-term meditation practitioners. | Luders E, Clark K, Narr KL, Toga AW | NeuroImage | 21664467 | Neuroimage | 2011 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/21664467 |
| 3D mapping of mini-mental state examination performance in clinical and preclinical Alzheimer disease. | Apostolova LG, Lu PH, Rogers S, Dutton RA, Hayashi KM, Toga AW, Cummings JL, Thompson PM | Alzheimer disease and associated disorders | 17132966 | Alzheimer Dis Assoc Disord | 2006 Oct-Dec | https://www.ncbi.nlm.nih.gov/pubmed/17132966 |
| Structural MRI and brain development. | Thompson PM, Sowell ER, Gogtay N, Giedd JN, Vidal CN, Hayashi KM, Leow A, Nicolson R, Rapoport JL, Toga AW | International review of neurobiology | 16291026 | Int Rev Neurobiol | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16291026 |
| Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene. | Wang Q, Barr I, Guo F, Lee C | RNA (New York, N.Y.) | 18974280 | RNA | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18974280 |
| Self-repelling snakes for topology-preserving segmentation models. | Le Guyader C, Vese LA | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 18390381 | IEEE Trans Image Process | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18390381 |
| Neurodevelopmental changes in verbal working memory load-dependency: an fMRI investigation. | O'Hare ED, Lu LH, Houston SM, Bookheimer SY, Sowell ER | NeuroImage | 18586110 | Neuroimage | 2008 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/18586110 |
| Relating alternative splicing to proteome complexity and genome evolution. | Xing Y, Lee C | Advances in experimental medicine and biology | 18380339 | Adv Exp Med Biol | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18380339 |
| Reduced white matter integrity in attention-deficit hyperactivity disorder. | Hamilton LS, Levitt JG, O'Neill J, Alger JR, Luders E, Phillips OR, Caplan R, Toga AW, McCracken J, Narr KL | Neuroreport | 18841089 | Neuroreport | 2008 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/18841089 |
| Decreased callosal thickness in attention-deficit/hyperactivity disorder. | Luders E, Narr KL, Hamilton LS, Phillips OR, Thompson PM, Valle JS, Del'Homme M, Strickland T, McCracken JT, Toga AW, Levitt JG | Biological psychiatry | 18842255 | Biol Psychiatry | 2009 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/18842255 |
| Brain surface contraction mapped in first-episode schizophrenia: a longitudinal magnetic resonance imaging study. | Sun D, Stuart GW, Jenkinson M, Wood SJ, McGorry PD, Velakoulis D, van Erp TG, Thompson PM, Toga AW, Smith DJ, Cannon TD, Pantelis C | Molecular psychiatry | 18607377 | Mol Psychiatry | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18607377 |
| Harmonic surface mapping with Laplace-Beltrami eigenmaps. | Shi Y, Lai R, Kern K, Sicotte N, Dinov I, Toga AW | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18982600 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18982600 |
| Ventricular enlargement and its clinical correlates in the imaging cohort from the ADCS MCI donepezil/vitamin E study. | Apostolova LG, Babakchanian S, Hwang KS, Green AE, Zlatev D, Chou YY, DeCarli C, Jack CR Jr, Petersen RC, Aisen PS, Cummings JL, Toga AW, Thompson PM | Alzheimer disease and associated disorders | 23694947 | Alzheimer Dis Assoc Disord | 2013 Apr-Jun | https://www.ncbi.nlm.nih.gov/pubmed/23694947 |
| Increased Cortical Thickness in Male-to-Female Transsexualism. | Luders E, Sánchez FJ, Tosun D, Shattuck DW, Gaser C, Vilain E, Toga AW | Journal of behavioral and brain science | 23724358 | J Behav Brain Sci | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23724358 |
| The Measurement of Local Variation in Shape. | Márquez EJ, Cabeen R, Woods RP, Houle D | Evolutionary biology | 23180896 | Evol Biol | 2012 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/23180896 |
| Adaptive reproducing kernel particle method for extraction of the cortical surface. | Xu M, Thompson PM, Toga AW | IEEE transactions on medical imaging | 16768240 | IEEE Trans Med Imaging | 2006 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16768240 |
| Normal variants of Microcephalin and ASPM do not account for brain size variability. | Woods RP, Freimer NB, De Young JA, Fears SC, Sicotte NL, Service SK, Valentino DJ, Toga AW, Mazziotta JC | Human molecular genetics | 16687438 | Hum Mol Genet | 2006 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/16687438 |
| 3D mapping of language networks in clinical and pre-clinical Alzheimer's disease. | Apostolova LG, Lu P, Rogers S, Dutton RA, Hayashi KM, Toga AW, Cummings JL, Thompson PM | Brain and language | 17485107 | Brain Lang | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17485107 |
| Cortical mapping of genotype-phenotype relationships in schizophrenia. | Bearden CE, van Erp TG, Thompson PM, Toga AW, Cannon TD | Human brain mapping | 17437284 | Hum Brain Mapp | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17437284 |
| Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. | Lee JA, Xing Y, Nguyen D, Xie J, Lee CJ, Black DL | PLoS biology | 17298178 | PLoS Biol | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17298178 |
| Automatic independent component labeling for artifact removal in fMRI. | Tohka J, Foerde K, Aron AR, Tom SM, Toga AW, Poldrack RA | NeuroImage | 18042495 | Neuroimage | 2008 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/18042495 |
| 3-D analysis of cortical morphometry in differential diagnosis of Parkinson's plus syndromes: mapping frontal lobe cortical atrophy in progressive supranuclear palsy patients. | Tosun D, Duchesne S, Rolland Y, Toga AW, Vérin M, Barillot C | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18044653 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18044653 |
| Direct mapping of hippocampal surfaces with intrinsic shape context. | Shi Y, Thompson PM, de Zubicaray GI, Rose SE, Tu Z, Dinov I, Toga AW | NeuroImage | 17625918 | Neuroimage | 2007 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/17625918 |
| Joint sulci detection using graphical models and boosted priors. | Shi Y, Tu Z, Reiss AL, Dutton RA, Lee AD, Galaburda AM, Dinov I, Thompson PM, Toga AW | Information processing in medical imaging : proceedings of the ... conference | 17633692 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633692 |
| What is where and why it is important. | Toga AW, Thompson PM | NeuroImage | 17720552 | Neuroimage | 2007 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/17720552 |
| Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization. | Kim N, Lee C | BMC bioinformatics | 17584922 | BMC Bioinformatics | 2007 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/17584922 |
| Construction of a 3D probabilistic atlas of human cortical structures. | Shattuck DW, Mirza M, Adisetiyo V, Hojatkashani C, Salamon G, Narr KL, Poldrack RA, Bilder RM, Toga AW | NeuroImage | 18037310 | Neuroimage | 2008 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/18037310 |
| Corpus callosum abnormalities in women with borderline personality disorder and comorbid attention-deficit hyperactivity disorder. | Rüsch N, Luders E, Lieb K, Zahn R, Ebert D, Thompson PM, Toga AW, van Elst LT | Journal of psychiatry & neuroscience : JPN | 18043765 | J Psychiatry Neurosci | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18043765 |
| Age effects on hippocampal structural changes in old men: the HAAS. | Xu Y, Valentino DJ, Scher AI, Dinov I, White LR, Thompson PM, Launer LJ, Toga AW | NeuroImage | 18280181 | Neuroimage | 2008 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/18280181 |
| Reduced hippocampal and parahippocampal volumes in murderers with schizophrenia. | Yang Y, Raine A, Han CB, Schug RA, Toga AW, Narr KL | Psychiatry research | 20227253 | Psychiatry Res | 2010 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/20227253 |
| LONI MiND: metadata in NIfTI for DWI. | Patel V, Dinov ID, Van Horn JD, Thompson PM, Toga AW | NeuroImage | 20206274 | Neuroimage | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20206274 |
| Sex and age differences in atrophic rates: an ADNI study with n=1368 MRI scans. | Hua X, Hibar DP, Lee S, Toga AW, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative | Neurobiology of aging | 20620666 | Neurobiol Aging | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20620666 |
| The development of the corpus callosum in the healthy human brain. | Luders E, Thompson PM, Toga AW | The Journal of neuroscience : the official journal of the Society for Neuroscience | 20720105 | J Neurosci | 2010 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/20720105 |
| Inverse-consistent surface mapping with Laplace-Beltrami eigen-features. | Shi Y, Morra JH, Thompson PM, Toga AW | Information processing in medical imaging : proceedings of the ... conference | 19694286 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694286 |
| Comparing registration methods for mapping brain change using tensor-based morphometry. | Yanovsky I, Leow AD, Lee S, Osher SJ, Thompson PM | Medical image analysis | 19631572 | Med Image Anal | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19631572 |
| Brain structure changes visualized in early- and late-onset blind subjects. | Leporé N, Voss P, Lepore F, Chou YY, Fortin M, Gougoux F, Lee AD, Brun C, Lassonde M, Madsen SK, Toga AW, Thompson PM | NeuroImage | 19643183 | Neuroimage | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19643183 |
| Callosal atrophy in mild cognitive impairment and Alzheimer's disease: different effects in different stages. | Di Paola M, Luders E, Di Iulio F, Cherubini A, Passafiume D, Thompson PM, Caltagirone C, Toga AW, Spalletta G | NeuroImage | 19643188 | Neuroimage | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19643188 |
| Cortical shape analysis in the Laplace-Beltrami feature space. | Shi Y, Dinov I, Toga AW | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426114 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426114 |
| Subregional hippocampal deformations in major depressive disorder. | Cole J, Toga AW, Hojatkashani C, Thompson P, Costafreda SG, Cleare AJ, Williams SC, Bullmore ET, Scott JL, Mitterschiffthaler MT, Walsh ND, Donaldson C, Mirza M, Marquand A, Nosarti C, McGuffin P, Fu CH | Journal of affective disorders | 20392498 | J Affect Disord | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20392498 |
| Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. | Stein JL, Hua X, Morra JH, Lee S, Hibar DP, Ho AJ, Leow AD, Toga AW, Sul JH, Kang HM, Eskin E, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen AN, Corneveaux JJ, Stephan DA, Webster J, DeChairo BM, Potkin SG, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative | NeuroImage | 20197096 | Neuroimage | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20197096 |
| Automated 3D mapping of baseline and 12-month associations between three verbal memory measures and hippocampal atrophy in 490 ADNI subjects. | Apostolova LG, Morra JH, Green AE, Hwang KS, Avedissian C, Woo E, Cummings JL, Toga AW, Jack CR Jr, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative | NeuroImage | 20083211 | Neuroimage | 2010 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/20083211 |
| Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline. | Dinov I, Lozev K, Petrosyan P, Liu Z, Eggert P, Pierce J, Zamanyan A, Chakrapani S, Van Horn J, Parker DS, Magsipoc R, Leung K, Gutman B, Woods R, Toga A | PloS one | 20927408 | PLoS One | 2010 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/20927408 |
| MRI RESOLUTION ENHANCEMENT USING TOTAL VARIATION REGULARIZATION. | Joshi SH, Marquina A, Osher SJ, Dinov I, Van Horn JD, Toga AW | Proceedings. IEEE International Symposium on Biomedical Imaging | 21113426 | Proc IEEE Int Symp Biomed Imaging | 2009 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/21113426 |
| Efficient path-based stereo matching with subpixel accuracy. | Donate A, Liu X, Collins EG | IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society | 20570775 | IEEE Trans Syst Man Cybern B Cybern | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20570775 |
| Double dissociation in the anatomy of socioemotional disinhibition and executive functioning in dementia. | Krueger CE, Laluz V, Rosen HJ, Neuhaus JM, Miller BL, Kramer JH | Neuropsychology | 21381829 | Neuropsychology | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21381829 |
| Regional brain volume reductions relate to facial dysmorphology and neurocognitive function in fetal alcohol spectrum disorders. | Roussotte FF, Sulik KK, Mattson SN, Riley EP, Jones KL, Adnams CM, May PA, O'Connor MJ, Narr KL, Sowell ER | Human brain mapping | 21416562 | Hum Brain Mapp | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21416562 |
| Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution. | Lee C, Kim N, Roy M, Graveley BR | RNA (New York, N.Y.) | 19934230 | RNA | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19934230 |
| Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. | Lu H, Lin L, Sato S, Xing Y, Lee CJ | PLoS computational biology | 20019791 | PLoS Comput Biol | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20019791 |
| TETRAHEDRAL MESH GENERATION FOR MEDICAL IMAGES WITH MULTIPLE REGIONS USING ACTIVE SURFACES. | Lederman C, Joshi A, Dinov I, Van Horn JD, Vese L, Toga A | Proceedings. IEEE International Symposium on Biomedical Imaging | 21278816 | Proc IEEE Int Symp Biomed Imaging | 2010 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/21278816 |
| The contribution of genes to cortical thickness and volume. | Joshi AA, Leporé N, Joshi SH, Lee AD, Barysheva M, Stein JL, McMahon KL, Johnson K, de Zubicaray GI, Martin NG, Wright MJ, Toga AW, Thompson PM | Neuroreport | 21233781 | Neuroreport | 2011 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/21233781 |
| A Novel Representation for Riemannian Analysis of Elastic Curves in ℝ. | Joshi SH, Klassen E, Srivastava A, Jermyn I | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 21311729 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2007 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/21311729 |
| Resting-state fMRI can reliably map neural networks in children. | Thomason ME, Dennis EL, Joshi AA, Joshi SH, Dinov ID, Chang C, Henry ML, Johnson RF, Thompson PM, Toga AW, Glover GH, Van Horn JD, Gotlib IH | NeuroImage | 21134471 | Neuroimage | 2011 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21134471 |
| Effects of ApoE4 and maternal history of dementia on hippocampal atrophy. | Andrawis JP, Hwang KS, Green AE, Kotlerman J, Elashoff D, Morra JH, Cummings JL, Toga AW, Thompson PM, Apostolova LG | Neurobiology of aging | 20833446 | Neurobiol Aging | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/20833446 |
| Developing image processing meta-algorithms with data mining of multiple metrics. | Leung K, Cunha A, Toga AW, Parker DS | Computational and mathematical methods in medicine | 24653748 | Comput Math Methods Med | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24653748 |
| Technology-enhanced Interactive Teaching of Marginal, Joint and Conditional Probabilities: The Special Case of Bivariate Normal Distribution. | Dinov ID, Kamino S, Bhakhrani B, Christou N | Teaching statistics | 25419016 | Teach Stat | 2013 Fall | https://www.ncbi.nlm.nih.gov/pubmed/25419016 |
| LANDMARK MATCHING ON THE SPHERE USING DISTANCE FUNCTIONS. | Leporé N, Leow A, Thompson P | Proceedings. IEEE International Symposium on Biomedical Imaging | 26877833 | Proc IEEE Int Symp Biomed Imaging | 2006 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26877833 |
| Human neuroimaging as a "Big Data" science. | Van Horn JD, Toga AW | Brain imaging and behavior | 24113873 | Brain Imaging Behav | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24113873 |
| Atlas-based hippocampus segmentation in Alzheimer's disease and mild cognitive impairment. | Carmichael OT, Aizenstein HA, Davis SW, Becker JT, Thompson PM, Meltzer CC, Liu Y | NeuroImage | 15990339 | Neuroimage | 2005 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/15990339 |
| Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms. | Roy M, Xu Q, Lee C | Nucleic acids research | 16147986 | Nucleic Acids Res | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16147986 |
| Brain structural mapping using a novel hybrid implicit/explicit framework based on the level-set method. | Leow A, Yu CL, Lee SJ, Huang SC, Protas H, Nicolson R, Hayashi KM, Toga AW, Thompson PM | NeuroImage | 15652325 | Neuroimage | 2005 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/15652325 |
| Automated diagnosis of brain tumours astrocytomas using probabilistic neural network clustering and support vector machines. | Glotsos D, Tohka J, Ravazoula P, Cavouras D, Nikiforidis G | International journal of neural systems | 15912578 | Int J Neural Syst | 2005 Feb-Apr | https://www.ncbi.nlm.nih.gov/pubmed/15912578 |
| Standard atlas space for C57BL/6J neonatal mouse brain. | Lee EF, Jacobs RE, Dinov I, Leow A, Toga AW | Anatomy and embryology | 16228227 | Anat Embryol (Berl) | 2005 Nov | https://www.ncbi.nlm.nih.gov/pubmed/16228227 |
| Hamilton-Jacobi skeleton on cortical surfaces. | Shi Y, Thompson PM, Dinov I, Toga AW | IEEE transactions on medical imaging | 18450539 | IEEE Trans Med Imaging | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18450539 |
| Brain anatomical structure segmentation by hybrid discriminative/generative models. | Tu Z, Narr KL, Dollar P, Dinov I, Thompson PM, Toga AW | IEEE transactions on medical imaging | 18390346 | IEEE Trans Med Imaging | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18390346 |
| Neural phenotypes of common and rare genetic variants. | Bearden CE, Glahn DC, Lee AD, Chiang MC, van Erp TG, Cannon TD, Reiss AL, Toga AW, Thompson PM | Biological psychology | 18395317 | Biol Psychol | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18395317 |
| Mapping progressive brain structural changes in early Alzheimer's disease and mild cognitive impairment. | Apostolova LG, Thompson PM | Neuropsychologia | 18395760 | Neuropsychologia | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18395760 |
| Hippocampal morphology and distinguishing late-onset from early-onset elderly depression. | Ballmaier M, Narr KL, Toga AW, Elderkin-Thompson V, Thompson PM, Hamilton L, Haroon E, Pham D, Heinz A, Kumar A | The American journal of psychiatry | 17986679 | Am J Psychiatry | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17986679 |
| Towards whole brain segmentation by a hybrid model. | Tu Z, Toga AW | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18044566 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18044566 |
| Detection and segmentation of pathological structures by the extended graph-shifts algorithm. | Corso JJ, Yuille A, Sicotte NL, Toga A | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051154 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051154 |
| Mapping brain maturation. | Toga AW, Thompson PM, Sowell ER | Trends in neurosciences | 16472876 | Trends Neurosci | 2006 Mar | https://www.ncbi.nlm.nih.gov/pubmed/16472876 |
| Lobar distribution of lesion volumes in late-life depression: the Biomedical Informatics Research Network (BIRN). | MacFall JR, Taylor WD, Rex DE, Pieper S, Payne ME, McQuoid DR, Steffens DC, Kikinis R, Toga AW, Krishnan KR | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 16341022 | Neuropsychopharmacology | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16341022 |
| Detection and mapping of hippocampal abnormalities in autism. | Nicolson R, DeVito TJ, Vidal CN, Sui Y, Hayashi KM, Drost DJ, Williamson PC, Rajakumar N, Toga AW, Thompson PM | Psychiatry research | 17056234 | Psychiatry Res | 2006 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/17056234 |
| Reduced neocortical thickness and complexity mapped in mesial temporal lobe epilepsy with hippocampal sclerosis. | Lin JJ, Salamon N, Lee AD, Dutton RA, Geaga JA, Hayashi KM, Luders E, Toga AW, Engel J Jr, Thompson PM | Cerebral cortex (New York, N.Y. : 1991) | 17088374 | Cereb Cortex | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17088374 |
| The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. | Kim N, Alekseyenko AV, Roy M, Lee C | Nucleic acids research | 17108355 | Nucleic Acids Res | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17108355 |
| Towards multimodal atlases of the human brain. | Toga AW, Thompson PM, Mori S, Amunts K, Zilles K | Nature reviews. Neuroscience | 17115077 | Nat Rev Neurosci | 2006 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17115077 |
| Relationships between IQ and regional cortical gray matter thickness in healthy adults. | Narr KL, Woods RP, Thompson PM, Szeszko P, Robinson D, Dimtcheva T, Gurbani M, Toga AW, Bilder RM | Cerebral cortex (New York, N.Y. : 1991) | 17118969 | Cereb Cortex | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17118969 |
| Increased local gyrification mapped in Williams syndrome. | Gaser C, Luders E, Thompson PM, Lee AD, Dutton RA, Geaga JA, Hayashi KM, Bellugi U, Galaburda AM, Korenberg JR, Mills DL, Toga AW, Reiss AL | NeuroImage | 16901723 | Neuroimage | 2006 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/16901723 |
| Conversion of mild cognitive impairment to Alzheimer disease predicted by hippocampal atrophy maps. | Apostolova LG, Dutton RA, Dinov ID, Hayashi KM, Toga AW, Cummings JL, Thompson PM | Archives of neurology | 16682538 | Arch Neurol | 2006 May | https://www.ncbi.nlm.nih.gov/pubmed/16682538 |
| CSF sub-compartments in relation to plasma osmolality in healthy controls and in patients with first episode schizophrenia. | Gunduz-Bruce H, Narr KL, Gueorguieva R, Toga AW, Szeszko PR, Ashtari M, Robinson DG, Sevy S, Kane JM, Bilder RM | Psychiatry research | 17398079 | Psychiatry Res | 2007 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/17398079 |
| Tracking Alzheimer's disease. | Thompson PM, Hayashi KM, Dutton RA, Chiang MC, Leow AD, Sowell ER, De Zubicaray G, Becker JT, Lopez OL, Aizenstein HJ, Toga AW | Annals of the New York Academy of Sciences | 17413023 | Ann N Y Acad Sci | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17413023 |
| White matter fiber tractography and color mapping of the normal human cerebellum with diffusion tensor imaging. | Salamon N, Sicotte N, Drain A, Frew A, Alger JR, Jen J, Perlman S, Salamon G | Journal of neuroradiology = Journal de neuroradiologie | 17481730 | J Neuroradiol | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17481730 |
| Positive correlations between corpus callosum thickness and intelligence. | Luders E, Narr KL, Bilder RM, Thompson PM, Szeszko PR, Hamilton L, Toga AW | NeuroImage | 17689267 | Neuroimage | 2007 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/17689267 |
| Structural correlates of apathy in Alzheimer's disease. | Apostolova LG, Akopyan GG, Partiali N, Steiner CA, Dutton RA, Hayashi KM, Dinov ID, Toga AW, Cummings JL, Thompson PM | Dementia and geriatric cognitive disorders | 17570907 | Dement Geriatr Cogn Disord | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17570907 |
| Diffusion tensor imaging of the superior longitudinal fasciculus and working memory in recent-onset schizophrenia. | Karlsgodt KH, van Erp TG, Poldrack RA, Bearden CE, Nuechterlein KH, Cannon TD | Biological psychiatry | 17720147 | Biol Psychiatry | 2008 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/17720147 |
| Three-dimensional gray matter atrophy mapping in mild cognitive impairment and mild Alzheimer disease. | Apostolova LG, Steiner CA, Akopyan GG, Dutton RA, Hayashi KM, Toga AW, Cummings JL, Thompson PM | Archives of neurology | 17923632 | Arch Neurol | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17923632 |
| Abnormal cortical thickness and brain-behavior correlation patterns in individuals with heavy prenatal alcohol exposure. | Sowell ER, Mattson SN, Kan E, Thompson PM, Riley EP, Toga AW | Cerebral cortex (New York, N.Y. : 1991) | 17443018 | Cereb Cortex | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17443018 |
| Iterative regularization and nonlinear inverse scale space applied to wavelet-based denoising. | Xu J, Osher S | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 17269645 | IEEE Trans Image Process | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17269645 |
| Callosal morphology in Williams syndrome: a new evaluation of shape and thickness. | Luders E, Di Paola M, Tomaiuolo F, Thompson PM, Toga AW, Vicari S, Petrides M, Caltagirone C | Neuroreport | 17314657 | Neuroreport | 2007 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/17314657 |
| Acceleration of cerebral ventricular expansion in the Cardiovascular Health Study. | Carmichael OT, Kuller LH, Lopez OL, Thompson PM, Dutton RA, Lu A, Lee SE, Lee JY, Aizenstein HJ, Meltzer CC, Liu Y, Toga AW, Becker JT | Neurobiology of aging | 16875759 | Neurobiol Aging | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16875759 |
| Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis. | MacKenzie-Graham A, Tinsley MR, Shah KP, Aguilar C, Strickland LV, Boline J, Martin M, Morales L, Shattuck DW, Jacobs RE, Voskuhl RR, Toga AW | NeuroImage | 16806982 | Neuroimage | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16806982 |
| Asymmetries of cortical shape: Effects of handedness, sex and schizophrenia. | Narr KL, Bilder RM, Luders E, Thompson PM, Woods RP, Robinson D, Szeszko PR, Dimtcheva T, Gurbani M, Toga AW | NeuroImage | 17166743 | Neuroimage | 2007 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/17166743 |
| Progressive brain structural changes mapped as psychosis develops in 'at risk' individuals. | Sun D, Phillips L, Velakoulis D, Yung A, McGorry PD, Wood SJ, van Erp TG, Thompson PM, Toga AW, Cannon TD, Pantelis C | Schizophrenia research | 19138834 | Schizophr Res | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19138834 |
| Subregional hippocampal atrophy predicts Alzheimer's dementia in the cognitively normal. | Apostolova LG, Mosconi L, Thompson PM, Green AE, Hwang KS, Ramirez A, Mistur R, Tsui WH, de Leon MJ | Neurobiology of aging | 18814937 | Neurobiol Aging | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18814937 |
| The effect of intron length on exon creation ratios during the evolution of mammalian genomes. | Roy M, Kim N, Xing Y, Lee C | RNA (New York, N.Y.) | 18796579 | RNA | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18796579 |
| Exploring predictors of outcome in the psychosis prodrome: implications for early identification and intervention. | Niendam TA, Jalbrzikowski M, Bearden CE | Neuropsychology review | 19597747 | Neuropsychol Rev | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19597747 |
| Comparing 3 T and 1.5 T MRI for tracking Alzheimer's disease progression with tensor-based morphometry. | Ho AJ, Hua X, Lee S, Leow AD, Yanovsky I, Gutman B, Dinov ID, Leporé N, Stein JL, Toga AW, Jack CR Jr, Bernstein MA, Reiman EM, Harvey DJ, Kornak J, Schuff N, Alexander GE, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative | Human brain mapping | 19780044 | Hum Brain Mapp | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19780044 |
| Classification of spatially unaligned fMRI scans. | Anderson A, Dinov ID, Sherin JE, Quintana J, Yuille AL, Cohen MS | NeuroImage | 19712744 | Neuroimage | 2010 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/19712744 |
| Cardiorespiratory fitness and brain atrophy in early Alzheimer disease. | Burns JM, Cronk BB, Anderson HS, Donnelly JE, Thomas GP, Harsha A, Brooks WM, Swerdlow RH | Neurology | 18625967 | Neurology | 2008 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/18625967 |
| Gene-environment interaction and covariation in schizophrenia: the role of obstetric complications. | Mittal VA, Ellman LM, Cannon TD | Schizophrenia bulletin | 18635675 | Schizophr Bull | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18635675 |
| Altered frontal-parietal functioning during verbal working memory in children and adolescents with heavy prenatal alcohol exposure. | O'Hare ED, Lu LH, Houston SM, Bookheimer SY, Mattson SN, O'Connor MJ, Sowell ER | Human brain mapping | 19263420 | Hum Brain Mapp | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19263420 |
| Total brain volume and corpus callosum size in medication-naïve adolescents and young adults with autism spectrum disorder. | Freitag CM, Luders E, Hulst HE, Narr KL, Thompson PM, Toga AW, Krick C, Konrad C | Biological psychiatry | 19409535 | Biol Psychiatry | 2009 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/19409535 |
| Multisite neuroimaging trials. | Van Horn JD, Toga AW | Current opinion in neurology | 19506479 | Curr Opin Neurol | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19506479 |
| Sex matters during adolescence: testosterone-related cortical thickness maturation differs between boys and girls. | Bramen JE, Hranilovich JA, Dahl RE, Chen J, Rosso C, Forbes EE, Dinov ID, Worthman CM, Sowell ER | PloS one | 22479458 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22479458 |
| Along-tract statistics allow for enhanced tractography analysis. | Colby JB, Soderberg L, Lebel C, Dinov ID, Thompson PM, Sowell ER | NeuroImage | 22094644 | Neuroimage | 2012 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/22094644 |
| Brain growth rate abnormalities visualized in adolescents with autism. | Hua X, Thompson PM, Leow AD, Madsen SK, Caplan R, Alger JR, O'Neill J, Joshi K, Smalley SL, Toga AW, Levitt JG | Human brain mapping | 22021093 | Hum Brain Mapp | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22021093 |
| FAST EDGE-FILTERED IMAGE UPSAMPLING. | Joshi SH, Marquina AL, Osher SJ, Dinov I, Toga AW, Van Horn JD | Proceedings. International Conference on Image Processing | 22323066 | Proc Int Conf Image Proc | 2011 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/22323066 |
| Right, left, and center: how does cerebral asymmetry mix with callosal connectivity? | Cherbuin N, Luders E, Chou YY, Thompson PM, Toga AW, Anstey KJ | Human brain mapping | 22419524 | Hum Brain Mapp | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22419524 |
| Central Limit Theorem: New SOCR Applet and Demonstration Activity. | Dinov ID, Christou N, Sanchez J | Journal of statistics education : an international journal on the teaching and learning of statistics | 21833159 | J Stat Educ | 2008 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/21833159 |
| A role for ephrin-A5 in axonal sprouting, recovery, and activity-dependent plasticity after stroke. | Overman JJ, Clarkson AN, Wanner IB, Overman WT, Eckstein I, Maguire JL, Dinov ID, Toga AW, Carmichael ST | Proceedings of the National Academy of Sciences of the United States of America | 22837401 | Proc Natl Acad Sci U S A | 2012 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/22837401 |
| The Cardiac Atlas Project--an imaging database for computational modeling and statistical atlases of the heart. | Fonseca CG, Backhaus M, Bluemke DA, Britten RD, Chung JD, Cowan BR, Dinov ID, Finn JP, Hunter PJ, Kadish AH, Lee DC, Lima JA, Medrano-Gracia P, Shivkumar K, Suinesiaputra A, Tao W, Young AA | Bioinformatics (Oxford, England) | 21737439 | Bioinformatics | 2011 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/21737439 |
| Applications of the pipeline environment for visual informatics and genomics computations. | Dinov ID, Torri F, Macciardi F, Petrosyan P, Liu Z, Zamanyan A, Eggert P, Pierce J, Genco A, Knowles JA, Clark AP, Van Horn JD, Ames J, Kesselman C, Toga AW | BMC bioinformatics | 21791102 | BMC Bioinformatics | 2011 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/21791102 |
| Brain surface conformal parameterization with the Ricci flow. | Wang Y, Shi J, Yin X, Gu X, Chan TF, Yau ST, Toga AW, Thompson PM | IEEE transactions on medical imaging | 21926017 | IEEE Trans Med Imaging | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21926017 |
| SOCR: Statistics Online Computational Resource. | Dinov ID | Journal of statistical software | 21451741 | J Stat Softw | 2006 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/21451741 |
| Fast approximate stochastic tractography. | Iglesias JE, Thompson PM, Liu CY, Tu Z | Neuroinformatics | 21476037 | Neuroinformatics | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21476037 |
| Preliminary evidence of within-subject changes in gray matter density associated with remission of bipolar depression. | Brooks JO 3rd, Foland-Ross LC, Thompson PM, Altshuler LL | Psychiatry research | 21561743 | Psychiatry Res | 2011 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/21561743 |
| A Study of Students' Learning Styles, Discipline Attitudes and Knowledge Acquisition in Technology-Enhanced Probability and Statistics Education. | Christou N, Dinov ID | Journal of online learning and teaching | 21603097 | J Online Learn Teach | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21603097 |
| Diffeomorphic Sulcal Shape Analysis for Cortical Surface Registration. | Joshi SH, Cabeen RP, Joshi AA, Woods RP, Narr KL, Toga AW | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 21076690 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2010 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/21076690 |
| A Computational Model of Multidimensional Shape. | Liu X, Shi Y, Dinov I, Mio W | International journal of computer vision | 21057668 | Int J Comput Vis | 2010 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/21057668 |
| Cortical sulcal atlas construction using a diffeomorphic mapping approach. | Joshi SH, Cabeen RP, Sun B, Joshi AA, Gutman B, Zamanyan A, Chakrapani S, Dinov I, Woods RP, Toga AW | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879251 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879251 |
| Synthetic MRI signal standardization: application to multi-atlas analysis. | Iglesias JE, Dinov I, Singh J, Tong G, Tu Z | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879386 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879386 |
| LAPLACE-BELTRAMI NODAL COUNTS: A NEW SIGNATURE FOR 3D SHAPE ANALYSIS. | Lai R, Shi Y, Dinov I, Chan TF, Toga AW | Proceedings. IEEE International Symposium on Biomedical Imaging | 21339849 | Proc IEEE Int Symp Biomed Imaging | 2009 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/21339849 |
| DigiWarp: a method for deformable mouse atlas warping to surface topographic data. | Joshi AA, Chaudhari AJ, Li C, Dutta J, Cherry SR, Shattuck DW, Toga AW, Leahy RM | Physics in medicine and biology | 20885019 | Phys Med Biol | 2010 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/20885019 |
| A web-based brain atlas of the vervet monkey, Chlorocebus aethiops. | Woods RP, Fears SC, Jorgensen MJ, Fairbanks LA, Toga AW, Freimer NB | NeuroImage | 20923706 | Neuroimage | 2011 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/20923706 |
| Differentiating prenatal exposure to methamphetamine and alcohol versus alcohol and not methamphetamine using tensor-based brain morphometry and discriminant analysis. | Sowell ER, Leow AD, Bookheimer SY, Smith LM, O'Connor MJ, Kan E, Rosso C, Houston S, Dinov ID, Thompson PM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 20237258 | J Neurosci | 2010 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/20237258 |
| Multivariate tensor-based brain anatomical surface morphometry via holomorphic one-forms. | Wang Y, Chan TF, Toga AW, Thompson PM | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426005 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426005 |
| A supermatrix-based molecular phylogeny of the family Drosophilidae. | van der Linde K, Houle D, Spicer GS, Steppan SJ | Genetics research | 20433773 | Genet Res (Camb) | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20433773 |
| Visualization of image data from cells to organisms. | Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché JK | Nature methods | 20195255 | Nat Methods | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20195255 |
| 3D PIB and CSF biomarker associations with hippocampal atrophy in ADNI subjects. | Apostolova LG, Hwang KS, Andrawis JP, Green AE, Babakchanian S, Morra JH, Cummings JL, Toga AW, Trojanowski JQ, Shaw LM, Jack CR Jr, Petersen RC, Aisen PS, Jagust WJ, Koeppe RA, Mathis CA, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative | Neurobiology of aging | 20538372 | Neurobiol Aging | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20538372 |
| Learning context-sensitive shape similarity by graph transduction. | Bai X, Yang X, Latecki LJ, Liu W, Tu Z | IEEE transactions on pattern analysis and machine intelligence | 20299710 | IEEE Trans Pattern Anal Mach Intell | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20299710 |
| Hippocampal, caudate, and ventricular changes in Parkinson's disease with and without dementia. | Apostolova LG, Beyer M, Green AE, Hwang KS, Morra JH, Chou YY, Avedissian C, Aarsland D, Janvin CC, Larsen JP, Cummings JL, Thompson PM | Movement disorders : official journal of the Movement Disorder Society | 20437538 | Mov Disord | 2010 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/20437538 |
| Mesh-based spherical deconvolution: a flexible approach to reconstruction of non-negative fiber orientation distributions. | Patel V, Shi Y, Thompson PM, Toga AW | NeuroImage | 20206705 | Neuroimage | 2010 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/20206705 |
| Multivariate tensor-based morphometry on surfaces: application to mapping ventricular abnormalities in HIV/AIDS. | Wang Y, Zhang J, Gutman B, Chan TF, Becker JT, Aizenstein HJ, Lopez OL, Tamburo RJ, Toga AW, Thompson PM | NeuroImage | 19900560 | Neuroimage | 2010 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/19900560 |
| Brain MRI tissue classification based on local Markov random fields. | Tohka J, Dinov ID, Shattuck DW, Toga AW | Magnetic resonance imaging | 20110151 | Magn Reson Imaging | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20110151 |
| Mapping Alzheimer's disease progression in 1309 MRI scans: power estimates for different inter-scan intervals. | Hua X, Lee S, Hibar DP, Yanovsky I, Leow AD, Toga AW, Jack CR Jr, Bernstein MA, Reiman EM, Harvey DJ, Kornak J, Schuff N, Alexander GE, Weiner MW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative | NeuroImage | 20139010 | Neuroimage | 2010 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/20139010 |
| Sex differences in orbitofrontal gray as a partial explanation for sex differences in antisocial personality. | Raine A, Yang Y, Narr KL, Toga AW | Molecular psychiatry | 20029391 | Mol Psychiatry | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20029391 |
| Grey and white matter loss along cerebral midline structures in myotonic dystrophy type 2. | Minnerop M, Luders E, Specht K, Ruhlmann J, Schneider-Gold C, Schröder R, Thompson PM, Toga AW, Klockgether T, Kornblum C | Journal of neurology | 19224318 | J Neurol | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19224318 |
| Plaque and tangle imaging and cognition in normal aging and Alzheimer's disease. | Braskie MN, Klunder AD, Hayashi KM, Protas H, Kepe V, Miller KJ, Huang SC, Barrio JR, Ercoli LM, Siddarth P, Satyamurthy N, Liu J, Toga AW, Bookheimer SY, Small GW, Thompson PM | Neurobiology of aging | 19004525 | Neurobiol Aging | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19004525 |
| Relationships between brain activation and brain structure in normally developing children. | Lu LH, Dapretto M, O'Hare ED, Kan E, McCourt ST, Thompson PM, Toga AW, Bookheimer SY, Sowell ER | Cerebral cortex (New York, N.Y. : 1991) | 19240138 | Cereb Cortex | 2009 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19240138 |
| Neuroanatomical Correlates of Intelligence. | Luders E, Narr KL, Thompson PM, Toga AW | Intelligence | 20160919 | Intelligence | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/20160919 |
| Reduced lean mass in early Alzheimer disease and its association with brain atrophy. | Burns JM, Johnson DK, Watts A, Swerdlow RH, Brooks WM | Archives of neurology | 20385908 | Arch Neurol | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20385908 |
| Quantitative in vivo evidence for broad regional gradients in the timing of white matter maturation during adolescence. | Colby JB, Van Horn JD, Sowell ER | NeuroImage | 20708693 | Neuroimage | 2011 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/20708693 |
| Puberty influences medial temporal lobe and cortical gray matter maturation differently in boys than girls matched for sexual maturity. | Bramen JE, Hranilovich JA, Dahl RE, Forbes EE, Chen J, Toga AW, Dinov ID, Worthman CM, Sowell ER | Cerebral cortex (New York, N.Y. : 1991) | 20713504 | Cereb Cortex | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20713504 |
| Mapping cortical atrophy in Parkinson's disease patients with dementia. | Hwang KS, Beyer MK, Green AE, Chung C, Thompson PM, Janvin C, Larsen JP, Aarsland D, Apostolova LG | Journal of Parkinson's disease | 23938313 | J Parkinsons Dis | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23938313 |
| Regional neuroplastic brain changes in patients with chronic inflammatory and non-inflammatory visceral pain. | Hong JY, Labus JS, Jiang Z, Ashe-Mcnalley C, Dinov I, Gupta A, Shi Y, Stains J, Heendeniya N, Smith SR, Tillisch K, Mayer EA | PloS one | 24416245 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24416245 |
| Web-based tools for modelling and analysis of multivariate data: California ozone pollution activity. | Dinov ID, Christou N | International journal of mathematical education in science and technology | 24465054 | Int J Math Educ Sci Technol | 2011 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/24465054 |
| Automated hippocampal shape analysis predicts the onset of dementia in mild cognitive impairment. | Costafreda SG, Dinov ID, Tu Z, Shi Y, Liu CY, Kloszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Wahlund LO, Spenger C, Toga AW, Lovestone S, Simmons A | NeuroImage | 21272654 | Neuroimage | 2011 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/21272654 |
| Statistics Online Computational Resource for Education. | Dinov ID, Christou N | Teaching statistics | 21297884 | Teach Stat | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/21297884 |
| Anisotropic Laplace-Beltrami Eigenmaps: Bridging Reeb Graphs and Skeletons. | Shi Y, Lai R, Krishna S, Sicotte N, Dinov I, Toga AW | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 21339850 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2008 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/21339850 |
| Structural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment. | Moon SW, Dinov ID, Hobel S, Zamanyan A, Choi YC, Shi R, Thompson PM, Toga AW, Alzheimer's Disease Neuroimaging Initiative | Journal of neuroimaging : official journal of the American Society of Neuroimaging | 25940587 | J Neuroimaging | 2015 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/25940587 |
| Gene interactions and structural brain change in early-onset Alzheimer's disease subjects using the pipeline environment. | Moon SW, Dinov ID, Zamanyan A, Shi R, Genco A, Hobel S, Thompson PM, Toga AW, Alzheimer's Disease Neuroimaging Initiative (ADNI) | Psychiatry investigation | 25670955 | Psychiatry Investig | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25670955 |
| Evolution of the central sulcus morphology in primates. | Hopkins WD, Meguerditchian A, Coulon O, Bogart S, Mangin JF, Sherwood CC, Grabowski MW, Bennett AJ, Pierre PJ, Fears S, Woods R, Hof PR, Vauclair J | Brain, behavior and evolution | 25139259 | Brain Behav Evol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25139259 |
| BRAIN PATTERN ANALYSIS OF CORTICAL VALUED DISTRIBUTIONS. | Joshi SH, Bowman I, Toga AW, Van Horn JD | Proceedings. IEEE International Symposium on Biomedical Imaging | 21743844 | Proc IEEE Int Symp Biomed Imaging | 2011 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/21743844 |
| Planum temporale grey matter asymmetries in chimpanzees (Pan troglodytes), vervet (Chlorocebus aethiops sabaeus), rhesus (Macaca mulatta) and bonnet (Macaca radiata) monkeys. | Lyn H, Pierre P, Bennett AJ, Fears S, Woods R, Hopkins WD | Neuropsychologia | 21447349 | Neuropsychologia | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21447349 |
| Populations with elevated mutation load do not benefit from the operation of sexual selection. | Hollis B, Houle D | Journal of evolutionary biology | 21658188 | J Evol Biol | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21658188 |
| Law of Large Numbers: the Theory, Applications and Technology-based Education. | Dinov ID, Christou N, Gould R | Journal of statistics education : an international journal on the teaching and learning of statistics | 21603584 | J Stat Educ | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21603584 |
| SOCR Motion Charts: An Efficient, Open-Source, Interactive and Dynamic Applet for Visualizing Longitudinal Multivariate Data. | Al-Aziz J, Christou N, Dinov ID | Journal of statistics education : an international journal on the teaching and learning of statistics | 21479108 | J Stat Educ | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21479108 |
| Callosal tissue loss in multiple system atrophy--a one-year follow-up study. | Minnerop M, Lüders E, Specht K, Ruhlmann J, Schimke N, Thompson PM, Chou YY, Toga AW, Abele M, Wüllner U, Klockgether T | Movement disorders : official journal of the Movement Disorder Society | 20623690 | Mov Disord | 2010 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/20623690 |
| Robust surface reconstruction via Laplace-Beltrami eigen-projection and boundary deformation. | Shi Y, Lai R, Morra JH, Dinov I, Thompson PM, Toga AW | IEEE transactions on medical imaging | 20624704 | IEEE Trans Med Imaging | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20624704 |
| Neurological imaging: statistics behind the pictures. | Dinov ID | Imaging in medicine | 22180753 | Imaging Med | 2011 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/22180753 |
| Confidence interval based parameter estimation--a new SOCR applet and activity. | Christou N, Dinov ID | PloS one | 21655319 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21655319 |
| Intelligence and cortical thickness in children with complex partial seizures. | Tosun D, Caplan R, Siddarth P, Seidenberg M, Gurbani S, Toga AW, Hermann B | NeuroImage | 21586333 | Neuroimage | 2011 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/21586333 |
| SOCR Analyses: Implementation and Demonstration of a New Graphical Statistics Educational Toolkit. | Chu A, Cui J, Dinov ID | Journal of statistical software | 21666874 | J Stat Softw | 2009 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/21666874 |
| Spatial-temporal atlas of human fetal brain development during the early second trimester. | Zhan J, Dinov ID, Li J, Zhang Z, Hobel S, Shi Y, Lin X, Zamanyan A, Feng L, Teng G, Fang F, Tang Y, Zang F, Toga AW, Liu S | NeuroImage | 23727529 | Neuroimage | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/23727529 |
| Fast diffusion tensor registration with exact reorientation and regularization. | Li J, Shi Y, Tran G, Dinov I, Wang DJ, Toga AW | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286042 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286042 |
| Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. | Xing Y, Lee CJ | PLoS genetics | 16170410 | PLoS Genet | 2005 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16170410 |
| A Web-based telemedicine system for diabetic retinopathy screening using digital fundus photography. | Wei JC, Valentino DJ, Bell DS, Baker RS | Telemedicine journal and e-health : the official journal of the American Telemedicine Association | 16478413 | Telemed J E Health | 2006 Feb | https://www.ncbi.nlm.nih.gov/pubmed/16478413 |
| The human cerebral cortex on MRI: value of the coronal plane. | Salamon N, Sicotte N, Mongkolwat P, Shattuck D, Salamon G | Surgical and radiologic anatomy : SRA | 16307199 | Surg Radiol Anat | 2005 Dec | https://www.ncbi.nlm.nih.gov/pubmed/16307199 |
| Three-dimensional patterns of hippocampal atrophy in mild cognitive impairment. | Becker JT, Davis SW, Hayashi KM, Meltzer CC, Toga AW, Lopez OL, Thompson PM, Imaging Methods and Analysis in Geriatrics Research Group | Archives of neurology | 16401741 | Arch Neurol | 2006 Jan | https://www.ncbi.nlm.nih.gov/pubmed/16401741 |
| A curvature-based approach to estimate local gyrification on the cortical surface. | Luders E, Thompson PM, Narr KL, Toga AW, Jancke L, Gaser C | NeuroImage | 16223589 | Neuroimage | 2006 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/16223589 |
| Hemispheric asymmetries in cortical thickness. | Luders E, Narr KL, Thompson PM, Rex DE, Jancke L, Toga AW | Cerebral cortex (New York, N.Y. : 1991) | 16267139 | Cereb Cortex | 2006 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16267139 |
| Mapping heritability and molecular genetic associations with cortical features using probabilistic brain atlases: methods and applications to schizophrenia. | Cannon TD, Thompson PM, van Erp TG, Huttunen M, Lonnqvist J, Kaprio J, Toga AW | Neuroinformatics | 16595856 | Neuroinformatics | 2006 Winter | https://www.ncbi.nlm.nih.gov/pubmed/16595856 |
| Colloquium papers: Numbering the hairs on our heads: the shared challenge and promise of phenomics. | Houle D | Proceedings of the National Academy of Sciences of the United States of America | 19858477 | Proc Natl Acad Sci U S A | 2010 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/19858477 |
| Alzheimer's Disease Neuroimaging Initiative (ADNI): clinical characterization. | Petersen RC, Aisen PS, Beckett LA, Donohue MC, Gamst AC, Harvey DJ, Jack CR Jr, Jagust WJ, Shaw LM, Toga AW, Trojanowski JQ, Weiner MW | Neurology | 20042704 | Neurology | 2010 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/20042704 |
| Surface feature-guided mapping of cerebral metabolic changes in cognitively normal and mildly impaired elderly. | Apostolova LG, Thompson PM, Rogers SA, Dinov ID, Zoumalan C, Steiner CA, Siu E, Green AE, Small GW, Toga AW, Cummings JL, Phelps ME, Silverman DH | Molecular imaging and biology | 19636640 | Mol Imaging Biol | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19636640 |
| Teichmöller shape space theory and its application to brain morphometry. | Wang Y, Dai W, Gu X, Chan TF, Yau ST, Toga AW, Thompson PM | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426105 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426105 |
| Lossless online ensemble learning (LOEL) and its application to subcortical segmentation. | Morra JH, Tu Z, Toga AW, Thompson PM | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426141 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426141 |
| The informatics core of the Alzheimer's Disease Neuroimaging Initiative. | Toga AW, Crawford KL, Alzheimer's Disease Neuroimaging Initiative | Alzheimer's & dementia : the journal of the Alzheimer's Association | 20451873 | Alzheimers Dement | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20451873 |
| Efficient, Distributed and Interactive Neuroimaging Data Analysis Using the LONI Pipeline. | Dinov ID, Van Horn JD, Lozev KM, Magsipoc R, Petrosyan P, Liu Z, Mackenzie-Graham A, Eggert P, Parker DS, Toga AW | Frontiers in neuroinformatics | 19649168 | Front Neuroinform | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19649168 |
| Conflict monitoring in early frontotemporal dementia. | Krueger CE, Bird AC, Growdon ME, Jang JY, Miller BL, Kramer JH | Neurology | 19652138 | Neurology | 2009 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/19652138 |
| Purkinje cell loss in experimental autoimmune encephalomyelitis. | MacKenzie-Graham A, Tiwari-Woodruff SK, Sharma G, Aguilar C, Vo KT, Strickland LV, Morales L, Fubara B, Martin M, Jacobs RE, Johnson GA, Toga AW, Voskuhl RR | NeuroImage | 19589388 | Neuroimage | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19589388 |
| A framework for brain registration via simultaneous surface and volume flow. | Joshi A, Leahy R, Toga AW, Shattuck D | Information processing in medical imaging : proceedings of the ... conference | 19694295 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694295 |
| Widespread cortical thinning is a robust anatomical marker for attention-deficit/hyperactivity disorder. | Narr KL, Woods RP, Lin J, Kim J, Phillips OR, Del'Homme M, Caplan R, Toga AW, McCracken JT, Levitt JG | Journal of the American Academy of Child and Adolescent Psychiatry | 19730275 | J Am Acad Child Adolesc Psychiatry | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19730275 |
| 3D comparison of low, intermediate, and advanced hippocampal atrophy in MCI. | Apostolova LG, Thompson PM, Green AE, Hwang KS, Zoumalan C, Jack CR Jr, Harvey DJ, Petersen RC, Thal LJ, Aisen PS, Toga AW, Cummings JL, Decarli CS | Human brain mapping | 20143386 | Hum Brain Mapp | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20143386 |
| Computer-assisted extraction of intracranial aneurysms on 3D rotational angiograms for computational fluid dynamics modeling. | Chang HH, Duckwiler GR, Valentine DJ, Chu WC | Medical physics | 20095274 | Med Phys | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20095274 |
| Voxelwise genome-wide association study (vGWAS). | Stein JL, Hua X, Lee S, Ho AJ, Leow AD, Toga AW, Saykin AJ, Shen L, Foroud T, Pankratz N, Huentelman MJ, Craig DW, Gerber JD, Allen AN, Corneveaux JJ, Dechairo BM, Potkin SG, Weiner MW, Thompson P, Alzheimer's Disease Neuroimaging Initiative | NeuroImage | 20171287 | Neuroimage | 2010 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/20171287 |
| When more is less: associations between corpus callosum size and handedness lateralization. | Luders E, Cherbuin N, Thompson PM, Gutman B, Anstey KJ, Sachdev P, Toga AW | NeuroImage | 20394828 | Neuroimage | 2010 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/20394828 |
| Registration of images with varying topology using embedded maps. | Li X, Long X, Laurienti P, Wyatt C, Alzheimer’s Disease Neuroimaging Initiative | IEEE transactions on medical imaging | 22194239 | IEEE Trans Med Imaging | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22194239 |
| Structural brain atlases: design, rationale, and applications in normal and pathological cohorts. | Mandal PK, Mahajan R, Dinov ID | Journal of Alzheimer's disease : JAD | 22647262 | J Alzheimers Dis | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22647262 |
| White matter integrity, language, and childhood onset schizophrenia. | Clark K, Narr KL, O'Neill J, Levitt J, Siddarth P, Phillips O, Toga A, Caplan R | Schizophrenia research | 22405729 | Schizophr Res | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22405729 |
| Frontostriatal connectivity in children during working memory and the effects of prenatal methamphetamine, alcohol, and polydrug exposure. | Roussotte FF, Rudie JD, Smith L, O'Connor MJ, Bookheimer SY, Narr KL, Sowell ER | Developmental neuroscience | 22472800 | Dev Neurosci | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22472800 |
| The right inhibition? Callosal correlates of hand performance in healthy children and adolescents callosal correlates of hand performance. | Kurth F, Mayer EA, Toga AW, Thompson PM, Luders E | Human brain mapping | 22438280 | Hum Brain Mapp | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22438280 |
| Hippocampal atrophy and ventricular enlargement in normal aging, mild cognitive impairment (MCI), and Alzheimer Disease. | Apostolova LG, Green AE, Babakchanian S, Hwang KS, Chou YY, Toga AW, Thompson PM | Alzheimer disease and associated disorders | 22343374 | Alzheimer Dis Assoc Disord | 2012 Jan-Mar | https://www.ncbi.nlm.nih.gov/pubmed/22343374 |
| Sex-related differences of cortical thickness in patients with chronic abdominal pain. | Jiang Z, Dinov ID, Labus J, Shi Y, Zamanyan A, Gupta A, Ashe-McNalley C, Hong JY, Tillisch K, Toga AW, Mayer EA | PloS one | 24040118 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24040118 |
| Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints. | Lin T, Guyader CL, Dinov I, Thompson P, Toga A, Vese L | Journal of scientific computing | 24273381 | J Sci Comput | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24273381 |
| Joint sulcal detection on cortical surfaces with graphical models and boosted priors. | Shi Y, Tu Z, Reiss AL, Dutton RA, Lee AD, Galaburda AM, Dinov I, Thompson PM, Toga AW | IEEE transactions on medical imaging | 19244008 | IEEE Trans Med Imaging | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19244008 |
| Performance measure characterization for evaluating neuroimage segmentation algorithms. | Chang HH, Zhuang AH, Valentino DJ, Chu WC | NeuroImage | 19345740 | Neuroimage | 2009 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/19345740 |
| Pattern of hippocampal shape and volume differences in blind subjects. | Leporé N, Shi Y, Lepore F, Fortin M, Voss P, Chou YY, Lord C, Lassonde M, Dinov ID, Toga AW, Thompson PM | NeuroImage | 19285559 | Neuroimage | 2009 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/19285559 |
| Disease classification with hippocampal shape invariants. | Gutman B, Wang Y, Morra J, Toga AW, Thompson PM | Hippocampus | 19437498 | Hippocampus | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19437498 |
| Regional patterns and clinical correlates of basal ganglia morphology in non-medicated schizophrenia. | Ballmaier M, Schlagenhauf F, Toga AW, Gallinat J, Koslowski M, Zoli M, Hojatkashani C, Narr KL, Heinz A | Schizophrenia research | 18818054 | Schizophr Res | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18818054 |
| Wagner and Dollo: a stochastic duet by composing two parsimonious solos. | Alekseyenko AV, Lee CJ, Suchard MA | Systematic biology | 18853363 | Syst Biol | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18853363 |
| Lifespan trajectory of myelin integrity and maximum motor speed. | Bartzokis G, Lu PH, Tingus K, Mendez MF, Richard A, Peters DG, Oluwadara B, Barrall KA, Finn JP, Villablanca P, Thompson PM, Mintz J | Neurobiology of aging | 18926601 | Neurobiol Aging | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18926601 |
| White matter integrity and prediction of social and role functioning in subjects at ultra-high risk for psychosis. | Karlsgodt KH, Niendam TA, Bearden CE, Cannon TD | Biological psychiatry | 19423081 | Biol Psychiatry | 2009 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/19423081 |
| Brain atlases and neuroanatomic imaging. | MacKenzie-Graham A, Boline J, Toga AW | Methods in molecular biology (Clifton, N.J.) | 18368367 | Methods Mol Biol | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18368367 |
| Re-evaluating dorsolateral prefrontal cortex activation during working memory in schizophrenia. | Karlsgodt KH, Sanz J, van Erp TG, Bearden CE, Nuechterlein KH, Cannon TD | Schizophrenia research | 19196494 | Schizophr Res | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19196494 |
| Models of normal variation and local contrasts in hippocampal anatomy. | Liu X, Mio W, Shi Y, Dinov I, Liu X, Leporé N, Leporé F, Fortin M, Voss P, Lassonde M, Thompson PM | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18982631 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18982631 |
| Remember and know judgments during recognition in chronic schizophrenia. | van Erp TG, Lesh TA, Knowlton BJ, Bearden CE, Hardt M, Karlsgodt KH, Shirinyan D, Rao V, Green MF, Subotnik KL, Nuechterlein K, Cannon TD | Schizophrenia research | 17964760 | Schizophr Res | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17964760 |
| Automated extraction of the cortical sulci based on a supervised learning approach. | Tu Z, Zheng S, Yuille AL, Reiss AL, Dutton RA, Lee AD, Galaburda AM, Dinov I, Thompson PM, Toga AW | IEEE transactions on medical imaging | 17427741 | IEEE Trans Med Imaging | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17427741 |
| Bioinformatics detection of alternative splicing. | Kim N, Lee C | Methods in molecular biology (Clifton, N.J.) | 18566765 | Methods Mol Biol | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18566765 |
| Reconstruction of full-length isoforms from splice graphs. | Xing Y, Lee C | Methods in molecular biology (Clifton, N.J.) | 18566766 | Methods Mol Biol | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18566766 |
| Thinning of sensorimotor cortices in children with Tourette syndrome. | Sowell ER, Kan E, Yoshii J, Thompson PM, Bansal R, Xu D, Toga AW, Peterson BS | Nature neuroscience | 18488025 | Nat Neurosci | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18488025 |
| Distinct regional atrophy in the corpus callosum of patients with temporal lobe epilepsy. | Weber B, Luders E, Faber J, Richter S, Quesada CM, Urbach H, Thompson PM, Toga AW, Elger CE, Helmstaedter C | Brain : a journal of neurology | 17728360 | Brain | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17728360 |
| Evidence for deficient modulation of amygdala response by prefrontal cortex in bipolar mania. | Foland LC, Altshuler LL, Bookheimer SY, Eisenberger N, Townsend J, Thompson PM | Psychiatry research | 18063349 | Psychiatry Res | 2008 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/18063349 |
| Detecting brain growth patterns in normal children using tensor-based morphometry. | Hua X, Leow AD, Levitt JG, Caplan R, Thompson PM, Toga AW | Human brain mapping | 18064588 | Hum Brain Mapp | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18064588 |
| Mapping the relationship between cortical convolution and intelligence: effects of gender. | Luders E, Narr KL, Bilder RM, Szeszko PR, Gurbani MN, Hamilton L, Toga AW, Gaser C | Cerebral cortex (New York, N.Y. : 1991) | 18089578 | Cereb Cortex | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18089578 |
| Strategies for identifying statistically significant dense regions in microarray data. | Yip AM, Ng MK, Wu EH, Chan TF | IEEE/ACM transactions on computational biology and bioinformatics | 17666761 | IEEE/ACM Trans Comput Biol Bioinform | 2007 Jul-Sep | https://www.ncbi.nlm.nih.gov/pubmed/17666761 |
| Statistical properties of Jacobian maps and the realization of unbiased large-deformation nonlinear image registration. | Leow AD, Yanovsky I, Chiang MC, Lee AD, Klunder AD, Lu A, Becker JT, Davis SW, Toga AW, Thompson PM | IEEE transactions on medical imaging | 17679333 | IEEE Trans Med Imaging | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17679333 |
| Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase. | Wang Q, Lee C | PloS one | 17726544 | PLoS One | 2007 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/17726544 |
| Genetics of brain structure and intelligence. | Toga AW, Thompson PM | Annual review of neuroscience | 15651931 | Annu Rev Neurosci | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/15651931 |
| Parasagittal asymmetries of the corpus callosum. | Luders E, Narr KL, Zaidel E, Thompson PM, Jancke L, Toga AW | Cerebral cortex (New York, N.Y. : 1991) | 15901651 | Cereb Cortex | 2006 Mar | https://www.ncbi.nlm.nih.gov/pubmed/15901651 |
| Skull-stripping magnetic resonance brain images using a model-based level set. | Zhuang AH, Valentino DJ, Toga AW | NeuroImage | 16697666 | Neuroimage | 2006 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/16697666 |
| Evolutionary divergence of exon flanks: a dissection of mutability and selection. | Xing Y, Wang Q, Lee C | Genetics | 16702427 | Genetics | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16702427 |
| The HIV positive selection mutation database. | Pan C, Kim J, Chen L, Wang Q, Lee C | Nucleic acids research | 17108357 | Nucleic Acids Res | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17108357 |
| 3D comparison of hippocampal atrophy in amnestic mild cognitive impairment and Alzheimer's disease. | Apostolova LG, Dinov ID, Dutton RA, Hayashi KM, Toga AW, Cummings JL, Thompson PM | Brain : a journal of neurology | 17018552 | Brain | 2006 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17018552 |
| An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. | Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C | Nucleic acids research | 16757580 | Nucleic Acids Res | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16757580 |
| Differential effects of typical and atypical antipsychotics on brain myelination in schizophrenia. | Bartzokis G, Lu PH, Nuechterlein KH, Gitlin M, Doi C, Edwards N, Lieu C, Altshuler LL, Mintz J | Schizophrenia research | 17407804 | Schizophr Res | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17407804 |
| Intrinsic Bayesian Active Contours for Extraction of Object Boundaries in Images. | Joshi SH, Srivastava A | International journal of computer vision | 21076692 | Int J Comput Vis | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21076692 |
| Abnormal brain activation during working memory in children with prenatal exposure to drugs of abuse: the effects of methamphetamine, alcohol, and polydrug exposure. | Roussotte FF, Bramen JE, Nunez SC, Quandt LC, Smith L, O'Connor MJ, Bookheimer SY, Sowell ER | NeuroImage | 21040792 | Neuroimage | 2011 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/21040792 |
| Agreement-based semi-supervised learning for skull stripping. | Iglesias JE, Liu CY, Thompson P, Tu Z | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879394 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879394 |
| Topographical relationships between arcuate fasciculus connectivity and cortical thickness. | Phillips OR, Clark KA, Woods RP, Subotnik KL, Asarnow RF, Nuechterlein KH, Toga AW, Narr KL | Human brain mapping | 20886580 | Hum Brain Mapp | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20886580 |
| Imaging genomics. | Thompson PM, Martin NG, Wright MJ | Current opinion in neurology | 20581684 | Curr Opin Neurol | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20581684 |
| The effects of physical activity, education, and body mass index on the aging brain. | Ho AJ, Raji CA, Becker JT, Lopez OL, Kuller LH, Hua X, Dinov ID, Stein JL, Rosano C, Toga AW, Thompson PM | Human brain mapping | 20715081 | Hum Brain Mapp | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20715081 |
| Optimization of Landmark Selection for Cortical Surface Registration. | Joshi A, Pantazis D, Damasio H, Shattuck D, Li Q, Leahy R | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 20717476 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2009 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/20717476 |
| CUDA optimization strategies for compute- and memory-bound neuroimaging algorithms. | Lee D, Dinov I, Dong B, Gutman B, Yanovsky I, Toga AW | Computer methods and programs in biomedicine | 21159404 | Comput Methods Programs Biomed | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21159404 |
| BDNF gene effects on brain circuitry replicated in 455 twins. | Chiang MC, Barysheva M, Toga AW, Medland SE, Hansell NK, James MR, McMahon KL, de Zubicaray GI, Martin NG, Wright MJ, Thompson PM | NeuroImage | 21195196 | Neuroimage | 2011 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/21195196 |
| Mean diffusivity and fractional anisotropy as indicators of disease and genetic liability to schizophrenia. | Clark KA, Nuechterlein KH, Asarnow RF, Hamilton LS, Phillips OR, Hageman NS, Woods RP, Alger JR, Toga AW, Narr KL | Journal of psychiatric research | 21306734 | J Psychiatr Res | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21306734 |
| Surface-based TBM boosts power to detect disease effects on the brain: an N=804 ADNI study. | Wang Y, Song Y, Rajagopalan P, An T, Liu K, Chou YY, Gutman B, Toga AW, Thompson PM, Alzheimer's Disease Neuroimaging Initiative | NeuroImage | 21440071 | Neuroimage | 2011 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/21440071 |
| Automated analysis of fundamental features of brain structures. | Lancaster JL, McKay DR, Cykowski MD, Martinez MJ, Tan X, Valaparla S, Zhang Y, Fox PT | Neuroinformatics | 21360205 | Neuroinformatics | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21360205 |
| Obesity is linked with lower brain volume in 700 AD and MCI patients. | Ho AJ, Raji CA, Becker JT, Lopez OL, Kuller LH, Hua X, Lee S, Hibar D, Dinov ID, Stein JL, Jack CR Jr, Weiner MW, Toga AW, Thompson PM, Cardiovascular Health Study, ADNI | Neurobiology of aging | 20570405 | Neurobiol Aging | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20570405 |
| Asymmetric and Symmetric Unbiased Image Registration: Statistical Assessment of Performance. | Yanovsky I, Thompson PM, Osher S, Leow AD | Conference on Computer Vision and Pattern Recognition Workshops. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops | 29152411 | Conf Comput Vis Pattern Recognit Workshops | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29152411 |
| Analysis of the volumetric relationship among human ocular, orbital and fronto-occipital cortical morphology. | Masters M, Bruner E, Queer S, Traynor S, Senjem J | Journal of anatomy | 26250048 | J Anat | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26250048 |
| Comparing 3T and 1.5T MRI for mapping hippocampal atrophy in the Alzheimer's Disease Neuroimaging Initiative. | Chow N, Hwang KS, Hurtz S, Green AE, Somme JH, Thompson PM, Elashoff DA, Jack CR, Weiner M, Apostolova LG, Alzheimer's Disease Neuroimaging Initiative | AJNR. American journal of neuroradiology | 25614473 | AJNR Am J Neuroradiol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25614473 |
| Probability Distributome: A Web Computational Infrastructure for Exploring the Properties, Interrelations, and Applications of Probability Distributions. | Dinov ID, Siegrist K, Pearl DK, Kalinin A, Christou N | Computational statistics | 27158191 | Comput Stat | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27158191 |
| Removing Shape-Preserving Transformations in Square-Root Elastic (SRE) Framework for Shape Analysis of Curves. | Joshi SH, Klassen E, Srivastava A, Jermyn I | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 21738385 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/21738385 |
| White matter microstructural alterations in children with prenatal methamphetamine/polydrug exposure. | Colby JB, Smith L, O'Connor MJ, Bookheimer SY, Van Horn JD, Sowell ER | Psychiatry research | 23149028 | Psychiatry Res | 2012 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/23149028 |
| Fast local trust region technique for diffusion tensor registration using exact reorientation and regularization. | Li J, Shi Y, Tran G, Dinov I, Wang DJ, Toga A | IEEE transactions on medical imaging | 23880040 | IEEE Trans Med Imaging | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/23880040 |
| In vivo neuropathology of the hippocampal formation in AD: a radial mapping MR-based study. | Frisoni GB, Sabattoli F, Lee AD, Dutton RA, Toga AW, Thompson PM | NeuroImage | 16631382 | Neuroimage | 2006 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/16631382 |
| A learning based algorithm for automatic extraction of the cortical sulci. | Zheng S, Tu Z, Yuille AL, Reiss AL, Dutton RA, Lee AD, Galaburda AM, Thompson PM, Dinov I, Toga AW | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354951 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354951 |
| Cerebral ventricular changes associated with transitions between normal cognitive function, mild cognitive impairment, and dementia. | Carmichael OT, Kuller LH, Lopez OL, Thompson PM, Dutton RA, Lu A, Lee SE, Lee JY, Aizenstein HJ, Meltzer CC, Liu Y, Toga AW, Becker JT | Alzheimer disease and associated disorders | 17334268 | Alzheimer Dis Assoc Disord | 2007 Jan-Mar | https://www.ncbi.nlm.nih.gov/pubmed/17334268 |
| Global analysis of alternative splicing differences between humans and chimpanzees. | Calarco JA, Xing Y, Cáceres M, Calarco JP, Xiao X, Pan Q, Lee C, Preuss TM, Blencowe BJ | Genes & development | 17978102 | Genes Dev | 2007 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/17978102 |
| Mapping white matter integrity and neurobehavioral correlates in children with fetal alcohol spectrum disorders. | Sowell ER, Johnson A, Kan E, Lu LH, Van Horn JD, Toga AW, O'Connor MJ, Bookheimer SY | The Journal of neuroscience : the official journal of the Society for Neuroscience | 18256251 | J Neurosci | 2008 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/18256251 |
| Segmentation of sub-cortical structures by the graph-shifts algorithm. | Corso JJ, Tu Z, Yuille A, Toga A | Information processing in medical imaging : proceedings of the ... conference | 17633699 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633699 |
| Deformation-based morphometry of prospective neurodevelopmental changes in new onset paediatric epilepsy. | Tosun D, Dabbs K, Caplan R, Siddarth P, Toga A, Seidenberg M, Hermann B | Brain : a journal of neurology | 21398377 | Brain | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21398377 |
| The link between callosal thickness and intelligence in healthy children and adolescents. | Luders E, Thompson PM, Narr KL, Zamanyan A, Chou YY, Gutman B, Dinov ID, Toga AW | NeuroImage | 20932920 | Neuroimage | 2011 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/20932920 |
| The contributions of disease and genetic factors towards regional cortical thinning in schizophrenia: the UCLA family study. | Yang Y, Nuechterlein KH, Phillips O, Hamilton LS, Subotnik KL, Asarnow RF, Toga AW, Narr KL | Schizophrenia research | 20817413 | Schizophr Res | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20817413 |
| Shape-based diffeomorphic registration on hippocampal surfaces using Beltrami holomorphic flow. | Lui LM, Wong TW, Thompson P, Chan T, Gu X, Yau ST | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879331 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879331 |
| Automated sulci identification via intrinsic modeling of cortical anatomy. | Shi Y, Sun B, Lai R, Dinov I, Toga AW | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879382 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879382 |
| Hippocampal morphology in lithium and non-lithium-treated bipolar I disorder patients, non-bipolar co-twins, and control twins. | van Erp TG, Thompson PM, Kieseppä T, Bearden CE, Marino AC, Hoftman GD, Haukka J, Partonen T, Huttunen M, Kaprio J, Lönnqvist J, Poutanen VP, Toga AW, Cannon TD | Human brain mapping | 21455943 | Hum Brain Mapp | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21455943 |
| SOCR Analyses - an Instructional Java Web-based Statistical Analysis Toolkit. | Chu A, Cui J, Dinov ID | Journal of online learning and teaching | 21546994 | J Online Learn Teach | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21546994 |
| The Center for Computational Biology: resources, achievements, and challenges. | Toga AW, Dinov ID, Thompson PM, Woods RP, Van Horn JD, Shattuck DW, Parker DS | Journal of the American Medical Informatics Association : JAMIA | 22081221 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22081221 |
| Disease and genetic contributions toward local tissue volume disturbances in schizophrenia: a tensor-based morphometry study. | Yang Y, Nuechterlein KH, Phillips OR, Gutman B, Kurth F, Dinov I, Thompson PM, Asarnow RF, Toga AW, Narr KL | Human brain mapping | 22241649 | Hum Brain Mapp | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22241649 |
| Anatomical global spatial normalization. | Lancaster JL, Cykowski MD, McKay DR, Kochunov PV, Fox PT, Rogers W, Toga AW, Zilles K, Amunts K, Mazziotta J | Neuroinformatics | 20582489 | Neuroinformatics | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20582489 |
| POSTURE MATCHING AND ELASTIC REGISTRATION OF A MOUSE ATLAS TO SURFACE TOPOGRAPHY RANGE DATA. | Joshi AA, Chaudhari AJ, Li C, Shattuck DW, Dutta J, Leahy RM, Toga AW | Proceedings. IEEE International Symposium on Biomedical Imaging | 21072317 | Proc IEEE Int Symp Biomed Imaging | 2009 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/21072317 |
| The generation of tetrahedral mesh models for neuroanatomical MRI. | Lederman C, Joshi A, Dinov I, Vese L, Toga A, Van Horn JD | NeuroImage | 21073968 | Neuroimage | 2011 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21073968 |
| The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. | Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P | Journal of biomedical informatics | 20955817 | J Biomed Inform | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20955817 |
| Apolipoprotein E genotype is associated with temporal and hippocampal atrophy rates in healthy elderly adults: a tensor-based morphometry study. | Lu PH, Thompson PM, Leow A, Lee GJ, Lee A, Yanovsky I, Parikshak N, Khoo T, Wu S, Geschwind D, Bartzokis G | Journal of Alzheimer's disease : JAD | 21098974 | J Alzheimers Dis | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21098974 |
| Structural, metabolic, and functional brain abnormalities as a result of prenatal exposure to drugs of abuse: evidence from neuroimaging. | Roussotte F, Soderberg L, Sowell E | Neuropsychology review | 20978945 | Neuropsychol Rev | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20978945 |
| Modeling Spatial Patterns of Shapes. | Srivastava A, Liu W, Joshi SH | Proceedings. International Conference on Image Processing | 21132063 | Proc Int Conf Image Proc | 2008 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/21132063 |
| Auto-context and its application to high-level vision tasks and 3D brain image segmentation. | Tu Z, Bai X | IEEE transactions on pattern analysis and machine intelligence | 20724753 | IEEE Trans Pattern Anal Mach Intell | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20724753 |
| HARDI DATA DENOISING USING VECTORIAL TOTAL VARIATION AND LOGARITHMIC BARRIER. | Kim Y, Thompson PM, Vese LA | Inverse problems and imaging (Springfield, Mo.) | 20802839 | Inverse Probl Imaging (Springfield) | 2010 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/20802839 |
| Interactive exploration of neuroanatomical meta-spaces. | Joshi SH, Horn JD, Toga AW | Frontiers in neuroinformatics | 19915734 | Front Neuroinform | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19915734 |
| The tensor distribution function. | Leow AD, Zhu S, Zhan L, McMahon K, de Zubicaray GI, Meredith M, Wright MJ, Toga AW, Thompson PM | Magnetic resonance in medicine | 19097208 | Magn Reson Med | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19097208 |
| Sexual selection accelerates the elimination of a deleterious mutant in Drosophila melanogaster. | Hollis B, Fierst JL, Houle D | Evolution; international journal of organic evolution | 19154371 | Evolution | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19154371 |
| A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. | Hageman NS, Toga AW, Narr KL, Shattuck DW | IEEE transactions on medical imaging | 19244007 | IEEE Trans Med Imaging | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19244007 |
| Active fibers: matching deformable tract templates to diffusion tensor images. | Eckstein I, Shattuck DW, Stein JL, McMahon KL, de Zubicaray G, Wright MJ, Thompson PM, Toga AW | NeuroImage | 19457360 | Neuroimage | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19457360 |
| Comparison of AdaBoost and support vector machines for detecting Alzheimer's disease through automated hippocampal segmentation. | Morra JH, Tu Z, Apostolova LG, Green AE, Toga AW, Thompson PM | IEEE transactions on medical imaging | 19457748 | IEEE Trans Med Imaging | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19457748 |
| Regional gray matter variation in male-to-female transsexualism. | Luders E, Sánchez FJ, Gaser C, Toga AW, Narr KL, Hamilton LS, Vilain E | NeuroImage | 19341803 | Neuroimage | 2009 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/19341803 |
| iTools: a framework for classification, categorization and integration of computational biology resources. | Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW | PloS one | 18509477 | PLoS One | 2008 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/18509477 |
| Automatic localization of anatomical point landmarks for brain image processing algorithms. | Neu SC, Toga AW | Neuroinformatics | 18512163 | Neuroinformatics | 2008 Summer | https://www.ncbi.nlm.nih.gov/pubmed/18512163 |
| Provenance in neuroimaging. | Mackenzie-Graham AJ, Van Horn JD, Woods RP, Crawford KL, Toga AW | NeuroImage | 18519166 | Neuroimage | 2008 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/18519166 |
| Level set method for positron emission tomography. | Chan TF, Li H, Lysaker M, Tai XC | International journal of biomedical imaging | 18354724 | Int J Biomed Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18354724 |
| Alterations in functional activation in euthymic bipolar disorder and schizophrenia during a working memory task. | Hamilton LS, Altshuler LL, Townsend J, Bookheimer SY, Phillips OR, Fischer J, Woods RP, Mazziotta JC, Toga AW, Nuechterlein KH, Narr KL | Human brain mapping | 19449330 | Hum Brain Mapp | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19449330 |
| DTNBP1 is associated with imaging phenotypes in schizophrenia. | Narr KL, Szeszko PR, Lencz T, Woods RP, Hamilton LS, Phillips O, Robinson D, Burdick KE, DeRosse P, Kucherlapati R, Thompson PM, Toga AW, Malhotra AK, Bilder RM | Human brain mapping | 19449336 | Hum Brain Mapp | 2009 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19449336 |
| Effects of prenatal methamphetamine exposure on verbal memory revealed with functional magnetic resonance imaging. | Lu LH, Johnson A, O'Hare ED, Bookheimer SY, Smith LM, O'Connor MJ, Sowell ER | Journal of developmental and behavioral pediatrics : JDBP | 19525715 | J Dev Behav Pediatr | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19525715 |
| Ventricular volume and dementia progression in the Cardiovascular Health Study. | Carmichael OT, Kuller LH, Lopez OL, Thompson PM, Dutton RA, Lu A, Lee SE, Lee JY, Aizenstein HJ, Meltzer CC, Liu Y, Toga AW, Becker JT | Neurobiology of aging | 16504345 | Neurobiol Aging | 2007 Mar | https://www.ncbi.nlm.nih.gov/pubmed/16504345 |
| LONI visualization environment. | Dinov ID, Valentino D, Shin BC, Konstantinidis F, Hu G, MacKenzie-Graham A, Lee EF, Shattuck D, Ma J, Schwartz C, Toga AW | Journal of digital imaging | 16598642 | J Digit Imaging | 2006 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16598642 |
| Brain surface conformal parameterization using Riemann surface structure. | Wang Y, Lui LM, Gu X, Hayashi KM, Chan TF, Toga AW, Thompson PM, Yau ST | IEEE transactions on medical imaging | 17679336 | IEEE Trans Med Imaging | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17679336 |
| Segmentation of brain MR images using a charged fluid model. | Chang HH, Valentino DJ, Duckwiler GR, Toga AW | IEEE transactions on bio-medical engineering | 17926678 | IEEE Trans Biomed Eng | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17926678 |
| An electrostatic deformable model for medical image segmentation. | Chang HH, Valentino DJ | Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society | 17933492 | Comput Med Imaging Graph | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17933492 |
| QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. | Kim N, Lee C | Bioinformatics (Oxford, England) | 17599926 | Bioinformatics | 2007 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/17599926 |
| Asymmetries of cortical thickness: effects of handedness, sex, and schizophrenia. | Hamilton LS, Narr KL, Luders E, Szeszko PR, Thompson PM, Bilder RM, Toga AW | Neuroreport | 17712268 | Neuroreport | 2007 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/17712268 |
| Mapping callosal morphology in early- and late-onset elderly depression: an index of distinct changes in cortical connectivity. | Ballmaier M, Kumar A, Elderkin-Thompson V, Narr KL, Luders E, Thompson PM, Hojatkashani C, Pham D, Heinz A, Toga AW | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 17712348 | Neuropsychopharmacology | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17712348 |
| Regional cortical thinning in subjects with violent antisocial personality disorder or schizophrenia. | Narayan VM, Narr KL, Kumari V, Woods RP, Thompson PM, Toga AW, Sharma T | The American journal of psychiatry | 17728428 | Am J Psychiatry | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17728428 |
| Sex differences in cortical thickness mapped in 176 healthy individuals between 7 and 87 years of age. | Sowell ER, Peterson BS, Kan E, Woods RP, Yoshii J, Bansal R, Xu D, Zhu H, Thompson PM, Toga AW | Cerebral cortex (New York, N.Y. : 1991) | 16945978 | Cereb Cortex | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16945978 |
| Integral invariants for shape matching. | Manay S, Cremers D, Hong BW, Yezzi AJ Jr, Soatto S | IEEE transactions on pattern analysis and machine intelligence | 16986542 | IEEE Trans Pattern Anal Mach Intell | 2006 Oct | https://www.ncbi.nlm.nih.gov/pubmed/16986542 |
| Normal developmental changes in inferior frontal gray matter are associated with improvement in phonological processing: a longitudinal MRI analysis. | Lu L, Leonard C, Thompson P, Kan E, Jolley J, Welcome S, Toga A, Sowell E | Cerebral cortex (New York, N.Y. : 1991) | 16782757 | Cereb Cortex | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/16782757 |
| Dynamic mapping of normal human hippocampal development. | Gogtay N, Nugent TF 3rd, Herman DH, Ordonez A, Greenstein D, Hayashi KM, Clasen L, Toga AW, Giedd JN, Rapoport JL, Thompson PM | Hippocampus | 16826559 | Hippocampus | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16826559 |
| Localisation of increased prefrontal white matter in pathological liars. | Yang Y, Raine A, Narr KL, Lencz T, LaCasse L, Colletti P, Toga AW | The British journal of psychiatry : the journal of mental science | 17267937 | Br J Psychiatry | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17267937 |
| Functional magnetic resonance imaging of verbal learning in children with heavy prenatal alcohol exposure. | Sowell ER, Lu LH, O'Hare ED, McCourt ST, Mattson SN, O'Connor MJ, Bookheimer SY | Neuroreport | 17426589 | Neuroreport | 2007 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/17426589 |
| Glial reactions and degeneration of myelinated processes in spinal cord gray matter in chronic experimental autoimmune encephalomyelitis. | Wu J, Ohlsson M, Warner EA, Loo KK, Hoang TX, Voskuhl RR, Havton LA | Neuroscience | 18718511 | Neuroscience | 2008 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/18718511 |
| Symptomatic and functional correlates of regional brain physiology during working memory processing in patients with recent onset schizophrenia. | Sanz JH, Karlsgodt KH, Bearden CE, van Erp TG, Nandy RR, Ventura J, Nuechterlein K, Cannon TD | Psychiatry research | 19692211 | Psychiatry Res | 2009 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/19692211 |
| HARDI denoising: variational regularization of the spherical apparent diffusion coefficient sADC. | Kim Y, Thompson PM, Toga AW, Vese L, Zhan L | Information processing in medical imaging : proceedings of the ... conference | 19694290 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694290 |
| Pedagogical Utilization and Assessment of the Statistic Online Computational Resource in Introductory Probability and Statistics Courses. | Dinov ID, Sanchez J, Christou N | Computers & education | 19750185 | Comput Educ | 2008 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19750185 |
| Demographic and genetic constraints on evolution. | Gomulkiewicz R, Houle D | The American naturalist | 19821744 | Am Nat | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19821744 |
| Why sex matters: brain size independent differences in gray matter distributions between men and women. | Luders E, Gaser C, Narr KL, Toga AW | The Journal of neuroscience : the official journal of the Society for Neuroscience | 19906974 | J Neurosci | 2009 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/19906974 |
| Wakefulness and loss of awareness: brain and brainstem interaction in the vegetative state. | Silva S, Alacoque X, Fourcade O, Samii K, Marque P, Woods R, Mazziotta J, Chollet F, Loubinoux I | Neurology | 20101037 | Neurology | 2010 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/20101037 |
| The construction of a Chinese MRI brain atlas: a morphometric comparison study between Chinese and Caucasian cohorts. | Tang Y, Hojatkashani C, Dinov ID, Sun B, Fan L, Lin X, Qi H, Hua X, Liu S, Toga AW | NeuroImage | 20152910 | Neuroimage | 2010 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/20152910 |
| Structural Neuroimaging Genetics Interactions in Alzheimer's Disease. | Moon SW, Dinov ID, Kim J, Zamanyan A, Hobel S, Thompson PM, Toga AW | Journal of Alzheimer's disease : JAD | 26444770 | J Alzheimers Dis | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26444770 |
| Small fitness effect of mutations in highly conserved non-coding regions. | Kryukov GV, Schmidt S, Sunyaev S | Human molecular genetics | 15994173 | Hum Mol Genet | 2005 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/15994173 |
| Biological process linkage networks. | Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S | PloS one | 19390589 | PLoS One | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19390589 |
| Genephony: a knowledge management tool for genome-wide research. | Nuzzo A, Riva A | BMC bioinformatics | 19728881 | BMC Bioinformatics | 2009 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/19728881 |
| Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. | Dreyfuss JM, Johnson MD, Park PJ | Molecular cancer | 19732454 | Mol Cancer | 2009 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/19732454 |
| BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis. | Bryan AW Jr, Menke M, Cowen LJ, Lindquist SL, Berger B | PLoS computational biology | 19325876 | PLoS Comput Biol | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19325876 |
| Power of deep, all-exon resequencing for discovery of human trait genes. | Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR | Proceedings of the National Academy of Sciences of the United States of America | 19202052 | Proc Natl Acad Sci U S A | 2009 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/19202052 |
| Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. | Deleger L, Molnar K, Savova G, Xia F, Lingren T, Li Q, Marsolo K, Jegga A, Kaiser M, Stoutenborough L, Solti I | Journal of the American Medical Informatics Association : JAMIA | 22859645 | J Am Med Inform Assoc | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/22859645 |
| Portability of an algorithm to identify rheumatoid arthritis in electronic health records. | Carroll RJ, Thompson WK, Eyler AE, Mandelin AM, Cai T, Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H, Karlson EW, Perez RG, Gainer VS, Murphy SN, Ruderman EM, Pope RM, Plenge RM, Kho AN, Liao KP, Denny JC | Journal of the American Medical Informatics Association : JAMIA | 22374935 | J Am Med Inform Assoc | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22374935 |
| Genome-wide association identifies the T gene as a novel asthma pharmacogenetic locus. | Tantisira KG, Damask A, Szefler SJ, Schuemann B, Markezich A, Su J, Klanderman B, Sylvia J, Wu R, Martinez F, Boushey HA, Chinchilli VM, Mauger D, Weiss ST, Israel E, SHARP Investigators | American journal of respiratory and critical care medicine | 22538805 | Am J Respir Crit Care Med | 2012 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/22538805 |
| Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease. | Ananthakrishnan AN, Gainer VS, Perez RG, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP | Alimentary pharmacology & therapeutics | 23289600 | Aliment Pharmacol Ther | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23289600 |
| Detecting concept relations in clinical text: insights from a state-of-the-art model. | Zhu X, Cherry C, Kiritchenko S, Martin J, de Bruijn B | Journal of biomedical informatics | 23380683 | J Biomed Inform | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23380683 |
| Active learning for clinical text classification: is it better than random sampling? | Figueroa RL, Zeng-Treitler Q, Ngo LH, Goryachev S, Wiechmann EP | Journal of the American Medical Informatics Association : JAMIA | 22707743 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22707743 |
| Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. | Jonnalagadda SR, Li D, Sohn S, Wu ST, Wagholikar K, Torii M, Liu H | Journal of the American Medical Informatics Association : JAMIA | 22707745 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22707745 |
| Federated queries of clinical data repositories: the sum of the parts does not equal the whole. | Weber GM | Journal of the American Medical Informatics Association : JAMIA | 23349080 | J Am Med Inform Assoc | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23349080 |
| QT interval and antidepressant use: a cross sectional study of electronic health records. | Castro VM, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Erb JL, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH | BMJ (Clinical research ed.) | 23360890 | BMJ | 2013 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/23360890 |
| Coreference resolution of medical concepts in discharge summaries by exploiting contextual information. | Dai HJ, Chen CY, Wu CY, Lai PT, Tsai RT, Hsu WL | Journal of the American Medical Informatics Association : JAMIA | 22556185 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22556185 |
| Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010. | de Bruijn B, Cherry C, Kiritchenko S, Martin J, Zhu X | Journal of the American Medical Informatics Association : JAMIA | 21565856 | J Am Med Inform Assoc | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21565856 |
| Influence of dietary sodium modulation on electrocardiographic voltage criteria for left ventricular hypertrophy in normotensive individuals. | Larson C, Vaidya A, Sun B, Williams JS | Journal of investigative medicine : the official publication of the American Federation for Clinical Research | 22089249 | J Investig Med | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22089249 |
| Qualitative analysis of workflow modifications used to generate the reference standard for the 2010 i2b2/VA challenge. | South BR, Shen S, Barrus R, DuVall SL, Uzuner O, Weir C | AMIA ... Annual Symposium proceedings. AMIA Symposium | 22195185 | AMIA Annu Symp Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22195185 |
| Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding. | Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML | Nature immunology | 22101729 | Nat Immunol | 2011 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/22101729 |
| Differential effects of the Huntington's disease CAG mutation in striatum and cerebellum are quantitative not qualitative. | Fossale E, Seong IS, Coser KR, Shioda T, Kohane IS, Wheeler VC, Gusella JF, MacDonald ME, Lee JM | Human molecular genetics | 21840924 | Hum Mol Genet | 2011 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/21840924 |
| Mapping tool for maintaining vocabulary relationships. | Hackett KL, Kohane IS, Chueh HC, Murphy SN | AMIA ... Annual Symposium proceedings. AMIA Symposium | 17238558 | AMIA Annu Symp Proc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17238558 |
| Integration of clinical and genetic data in the i2b2 architecture. | Murphy SN, Mendis ME, Berkowitz DA, Kohane I, Chueh HC | AMIA ... Annual Symposium proceedings. AMIA Symposium | 17238659 | AMIA Annu Symp Proc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17238659 |
| Absolute enrichment: gene set enrichment analysis for homeostatic systems. | Saxena V, Orgill D, Kohane I | Nucleic acids research | 17130162 | Nucleic Acids Res | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17130162 |
| Biological context networks: a mosaic view of the interactome. | Rachlin J, Cohen DD, Cantor C, Kasif S | Molecular systems biology | 17130868 | Mol Syst Biol | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17130868 |
| Machine learning and rule-based approaches to assertion classification. | Uzuner O, Zhang X, Sibanda T | Journal of the American Medical Informatics Association : JAMIA | 18952931 | J Am Med Inform Assoc | 2009 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/18952931 |
| A la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge. | Cherry C, Zhu X, Martin J, de Bruijn B | Journal of the American Medical Informatics Association : JAMIA | 23523875 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23523875 |
| A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text. | Roberts K, Rink B, Harabagiu SM | Journal of the American Medical Informatics Association : JAMIA | 23686936 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23686936 |
| Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls. | Liao KP, Diogo D, Cui J, Cai T, Okada Y, Gainer VS, Murphy SN, Gupta N, Mirel D, Ananthakrishnan AN, Szolovits P, Shaw SY, Raychaudhuri S, Churchill S, Kohane I, Karlson EW, Plenge RM | Annals of the rheumatic diseases | 23716066 | Ann Rheum Dis | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23716066 |
| Copy fees and patients' rights to obtain a copy of their medical records: from law to reality. | Fioriglio G, Szolovits P | AMIA ... Annual Symposium proceedings. AMIA Symposium | 16779040 | AMIA Annu Symp Proc | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16779040 |
| Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. | Lee H, Kong SW, Park PJ | Bioinformatics (Oxford, England) | 18263644 | Bioinformatics | 2008 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/18263644 |
| Electronic health records: high-quality electronic data for higher-quality clinical research. | Weiner MG, Lyman JA, Murphy S, Weiner M | Informatics in primary care | 17877874 | Inform Prim Care | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17877874 |
| Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia. | Cohen J, Van Marter LJ, Sun Y, Allred E, Leviton A, Kohane IS | Genome biology | 17916252 | Genome Biol | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17916252 |
| Analysis of sequence conservation at nucleotide resolution. | Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S | PLoS computational biology | 18166073 | PLoS Comput Biol | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18166073 |
| Triplet repeat length bias and variation in the human transcriptome. | Molla M, Delcher A, Sunyaev S, Cantor C, Kasif S | Proceedings of the National Academy of Sciences of the United States of America | 19805156 | Proc Natl Acad Sci U S A | 2009 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/19805156 |
| Pharmacologic therapies for obesity. | Kaplan LM | Gastroenterology clinics of North America | 20202580 | Gastroenterol Clin North Am | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20202580 |
| Evaluating the informatics for integrating biology and the bedside system for clinical research. | Deshmukh VG, Meystre SM, Mitchell JA | BMC medical research methodology | 19863809 | BMC Med Res Methodol | 2009 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/19863809 |
| Different gene regulation strategies revealed by analysis of binding motifs. | Wunderlich Z, Mirny LA | Trends in genetics : TIG | 19815308 | Trends Genet | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19815308 |
| Community annotation experiment for ground truth generation for the i2b2 medication challenge. | Uzuner O, Solti I, Xia F, Cadag E | Journal of the American Medical Informatics Association : JAMIA | 20819855 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819855 |
| Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents. | Meystre SM, Thibault J, Shen S, Hurdle JF, South BR | Journal of the American Medical Informatics Association : JAMIA | 20819864 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819864 |
| Association between fine particulate matter and diabetes prevalence in the U.S. | Pearson JF, Bachireddy C, Shyamprasad S, Goldfine AB, Brownstein JS | Diabetes care | 20628090 | Diabetes Care | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20628090 |
| Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench. | Lazarus R, Taylor J, Qiu W, Nekrutenko A | Summit on translational bioinformatics | 21347127 | Summit Transl Bioinform | 2008 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347127 |
| Improving textual medication extraction using combined conditional random fields and rule-based systems. | Tikk D, Solt I | Journal of the American Medical Informatics Association : JAMIA | 20819860 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819860 |
| Automatic extraction of medication information from medical discharge summaries. | Yang H | Journal of the American Medical Informatics Association : JAMIA | 20819861 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819861 |
| Efficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records. | Luo Y, Szolovits P | Biomedical informatics insights | 27478379 | Biomed Inform Insights | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27478379 |
| Automated systems for the de-identification of longitudinal clinical narratives: Overview of 2014 i2b2/UTHealth shared task Track 1. | Stubbs A, Kotfila C, Uzuner Ö | Journal of biomedical informatics | 26225918 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26225918 |
| Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort. | Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I | Inflammatory bowel diseases | 26332313 | Inflamm Bowel Dis | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26332313 |
| TEMPTING system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries. | Chang YC, Dai HJ, Wu JC, Chen JM, Tsai RT, Hsu WL | Journal of biomedical informatics | 24060600 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24060600 |
| Discovering body site and severity modifiers in clinical texts. | Dligach D, Bethard S, Becker L, Miller T, Savova GK | Journal of the American Medical Informatics Association : JAMIA | 24091648 | J Am Med Inform Assoc | 2014 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/24091648 |
| Extraction of events and temporal expressions from clinical narratives. | Jindal P, Roth D | Journal of biomedical informatics | 24022023 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24022023 |
| Landmark Estimation of Survival and Treatment Effect in a Randomized Clinical Trial. | Parast L, Tian L, Cai T | Journal of the American Statistical Association | 24659838 | J Am Stat Assoc | 2014 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/24659838 |
| Mission and Sustainability of Informatics for Integrating Biology and the Bedside (i2b2). | Murphy S, Wilcox A | EGEMS (Washington, DC) | 25848608 | EGEMS (Wash DC) | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25848608 |
| Classification of CT pulmonary angiography reports by presence, chronicity, and location of pulmonary embolism with natural language processing. | Yu S, Kumamaru KK, George E, Dunne RM, Bedayat A, Neykov M, Hunsaker AR, Dill KE, Cai T, Rybicki FJ | Journal of biomedical informatics | 25117751 | J Biomed Inform | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25117751 |
| Treatment selections using risk-benefit profiles based on data from comparative randomized clinical trials with multiple endpoints. | Claggett B, Tian L, Castagno D, Wei LJ | Biostatistics (Oxford, England) | 25122189 | Biostatistics | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25122189 |
| Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes. | Nogiec C, Burkart A, Dreyfuss JM, Lerin C, Kasif S, Patti ME | Molecular metabolism | 25737951 | Mol Metab | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25737951 |
| Development of phenotype algorithms using electronic medical records and incorporating natural language processing. | Liao KP, Cai T, Savova GK, Murphy SN, Karlson EW, Ananthakrishnan AN, Gainer VS, Shaw SY, Xia Z, Szolovits P, Churchill S, Kohane I | BMJ (Clinical research ed.) | 25911572 | BMJ | 2015 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/25911572 |
| Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. | Yu S, Liao KP, Shaw SY, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T | Journal of the American Medical Informatics Association : JAMIA | 25929596 | J Am Med Inform Assoc | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25929596 |
| Practical applications for natural language processing in clinical research: The 2014 i2b2/UTHealth shared tasks. | Uzuner Ö, Stubbs A | Journal of biomedical informatics | 26515500 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26515500 |
| Development and Validation of an Algorithm to Identify Nonalcoholic Fatty Liver Disease in the Electronic Medical Record. | Corey KE, Kartoun U, Zheng H, Shaw SY | Digestive diseases and sciences | 26537487 | Dig Dis Sci | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26537487 |
| Creation of a new longitudinal corpus of clinical narratives. | Kumar V, Stubbs A, Shaw S, Uzuner Ö | Journal of biomedical informatics | 26433122 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26433122 |
| Temporal Annotation in the Clinical Domain. | Styler WF 4th, Bethard S, Finan S, Palmer M, Pradhan S, de Groen PC, Erickson B, Miller T, Lin C, Savova G, Pustejovsky J | Transactions of the Association for Computational Linguistics | 29082229 | Trans Assoc Comput Linguist | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29082229 |
| Leveraging electronic health records to notify pediatric patients of a drug recall. | Mendelson MM, Zachariah JP, de Ferranti SD, Bickel JP | JAMA pediatrics | 24165895 | JAMA Pediatr | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24165895 |
| Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease. | Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Journal of Crohn's & colitis | 24559536 | J Crohns Colitis | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24559536 |
| Evaluating marker-guided treatment selection strategies. | Matsouaka RA, Li J, Cai T | Biometrics | 24779731 | Biometrics | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24779731 |
| Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. | Sun W, Rumshisky A, Uzuner O | Journal of the American Medical Informatics Association : JAMIA | 23564629 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23564629 |
| Eventual situations for timeline extraction from clinical reports. | Grouin C, Grabar N, Hamon T, Rosset S, Tannier X, Zweigenbaum P | Journal of the American Medical Informatics Association : JAMIA | 23571851 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23571851 |
| Associations of smoking and alcohol consumption with disease activity and functional status in rheumatoid arthritis. | Lu B, Rho YH, Cui J, Iannaccone CK, Frits ML, Karlson EW, Shadick NA | The Journal of rheumatology | 24293566 | J Rheumatol | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24293566 |
| Dominant effects of the Huntington's disease HTT CAG repeat length are captured in gene-expression data sets by a continuous analysis mathematical modeling strategy. | Lee JM, Galkina EI, Levantovsky RM, Fossale E, Anne Anderson M, Gillis T, Srinidhi Mysore J, Coser KR, Shioda T, Zhang B, Furia MD, Derry J, Kohane IS, Seong IS, Wheeler VC, Gusella JF, MacDonald ME | Human molecular genetics | 23595883 | Hum Mol Genet | 2013 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/23595883 |
| Biases in electronic health record data due to processes within the healthcare system: retrospective observational study. | Agniel D, Kohane IS, Weber GM | BMJ (Clinical research ed.) | 29712648 | BMJ | 2018 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/29712648 |
| Association between inflammation and systolic blood pressure in RA compared to patients without RA. | Yu Z, Kim SC, Vanni K, Huang J, Desai R, Murphy SN, Solomon DH, Liao KP | Arthritis research & therapy | 29855349 | Arthritis Res Ther | 2018 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/29855349 |
| Developing a portable natural language processing based phenotyping system. | Sharma H, Mao C, Zhang Y, Vatani H, Yao L, Zhong Y, Rasmussen L, Jiang G, Pathak J, Luo Y | BMC medical informatics and decision making | 30943974 | BMC Med Inform Decis Mak | 2019 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/30943974 |
| Precursor-induced conditional random fields: connecting separate entities by induction for improved clinical named entity recognition. | Lee W, Choi J | BMC medical informatics and decision making | 31307440 | BMC Med Inform Decis Mak | 2019 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/31307440 |
| High-throughput phenotyping with electronic medical record data using a common semi-supervised approach (PheCAP). | Zhang Y, Cai T, Yu S, Cho K, Hong C, Sun J, Huang J, Ho YL, Ananthakrishnan AN, Xia Z, Shaw SY, Gainer V, Castro V, Link N, Honerlaw J, Huang S, Gagnon D, Karlson EW, Plenge RM, Szolovits P, Savova G, Churchill S, O'Donnell C, Murphy SN, Gaziano JM, Kohane I, Cai T, Liao KP | Nature protocols | 31748751 | Nat Protoc | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31748751 |
| Implementing electronic medical record systems in developing countries. | Fraser HS, Biondich P, Moodley D, Choi S, Mamlin BW, Szolovits P | Informatics in primary care | 15992493 | Inform Prim Care | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/15992493 |
| A susceptible-infected model of early detection of respiratory infection outbreaks on a background of influenza. | Mohtashemi M, Szolovits P, Dunyak J, Mandl KD | Journal of theoretical biology | 16556450 | J Theor Biol | 2006 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/16556450 |
| An unsupervised classification method for inferring original case locations from low-resolution disease maps. | Brownstein JS, Cassa CA, Kohane IS, Mandl KD | International journal of health geographics | 17156451 | Int J Health Geogr | 2006 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/17156451 |
| A multivariate approach for integrating genome-wide expression data and biological knowledge. | Kong SW, Pu WT, Park PJ | Bioinformatics (Oxford, England) | 16877751 | Bioinformatics | 2006 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/16877751 |
| DITTO - a tool for identification of patient cohorts from the text of physician notes in the electronic medical record. | Turchin A, Pendergrass ML, Kohane IS | AMIA ... Annual Symposium proceedings. AMIA Symposium | 16779139 | AMIA Annu Symp Proc | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16779139 |
| The incidentalome: a threat to genomic medicine. | Kohane IS, Masys DR, Altman RB | JAMA | 16835427 | JAMA | 2006 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/16835427 |
| Computational analysis of non-adherence and non-attendance using the text of narrative physician notes in the electronic medical record. | Turchin A, Kolatkar NS, Pendergrass ML, Kohane IS | Medical informatics and the Internet in medicine | 17541859 | Med Inform Internet Med | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17541859 |
| Network-based analysis of affected biological processes in type 2 diabetes models. | Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, Kohane IS, Kasif S | PLoS genetics | 17571924 | PLoS Genet | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17571924 |
| Hypermutable non-synonymous sites are under stronger negative selection. | Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Adzuhbei IA, Kondrashov AS, Sunyaev S | PLoS genetics | 19043566 | PLoS Genet | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19043566 |
| The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. | Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS | Journal of the American Medical Informatics Association : JAMIA | 19567788 | J Am Med Inform Assoc | 2009 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/19567788 |
| Transcriptomic analysis of human lung development. | Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS, Kohane IS, Weiss ST, Mariani TJ | American journal of respiratory and critical care medicine | 19815808 | Am J Respir Crit Care Med | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19815808 |
| Recognizing obesity and comorbidities in sparse data. | Uzuner O | Journal of the American Medical Informatics Association : JAMIA | 19390096 | J Am Med Inform Assoc | 2009 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/19390096 |
| Using genome-wide measurements for computational prediction of SH2-peptide interactions. | Wunderlich Z, Mirny LA | Nucleic acids research | 19502496 | Nucleic Acids Res | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19502496 |
| Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside. | Murphy SN, Mendis M, Hackett K, Kuttan R, Pan W, Phillips LC, Gainer V, Berkowicz D, Glaser JP, Kohane I, Chueh HC | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18693896 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18693896 |
| Integration of Hive and cell software in the i2b2 architecture. | Mendis M, Wattanasin N, Kuttan R, Pan W, Philips L, Hackett K, Gainer V, Chueh HC, Murphy S | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18694146 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18694146 |
| Genetic susceptibility to coronary heart disease in type 2 diabetes: 3 independent studies. | Qi L, Parast L, Cai T, Powers C, Gervino EV, Hauser TH, Hu FB, Doria A | Journal of the American College of Cardiology | 22152955 | J Am Coll Cardiol | 2011 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/22152955 |
| A system for coreference resolution for the clinical narrative. | Zheng J, Chapman WW, Miller TA, Lin C, Crowley RS, Savova GK | Journal of the American Medical Informatics Association : JAMIA | 22298565 | J Am Med Inform Assoc | 2012 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/22298565 |
| A classification approach to coreference in discharge summaries: 2011 i2b2 challenge. | Xu Y, Liu J, Wu J, Wang Y, Tu Z, Sun JT, Tsujii J, Chang EI | Journal of the American Medical Informatics Association : JAMIA | 22505762 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22505762 |
| MCORES: a system for noun phrase coreference resolution for clinical records. | Bodnari A, Szolovits P, Uzuner Ö | Journal of the American Medical Informatics Association : JAMIA | 22419739 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22419739 |
| A cascade of classifiers for extracting medication information from discharge summaries. | Halgrim SR, Xia F, Solti I, Cadag E, Uzuner O | Journal of biomedical semantics | 21992591 | J Biomed Semantics | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21992591 |
| Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease. | Ananthakrishnan AN, Guzman-Perez R, Gainer V, Cai T, Churchill S, Kohane I, Plenge RM, Murphy S | Alimentary pharmacology & therapeutics | 22360370 | Aliment Pharmacol Ther | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22360370 |
| Novel data-mining methodologies for adverse drug event discovery and analysis. | Harpaz R, DuMouchel W, Shah NH, Madigan D, Ryan P, Friedman C | Clinical pharmacology and therapeutics | 22549283 | Clin Pharmacol Ther | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22549283 |
| Graphical procedures for evaluating overall and subject-specific incremental values from new predictors with censored event time data. | Uno H, Cai T, Tian L, Wei LJ | Biometrics | 21504421 | Biometrics | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21504421 |
| Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification. | Minard AL, Ligozat AL, Ben Abacha A, Bernhard D, Cartoni B, Deléger L, Grau B, Rosset S, Zweigenbaum P, Grouin C | Journal of the American Medical Informatics Association : JAMIA | 21597105 | J Am Med Inform Assoc | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21597105 |
| Meta-analysis for rare events. | Cai T, Parast L, Ryan L | Statistics in medicine | 20623822 | Stat Med | 2010 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/20623822 |
| Lancet: a high precision medication event extraction system for clinical text. | Li Z, Liu F, Antieau L, Cao Y, Yu H | Journal of the American Medical Informatics Association : JAMIA | 20819865 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819865 |
| The association of plasma resistin with dietary sodium manipulation, the renin-angiotensin-aldosterone system, and 25-hydroxyvitamin D3 in human hypertension. | Vaidya A, Pojoga L, Underwood PC, Forman JP, Hopkins PN, Williams GH, Williams JS | Clinical endocrinology | 21050256 | Clin Endocrinol (Oxf) | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21050256 |
| Using electronic medical records to enable large-scale studies in psychiatry: treatment resistant depression as a model. | Perlis RH, Iosifescu DV, Castro VM, Murphy SN, Gainer VS, Minnier J, Cai T, Goryachev S, Zeng Q, Gallagher PJ, Fava M, Weilburg JB, Churchill SE, Kohane IS, Smoller JW | Psychological medicine | 21682950 | Psychol Med | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21682950 |
| 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. | Uzuner Ö, South BR, Shen S, DuVall SL | Journal of the American Medical Informatics Association : JAMIA | 21685143 | J Am Med Inform Assoc | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21685143 |
| Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). | Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, Kohane I | Journal of the American Medical Informatics Association : JAMIA | 20190053 | J Am Med Inform Assoc | 2010 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/20190053 |
| The role of mitochondria in the pathogenesis of type 2 diabetes. | Patti ME, Corvera S | Endocrine reviews | 20156986 | Endocr Rev | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20156986 |
| Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical records. | Brownstein JS, Murphy SN, Goldfine AB, Grant RW, Sordo M, Gainer V, Colecchi JA, Dubey A, Nathan DM, Glaser JP, Kohane IS | Diabetes care | 20009093 | Diabetes Care | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20009093 |
| Classifying temporal relations in clinical data: a hybrid, knowledge-rich approach. | D'Souza J, Ng V | Journal of biomedical informatics | 23954311 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23954311 |
| Chronology of your health events: approaches to extracting temporal relations from medical narratives. | Uzuner Ö, Stubbs A, Sun W | Journal of biomedical informatics | 24286753 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24286753 |
| Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods. | Chasin R, Rumshisky A, Uzuner O, Szolovits P | Journal of the American Medical Informatics Association : JAMIA | 24441986 | J Am Med Inform Assoc | 2014 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/24441986 |
| EFFECTIVELY SELECTING A TARGET POPULATION FOR A FUTURE COMPARATIVE STUDY. | Zhao L, Tian L, Cai T, Claggett B, Wei LJ | Journal of the American Statistical Association | 24058223 | J Am Stat Assoc | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/24058223 |
| Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases. | Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 24161349 | Clin Gastroenterol Hepatol | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24161349 |
| Extracting physician group intelligence from electronic health records to support evidence based medicine. | Weber GM, Kohane IS | PloS one | 23734227 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23734227 |
| Normalization of plasma 25-hydroxy vitamin D is associated with reduced risk of surgery in Crohn's disease. | Ananthakrishnan AN, Cagan A, Gainer VS, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Plenge RM, Murphy SN, Liao KP | Inflammatory bowel diseases | 23751398 | Inflamm Bowel Dis | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23751398 |
| Improved de-identification of physician notes through integrative modeling of both public and private medical text. | McMurry AJ, Fitch B, Savova G, Kohane IS, Reis BY | BMC medical informatics and decision making | 24083569 | BMC Med Inform Decis Mak | 2013 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/24083569 |
| Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records. | Lin C, Karlson EW, Canhao H, Miller TA, Dligach D, Chen PJ, Perez RN, Shen Y, Weinblatt ME, Shadick NA, Plenge RM, Savova GK | PloS one | 23976944 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23976944 |
| Modeling disease severity in multiple sclerosis using electronic health records. | Xia Z, Secor E, Chibnik LB, Bove RM, Cheng S, Chitnis T, Cagan A, Gainer VS, Chen PJ, Liao KP, Shaw SY, Ananthakrishnan AN, Szolovits P, Weiner HL, Karlson EW, Murphy SN, Savova GK, Cai T, Churchill SE, Plenge RM, Kohane IS, De Jager PL | PloS one | 24244385 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24244385 |
| Potential for electronic health records and online social networking to redefine medical research. | Pearson JF, Brownstein CA, Brownstein JS | Clinical chemistry | 21159898 | Clin Chem | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21159898 |
| Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records. | Kurreeman F, Liao K, Chibnik L, Hickey B, Stahl E, Gainer V, Li G, Bry L, Mahan S, Ardlie K, Thomson B, Szolovits P, Churchill S, Murphy SN, Cai T, Raychaudhuri S, Kohane I, Karlson E, Plenge RM | American journal of human genetics | 21211616 | Am J Hum Genet | 2011 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/21211616 |
| The emerging role of electronic medical records in pharmacogenomics. | Wilke RA, Xu H, Denny JC, Roden DM, Krauss RM, McCarty CA, Davis RL, Skaar T, Lamba J, Savova G | Clinical pharmacology and therapeutics | 21248726 | Clin Pharmacol Ther | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21248726 |
| The association of the angiotensinogen gene with insulin sensitivity in humans: a tagging single nucleotide polymorphism and haplotype approach. | Underwood PC, Sun B, Williams JS, Pojoga LH, Raby B, Lasky-Su J, Hunt S, Hopkins PN, Jeunemaitre X, Adler GK, Williams GH | Metabolism: clinical and experimental | 21306748 | Metabolism | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21306748 |
| Comprehensive genetic assessment of a functional TLR9 promoter polymorphism: no replicable association with asthma or asthma-related phenotypes. | Lange NE, Zhou X, Lasky-Su J, Himes BE, Lazarus R, Soto-Quirós M, Avila L, Celedón JC, Hawrylowicz CM, Raby BA, Litonjua AA | BMC medical genetics | 21324137 | BMC Med Genet | 2011 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/21324137 |
| A controlled greedy supervised approach for co-reference resolution on clinical text. | Chowdhury MF, Zweigenbaum P | Journal of biomedical informatics | 23562650 | J Biomed Inform | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23562650 |
| Temporal reasoning over clinical text: the state of the art. | Sun W, Rumshisky A, Uzuner O | Journal of the American Medical Informatics Association : JAMIA | 23676245 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23676245 |
| A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. | Palmer NP, Schmid PR, Berger B, Kohane IS | Genome biology | 22909066 | Genome Biol | 2012 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/22909066 |
| Antidepressant response in patients with major depression exposed to NSAIDs: a pharmacovigilance study. | Gallagher PJ, Castro V, Fava M, Weilburg JB, Murphy SN, Gainer VS, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH | The American journal of psychiatry | 23032386 | Am J Psychiatry | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23032386 |
| A unified inference procedure for a class of measures to assess improvement in risk prediction systems with survival data. | Uno H, Tian L, Cai T, Kohane IS, Wei LJ | Statistics in medicine | 23037800 | Stat Med | 2013 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/23037800 |
| Salt sensitivity of blood pressure is associated with polymorphisms in the sodium-bicarbonate cotransporter. | Carey RM, Schoeffel CD, Gildea JJ, Jones JE, McGrath HE, Gordon LN, Park MJ, Sobota RS, Underwood PC, Williams J, Sun B, Raby B, Lasky-Su J, Hopkins PN, Adler GK, Williams SM, Jose PA, Felder RA | Hypertension (Dallas, Tex. : 1979) | 22987918 | Hypertension | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22987918 |
| The relationship between structural characteristics of 2010 challenge documents and ratings of document quality. | Shen S, South BR, Butler J, Barrus R, Weir C | AMIA ... Annual Symposium proceedings. AMIA Symposium | 23304359 | AMIA Annu Symp Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23304359 |
| Landmark risk prediction of residual life for breast cancer survival. | Parast L, Cai T | Statistics in medicine | 23494768 | Stat Med | 2013 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/23494768 |
| Federated queries of clinical data repositories: Scaling to a national network. | Weber GM | Journal of biomedical informatics | 25957825 | J Biomed Inform | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25957825 |
| Higher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases. | Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Alimentary pharmacology & therapeutics | 24641590 | Aliment Pharmacol Ther | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24641590 |
| Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases. | Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 26905907 | Clin Gastroenterol Hepatol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26905907 |
| Ease of adoption of clinical natural language processing software: An evaluation of five systems. | Zheng K, Vydiswaran VGV, Liu Y, Wang Y, Stubbs A, Uzuner Ö, Gururaj AE, Bayer S, Aberdeen J, Rumshisky A, Pakhomov S, Liu H, Xu H | Journal of biomedical informatics | 26210361 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26210361 |
| Response to letters regarding article, "unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine". | Ghebremariam YT, Lee JC, LePendu P, Erlanson DA, Slaviero A, Shah NH, Leiper JM, Cooke JP | Circulation | 24687654 | Circulation | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24687654 |
| HD CAGnome: a search tool for huntingtin CAG repeat length-correlated genes. | Galkina EI, Shin A, Coser KR, Shioda T, Kohane IS, Seong IS, Wheeler VC, Gusella JF, Macdonald ME, Lee JM | PloS one | 24751919 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24751919 |
| Colonoscopy is associated with a reduced risk for colon cancer and mortality in patients with inflammatory bowel diseases. | Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 25041865 | Clin Gastroenterol Hepatol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25041865 |
| Genetic Misdiagnoses and the Potential for Health Disparities. | Manrai AK, Funke BH, Rehm HL, Olesen MS, Maron BA, Szolovits P, Margulies DM, Loscalzo J, Kohane IS | The New England journal of medicine | 27532831 | N Engl J Med | 2016 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/27532831 |
| Using an Electronic Medical Records Database to Identify Non-Traditional Cardiovascular Risk Factors in Nonalcoholic Fatty Liver Disease. | Corey KE, Kartoun U, Zheng H, Chung RT, Shaw SY | The American journal of gastroenterology | 26925881 | Am J Gastroenterol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26925881 |
| Exploiting Unlabeled Texts with Clustering-based Instance Selection for Medical Relation Classification. | Kim Y, Riloff E, Meystre SM | AMIA ... Annual Symposium proceedings. AMIA Symposium | 29854174 | AMIA Annu Symp Proc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29854174 |
| Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes. | Luo Y, Cheng Y, Uzuner Ö, Szolovits P, Starren J | Journal of the American Medical Informatics Association : JAMIA | 29025149 | J Am Med Inform Assoc | 2018 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/29025149 |
| Renin Phenotypes Characterize Vascular Disease, Autonomous Aldosteronism, and Mineralocorticoid Receptor Activity. | Hundemer GL, Baudrand R, Brown JM, Curhan G, Williams GH, Vaidya A | The Journal of clinical endocrinology and metabolism | 28323995 | J Clin Endocrinol Metab | 2017 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/28323995 |
| A Preliminary Study of Clinical Concept Detection Using Syntactic Relations. | Torii M, Yang EW, Doan S | AMIA ... Annual Symposium proceedings. AMIA Symposium | 30815146 | AMIA Annu Symp Proc | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30815146 |
| A knowledge discovery and reuse pipeline for information extraction in clinical notes. | Patrick JD, Nguyen DH, Wang Y, Li M | Journal of the American Medical Informatics Association : JAMIA | 21737844 | J Am Med Inform Assoc | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21737844 |
| Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions. | Chapman WW, Nadkarni PM, Hirschman L, D'Avolio LW, Savova GK, Uzuner O | Journal of the American Medical Informatics Association : JAMIA | 21846785 | J Am Med Inform Assoc | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21846785 |
| HD CAG-correlated gene expression changes support a simple dominant gain of function. | Jacobsen JC, Gregory GC, Woda JM, Thompson MN, Coser KR, Murthy V, Kohane IS, Gusella JF, Seong IS, MacDonald ME, Shioda T, Lee JM | Human molecular genetics | 21536587 | Hum Mol Genet | 2011 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/21536587 |
| Strategies for maintaining patient privacy in i2b2. | Murphy SN, Gainer V, Mendis M, Churchill S, Kohane I | Journal of the American Medical Informatics Association : JAMIA | 21984588 | J Am Med Inform Assoc | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21984588 |
| Phenotyping patient-derived cells for translational studies in cardiovascular disease. | Shaw SY, Brettman AD | Circulation | 22125190 | Circulation | 2011 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/22125190 |
| Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. | Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML | Molecular systems biology | 22146299 | Mol Syst Biol | 2011 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/22146299 |
| Regulation of X-chromosome inactivation by the X-inactivation centre. | Augui S, Nora EP, Heard E | Nature reviews. Genetics | 21587299 | Nat Rev Genet | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21587299 |
| The Fok1 vitamin D receptor gene polymorphism is associated with plasma renin activity in Caucasians. | Vaidya A, Sun B, Forman JP, Hopkins PN, Brown NJ, Kolatkar NS, Williams GH, Williams JS | Clinical endocrinology | 21521263 | Clin Endocrinol (Oxf) | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21521263 |
| Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. | Kovacevic A, Dehghan A, Filannino M, Keane JA, Nenadic G | Journal of the American Medical Informatics Association : JAMIA | 23605114 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23605114 |
| SHRINE: enabling nationally scalable multi-site disease studies. | McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, Bickel J, Wattanasin N, Gilbert C, Trevvett P, Churchill S, Kohane IS | PloS one | 23533569 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23533569 |
| Evaluating incremental values from new predictors with net reclassification improvement in survival analysis. | Zheng Y, Parast L, Cai T, Brown M | Lifetime data analysis | 23254468 | Lifetime Data Anal | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23254468 |
| Subgroup specific incremental value of new markers for risk prediction. | Zhou QM, Zheng Y, Cai T | Lifetime data analysis | 23263882 | Lifetime Data Anal | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23263882 |
| Abnormal aldosterone physiology and cardiometabolic risk factors. | Vaidya A, Underwood PC, Hopkins PN, Jeunemaitre X, Ferri C, Williams GH, Adler GK | Hypertension (Dallas, Tex. : 1979) | 23399714 | Hypertension | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23399714 |
| Evaluating the predictive value of biomarkers with stratified case-cohort design. | Liu D, Cai T, Zheng Y | Biometrics | 23173848 | Biometrics | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23173848 |
| Landmark Prediction of Long Term Survival Incorporating Short Term Event Time Information. | Parast L, Cheng SC, Cai T | Journal of the American Statistical Association | 23293405 | J Am Stat Assoc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23293405 |
| MedTime: a temporal information extraction system for clinical narratives. | Lin YK, Chen H, Brown RA | Journal of biomedical informatics | 23911344 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23911344 |
| Improving case definition of Crohn's disease and ulcerative colitis in electronic medical records using natural language processing: a novel informatics approach. | Ananthakrishnan AN, Cai T, Savova G, Cheng SC, Chen P, Perez RG, Gainer VS, Murphy SN, Szolovits P, Xia Z, Shaw S, Churchill S, Karlson EW, Kohane I, Plenge RM, Liao KP | Inflammatory bowel diseases | 23567779 | Inflamm Bowel Dis | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23567779 |
| Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: a pilot study. | Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV | Psychiatry research | 23149041 | Psychiatry Res | 2013 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/23149041 |
| Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis. | Diogo D, Kurreeman F, Stahl EA, Liao KP, Gupta N, Greenberg JD, Rivas MA, Hickey B, Flannick J, Thomson B, Guiducci C, Ripke S, Adzhubey I, Barton A, Kremer JM, Alfredsson L, Consortium of Rheumatology Researchers of North America, Rheumatoid Arthritis Consortium International, Sunyaev S, Martin J, Zhernakova A, Bowes J, Eyre S, Siminovitch KA, Gregersen PK, Worthington J, Klareskog L, Padyukov L, Raychaudhuri S, Plenge RM | American journal of human genetics | 23261300 | Am J Hum Genet | 2013 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/23261300 |
| Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. | Liao KP, Kurreeman F, Li G, Duclos G, Murphy S, Guzman R, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM | Arthritis and rheumatism | 23233247 | Arthritis Rheum | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23233247 |
| Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. | Wolfe CJ, Kohane IS, Butte AJ | BMC bioinformatics | 16162296 | BMC Bioinformatics | 2005 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/16162296 |
| Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. | Lee S, Kohane I, Kasif S | BMC genomics | 16309559 | BMC Genomics | 2005 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/16309559 |
| Creation and implications of a phenome-genome network. | Butte AJ, Kohane IS | Nature biotechnology | 16404398 | Nat Biotechnol | 2006 Jan | https://www.ncbi.nlm.nih.gov/pubmed/16404398 |
| GEMS: a web server for biclustering analysis of expression data. | Wu CJ, Kasif S | Nucleic acids research | 15980544 | Nucleic Acids Res | 2005 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/15980544 |
| Expression differences by continent of origin point to the immortalization process. | Davis AR, Kohane IS | Human molecular genetics | 19628477 | Hum Mol Genet | 2009 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/19628477 |
| Electronic medical records for discovery research in rheumatoid arthritis. | Liao KP, Cai T, Gainer V, Goryachev S, Zeng-treitler Q, Raychaudhuri S, Szolovits P, Churchill S, Murphy S, Kohane I, Karlson EW, Plenge RM | Arthritis care & research | 20235204 | Arthritis Care Res (Hoboken) | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20235204 |
| Part-of-speech tagging for clinical text: wall or bridge between institutions? | Fan JW, Prasad R, Yabut RM, Loomis RM, Zisook DS, Mattison JE, Huang Y | AMIA ... Annual Symposium proceedings. AMIA Symposium | 22195091 | AMIA Annu Symp Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22195091 |
| Technical desiderata for the integration of genomic data into Electronic Health Records. | Masys DR, Jarvik GP, Abernethy NF, Anderson NR, Papanicolaou GJ, Paltoo DN, Hoffman MA, Kohane IS, Levy HP | Journal of biomedical informatics | 22223081 | J Biomed Inform | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22223081 |
| Polymorphisms in the serum- and glucocorticoid-inducible kinase 1 gene are associated with blood pressure and renin response to dietary salt intake. | Rao AD, Sun B, Saxena A, Hopkins PN, Jeunemaitre X, Brown NJ, Adler GK, Williams JS | Journal of human hypertension | 22648267 | J Hum Hypertens | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22648267 |
| Limbic system white matter microstructure and long-term treatment outcome in major depressive disorder: a diffusion tensor imaging study using legacy data. | Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV | The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry | 22540406 | World J Biol Psychiatry | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22540406 |
| The coming age of data-driven medicine: translational bioinformatics' next frontier. | Shah NH, Tenenbaum JD | Journal of the American Medical Informatics Association : JAMIA | 22718035 | J Am Med Inform Assoc | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22718035 |
| Recognition of medication information from discharge summaries using ensembles of classifiers. | Doan S, Collier N, Xu H, Pham HD, Tu MP | BMC medical informatics and decision making | 22564405 | BMC Med Inform Decis Mak | 2012 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/22564405 |
| A supervised framework for resolving coreference in clinical records. | Rink B, Roberts K, Harabagiu SM | Journal of the American Medical Informatics Association : JAMIA | 22610493 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22610493 |
| Towards automatic diabetes case detection and ABCS protocol compliance assessment. | Mishra NK, Son RY, Arnzen JJ | Clinical medicine & research | 22634542 | Clin Med Res | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22634542 |
| A mega-analysis of genome-wide association studies for major depressive disorder. | Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium, Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, Breen G, Byrne EM, Blackwood DH, Boomsma DI, Cichon S, Heath AC, Holsboer F, Lucae S, Madden PA, Martin NG, McGuffin P, Muglia P, Noethen MM, Penninx BP, Pergadia ML, Potash JB, Rietschel M, Lin D, Müller-Myhsok B, Shi J, Steinberg S, Grabe HJ, Lichtenstein P, Magnusson P, Perlis RH, Preisig M, Smoller JW, Stefansson K, Uher R, Kutalik Z, Tansey KE, Teumer A, Viktorin A, Barnes MR, Bettecken T, Binder EB, Breuer R, Castro VM, Churchill SE, Coryell WH, Craddock N, Craig IW, Czamara D, De Geus EJ, Degenhardt F, Farmer AE, Fava M, Frank J, Gainer VS, Gallagher PJ, Gordon SD, Goryachev S, Gross M, Guipponi M, Henders AK, Herms S, Hickie IB, Hoefels S, Hoogendijk W, Hottenga JJ, Iosifescu DV, Ising M, Jones I, Jones L, Jung-Ying T, Knowles JA, Kohane IS, Kohli MA, Korszun A, Landen M, Lawson WB, Lewis G, Macintyre D, Maier W, Mattheisen M, McGrath PJ, McIntosh A, McLean A, Middeldorp CM, Middleton L, Montgomery GM, Murphy SN, Nauck M, Nolen WA, Nyholt DR, O'Donovan M, Oskarsson H, Pedersen N, Scheftner WA, Schulz A, Schulze TG, Shyn SI, Sigurdsson E, Slager SL, Smit JH, Stefansson H, Steffens M, Thorgeirsson T, Tozzi F, Treutlein J, Uhr M, van den Oord EJ, Van Grootheest G, Völzke H, Weilburg JB, Willemsen G, Zitman FG, Neale B, Daly M, Levinson DF, Sullivan PF | Molecular psychiatry | 22472876 | Mol Psychiatry | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22472876 |
| The co-morbidity burden of children and young adults with autism spectrum disorders. | Kohane IS, McMurry A, Weber G, MacFadden D, Rappaport L, Kunkel L, Bickel J, Wattanasin N, Spence S, Murphy S, Churchill S | PloS one | 22511918 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22511918 |
| Machine learning-based coreference resolution of concepts in clinical documents. | Ware H, Mullett CJ, Jagannathan V, El-Rawas O | Journal of the American Medical Informatics Association : JAMIA | 22582205 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22582205 |
| Thromboprophylaxis is associated with reduced post-hospitalization venous thromboembolic events in patients with inflammatory bowel diseases. | Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Scoville E, Konijeti GG, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 24632349 | Clin Gastroenterol Hepatol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24632349 |
| Opportunities for genomic clinical decision support interventions. | Overby CL, Kohane I, Kannry JL, Williams MS, Starren J, Bottinger E, Gottesman O, Denny JC, Weng C, Tarczy-Hornoch P, Hripcsak G | Genetics in medicine : official journal of the American College of Medical Genetics | 24051479 | Genet Med | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24051479 |
| Predicting the restricted mean event time with the subject's baseline covariates in survival analysis. | Tian L, Zhao L, Wei LJ | Biostatistics (Oxford, England) | 24292992 | Biostatistics | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24292992 |
| Omnibus risk assessment via accelerated failure time kernel machine modeling. | Sinnott JA, Cai T | Biometrics | 24328713 | Biometrics | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24328713 |
| Rare copy number variation in treatment-resistant major depressive disorder. | O'Dushlaine C, Ripke S, Ruderfer DM, Hamilton SP, Fava M, Iosifescu DV, Kohane IS, Churchill SE, Castro VM, Clements CC, Blumenthal SR, Murphy SN, Smoller JW, Perlis RH | Biological psychiatry | 24529801 | Biol Psychiatry | 2014 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/24529801 |
| Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. | Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ | Cell | 24183448 | Cell | 2013 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/24183448 |
| Using search queries for malaria surveillance, Thailand. | Ocampo AJ, Chunara R, Brownstein JS | Malaria journal | 24188069 | Malar J | 2013 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/24188069 |
| Assessment of biomarkers for risk prediction with nested case-control studies. | Zhou QM, Zheng Y, Cai T | Clinical trials (London, England) | 24013405 | Clin Trials | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24013405 |
| Three approaches to automatic assignment of ICD-9-CM codes to radiology reports. | Goldstein I, Arzrumtsyan A, Uzuner O | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18693842 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18693842 |
| Second i2b2 workshop on natural language processing challenges for clinical records. | Uzuner O | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18998924 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18998924 |
| Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancy. | Liu H, Kohane IS | PloS one | 19415117 | PLoS One | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19415117 |
| Human mutation rate associated with DNA replication timing. | Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR | Nature genetics | 19287383 | Nat Genet | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19287383 |
| Exact and efficient inference procedure for meta-analysis and its application to the analysis of independent 2 x 2 tables with all available data but without artificial continuity correction. | Tian L, Cai T, Pfeffer MA, Piankov N, Cremieux PY, Wei LJ | Biostatistics (Oxford, England) | 18922759 | Biostatistics | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18922759 |
| Two approaches to assertion classification. | Uzuner O, Zhang X, Sibanda T | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18999049 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18999049 |
| Optimal screening for promising genes in 2-stage designs. | Moerkerke B, Goetghebeur E | Biostatistics (Oxford, England) | 18349035 | Biostatistics | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18349035 |
| Integrating outside modules into the i2b2 architecture. | Mendis M, Phillips LC, Kuttan R, Pan W, Gainer V, Kohane I, Murphy SN | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18999021 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18999021 |
| Identification and extraction of family history information from clinical reports. | Goryachev S, Kim H, Zeng-Treitler Q | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18999129 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18999129 |
| Hierarchical tree snipping: clustering guided by prior knowledge. | Dotan-Cohen D, Melkman AA, Kasif S | Bioinformatics (Oxford, England) | 17989094 | Bioinformatics | 2007 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/17989094 |
| A de-identifier for medical discharge summaries. | Uzuner O, Sibanda TC, Luo Y, Szolovits P | Artificial intelligence in medicine | 18053696 | Artif Intell Med | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18053696 |
| The tell-tale heart: population-based surveillance reveals an association of rofecoxib and celecoxib with myocardial infarction. | Brownstein JS, Sordo M, Kohane IS, Mandl KD | PloS one | 17786211 | PLoS One | 2007 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/17786211 |
| Effect of acute aldosterone administration on gene expression profile in the heart. | Turchin A, Guo CZ, Adler GK, Ricchiuti V, Kohane IS, Williams GH | Endocrinology | 16601137 | Endocrinology | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16601137 |
| Syntactically-informed semantic category recognition in discharge summaries. | Sibanda T, He T, Szolovits P, Uzuner O | AMIA ... Annual Symposium proceedings. AMIA Symposium | 17238434 | AMIA Annu Symp Proc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17238434 |
| Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. | Kryukov GV, Pennacchio LA, Sunyaev SR | American journal of human genetics | 17357078 | Am J Hum Genet | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17357078 |
| Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development. | Liu H, Kho AT, Kohane IS, Sun Y | PLoS medicine | 16800721 | PLoS Med | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16800721 |
| Phase II study of neoadjuvant bevacizumab and radiotherapy for resectable soft tissue sarcomas. | Yoon SS, Duda DG, Karl DL, Kim TM, Kambadakone AR, Chen YL, Rothrock C, Rosenberg AE, Nielsen GP, Kirsch DG, Choy E, Harmon DC, Hornicek FJ, Dreyfuss J, Ancukiewicz M, Sahani DV, Park PJ, Jain RK, Delaney TF | International journal of radiation oncology, biology, physics | 20932656 | Int J Radiat Oncol Biol Phys | 2011 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/20932656 |
| Medication information extraction with linguistic pattern matching and semantic rules. | Spasic I, Sarafraz F, Keane JA, Nenadic G | Journal of the American Medical Informatics Association : JAMIA | 20819858 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819858 |
| Phosphoproteomics. | Ozlu N, Akten B, Timm W, Haseley N, Steen H, Steen JAJ | Wiley interdisciplinary reviews. Systems biology and medicine | 20836028 | Wiley Interdiscip Rev Syst Biol Med | 2010 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/20836028 |
| Analysis of randomized comparative clinical trial data for personalized treatment selections. | Cai T, Tian L, Wong PH, Wei LJ | Biostatistics (Oxford, England) | 20876663 | Biostatistics | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20876663 |
| The relationship between peroxisome proliferator-activated receptor-gamma and renin: a human genetics study. | Underwood PC, Sun B, Williams JS, Pojoga LH, Chamarthi B, Lasky-Su J, Raby BA, Hopkins PN, Jeunemaitre X, Brown NJ, Adler GK, Williams GH | The Journal of clinical endocrinology and metabolism | 20631015 | J Clin Endocrinol Metab | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20631015 |
| Semantic relations for problem-oriented medical records. | Uzuner O, Mailoa J, Ryan R, Sibanda T | Artificial intelligence in medicine | 20646918 | Artif Intell Med | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20646918 |
| Increased SRF transcriptional activity in human and mouse skeletal muscle is a signature of insulin resistance. | Jin W, Goldfine AB, Boes T, Henry RR, Ciaraldi TP, Kim EY, Emecan M, Fitzpatrick C, Sen A, Shah A, Mun E, Vokes V, Schroeder J, Tatro E, Jimenez-Chillaron J, Patti ME | The Journal of clinical investigation | 21393865 | J Clin Invest | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21393865 |
| Extracting Rx information from clinical narrative. | Mork JG, Bodenreider O, Demner-Fushman D, Dogan RI, Lang FM, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR | Journal of the American Medical Informatics Association : JAMIA | 20819859 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819859 |
| Extracting medical information from narrative patient records: the case of medication-related information. | Deléger L, Grouin C, Zweigenbaum P | Journal of the American Medical Informatics Association : JAMIA | 20819863 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819863 |
| Age-Related Autonomous Aldosteronism. | Nanba K, Vaidya A, Williams GH, Zheng I, Else T, Rainey WE | Circulation | 28566337 | Circulation | 2017 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/28566337 |
| The MELD-Plus: A generalizable prediction risk score in cirrhosis. | Kartoun U, Corey KE, Simon TG, Zheng H, Aggarwal R, Ng K, Shaw SY | PloS one | 29069090 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29069090 |
| Recurrent neural networks for classifying relations in clinical notes. | Luo Y | Journal of biomedical informatics | 28694119 | J Biomed Inform | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28694119 |
| Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. | Kuo TT, Rao P, Maehara C, Doan S, Chaparro JD, Day ME, Farcas C, Ohno-Machado L, Hsu CN | AMIA ... Annual Symposium proceedings. AMIA Symposium | 28269947 | AMIA Annu Symp Proc | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28269947 |
| PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. | Sinnott JA, Cai F, Yu S, Hejblum BP, Hong C, Kohane IS, Liao KP | Journal of the American Medical Informatics Association : JAMIA | 29788308 | J Am Med Inform Assoc | 2018 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/29788308 |
| Qualitative analysis of manual annotations of clinical text with SNOMED CT. | Miñarro-Giménez JA, Martínez-Costa C, Karlsson D, Schulz S, Gøeg KR | PloS one | 30589855 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30589855 |
| Classifying relations in clinical narratives using segment graph convolutional and recurrent neural networks (Seg-GCRNs). | Li Y, Jin R, Luo Y | Journal of the American Medical Informatics Association : JAMIA | 30590613 | J Am Med Inform Assoc | 2019 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/30590613 |
| Ensemble-based Methods to Improve De-identification of Electronic Health Record Narratives. | Kim Y, Heider P, Meystre S | AMIA ... Annual Symposium proceedings. AMIA Symposium | 30815108 | AMIA Annu Symp Proc | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30815108 |
| Semi-supervised Learning for Phenotyping Tasks. | Dligach D, Miller T, Savova GK | AMIA ... Annual Symposium proceedings. AMIA Symposium | 26958183 | AMIA Annu Symp Proc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26958183 |
| Building a tobacco user registry by extracting multiple smoking behaviors from clinical notes. | Palmer EL, Hassanpour S, Higgins J, Doherty JA, Onega T | BMC medical informatics and decision making | 31340796 | BMC Med Inform Decis Mak | 2019 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/31340796 |
| ClinicalTrials.gov as a data source for semi-automated point-of-care trial eligibility screening. | Pfiffner PB, Oh J, Miller TA, Mandl KD | PloS one | 25334031 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25334031 |
| Identifying risk factors for heart disease over time: Overview of 2014 i2b2/UTHealth shared task Track 2. | Stubbs A, Kotfila C, Xu H, Uzuner Ö | Journal of biomedical informatics | 26210362 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26210362 |
| Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases. | Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ | Inflammatory bowel diseases | 26241000 | Inflamm Bowel Dis | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26241000 |
| Text mining in cancer gene and pathway prioritization. | Luo Y, Riedlinger G, Szolovits P | Cancer informatics | 25392685 | Cancer Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25392685 |
| Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts. | Liao KP, Ananthakrishnan AN, Kumar V, Xia Z, Cagan A, Gainer VS, Goryachev S, Chen P, Savova GK, Agniel D, Churchill S, Lee J, Murphy SN, Plenge RM, Szolovits P, Kohane I, Shaw SY, Karlson EW, Cai T | PloS one | 26301417 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26301417 |
| Coronary artery disease risk assessment from unstructured electronic health records using text mining. | Jonnagaddala J, Liaw ST, Ray P, Kumar M, Chang NW, Dai HJ | Journal of biomedical informatics | 26319542 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26319542 |
| Identification of rare germline copy number variations over-represented in five human cancer types. | Park RW, Kim TM, Kasif S, Park PJ | Molecular cancer | 25644941 | Mol Cancer | 2015 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/25644941 |
| Identification and Progression of Heart Disease Risk Factors in Diabetic Patients from Longitudinal Electronic Health Records. | Jonnagaddala J, Liaw ST, Ray P, Kumar M, Dai HJ, Hsu CY | BioMed research international | 26380290 | Biomed Res Int | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26380290 |
| Improving the power of genetic association tests with imperfect phenotype derived from electronic medical records. | Sinnott JA, Dai W, Liao KP, Shaw SY, Ananthakrishnan AN, Gainer VS, Karlson EW, Churchill S, Szolovits P, Murphy S, Kohane I, Plenge R, Cai T | Human genetics | 25062868 | Hum Genet | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25062868 |
| Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. | Lin C, Karlson EW, Dligach D, Ramirez MP, Miller TA, Mo H, Braggs NS, Cagan A, Gainer V, Denny JC, Savova GK | Journal of the American Medical Informatics Association : JAMIA | 25344930 | J Am Med Inform Assoc | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25344930 |
| Predictors of plasma and urinary catecholamine levels in normotensive and hypertensive men and women. | Saxena AR, Chamarthi B, Williams GH, Hopkins PN, Seely EW | Journal of human hypertension | 24226101 | J Hum Hypertens | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24226101 |
| Population-level evidence for an autoimmune etiology of epilepsy. | Ong MS, Kohane IS, Cai T, Gorman MP, Mandl KD | JAMA neurology | 24687183 | JAMA Neurol | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24687183 |
| Multilayered temporal modeling for the clinical domain. | Lin C, Dligach D, Miller TA, Bethard S, Savova GK | Journal of the American Medical Informatics Association : JAMIA | 26521301 | J Am Med Inform Assoc | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26521301 |
| Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. | Luo Y, Uzuner Ö, Szolovits P | Briefings in bioinformatics | 26851224 | Brief Bioinform | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26851224 |
| Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study. | Castro VM, Kong SW, Clements CC, Brady R, Kaimal AJ, Doyle AE, Robinson EB, Churchill SE, Kohane IS, Perlis RH | Translational psychiatry | 26731445 | Transl Psychiatry | 2016 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/26731445 |
| A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. | Liu F, Park PJ, Lai W, Maher E, Chakravarti A, Durso L, Jiang X, Yu Y, Brosius A, Thomas M, Chin L, Brennan C, DePinho RA, Kohane I, Carroll RS, Black PM, Johnson MD | Cancer research | 17090523 | Cancer Res | 2006 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/17090523 |
| Genetic criteria for Huntington's disease pathogenesis. | Gusella JF, Macdonald M | Brain research bulletin | 17352930 | Brain Res Bull | 2007 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/17352930 |
| Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location. | Inaoka H, Fukuoka Y, Kohane IS | Proceedings of the National Academy of Sciences of the United States of America | 17360362 | Proc Natl Acad Sci U S A | 2007 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/17360362 |
| Selecting "significant" differentially expressed genes from the combined perspective of the null and the alternative. | Moerkerke B, Goetghebeur E | Journal of computational biology : a journal of computational molecular cell biology | 17147475 | J Comput Biol | 2006 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17147475 |
| Finding temporal order in discharge summaries. | Bramsen P, Deshpande P, Lee YK, Barzilay R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 17238307 | AMIA Annu Symp Proc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17238307 |
| Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system. | Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus R | BMC medical informatics and decision making | 16872495 | BMC Med Inform Decis Mak | 2006 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/16872495 |
| A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. | Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z | Nature genetics | 16921376 | Nat Genet | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16921376 |
| Huntington's disease: seeing the pathogenic process through a genetic lens. | Gusella JF, MacDonald ME | Trends in biochemical sciences | 16829072 | Trends Biochem Sci | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16829072 |
| Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. | Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z | BMC bioinformatics | 15850491 | BMC Bioinformatics | 2005 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/15850491 |
| Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol. | Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev SR | American journal of human genetics | 17952847 | Am J Hum Genet | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17952847 |
| Identifying patient smoking status from medical discharge records. | Uzuner O, Goldstein I, Luo Y, Kohane I | Journal of the American Medical Informatics Association : JAMIA | 17947624 | J Am Med Inform Assoc | 2008 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/17947624 |
| Aging elevates metabolic gene expression in brain cholinergic neurons. | Baskerville KA, Kent C, Personett D, Lai WR, Park PJ, Coleman P, McKinney M | Neurobiology of aging | 17560690 | Neurobiol Aging | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17560690 |
| Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism. | Lee JM, Ivanova EV, Seong IS, Cashorali T, Kohane I, Gusella JF, MacDonald ME | PLoS genetics | 17708681 | PLoS Genet | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17708681 |
| Evaluating the state-of-the-art in automatic de-identification. | Uzuner O, Luo Y, Szolovits P | Journal of the American Medical Informatics Association : JAMIA | 17600094 | J Am Med Inform Assoc | 2007 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/17600094 |
| A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease. | Mori MA, Liu M, Bezy O, Almind K, Shapiro H, Kasif S, Kahn CR | Diabetes | 20713682 | Diabetes | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20713682 |
| A Perturbation Method for Inference on Regularized Regression Estimates. | Minnier J, Tian L, Cai T | Journal of the American Statistical Association | 22844171 | J Am Stat Assoc | 2011 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/22844171 |
| The influence of sodium- and calcium-regulatory hormone interventions on adipocytokines in obesity and diabetes. | Vaidya A, Underwood PC, Annes JP, Sun B, Williams GH, Forman JP, Williams JS | Metabolism: clinical and experimental | 23142162 | Metabolism | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23142162 |
| Longitudinal analysis of pain in patients with metastatic prostate cancer using natural language processing of medical record text. | Heintzelman NH, Taylor RJ, Simonsen L, Lustig R, Anderko D, Haythornthwaite JA, Childs LC, Bova GS | Journal of the American Medical Informatics Association : JAMIA | 23144336 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23144336 |
| Similar risk of depression and anxiety following surgery or hospitalization for Crohn's disease and ulcerative colitis. | Ananthakrishnan AN, Gainer VS, Cai T, Perez RG, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw S, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP | The American journal of gastroenterology | 23337479 | Am J Gastroenterol | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23337479 |
| Nonmodulation as the mechanism for salt sensitivity of blood pressure in individuals with hypertension and type 2 diabetes mellitus. | Underwood PC, Chamarthi B, Williams JS, Vaidya A, Garg R, Adler GK, Grotzke MP, Staskus G, Wadwekar D, Hopkins PN, Ferri C, McCall A, McClain D, Williams GH | The Journal of clinical endocrinology and metabolism | 22865897 | J Clin Endocrinol Metab | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22865897 |
| A rule based solution to co-reference resolution in clinical text. | Chen P, Hinote D, Chen G | Journal of the American Medical Informatics Association : JAMIA | 23059732 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23059732 |
| Utilizing the integrated difference of two survival functions to quantify the treatment contrast for designing, monitoring, and analyzing a comparative clinical study. | Zhao L, Tian L, Uno H, Solomon SD, Pfeffer MA, Schindler JS, Wei LJ | Clinical trials (London, England) | 22914867 | Clin Trials | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22914867 |
| Designing a public square for research computing. | Masys DR, Harris PA, Fearn PA, Kohane IS | Science translational medicine | 22932220 | Sci Transl Med | 2012 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/22932220 |
| A survey of informatics platforms that enable distributed comparative effectiveness research using multi-institutional heterogenous clinical data. | Sittig DF, Hazlehurst BL, Brown J, Murphy S, Rosenman M, Tarczy-Hornoch P, Wilcox AB | Medical care | 22692259 | Med Care | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22692259 |
| Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives. | Jindal P, Roth D | Journal of the American Medical Informatics Association : JAMIA | 22781192 | J Am Med Inform Assoc | 2013 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22781192 |
| Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test. | Cai T, Lin X, Carroll RJ | Biostatistics (Oxford, England) | 22734045 | Biostatistics | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22734045 |
| Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases. | Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 24407106 | Clin Gastroenterol Hepatol | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24407106 |
| Comorbidity clusters in autism spectrum disorders: an electronic health record time-series analysis. | Doshi-Velez F, Ge Y, Kohane I | Pediatrics | 24323995 | Pediatrics | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24323995 |
| Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): architecture. | Mandl KD, Kohane IS, McFadden D, Weber GM, Natter M, Mandel J, Schneeweiss S, Weiler S, Klann JG, Bickel J, Adams WG, Ge Y, Zhou X, Perkins J, Marsolo K, Bernstam E, Showalter J, Quarshie A, Ofili E, Hripcsak G, Murphy SN | Journal of the American Medical Informatics Association : JAMIA | 24821734 | J Am Med Inform Assoc | 2014 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/24821734 |
| Aldosterone dysregulation with aging predicts renal vascular function and cardiovascular risk. | Brown JM, Underwood PC, Ferri C, Hopkins PN, Williams GH, Adler GK, Vaidya A | Hypertension (Dallas, Tex. : 1979) | 24664291 | Hypertension | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24664291 |
| Resampling Procedures for Making Inference under Nested Case-control Studies. | Cai T, Zheng Y | Journal of the American Statistical Association | 24436503 | J Am Stat Assoc | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/24436503 |
| Automatic lymphoma classification with sentence subgraph mining from pathology reports. | Luo Y, Sohani AR, Hochberg EP, Szolovits P | Journal of the American Medical Informatics Association : JAMIA | 24431333 | J Am Med Inform Assoc | 2014 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/24431333 |
| A new tool for sharing and querying of clinical documents modeled using HL7 Version 3 standard. | Slavov V, Rao P, Paturi S, Swami TK, Barnes M, Rao D, Palvai R | Computer methods and programs in biomedicine | 24001923 | Comput Methods Programs Biomed | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24001923 |
| Combining an expert-based medical entity recognizer to a machine-learning system: methods and a case study. | Zweigenbaum P, Lavergne T, Grabar N, Hamon T, Rosset S, Grouin C | Biomedical informatics insights | 24052691 | Biomed Inform Insights | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24052691 |
| Transfer learning based clinical concept extraction on data from multiple sources. | Lv X, Guan Y, Deng B | Journal of biomedical informatics | 24859154 | J Biomed Inform | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24859154 |
| High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge. | Patrick J, Li M | Journal of the American Medical Informatics Association : JAMIA | 20819856 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819856 |
| Integrating existing natural language processing tools for medication extraction from discharge summaries. | Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H | Journal of the American Medical Informatics Association : JAMIA | 20819857 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819857 |
| Extracting medication information from French clinical texts. | Deléger L, Grouin C, Zweigenbaum P | Studies in health technology and informatics | 20841824 | Stud Health Technol Inform | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20841824 |
| CYP4A11 T8590C polymorphism, salt-sensitive hypertension, and renal blood flow. | Williams JS, Hopkins PN, Jeunemaitre X, Brown NJ | Journal of hypertension | 21873888 | J Hypertens | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21873888 |
| Evaluating the state of the art in coreference resolution for electronic medical records. | Uzuner O, Bodnari A, Shen S, Forbush T, Pestian J, South BR | Journal of the American Medical Informatics Association : JAMIA | 22366294 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22366294 |
| Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. | Gooch P, Roudsari A | Journal of biomedical informatics | 22449720 | J Biomed Inform | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22449720 |
| Lysine-specific demethylase 1: an epigenetic regulator of salt-sensitive hypertension. | Williams JS, Chamarthi B, Goodarzi MO, Pojoga LH, Sun B, Garza AE, Raby BA, Adler GK, Hopkins PN, Brown NJ, Jeunemaitre X, Ferri C, Fang R, Leonor T, Cui J, Guo X, Taylor KD, Ida Chen YD, Xiang A, Raffel LJ, Buchanan TA, Rotter JI, Williams GH, Shi Y | American journal of hypertension | 22534796 | Am J Hypertens | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22534796 |
| Vitamin D3 therapy corrects the tissue sensitivity to angiotensin ii akin to the action of a converting enzyme inhibitor in obese hypertensives: an interventional study. | Vaidya A, Sun B, Larson C, Forman JP, Williams JS | The Journal of clinical endocrinology and metabolism | 22539586 | J Clin Endocrinol Metab | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22539586 |
| A translational engine at the national scale: informatics for integrating biology and the bedside. | Kohane IS, Churchill SE, Murphy SN | Journal of the American Medical Informatics Association : JAMIA | 22081225 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22081225 |
| Replication and meta-analysis of the gene-environment interaction between body mass index and the interleukin-6 promoter polymorphism with higher insulin resistance. | Underwood PC, Chamarthi B, Williams JS, Sun B, Vaidya A, Raby BA, Lasky-Su J, Hopkins PN, Adler GK, Williams GH | Metabolism: clinical and experimental | 22075267 | Metabolism | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22075267 |
| Sentiment Analysis of Suicide Notes: A Shared Task. | Pestian JP, Matykiewicz P, Linn-Gust M, South B, Uzuner O, Wiebe J, Cohen KB, Hurdle J, Brew C | Biomedical informatics insights | 22419877 | Biomed Inform Insights | 2012 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/22419877 |
| On the covariate-adjusted estimation for an overall treatment difference with data from a randomized comparative clinical trial. | Tian L, Cai T, Zhao L, Wei LJ | Biostatistics (Oxford, England) | 22294672 | Biostatistics | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22294672 |
| The influence of body mass index and renin-angiotensin-aldosterone system activity on the relationship between 25-hydroxyvitamin D and adiponectin in Caucasian men. | Vaidya A, Forman JP, Underwood PC, Hopkins PN, Williams GH, Pojoga LH, Williams JS | European journal of endocrinology | 21402748 | Eur J Endocrinol | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21402748 |
| Using machine learning for concept extraction on clinical documents from multiple data sources. | Torii M, Wagholikar K, Liu H | Journal of the American Medical Informatics Association : JAMIA | 21709161 | J Am Med Inform Assoc | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21709161 |
| Variants of the caveolin-1 gene: a translational investigation linking insulin resistance and hypertension. | Pojoga LH, Underwood PC, Goodarzi MO, Williams JS, Adler GK, Jeunemaitre X, Hopkins PN, Raby BA, Lasky-Su J, Sun B, Cui J, Guo X, Taylor KD, Chen YD, Xiang A, Raffel LJ, Buchanan TA, Rotter JI, Williams GH | The Journal of clinical endocrinology and metabolism | 21613355 | J Clin Endocrinol Metab | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21613355 |
| Structure-based prediction reveals capping motifs that inhibit β-helix aggregation. | Bryan AW Jr, Starner-Kreinbrink JL, Hosur R, Clark PL, Berger B | Proceedings of the National Academy of Sciences of the United States of America | 21685332 | Proc Natl Acad Sci U S A | 2011 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/21685332 |
| Extracting medication information from clinical text. | Uzuner O, Solti I, Cadag E | Journal of the American Medical Informatics Association : JAMIA | 20819854 | J Am Med Inform Assoc | 2010 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/20819854 |
| Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. | Park PJ, Kong SW, Tebaldi T, Lai WR, Kasif S, Kohane IS | Bioinformatics (Oxford, England) | 19786482 | Bioinformatics | 2009 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/19786482 |
| Characterization of patients who suffer asthma exacerbations using data extracted from electronic medical records. | Himes BE, Kohane IS, Ramoni MF, Weiss ST | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18999057 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18999057 |
| Specializing for predicting obesity and its co-morbidities. | Goldstein I, Uzuner O | Journal of biomedical informatics | 19041423 | J Biomed Inform | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19041423 |
| Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using electronic medical records. | Himes BE, Dai Y, Kohane IS, Weiss ST, Ramoni MF | Journal of the American Medical Informatics Association : JAMIA | 19261943 | J Am Med Inform Assoc | 2009 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/19261943 |
| Prenatal antidepressant exposure is associated with risk for attention-deficit hyperactivity disorder but not autism spectrum disorder in a large health system. | Clements CC, Castro VM, Blumenthal SR, Rosenfield HR, Murphy SN, Fava M, Erb JL, Churchill SE, Kaimal AJ, Doyle AE, Robinson EB, Smoller JW, Kohane IS, Perlis RH | Molecular psychiatry | 25155880 | Mol Psychiatry | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25155880 |
| Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases. | Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Alimentary pharmacology & therapeutics | 25864945 | Aliment Pharmacol Ther | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25864945 |
| Normalization of relative and incomplete temporal expressions in clinical narratives. | Sun W, Rumshisky A, Uzuner O | Journal of the American Medical Informatics Association : JAMIA | 25868462 | J Am Med Inform Assoc | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25868462 |
| A clinical use case to evaluate the i2b2 Hive: predicting asthma exacerbations. | Meystre SM, Deshmukh VG, Mitchell J | AMIA ... Annual Symposium proceedings. AMIA Symposium | 20351896 | AMIA Annu Symp Proc | 2009 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/20351896 |
| Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. | Fan JW, Yang EW, Jiang M, Prasad R, Loomis RM, Zisook DS, Denny JC, Xu H, Huang Y | Journal of the American Medical Informatics Association : JAMIA | 23907286 | J Am Med Inform Assoc | 2013 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/23907286 |
| Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population. | Liao KP, Cai T, Gainer VS, Cagan A, Murphy SN, Liu C, Churchill S, Shaw SY, Kohane I, Solomon DH, Plenge RM, Karlson EW | Arthritis care & research | 23925980 | Arthritis Care Res (Hoboken) | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23925980 |
| Adopting nested case-control quota sampling designs for the evaluation of risk markers. | Zheng Y, Cai T, Pepe MS | Lifetime data analysis | 23807695 | Lifetime Data Anal | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23807695 |
| Unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine. | Ghebremariam YT, LePendu P, Lee JC, Erlanson DA, Slaviero A, Shah NH, Leiper J, Cooke JP | Circulation | 23825361 | Circulation | 2013 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/23825361 |
| Annotating temporal information in clinical narratives. | Sun W, Rumshisky A, Uzuner O | Journal of biomedical informatics | 23872518 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23872518 |
| Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. | Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H | Journal of the American Medical Informatics Association : JAMIA | 23558168 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23558168 |
| Pharmacovigilance using clinical notes. | LePendu P, Iyer SV, Bauer-Mehren A, Harpaz R, Mortensen JM, Podchiyska T, Ferris TA, Shah NH | Clinical pharmacology and therapeutics | 23571773 | Clin Pharmacol Ther | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23571773 |
| Automating the study of population variation of electrocardiographic features. | Kohane IS | Circulation | 23463856 | Circulation | 2013 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/23463856 |
| An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge. | Xu Y, Wang Y, Liu T, Tsujii J, Chang EI | Journal of the American Medical Informatics Association : JAMIA | 23467472 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23467472 |
| A hybrid system for temporal information extraction from clinical text. | Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H | Journal of the American Medical Informatics Association : JAMIA | 23571849 | J Am Med Inform Assoc | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23571849 |
| Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway. | Li G, Diogo D, Wu D, Spoonamore J, Dancik V, Franke L, Kurreeman F, Rossin EJ, Duclos G, Hartland C, Zhou X, Li K, Liu J, De Jager PL, Siminovitch KA, Zhernakova A, Raychaudhuri S, Bowes J, Eyre S, Padyukov L, Gregersen PK, Worthington J, Rheumatoid Arthritis Consortium International (RACI), Gupta N, Clemons PA, Stahl E, Tolliday N, Plenge RM | PLoS genetics | 23696745 | PLoS Genet | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23696745 |
| Towards generating a patient's timeline: extracting temporal relationships from clinical notes. | Nikfarjam A, Emadzadeh E, Gonzalez G | Journal of biomedical informatics | 24212118 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24212118 |
| Temporal relation discovery between events and temporal expressions identified in clinical narrative. | Cheng Y, Anick P, Hong P, Xue N | Journal of biomedical informatics | 24076508 | J Biomed Inform | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24076508 |
| Genetic effects influencing risk for major depressive disorder in China and Europe. | Bigdeli TB, Ripke S, Peterson RE, Trzaskowski M, Bacanu SA, Abdellaoui A, Andlauer TF, Beekman AT, Berger K, Blackwood DH, Boomsma DI, Breen G, Buttenschøn HN, Byrne EM, Cichon S, Clarke TK, Couvy-Duchesne B, Craddock N, de Geus EJ, Degenhardt F, Dunn EC, Edwards AC, Fanous AH, Forstner AJ, Frank J, Gill M, Gordon SD, Grabe HJ, Hamilton SP, Hardiman O, Hayward C, Heath AC, Henders AK, Herms S, Hickie IB, Hoffmann P, Homuth G, Hottenga JJ, Ising M, Jansen R, Kloiber S, Knowles JA, Lang M, Li QS, Lucae S, MacIntyre DJ, Madden PA, Martin NG, McGrath PJ, McGuffin P, McIntosh AM, Medland SE, Mehta D, Middeldorp CM, Milaneschi Y, Montgomery GW, Mors O, Müller-Myhsok B, Nauck M, Nyholt DR, Nöthen MM, Owen MJ, Penninx BW, Pergadia ML, Perlis RH, Peyrot WJ, Porteous DJ, Potash JB, Rice JP, Rietschel M, Riley BP, Rivera M, Schoevers R, Schulze TG, Shi J, Shyn SI, Smit JH, Smoller JW, Streit F, Strohmaier J, Teumer A, Treutlein J, Van der Auwera S, van Grootheest G, van Hemert AM, Völzke H, Webb BT, Weissman MM, Wellmann J, Willemsen G, Witt SH, Levinson DF, Lewis CM, Wray NR, Flint J, Sullivan PF, Kendler KS | Translational psychiatry | 28350396 | Transl Psychiatry | 2017 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/28350396 |
| Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text. | Luo Y, Xin Y, Hochberg E, Joshi R, Uzuner O, Szolovits P | Journal of the American Medical Informatics Association : JAMIA | 25862765 | J Am Med Inform Assoc | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25862765 |
| Semi-Supervised Learning to Identify UMLS Semantic Relations. | Luo Y, Uzuner O | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 25954580 | AMIA Jt Summits Transl Sci Proc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25954580 |
| Annotating risk factors for heart disease in clinical narratives for diabetic patients. | Stubbs A, Uzuner Ö | Journal of biomedical informatics | 26004790 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26004790 |
| Risk Classification with an Adaptive Naive Bayes Kernel Machine Model. | Minnier J, Yuan M, Liu JS, Cai T | Journal of the American Statistical Association | 26236061 | J Am Stat Assoc | 2015 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/26236061 |
| Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis. | Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Kohane I, Liao KP, Murphy SN | Inflammatory bowel diseases | 26933751 | Inflamm Bowel Dis | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26933751 |
| Tensor factorization toward precision medicine. | Luo Y, Wang F, Szolovits P | Briefings in bioinformatics | 26994614 | Brief Bioinform | 2017 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/26994614 |
| REPRODUCIBLE AND SHAREABLE QUANTIFICATIONS OF PATHOGENICITY. | Manrai AK, Wang BL, Patel CJ, Kohane IS | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 26776189 | Pac Symp Biocomput | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26776189 |
| Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. | Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA | Nature genetics | 26808112 | Nat Genet | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26808112 |
| Annotating longitudinal clinical narratives for de-identification: The 2014 i2b2/UTHealth corpus. | Stubbs A, Uzuner Ö | Journal of biomedical informatics | 26319540 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26319540 |
| Sparse kernel machine regression for ordinal outcomes. | Shen Y, Liao KP, Cai T | Biometrics | 25196727 | Biometrics | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25196727 |
| Mode of childbirth and long-term outcomes in women with inflammatory bowel diseases. | Ananthakrishnan AN, Cheng A, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP | Digestive diseases and sciences | 25213079 | Dig Dis Sci | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25213079 |
| Genome-wide association study of short-acting β2-agonists. A novel genome-wide significant locus on chromosome 2 near ASB3. | Israel E, Lasky-Su J, Markezich A, Damask A, Szefler SJ, Schuemann B, Klanderman B, Sylvia J, Kazani S, Wu R, Martinez F, Boushey HA, Chinchilli VM, Mauger D, Weiss ST, Tantisira KG, SHARP Investigators | American journal of respiratory and critical care medicine | 25562107 | Am J Respir Crit Care Med | 2015 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/25562107 |
| CRFs based de-identification of medical records. | He B, Guan Y, Cheng J, Cen K, Hua W | Journal of biomedical informatics | 26315662 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26315662 |
| The association between lower educational attainment and depression owing to shared genetic effects? Results in ~25,000 subjects. | Peyrot WJ, Lee SH, Milaneschi Y, Abdellaoui A, Byrne EM, Esko T, de Geus EJ, Hemani G, Hottenga JJ, Kloiber S, Levinson DF, Lucae S, Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium (Corporate Collaborator), Martin NG, Medland SE, Metspalu A, Milani L, Noethen MM, Potash JB, Rietschel M, Rietveld CA, Ripke S, Shi J, Social Science Genetic Association Consortium Corporate Collaborator, Willemsen G, Zhu Z, Boomsma DI, Wray NR, Penninx BW, Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium Corporate Collaborator, Social Science Genetic Association Consortium Corporate Collaborator | Molecular psychiatry | 25917368 | Mol Psychiatry | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25917368 |
| Enabling phenotypic big data with PheNorm. | Yu S, Ma Y, Gronsbell J, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Liao KP, Cai T | Journal of the American Medical Informatics Association : JAMIA | 29126253 | J Am Med Inform Assoc | 2018 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/29126253 |
| Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context. | Fan JW, Li J, Lussier YA | Journal of healthcare engineering | 29065591 | J Healthc Eng | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29065591 |
| Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. | Nazeen S, Palmer NP, Berger B, Kohane IS | Genome biology | 27842596 | Genome Biol | 2016 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/27842596 |
| Unsupervised concept extraction from clinical text through semantic composition. | Tulkens S, Šuster S, Daelemans W | Journal of biomedical informatics | 30753949 | J Biomed Inform | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30753949 |
| Clinical text classification with rule-based features and knowledge-guided convolutional neural networks. | Yao L, Mao C, Luo Y | BMC medical informatics and decision making | 30943960 | BMC Med Inform Decis Mak | 2019 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/30943960 |
| RAPID detection of gene-gene interactions in genome-wide association studies. | Brinza D, Schultz M, Tesler G, Bafna V | Bioinformatics (Oxford, England) | 20871107 | Bioinformatics | 2010 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/20871107 |
| AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. | Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L | BMC bioinformatics | 21410990 | BMC Bioinformatics | 2011 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/21410990 |
| Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. | Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V | Bioinformatics (Oxford, England) | 21330288 | Bioinformatics | 2011 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/21330288 |
| Strobe sequence design for haplotype assembly. | Lo C, Bashir A, Bansal V, Bafna V | BMC bioinformatics | 21342554 | BMC Bioinformatics | 2011 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/21342554 |
| An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. | Zakov S, Kinsella M, Bafna V | Proceedings of the National Academy of Sciences of the United States of America | 23503850 | Proc Natl Acad Sci U S A | 2013 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/23503850 |
| Natural Language Processing to identify pneumonia from radiology reports. | Dublin S, Baldwin E, Walker RL, Christensen LM, Haug PJ, Jackson ML, Nelson JC, Ferraro J, Carrell D, Chapman WW | Pharmacoepidemiology and drug safety | 23554109 | Pharmacoepidemiol Drug Saf | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23554109 |
| Recent trends in biomedical informatics: a study based on JAMIA articles. | Jiang X, Tse K, Wang S, Doan S, Kim H, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 24214018 | J Am Med Inform Assoc | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24214018 |
| Using twitter to examine smoking behavior and perceptions of emerging tobacco products. | Myslín M, Zhu SH, Chapman W, Conway M | Journal of medical Internet research | 23989137 | J Med Internet Res | 2013 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/23989137 |
| Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. | South BR, Mowery D, Suo Y, Leng J, Ferrández Ó, Meystre SM, Chapman WW | Journal of biomedical informatics | 24859155 | J Biomed Inform | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24859155 |
| Privacy preserving RBF kernel support vector machine. | Li H, Xiong L, Ohno-Machado L, Jiang X | BioMed research international | 25013805 | Biomed Res Int | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25013805 |
| "Big data" and the electronic health record. | Ross MK, Wei W, Ohno-Machado L | Yearbook of medical informatics | 25123728 | Yearb Med Inform | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/25123728 |
| Ensuring privacy in the study of pathogen genetics. | Mehta SR, Vinterbo SA, Little SJ | The Lancet. Infectious diseases | 24721230 | Lancet Infect Dis | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24721230 |
| Fluoroquinolone resistant rectal colonization predicts risk of infectious complications after transrectal prostate biopsy. | Liss MA, Taylor SA, Batura D, Steensels D, Chayakulkeeree M, Soenens C, Rao GG, Dash A, Park S, Patel N, Woo J, McDonald M, Nseyo U, Banapour P, Unterberg S, Ahlering TE, Van Poppel H, Sakamoto K, Fierer J, Black PC | The Journal of urology | 24928266 | J Urol | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24928266 |
| Selecting cases for whom additional tests can improve prognostication. | Jiang X, Kim J, Wu Y, Wang S, Ohno-Machado L | AMIA ... Annual Symposium proceedings. AMIA Symposium | 23304404 | AMIA Annu Symp Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23304404 |
| Reviewing social media use by clinicians. | von Muhlen M, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 22759618 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22759618 |
| Sharing data for the public good and protecting individual privacy: informatics solutions to combine different goals. | Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 23243087 | J Am Med Inform Assoc | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23243087 |
| A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support. | Jiang X, Boxwala AA, El-Kareh R, Kim J, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 22493049 | J Am Med Inform Assoc | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22493049 |
| Adaptive Distributed Video Coding with Correlation Estimation using Expectation Propagation. | Cui L, Wang S, Jiang X, Cheng S | Proceedings of SPIE--the International Society for Optical Engineering | 23750314 | Proc SPIE Int Soc Opt Eng | 2012 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/23750314 |
| HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. | Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 24368726 | J Am Med Inform Assoc | 2014 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/24368726 |
| Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. | Patel A, Schwab R, Liu YT, Bafna V | Genome research | 24307551 | Genome Res | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24307551 |
| Calibrating predictive model estimates to support personalized medicine. | Jiang X, Osl M, Kim J, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 21984587 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/21984587 |
| Differentially Private Empirical Risk Minimization. | Chaudhuri K, Monteleoni C, Sarwate AD | Journal of machine learning research : JMLR | 21892342 | J Mach Learn Res | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21892342 |
| An approach to improve LOINC mapping through augmentation of local test names. | Kim H, El-Kareh R, Goel A, Vineet FN, Chapman WW | Journal of biomedical informatics | 22210167 | J Biomed Inform | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22210167 |
| Trends in biomedical informatics: most cited topics from recent years. | Kim HE, Jiang X, Kim J, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 22180873 | J Am Med Inform Assoc | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22180873 |
| Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment. | Roozgard A, Barzigar N, Wang S, Jiang X, Cheng S | Cancer informatics | 25983537 | Cancer Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25983537 |
| Overcome support vector machine diagnosis overfitting. | Han H, Jiang X | Cancer informatics | 25574125 | Cancer Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25574125 |
| A community assessment of privacy preserving techniques for human genomes. | Jiang X, Zhao Y, Wang X, Malin B, Wang S, Ohno-Machado L, Tang H | BMC medical informatics and decision making | 25521230 | BMC Med Inform Decis Mak | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25521230 |
| Fine specificities of natural regulatory T cells after IVIG therapy in patients with Kawasaki disease. | Burns JC, Touma R, Song Y, Padilla RL, Tremoulet AH, Sidney J, Sette A, Franco A | Autoimmunity | 25822882 | Autoimmunity | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25822882 |
| Role of TGF-β Signaling in Remodeling of Noncoronary Artery Aneurysms in Kawasaki Disease. | Lee AM, Shimizu C, Oharaseki T, Takahashi K, Daniels LB, Kahn A, Adamson R, Dembitsky W, Gordon JB, Burns JC | Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society | 25856633 | Pediatr Dev Pathol | 2015 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/25856633 |
| Trends in biomedical informatics: automated topic analysis of JAMIA articles. | Han D, Wang S, Jiang C, Jiang X, Kim HE, Sun J, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 26555018 | J Am Med Inform Assoc | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26555018 |
| Structured Set Intra Prediction With Discriminative Learning in a Max-Margin Markov Network for High Efficiency Video Coding. | Dai W, Xiong H, Jiang X, Chen CW | IEEE transactions on circuits and systems for video technology : a publication of the Circuits and Systems Society | 25505829 | IEEE Trans Circuits Syst Video Technol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25505829 |
| Ranking Medical Subject Headings using a factor graph model. | Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 26306236 | AMIA Jt Summits Transl Sci Proc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26306236 |
| Abstractions for Genomics. | Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G | Communications of the ACM | 25284821 | Commun ACM | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25284821 |
| Convergence Rates for Differentially Private Statistical Estimation. | Chaudhuri K, Hsu D | Proceedings of the ... International Conference on Machine Learning. International Conference on Machine Learning | 25302341 | Proc Int Conf Mach Learn | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25302341 |
| How Do You #relax When You're #stressed? A Content Analysis and Infodemiology Study of Stress-Related Tweets. | Doan S, Ritchart A, Perry N, Chaparro JD, Conway M | JMIR public health and surveillance | 28611016 | JMIR Public Health Surveill | 2017 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/28611016 |
| A Methodology to Compare Insulin Dosing Recommendations in Real-Life Settings. | Groat D, Grando MA, Thompson B, Neto P, Soni H, Boyle ME, Bailey M, Cook CB | Journal of diabetes science and technology | 28406039 | J Diabetes Sci Technol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28406039 |
| Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. | Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP | Journal of the American Medical Informatics Association : JAMIA | 28339683 | J Am Med Inform Assoc | 2017 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/28339683 |
| Secure large-scale genome data storage and query. | Chen L, Aziz MM, Mohammed N, Jiang X | Computer methods and programs in biomedicine | 30337067 | Comput Methods Programs Biomed | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30337067 |
| Self-Reported Compensation Techniques for Carbohydrate, Exercise, and Alcohol Behaviors in Patients With Type 1 Diabetes on Insulin Pump Therapy. | Groat D, Soni H, Grando MA, Thompson B, Cook CB | Journal of diabetes science and technology | 28677414 | J Diabetes Sci Technol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28677414 |
| The Real-World Effectiveness and Safety of Vedolizumab for Moderate-Severe Crohn's Disease: Results From the US VICTORY Consortium. | Dulai PS, Singh S, Jiang X, Peerani F, Narula N, Chaudrey K, Whitehead D, Hudesman D, Lukin D, Swaminath A, Shmidt E, Wang S, Boland BS, Chang JT, Kane S, Siegel CA, Loftus EV, Sandborn WJ, Sands BE, Colombel JF | The American journal of gastroenterology | 27296941 | Am J Gastroenterol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27296941 |
| Differences in GlycA and lipoprotein particle parameters may help distinguish acute kawasaki disease from other febrile illnesses in children. | Connelly MA, Shimizu C, Winegar DA, Shalaurova I, Pourfarzib R, Otvos JD, Kanegaye JT, Tremoulet AH, Burns JC | BMC pediatrics | 27596163 | BMC Pediatr | 2016 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/27596163 |
| PALME: PAtients Like My gEnome. | Wang L, Fang Y, Aref D, Rathi S, Shen L, Jiang X, Wang S | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 27570674 | AMIA Jt Summits Transl Sci Proc | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27570674 |
| FERI: A Multitask-based Fairness Achieving Algorithm with Applications to Fair Organ Transplantation. | Li C, Lai D, Jiang X, Zhang K | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 38827050 | AMIA Jt Summits Transl Sci Proc | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38827050 |
| Translational bioinformatics: linking knowledge across biological and clinical realms. | Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 21561873 | J Am Med Inform Assoc | 2011 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/21561873 |
| A potential role for intragenic miRNAs on their hosts' interactome. | Hinske LC, Galante PA, Kuo WP, Ohno-Machado L | BMC genomics | 20920310 | BMC Genomics | 2010 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/20920310 |
| Improving predictions in imbalanced data using Pairwise Expanded Logistic Regression. | Jiang X, El-Kareh R, Ohno-Machado L | AMIA ... Annual Symposium proceedings. AMIA Symposium | 22195118 | AMIA Annu Symp Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22195118 |
| Empirical comparison of cross-platform normalization methods for gene expression data. | Rudy J, Valafar F | BMC bioinformatics | 22151536 | BMC Bioinformatics | 2011 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/22151536 |
| iDASH: integrating data for analysis, anonymization, and sharing. | Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, Day ME, Farcas C, Heintzman ND, Jiang X, Kim H, Kim J, Matheny ME, Resnic FS, Vinterbo SA, iDASH team | Journal of the American Medical Informatics Association : JAMIA | 22081224 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22081224 |
| Grid Binary LOgistic REgression (GLORE): building shared models without sharing data. | Wu Y, Jiang X, Kim J, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 22511014 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22511014 |
| Genetics insights into the pathogenesis of Kawasaki disease. | Burns JC, Newburger JW | Circulation. Cardiovascular genetics | 22715279 | Circ Cardiovasc Genet | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22715279 |
| MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. | Kim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L | Bioinformatics (Oxford, England) | 24907367 | Bioinformatics | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24907367 |
| Impact of family history on prostate cancer mortality in white men undergoing prostate specific antigen based screening. | Liss MA, Chen H, Hemal S, Krane S, Kane CJ, Xu J, Kader AK | The Journal of urology | 25066872 | J Urol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25066872 |
| The genetic basis of chronic mountain sickness. | Ronen R, Zhou D, Bafna V, Haddad GG | Physiology (Bethesda, Md.) | 25362634 | Physiology (Bethesda) | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25362634 |
| Text Mining Driven Drug-Drug Interaction Detection. | Yan S, Jiang X, Chen Y | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 25131635 | Proceedings (IEEE Int Conf Bioinformatics Biomed) | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/25131635 |
| Immune-monitoring in Kawasaki disease patients treated with infliximab and intravenous immunoglobulin. | Burns JC, Song Y, Bujold M, Shimizu C, Kanegaye JT, Tremoulet AH, Franco A | Clinical and experimental immunology | 23901839 | Clin Exp Immunol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23901839 |
| Evaluating genome architecture of a complex region via generalized bipartite matching. | Lo C, Kim S, Zakov S, Bafna V | BMC bioinformatics | 23734567 | BMC Bioinformatics | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23734567 |
| On the design of clone-based haplotyping. | Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K | Genome biology | 24028704 | Genome Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24028704 |
| Privacy technology to support data sharing for comparative effectiveness research: a systematic review. | Jiang X, Sarwate AD, Ohno-Machado L | Medical care | 23774511 | Med Care | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23774511 |
| Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. | Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG | American journal of human genetics | 23954164 | Am J Hum Genet | 2013 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/23954164 |
| Reprever: resolving low-copy duplicated sequences using template driven assembly. | Kim S, Medvedev P, Paton TA, Bafna V | Nucleic acids research | 23658221 | Nucleic Acids Res | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23658221 |
| EXpectation Propagation LOgistic REgRession (EXPLORER): distributed privacy-preserving online model learning. | Wang S, Jiang X, Wu Y, Cui L, Cheng S, Ohno-Machado L | Journal of biomedical informatics | 23562651 | J Biomed Inform | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23562651 |
| Signal Processing and Machine Learning with Differential Privacy: Algorithms and challenges for continuous data. | Sarwate AD, Chaudhuri K | IEEE signal processing magazine | 24737929 | IEEE Signal Process Mag | 2013 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/24737929 |
| The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL. | Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM | Proceedings of the National Academy of Sciences of the United States of America | 24371310 | Proc Natl Acad Sci U S A | 2014 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/24371310 |
| Building and evaluating an ontology-based tool for reasoning about consent permission. | Grando A, Schwab R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 24551354 | AMIA Annu Symp Proc | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24551354 |
| DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique. | Li P, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X | PloS one | 24282536 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24282536 |
| When you can't tell when it hurts: a preliminary algorithm to assess pain in patients who can't communicate. | Wang S, Jiang X, Ji Z, El-Kareh R, Choi J, Kim H | AMIA ... Annual Symposium proceedings. AMIA Symposium | 24551418 | AMIA Annu Symp Proc | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24551418 |
| Privacy-preserving heterogeneous health data sharing. | Mohammed N, Jiang X, Chen R, Fung BC, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 23242630 | J Am Med Inform Assoc | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23242630 |
| A Randomized Response Model For Privacy Preserving Smart Metering. | Wang S, Cui L, Que J, Choi DH, Jiang X, Cheng S, Xie L | IEEE transactions on smart grid | 23243488 | IEEE Trans Smart Grid | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23243488 |
| The role of TGF-β and myofibroblasts in the arteritis of Kawasaki disease. | Shimizu C, Oharaseki T, Takahashi K, Kottek A, Franco A, Burns JC | Human pathology | 22955109 | Hum Pathol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22955109 |
| Differential expression of miR-145 in children with Kawasaki disease. | Shimizu C, Kim J, Stepanowsky P, Trinh C, Lau HD, Akers JC, Chen C, Kanegaye JT, Tremoulet A, Ohno-Machado L, Burns JC | PloS one | 23483985 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23483985 |
| Exact statistical tests for the intersection of independent lists of genes. | Natarajan L, Pu M, Messer K | The annals of applied statistics | 23335952 | Ann Appl Stat | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23335952 |
| Classic "broken cell" techniques and newer live cell methods for cell cycle assessment. | Henderson L, Bortone DS, Lim C, Zambon AC | American journal of physiology. Cell physiology | 23392113 | Am J Physiol Cell Physiol | 2013 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/23392113 |
| Setting up an intronic miRNA database. | Hinske LC, Heyn J, Galante PA, Ohno-Machado L, Kreth S | Methods in molecular biology (Clifton, N.J.) | 23007499 | Methods Mol Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23007499 |
| Development of a web service for analysis in a distributed network. | Jiang X, Wu Y, Marsolo K, Ohno-Machado L | EGEMS (Washington, DC) | 25848586 | EGEMS (Wash DC) | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25848586 |
| Grid multi-category response logistic models. | Wu Y, Jiang X, Wang S, Jiang W, Li P, Ohno-Machado L | BMC medical informatics and decision making | 25886151 | BMC Med Inform Decis Mak | 2015 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/25886151 |
| A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research. | Meeker D, Jiang X, Matheny ME, Farcas C, D'Arcy M, Pearlman L, Nookala L, Day ME, Kim KK, Kim H, Boxwala A, El-Kareh R, Kuo GM, Resnic FS, Kesselman C, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 26142423 | J Am Med Inform Assoc | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26142423 |
| Novel data-mining approach identifies biomarkers for diagnosis of Kawasaki disease. | Tremoulet AH, Dutkowski J, Sato Y, Kanegaye JT, Ling XB, Burns JC | Pediatric research | 26237629 | Pediatr Res | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26237629 |
| PRECISE:PRivacy-prEserving Cloud-assisted quality Improvement Service in hEalthcare. | Chen F, Wang S, Mohammed N, Cheng S, Jiang X | IEEE International Conference on Systems Biology : [proceedings]. IEEE International Conference on Systems Biology | 26146645 | IEEE Int Conf Systems Biol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26146645 |
| Privacy-Preserving Patient Similarity Learning in a Federated Environment: Development and Analysis. | Lee J, Sun J, Wang F, Wang S, Jun CH, Jiang X | JMIR medical informatics | 29653917 | JMIR Med Inform | 2018 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/29653917 |
| A Scalable Privacy-preserving Data Generation Methodology for Exploratory Analysis. | Vaidya J, Shafiq B, Asani M, Adam N, Jiang X, Ohno-Machado L | AMIA ... Annual Symposium proceedings. AMIA Symposium | 29854240 | AMIA Annu Symp Proc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29854240 |
| Perfectly Secure and Efficient Two-Party Electronic-Health-Record Linkage. | Chen F, Jiang X, Wang S, Schilling LM, Meeker D, Ong T, Matheny ME, Doctor JN, Ohno-Machado L, Vaidya J | IEEE internet computing | 29867290 | IEEE Internet Comput | 2018 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/29867290 |
| Creating a Common Data Model for Comparative Effectiveness with the Observational Medical Outcomes Partnership. | FitzHenry F, Resnic FS, Robbins SL, Denton J, Nookala L, Meeker D, Ohno-Machado L, Matheny ME | Applied clinical informatics | 26448797 | Appl Clin Inform | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26448797 |
| Building a Natural Language Processing Tool to Identify Patients With High Clinical Suspicion for Kawasaki Disease from Emergency Department Notes. | Doan S, Maehara CK, Chaparro JD, Lu S, Liu R, Graham A, Berry E, Hsu CN, Kanegaye JT, Lloyd DD, Ohno-Machado L, Burns JC, Tremoulet AH, Pediatric Emergency Medicine Kawasaki Disease Research Group | Academic emergency medicine : official journal of the Society for Academic Emergency Medicine | 26826020 | Acad Emerg Med | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26826020 |
| Participation of low-income women in genetic cancer risk assessment and BRCA 1/2 testing: the experience of a safety-net institution. | Komenaka IK, Nodora JN, Madlensky L, Winton LM, Heberer MA, Schwab RB, Weitzel JN, Martinez ME | Journal of community genetics | 26690931 | J Community Genet | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26690931 |
| Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR. | Hinske LC, Galante PA, Limbeck E, Möhnle P, Parmigiani RB, Ohno-Machado L, Camargo AA, Kreth S | PloS one | 25799583 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25799583 |
| Human pre-valvular endocardial cells derived from pluripotent stem cells recapitulate cardiac pathophysiological valvulogenesis. | Neri T, Hiriart E, van Vliet PP, Faure E, Norris RA, Farhat B, Jagla B, Lefrancois J, Sugi Y, Moore-Morris T, Zaffran S, Faustino RS, Zambon AC, Desvignes JP, Salgado D, Levine RA, de la Pompa JL, Terzic A, Evans SM, Markwald R, Pucéat M | Nature communications | 31028265 | Nat Commun | 2019 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/31028265 |
| HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease. | Shimizu C, Kim J, Eleftherohorinou H, Wright VJ, Hoang LT, Tremoulet AH, Franco A, Hibberd ML, Takahashi A, Kubo M, Ito K, Tanaka T, Onouchi Y, Coin LJM, Levin M, Burns JC, Shike H, International Kawasaki Disease Genetic Consortium | Human immunology | 31122742 | Hum Immunol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31122742 |
| Privacy-preserving GWAS analysis on federated genomic datasets. | Constable SD, Tang Y, Wang S, Jiang X, Chapin S | BMC medical informatics and decision making | 26733045 | BMC Med Inform Decis Mak | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26733045 |
| Protecting genomic data analytics in the cloud: state of the art and opportunities. | Tang H, Jiang X, Wang X, Wang S, Sofia H, Fox D, Lauter K, Malin B, Telenti A, Xiong L, Ohno-Machado L | BMC medical genomics | 27733153 | BMC Med Genomics | 2016 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/27733153 |
| Self-Management Behaviors in Adults on Insulin Pump Therapy. | Groat D, Grando MA, Soni H, Thompson B, Boyle M, Bailey M, Cook CB | Journal of diabetes science and technology | 27587370 | J Diabetes Sci Technol | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27587370 |
| A Predictive Model for Medical Events Based on Contextual Embedding of Temporal Sequences. | Farhan W, Wang Z, Huang Y, Wang S, Wang F, Jiang X | JMIR medical informatics | 27888170 | JMIR Med Inform | 2016 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/27888170 |
| An Adaptive Difference Distribution-based Coding with Hierarchical Tree Structure for DNA Sequence Compression. | Dai W, Xiong H, Jiang X, Ohno-Machado L | Proceedings. Data Compression Conference | 26501129 | Proc Data Compress Conf | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/26501129 |
| Secure Multi-pArty Computation Grid LOgistic REgression (SMAC-GLORE). | Shi H, Jiang C, Dai W, Jiang X, Tang Y, Ohno-Machado L, Wang S | BMC medical informatics and decision making | 27454168 | BMC Med Inform Decis Mak | 2016 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/27454168 |
| Annual Burden and Costs of Hospitalization for High-Need, High-Cost Patients With Chronic Gastrointestinal and Liver Diseases. | Nguyen NH, Khera R, Ohno-Machado L, Sandborn WJ, Singh S | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 29474966 | Clin Gastroenterol Hepatol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29474966 |
| Differentially Private Histogram Publication For Dynamic Datasets: An Adaptive Sampling Approach. | Li H, Jiang X, Xiong L, Liu J | Proceedings of the ... ACM International Conference on Information & Knowledge Management. ACM International Conference on Information and Knowledge Management | 26973795 | Proc ACM Int Conf Inf Knowl Manag | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26973795 |
| FGFR1 and NTRK3 actionable alterations in "Wild-Type" gastrointestinal stromal tumors. | Shi E, Chmielecki J, Tang CM, Wang K, Heinrich MC, Kang G, Corless CL, Hong D, Fero KE, Murphy JD, Fanta PT, Ali SM, De Siena M, Burgoyne AM, Movva S, Madlensky L, Heestand GM, Trent JC, Kurzrock R, Morosini D, Ross JS, Harismendy O, Sicklick JK | Journal of translational medicine | 27974047 | J Transl Med | 2016 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/27974047 |
| Active Surveillance of the Implantable Cardioverter-Defibrillator Registry for Defibrillator Lead Failures. | Resnic FS, Majithia A, Dhruva SS, Ssemaganda H, Robbins S, Marinac-Dabic D, Hewitt K, Ohno-Machado L, Reynolds MR, Matheny ME | Circulation. Cardiovascular quality and outcomes | 32283971 | Circ Cardiovasc Qual Outcomes | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32283971 |
| Wessim: a whole-exome sequencing simulator based on in silico exome capture. | Kim S, Jeong K, Bafna V | Bioinformatics (Oxford, England) | 23413434 | Bioinformatics | 2013 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/23413434 |
| Preserving Institutional Privacy in Distributed binary Logistic Regression. | Wu Y, Jiang X, Ohno-Machado L | AMIA ... Annual Symposium proceedings. AMIA Symposium | 23304425 | AMIA Annu Symp Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23304425 |
| Extending the NegEx lexicon for multiple languages. | Chapman WW, Hillert D, Velupillai S, Kvist M, Skeppstedt M, Chapman BE, Conway M, Tharp M, Mowery DL, Deleger L | Studies in health technology and informatics | 23920642 | Stud Health Technol Inform | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23920642 |
| Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis. | Thawait SK, Kim J, Klufas RA, Morrison WB, Flanders AE, Carrino JA, Ohno-Machado L | AJR. American journal of roentgenology | 23436836 | AJR Am J Roentgenol | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23436836 |
| Smooth isotonic regression: a new method to calibrate predictive models. | Jiang X, Osl M, Kim J, Ohno-Machado L | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22211175 | AMIA Jt Summits Transl Sci Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22211175 |
| Analysis of high-throughput screening assays using cluster enrichment. | Pu M, Hayashi T, Cottam H, Mulvaney J, Arkin M, Corr M, Carson D, Messer K | Statistics in medicine | 22763983 | Stat Med | 2012 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/22763983 |
| Pregnancy in women with a history of Kawasaki disease: management and outcomes. | Gordon CT, Jimenez-Fernandez S, Daniels LB, Kahn AM, Tarsa M, Matsubara T, Shimizu C, Burns JC, Gordon JB | BJOG : an international journal of obstetrics and gynaecology | 24597833 | BJOG | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24597833 |
| Detecting Inappropriate Access to Electronic Health Records Using Collaborative Filtering. | Menon AK, Jiang X, Kim J, Vaidya J, Ohno-Machado L | Machine learning | 24683293 | Mach Learn | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24683293 |
| Seasonality of Kawasaki disease: a global perspective. | Burns JC, Herzog L, Fabri O, Tremoulet AH, Rodó X, Uehara R, Burgner D, Bainto E, Pierce D, Tyree M, Cayan D, Kawasaki Disease Global Climate Consortium | PloS one | 24058585 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24058585 |
| Nucleotide sequence alignment using sparse coding and belief propagation. | Roozgard A, Barzigar N, Wang S, Jiang X, Ohno-Machado L, Cheng S | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 24109755 | Annu Int Conf IEEE Eng Med Biol Soc | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24109755 |
| Differential privacy based on importance weighting. | Ji Z, Elkan C | Machine learning | 24482559 | Mach Learn | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24482559 |
| PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. | Doan S, Lin KW, Conway M, Ohno-Machado L, Hsieh A, Feupe SF, Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim HE | Journal of the American Medical Informatics Association : JAMIA | 23989082 | J Am Med Inform Assoc | 2014 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/23989082 |
| Nocturnal continuous glucose and sleep stage data in adults with type 1 diabetes in real-world conditions. | Feupe SF, Frias PF, Mednick SC, McDevitt EA, Heintzman ND | Journal of diabetes science and technology | 24124962 | J Diabetes Sci Technol | 2013 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/24124962 |
| Specificity of regulatory T cells that modulate vascular inflammation. | Franco A, Touma R, Song Y, Shimizu C, Tremoulet AH, Kanegaye JT, Burns JC | Autoimmunity | 24490882 | Autoimmunity | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24490882 |
| Differential-Private Data Publishing Through Component Analysis. | Jiang X, Ji Z, Wang S, Mohammed N, Cheng S, Ohno-Machado L | Transactions on data privacy | 24409205 | Trans Data Priv | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24409205 |
| Treatment response in Kawasaki disease is associated with sialylation levels of endogenous but not therapeutic intravenous immunoglobulin G. | Ogata S, Shimizu C, Franco A, Touma R, Kanegaye JT, Choudhury BP, Naidu NN, Kanda Y, Hoang LT, Hibberd ML, Tremoulet AH, Varki A, Burns JC | PloS one | 24324693 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24324693 |
| Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. | Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW, Rowley AH, Shulman ST, Burgner D, Breunis WB, Kuijpers TW, Wright VJ, Levin M, Eleftherohorinou H, Coin L, Popper SJ, Relman DA, Fury W, Lin C, Mellis S, Tremoulet AH, Burns JC | Circulation. Cardiovascular genetics | 21127203 | Circ Cardiovasc Genet | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21127203 |
| Duodenal-Jejunal Flexure GI Stromal Tumor Frequently Heralds Somatic NF1 and Notch Pathway Mutations. | Burgoyne AM, De Siena M, Alkhuziem M, Tang CM, Medina B, Fanta PT, Belinsky MG, von Mehren M, Thorson JA, Madlensky L, Bowler T, D'Angelo F, Stupack DG, Harismendy O, DeMatteo RP, Sicklick JK | JCO precision oncology | 29938249 | JCO Precis Oncol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29938249 |
| Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease. | Azad P, Zhao HW, Cabrales PJ, Ronen R, Zhou D, Poulsen O, Appenzeller O, Hsiao YH, Bafna V, Haddad GG | The Journal of experimental medicine | 27821551 | J Exp Med | 2016 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/27821551 |
| Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States. | Wang S, Jiang X, Singh S, Marmor R, Bonomi L, Fox D, Dow M, Ohno-Machado L | Annals of the New York Academy of Sciences | 27681358 | Ann N Y Acad Sci | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27681358 |
| Machine Learning-Based Predictive Modeling of Surgical Intervention in Glaucoma Using Systemic Data From Electronic Health Records. | Baxter SL, Marks C, Kuo TT, Ohno-Machado L, Weinreb RN | American journal of ophthalmology | 31323204 | Am J Ophthalmol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31323204 |
| miRIAD-integrating microRNA inter- and intragenic data. | Hinske LC, França GS, Torres HA, Ohara DT, Lopes-Ramos CM, Heyn J, Reis LF, Ohno-Machado L, Kreth S, Galante PA | Database : the journal of biological databases and curation | 25288656 | Database (Oxford) | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25288656 |
| Prediction of MicroRNA Precursors Using Parsimonious Feature Sets. | Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L | Cancer informatics | 25392687 | Cancer Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25392687 |
| Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. | Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL | Molecular biology and evolution | 25697341 | Mol Biol Evol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25697341 |
| BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. | Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM, Harismendy O | Journal of translational medicine | 25889843 | J Transl Med | 2015 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/25889843 |
| Galectin-3 is a marker of myocardial and vascular fibrosis in Kawasaki disease patients with giant aneurysms. | Numano F, Shimizu C, Jimenez-Fernandez S, Vejar M, Oharaseki T, Takahashi K, Salgado A, Tremoulet AH, Gordon JB, Burns JC, Daniels LB | International journal of cardiology | 26313861 | Int J Cardiol | 2015 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/26313861 |
| Differentially private distributed logistic regression using private and public data. | Ji Z, Jiang X, Wang S, Xiong L, Ohno-Machado L | BMC medical genomics | 25079786 | BMC Med Genomics | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25079786 |
| IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. | Hepler NL, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL | PLoS computational biology | 25254639 | PLoS Comput Biol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25254639 |
| SAPPIRE: a prototype mobile tool for pressure ulcer risk assessment. | Kim H, Chung H, Wang S, Jiang X, Choi J | Studies in health technology and informatics | 24943578 | Stud Health Technol Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24943578 |
| Big Data Privacy in Biomedical Research. | Wang S, Bonomi L, Dai W, Chen F, Cheung C, Bloss CS, Cheng S, Jiang X | IEEE transactions on big data | 32478127 | IEEE Trans Big Data | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32478127 |
| Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice. | Eguchi A, Yan R, Pan SQ, Wu R, Kim J, Chen Y, Ansong C, Smith RD, Tempaku M, Ohno-Machado L, Takei Y, Feldstein AE, Tsukamoto H | Journal of molecular medicine (Berlin, Germany) | 32556367 | J Mol Med (Berl) | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32556367 |
| VERTIcal Grid lOgistic regression (VERTIGO). | Li Y, Jiang X, Wang S, Xiong H, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 26554428 | J Am Med Inform Assoc | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26554428 |
| Using Kepler for Tool Integration in Microarray Analysis Workflows. | Gan Z, Stowe JC, Altintas I, McCulloch AD, Zambon AC | Procedia computer science | 26605000 | Procedia Comput Sci | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/26605000 |
| Cardiovascular pathology in 2 young adults with sudden, unexpected death due to coronary aneurysms from Kawasaki disease in childhood. | Shimizu C, Sood A, Lau HD, Oharaseki T, Takahashi K, Krous HF, Campman S, Burns JC | Cardiovascular pathology : the official journal of the Society for Cardiovascular Pathology | 25791439 | Cardiovasc Pathol | 2015 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/25791439 |
| Trends in publication of nursing informatics research. | Kim H, Ohno-Machado L, Oh J, Jiang X | AMIA ... Annual Symposium proceedings. AMIA Symposium | 25954387 | AMIA Annu Symp Proc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25954387 |
| Sharing my health data: a survey of data sharing preferences of healthy individuals. | Bell EA, Ohno-Machado L, Grando MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 25954442 | AMIA Annu Symp Proc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25954442 |
| Immune DNA signature of T-cell infiltration in breast tumor exomes. | Levy E, Marty R, Gárate Calderón V, Woo B, Dow M, Armisen R, Carter H, Harismendy O | Scientific reports | 27452728 | Sci Rep | 2016 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/27452728 |
| RELAX: detecting relaxed selection in a phylogenetic framework. | Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K | Molecular biology and evolution | 25540451 | Mol Biol Evol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25540451 |
| The immunomodulatory effects of intravenous immunoglobulin therapy in Kawasaki disease. | Burns JC, Franco A | Expert review of clinical immunology | 26099344 | Expert Rev Clin Immunol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26099344 |
| WebDISCO: a web service for distributed cox model learning without patient-level data sharing. | Lu CL, Wang S, Ji Z, Wu Y, Xiong L, Jiang X, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 26159465 | J Am Med Inform Assoc | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26159465 |
| Automated generation of directed graphs from vascular segmentations. | Chapman BE, Berty HP, Schulthies SL | Journal of biomedical informatics | 26165778 | J Biomed Inform | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26165778 |
| DPSynthesizer: Differentially Private Data Synthesizer for Privacy Preserving Data Sharing. | Li H, Xiong L, Zhang L, Jiang X | Proceedings of the VLDB Endowment. International Conference on Very Large Data Bases | 26167358 | Proceedings VLDB Endowment | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26167358 |
| Assigning and visualizing germline genes in antibody repertoires. | Frost SD, Murrell B, Hossain AS, Silverman GJ, Pond SL | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 26194754 | Philos Trans R Soc Lond B Biol Sci | 2015 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/26194754 |
| Learning from Data with Heterogeneous Noise using SGD. | Song S, Chaudhuri K, Sarwate AD | JMLR workshop and conference proceedings | 26705435 | JMLR Workshop Conf Proc | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26705435 |
| Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. | Herberg JA, Kaforou M, Wright VJ, Shailes H, Eleftherohorinou H, Hoggart CJ, Cebey-López M, Carter MJ, Janes VA, Gormley S, Shimizu C, Tremoulet AH, Barendregt AM, Salas A, Kanegaye J, Pollard AJ, Faust SN, Patel S, Kuijpers T, Martinón-Torres F, Burns JC, Coin LJ, Levin M, IRIS Consortium | JAMA | 27552617 | JAMA | 2016 Aug 23-30 | https://www.ncbi.nlm.nih.gov/pubmed/27552617 |
| An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. | Ghosh P, Katkar GD, Shimizu C, Kim J, Khandelwal S, Tremoulet AH, Kanegaye JT, Pediatric Emergency Medicine Kawasaki Disease Research Group, Bocchini J, Das S, Burns JC, Sahoo D | Nature communications | 35577777 | Nat Commun | 2022 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/35577777 |
| To share or not to share: that is not the question. | Ohno-Machado L | Science translational medicine | 23253606 | Sci Transl Med | 2012 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/23253606 |
| A semi-automated quantification of pulmonary artery dimensions in computed tomography angiography images. | Berty HL, Simon M, Chapman BE | AMIA ... Annual Symposium proceedings. AMIA Symposium | 23304270 | AMIA Annu Symp Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23304270 |
| SHARE: system design and case studies for statistical health information release. | Gardner J, Xiong L, Xiao Y, Gao J, Post AR, Jiang X, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 23059729 | J Am Med Inform Assoc | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23059729 |
| Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): an algorithm for joint optimization of discrimination and calibration. | Jiang X, Menon A, Wang S, Kim J, Ohno-Machado L | PloS one | 23139819 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23139819 |
| Natural language processing in biomedicine: a unified system architecture overview. | Doan S, Conway M, Phuong TM, Ohno-Machado L | Methods in molecular biology (Clifton, N.J.) | 24870142 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24870142 |
| Inferring gene ontologies from pairwise similarity data. | Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T | Bioinformatics (Oxford, England) | 24932003 | Bioinformatics | 2014 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/24932003 |
| The elusive evidence for chromothripsis. | Kinsella M, Patel A, Bafna V | Nucleic acids research | 24939897 | Nucleic Acids Res | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24939897 |
| Lipoprotein particle concentrations in children and adults following Kawasaki disease. | Lin J, Jain S, Sun X, Liu V, Sato YZ, Jimenez-Fernandez S, Newfield RS, Pourfarzib R, Tremoulet AH, Gordon JB, Daniels LB, Burns JC | The Journal of pediatrics | 25039043 | J Pediatr | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25039043 |
| pSCANNER: patient-centered Scalable National Network for Effectiveness Research. | Ohno-Machado L, Agha Z, Bell DS, Dahm L, Day ME, Doctor JN, Gabriel D, Kahlon MK, Kim KK, Hogarth M, Matheny ME, Meeker D, Nebeker JR, pSCANNER team | Journal of the American Medical Informatics Association : JAMIA | 24780722 | J Am Med Inform Assoc | 2014 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/24780722 |
| Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. | Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG | Genome biology | 24555826 | Genome Biol | 2014 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/24555826 |
| MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. | Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch AD, Altintas I, Zambon AC | BMC bioinformatics | 24621103 | BMC Bioinformatics | 2014 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/24621103 |
| Protecting count queries in study design. | Vinterbo SA, Sarwate AD, Boxwala AA | Journal of the American Medical Informatics Association : JAMIA | 22511018 | J Am Med Inform Assoc | 2012 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/22511018 |
| Anomaly and signature filtering improve classifier performance for detection of suspicious access to EHRs. | Kim J, Grillo JM, Boxwala AA, Jiang X, Mandelbaum RB, Patel BA, Mikels D, Vinterbo SA, Ohno-Machado L | AMIA ... Annual Symposium proceedings. AMIA Symposium | 22195129 | AMIA Annu Symp Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22195129 |
| Natural language processing: an introduction. | Nadkarni PM, Ohno-Machado L, Chapman WW | Journal of the American Medical Informatics Association : JAMIA | 21846786 | J Am Med Inform Assoc | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21846786 |
| Using statistical and machine learning to help institutions detect suspicious access to electronic health records. | Boxwala AA, Kim J, Grillo JM, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 21672912 | J Am Med Inform Assoc | 2011 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/21672912 |
| Compressing genomic sequence fragments using SlimGene. | Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G | Journal of computational biology : a journal of computational molecular cell biology | 21385043 | J Comput Biol | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21385043 |
| Streamlined Genome Sequence Compression using Distributed Source Coding. | Wang S, Jiang X, Chen F, Cui L, Cheng S | Cancer informatics | 25520552 | Cancer Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25520552 |
| Scalable privacy-preserving data sharing methodology for genome-wide association studies: an application to iDASH healthcare privacy protection challenge. | Yu F, Ji Z | BMC medical informatics and decision making | 25521367 | BMC Med Inform Decis Mak | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25521367 |
| Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery. | Zhao Y, Wang X, Jiang X, Ohno-Machado L, Tang H | Journal of the American Medical Informatics Association : JAMIA | 25352565 | J Am Med Inform Assoc | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25352565 |
| Sample Complexity Bounds for Differentially Private Learning. | Chaudhuri K, Hsu D | JMLR workshop and conference proceedings | 25285183 | JMLR Workshop Conf Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/25285183 |
| Policy Driven Development: Flexible Policy Insertion for Large Scale Systems. | Demchak B, Krüger I | Proceedings. IEEE International Symposium on Policies for Distributed Systems and Networks | 25383258 | Proc IEEE Int Symp Policies Distrib Syst Netw | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25383258 |
| Disease Biomarker Query from RNA-Seq Data. | Han H, Jiang X | Cancer informatics | 25392686 | Cancer Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25392686 |
| Differentially private genome data dissemination through top-down specialization. | Wang S, Mohammed N, Chen R | BMC medical informatics and decision making | 25521306 | BMC Med Inform Decis Mak | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25521306 |
| Gene-wide identification of episodic selection. | Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL | Molecular biology and evolution | 25701167 | Mol Biol Evol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25701167 |
| DSGeo: software tools for cross-platform analysis of gene expression data in GEO. | Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L | Journal of biomedical informatics | 20435161 | J Biomed Inform | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20435161 |
| Using Genome Query Language to uncover genetic variation. | Kozanitis C, Heiberg A, Varghese G, Bafna V | Bioinformatics (Oxford, England) | 23751181 | Bioinformatics | 2014 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23751181 |
| Virmid: accurate detection of somatic mutations with sample impurity inference. | Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V | Genome biology | 23987214 | Genome Biol | 2013 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/23987214 |
| SEMI-SUPERVISED OBJECT RECOGNITION USING STRUCTURE KERNEL. | Wang B, Xiong H, Jiang X, Ling F | Proceedings. International Conference on Image Processing | 23666108 | Proc Int Conf Image Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23666108 |
| Comparison of consumers' views on electronic data sharing for healthcare and research. | Kim KK, Joseph JG, Ohno-Machado L | Journal of the American Medical Informatics Association : JAMIA | 25829461 | J Am Med Inform Assoc | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25829461 |
| Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data. | Kroll JE, Kim J, Ohno-Machado L, de Souza SJ | PeerJ | 26618088 | PeerJ | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26618088 |
| FORESEE: Fully Outsourced secuRe gEnome Study basEd on homomorphic Encryption. | Zhang Y, Dai W, Jiang X, Xiong H, Wang S | BMC medical informatics and decision making | 26733391 | BMC Med Inform Decis Mak | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26733391 |
| Predicting accurate probabilities with a ranking loss. | Menon AK, Jiang XJ, Vembu S, Elkan C, Ohno-Machado L | Proceedings of the ... International Conference on Machine Learning. International Conference on Machine Learning | 25285328 | Proc Int Conf Mach Learn | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/25285328 |
| HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS. | Wang S, Zhang Y, Dai W, Lauter K, Kim M, Tang Y, Xiong H, Jiang X | Bioinformatics (Oxford, England) | 26446135 | Bioinformatics | 2016 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/26446135 |
| iDECIDE: A Mobile Application for Insulin Dosing Using an Evidence Based Equation to Account for Patient Preferences. | Lloyd B, Groat D, Cook CB, Kaufman D, Grando A | Studies in health technology and informatics | 26262017 | Stud Health Technol Inform | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26262017 |
| Medical subdomain classification of clinical notes using a machine learning-based natural language processing approach. | Weng WH, Wagholikar KB, McCray AT, Szolovits P, Chueh HC | BMC medical informatics and decision making | 29191207 | BMC Med Inform Decis Mak | 2017 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/29191207 |
| PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. | Spahn PN, Bath T, Weiss RJ, Kim J, Esko JD, Lewis NE, Harismendy O | Scientific reports | 29158538 | Sci Rep | 2017 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/29158538 |
| Cronkhite Canada Syndrome: Significant Response to Infliximab and a Possible Clue to Pathogenesis. | Boland BS, Bagi P, Valasek MA, Chang JT, Bustamante R, Madlensky L, Sandborn WJ, Harismendy O, Gupta S | The American journal of gastroenterology | 27151126 | Am J Gastroenterol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27151126 |
| PATTERN: Pain Assessment for paTients who can't TEll using Restricted Boltzmann machiNe. | Yang L, Wang S, Jiang X, Cheng S, Kim HE | BMC medical informatics and decision making | 27454233 | BMC Med Inform Decis Mak | 2016 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/27454233 |
| PREMIX: PRivacy-preserving EstiMation of Individual admiXture. | Chen F, Dow M, Ding S, Lu Y, Jiang X, Tang H, Wang S | AMIA ... Annual Symposium proceedings. AMIA Symposium | 28269933 | AMIA Annu Symp Proc | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28269933 |
| PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. | Chen F, Wang S, Jiang X, Ding S, Lu Y, Kim J, Sahinalp SC, Shimizu C, Burns JC, Wright VJ, Png E, Hibberd ML, Lloyd DD, Yang H, Telenti A, Bloss CS, Fox D, Lauter K, Ohno-Machado L | Bioinformatics (Oxford, England) | 28065902 | Bioinformatics | 2017 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/28065902 |
| Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. | Kim J, Shimizu C, Kingsmore SF, Veeraraghavan N, Levy E, Ribeiro Dos Santos AM, Yang H, Flatley J, Hoang LT, Hibberd ML, Tremoulet AH, Harismendy O, Ohno-Machado L, Burns JC | PloS one | 28151979 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28151979 |
| Characterization of Exercise and Alcohol Self-Management Behaviors of Type 1 Diabetes Patients on Insulin Pump Therapy. | Grando MA, Groat D, Soni H, Boyle M, Bailey M, Thompson B, Cook CB | Journal of diabetes science and technology | 27595712 | J Diabetes Sci Technol | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27595712 |
| Extracellular vesicles released by hepatocytes from gastric infusion model of alcoholic liver disease contain a MicroRNA barcode that can be detected in blood. | Eguchi A, Lazaro RG, Wang J, Kim J, Povero D, Willliams B, Ho SB, Stärkel P, Schnabl B, Ohno-Machado L, Tsukamoto H, Feldstein AE | Hepatology (Baltimore, Md.) | 27639178 | Hepatology | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27639178 |
| Distributed learning from multiple EHR databases: Contextual embedding models for medical events. | Li Z, Roberts K, Jiang X, Long Q | Journal of biomedical informatics | 30825539 | J Biomed Inform | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30825539 |
| Activation of hedgehog signaling associates with early disease progression in chronic lymphocytic leukemia. | Ghia EM, Rassenti LZ, Neuberg DS, Blanco A, Yousif F, Smith EN, McPherson JD, Hudson TJ, HALT Pan-Leukemia Gene Panel Consortium, Harismendy O, Frazer KA, Kipps TJ | Blood | 30923040 | Blood | 2019 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/30923040 |
| Privacy Policy and Technology in Biomedical Data Science. | Arellano AM, Dai W, Wang S, Jiang X, Ohno-Machado L | Annual review of biomedical data science | 31058261 | Annu Rev Biomed Data Sci | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31058261 |
| Integrating phenotype ontologies across multiple species. | Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M | Genome biology | 20064205 | Genome Biol | 2010 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/20064205 |
| Patients' perceptions of self-management of chronic low back pain: evidence for enhancing patient education and support. | Cooper K, Smith BH, Hancock E | Physiotherapy | 19627685 | Physiotherapy | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19627685 |
| Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages. | Noy NF, de Coronado S, Solbrig H, Fragoso G, Hartel FW, Musen MA | Applied ontology | 19789731 | Appl Ontol | 2008 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19789731 |
| The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system. | Brochhausen M, Spear AD, Cocos C, Weiler G, Martín L, Anguita A, Stenzhorn H, Daskalaki E, Schera F, Schwarz U, Sfakianakis S, Kiefer S, Dörr M, Graf N, Tsiknakis M | Journal of biomedical informatics | 20438862 | J Biomed Inform | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20438862 |
| Towards an ontological representation of resistance: the case of MRSA. | Goldfain A, Smith B, Cowell LG | Journal of biomedical informatics | 20206294 | J Biomed Inform | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20206294 |
| Strengths and limitations of formal ontologies in the biomedical domain. | Schulz S, Stenzhorn H, Boeker M, Smith B | Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS | 20640238 | Rev Electron Comun Inf Inov Saude | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/20640238 |
| Adapting Clinical Ontologies in Real-World Environments. | Stenzhorn H, Schulz S, Boeker M, Smith B | Journal of universal computer science : J. UCS | 20390048 | J Univers. Comput Sci | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/20390048 |
| Dealing with socially constructed concepts in an ontology. | Koepsell D, Smith B | Journal of empirical research on human research ethics : JERHRE | 19480594 | J Empir Res Hum Res Ethics | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19480594 |
| Computational neuroanatomy: ontology-based representation of neural components and connectivity. | Rubin DL, Talos IF, Halle M, Musen MA, Kikinis R | BMC bioinformatics | 19208191 | BMC Bioinformatics | 2009 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/19208191 |
| Survey-based naming conventions for use in OBO Foundry ontology development. | Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA | BMC bioinformatics | 19397794 | BMC Bioinformatics | 2009 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/19397794 |
| Working together to put molecules on the map. | Field D | Nature | 18563126 | Nature | 2008 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/18563126 |
| The minimum information about a genome sequence (MIGS) specification. | Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A | Nature biotechnology | 18464787 | Nat Biotechnol | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18464787 |
| Protégé: a tool for managing and using terminology in radiology applications. | Rubin DL, Noy NF, Musen MA | Journal of digital imaging | 17687607 | J Digit Imaging | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17687607 |
| Negative findings in electronic health records and biomedical ontologies: a realist approach. | Ceusters W, Elkin P, Smith B | International journal of medical informatics | 17369081 | Int J Med Inform | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17369081 |
| Phenotype ontologies: the bridge between genomics and evolution. | Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M | Trends in ecology & evolution | 17416439 | Trends Ecol Evol | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17416439 |
| A prototype symbolic model of canonical functional neuroanatomy of the motor system. | Talos IF, Rubin DL, Halle M, Musen M, Kikinis R | Journal of biomedical informatics | 18164666 | J Biomed Inform | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18164666 |
| Knowledge Zone: a public repository of peer-reviewed biomedical ontologies. | Supekar K, Rubin D, Noy N, Musen M | Studies in health technology and informatics | 17911829 | Stud Health Technol Inform | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17911829 |
| Current progress in network research: toward reference networks for key model organisms. | Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S | Briefings in bioinformatics | 17728341 | Brief Bioinform | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17728341 |
| The Protein Ontology: a structured representation of protein forms and complexes. | Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH | Nucleic acids research | 20935045 | Nucleic Acids Res | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20935045 |
| The BioPAX community standard for pathway data sharing. | Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD | Nature biotechnology | 20829833 | Nat Biotechnol | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20829833 |
| A unified framework for biomedical terminologies and ontologies. | Ceusters W, Smith B | Studies in health technology and informatics | 20841844 | Stud Health Technol Inform | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20841844 |
| Toward an ontological treatment of disease and diagnosis. | Scheuermann RH, Ceusters W, Smith B | Summit on translational bioinformatics | 21347182 | Summit Transl Bioinform | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347182 |
| Extraction of Conditional Probabilities of the Relationships Between Drugs, Diseases, and Genes from PubMed Guided by Relationships in PharmGKB. | Theobald M, Shah N, Shrager J | Summit on translational bioinformatics | 21347183 | Summit Transl Bioinform | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347183 |
| Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. | Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL | Standards in genomic sciences | 21304730 | Stand Genomic Sci | 2010 Dec 25 | https://www.ncbi.nlm.nih.gov/pubmed/21304730 |
| Towards BioDBcore: a community-defined information specification for biological databases. | Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C, BioDBCore Working Group | Database : the journal of biological databases and curation | 21205783 | Database (Oxford) | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21205783 |
| Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. | Butte AJ, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 21672904 | J Am Med Inform Assoc | 2011 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/21672904 |
| Referent tracking for treatment optimisation in schizophrenic patients: A case study in applying philosophical ontology to diagnostic algorithms. | Ceusters W, Smith B | Web semantics (Online) | 23459504 | Web Semant | 2006 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/23459504 |
| Web-scale pharmacovigilance: listening to signals from the crowd. | White RW, Tatonetti NP, Shah NH, Altman RB, Horvitz E | Journal of the American Medical Informatics Association : JAMIA | 23467469 | J Am Med Inform Assoc | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23467469 |
| Performance of pharmacovigilance signal-detection algorithms for the FDA adverse event reporting system. | Harpaz R, DuMouchel W, LePendu P, Bauer-Mehren A, Ryan P, Shah NH | Clinical pharmacology and therapeutics | 23571771 | Clin Pharmacol Ther | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23571771 |
| Toward personalizing treatment for depression: predicting diagnosis and severity. | Huang SH, LePendu P, Iyer SV, Tai-Seale M, Carrell D, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 24988898 | J Am Med Inform Assoc | 2014 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/24988898 |
| Toward enhanced pharmacovigilance using patient-generated data on the internet. | White RW, Harpaz R, Shah NH, DuMouchel W, Horvitz E | Clinical pharmacology and therapeutics | 24713590 | Clin Pharmacol Ther | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24713590 |
| Patient-level temporal aggregation for text-based asthma status ascertainment. | Wu ST, Juhn YJ, Sohn S, Liu H | Journal of the American Medical Informatics Association : JAMIA | 24833775 | J Am Med Inform Assoc | 2014 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/24833775 |
| ArrayExpress update--trends in database growth and links to data analysis tools. | Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U | Nucleic acids research | 23193272 | Nucleic Acids Res | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23193272 |
| Towards the creation of a visual ontology of biomedical imaging entities. | Simpson MS, You D, Rahman MM, Antani SK, Thoma GR, Demner-Fushman D | AMIA ... Annual Symposium proceedings. AMIA Symposium | 23304361 | AMIA Annu Symp Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23304361 |
| Genetic correction of Huntington's disease phenotypes in induced pluripotent stem cells. | An MC, Zhang N, Scott G, Montoro D, Wittkop T, Mooney S, Melov S, Ellerby LM | Cell stem cell | 22748967 | Cell Stem Cell | 2012 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/22748967 |
| Context-specific ontology integration: a bayesian approach. | Marwah K, Katzin D, Zollanvari A, Noy NF, Ramoni M, Alterovitz G | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22779057 | AMIA Jt Summits Transl Sci Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22779057 |
| Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. | Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, Adzhubey IA, Li B, Bell R, Feng B, Mooney SD, Radivojac P, Sunyaev SR, Frebourg T, Hofstra RM, Sijmons RH, Boucher K, Thomas A, Goldgar DE, Spurdle AB, Tavtigian SV | Human mutation | 22949387 | Hum Mutat | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22949387 |
| Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions. | Harpaz R, Vilar S, Dumouchel W, Salmasian H, Haerian K, Shah NH, Chase HS, Friedman C | Journal of the American Medical Informatics Association : JAMIA | 23118093 | J Am Med Inform Assoc | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23118093 |
| Practice-based evidence: profiling the safety of cilostazol by text-mining of clinical notes. | Leeper NJ, Bauer-Mehren A, Iyer SV, Lependu P, Olson C, Shah NH | PloS one | 23717437 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23717437 |
| Improving data and knowledge management to better integrate health care and research. | Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark TW, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, López-Bigas N, Maojo V, Mons B, Musen M, Oliveira JL, Rowe A, Ruch P, Shabo A, Shortliffe EH, Valencia A, van der Lei J, Mayer MA, Sanz F | Journal of internal medicine | 23808970 | J Intern Med | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23808970 |
| Computational semantics in clinical text. | Wu S | Biomedical informatics insights | 23847422 | Biomed Inform Insights | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23847422 |
| Annotating the structure and components of a nanoparticle formulation using computable string expressions. | Thomas DG, Chikkagoudar S, Chappell AR, Baker NA | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 24533226 | Proceedings (IEEE Int Conf Bioinformatics Biomed) | 2012 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/24533226 |
| Learning signals of adverse drug-drug interactions from the unstructured text of electronic health records. | Iyer SV, Lependu P, Harpaz R, Bauer-Mehren A, Shah NH | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 24303305 | AMIA Jt Summits Transl Sci Proc | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24303305 |
| NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. | Jonquet C, Lependu P, Falconer S, Coulet A, Noy NF, Musen MA, Shah NH | Web semantics (Online) | 21918645 | Web Semant | 2011 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/21918645 |
| ARGOS policy brief on semantic interoperability. | Kalra D, Musen M, Smith B, Ceusters W, De Moor G | Studies in health technology and informatics | 21893897 | Stud Health Technol Inform | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21893897 |
| Building the graph of medicine from millions of clinical narratives. | Finlayson SG, LePendu P, Shah NH | Scientific data | 25977789 | Sci Data | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25977789 |
| Feasibility of Prioritizing Drug-Drug-Event Associations Found in Electronic Health Records. | Banda JM, Callahan A, Winnenburg R, Strasberg HR, Cami A, Reis BY, Vilar S, Hripcsak G, Dumontier M, Shah NH | Drug safety | 26446143 | Drug Saf | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26446143 |
| A time-indexed reference standard of adverse drug reactions. | Harpaz R, Odgers D, Gaskin G, DuMouchel W, Winnenburg R, Bodenreider O, Ripple A, Szarfman A, Sorbello A, Horvitz E, White RW, Shah NH | Scientific data | 25632348 | Sci Data | 2014 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/25632348 |
| A method for systematic discovery of adverse drug events from clinical notes. | Wang G, Jung K, Winnenburg R, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 26232442 | J Am Med Inform Assoc | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26232442 |
| Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies. | Winnenburg R, Sorbello A, Ripple A, Harpaz R, Tonning J, Szarfman A, Francis H, Bodenreider O | Journal of biomedical informatics | 26342964 | J Biomed Inform | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26342964 |
| Recommendations for minimum information for publication of experimental pathology data: MINPEPA guidelines. | Scudamore CL, Soilleux EJ, Karp NA, Smith K, Poulsom R, Herrington CS, Day MJ, Brayton CF, Bolon B, Whitelaw B, White ES, Everitt JI, Arends MJ | The Journal of pathology | 26387837 | J Pathol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26387837 |
| An empirical analysis of ontology reuse in BioPortal. | Ochs C, Perl Y, Geller J, Arabandi S, Tudorache T, Musen MA | Journal of biomedical informatics | 28583809 | J Biomed Inform | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28583809 |
| NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. | Martínez-Romero M, Jonquet C, O'Connor MJ, Graybeal J, Pazos A, Musen MA | Journal of biomedical semantics | 28592275 | J Biomed Semantics | 2017 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/28592275 |
| The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). | MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H | Nucleic acids research | 27899670 | Nucleic Acids Res | 2017 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/27899670 |
| Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. | Martínez-Romero M, O'Connor MJ, Shankar RD, Panahiazar M, Willrett D, Egyedi AL, Gevaert O, Graybeal J, Musen MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 29854196 | AMIA Annu Symp Proc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29854196 |
| WaveformECG: A Platform for Visualizing, Annotating, and Analyzing ECG Data. | Winslow RL, Granite S, Jurado C | Computing in science & engineering | 28642673 | Comput Sci Eng | 2016 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/28642673 |
| Enabling Web-scale data integration in biomedicine through Linked Open Data. | Kamdar MR, Fernández JD, Polleres A, Tudorache T, Musen MA | NPJ digital medicine | 31531395 | NPJ Digit Med | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31531395 |
| Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates. | Jupp S, Burdett T, Welter D, Sarntivijai S, Parkinson H, Malone J | Journal of biomedical semantics | 27042287 | J Biomed Semantics | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27042287 |
| Learning statistical models of phenotypes using noisy labeled training data. | Agarwal V, Podchiyska T, Banda JM, Goel V, Leung TI, Minty EP, Sweeney TE, Gyang E, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 27174893 | J Am Med Inform Assoc | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27174893 |
| An empirical meta-analysis of the life sciences linked open data on the web. | Kamdar MR, Musen MA | Scientific data | 33479214 | Sci Data | 2021 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/33479214 |
| The GA4GH Phenopacket schema defines a computable representation of clinical data. | Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, GAGH Phenopacket Modeling Consortium, Haendel MA, Robinson PN | Nature biotechnology | 35705716 | Nat Biotechnol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35705716 |
| Relations in biomedical ontologies. | Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C | Genome biology | 15892874 | Genome Biol | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/15892874 |
| Ontology metadata to support the building of a library of biomedical ontologies. | Supekar K, Musen M | AMIA ... Annual Symposium proceedings. AMIA Symposium | 16779413 | AMIA Annu Symp Proc | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16779413 |
| National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. | Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA | Omics : a journal of integrative biology | 16901225 | OMICS | 2006 Summer | https://www.ncbi.nlm.nih.gov/pubmed/16901225 |
| Bridging the gap between medical and bioinformatics: an ontological case study in colon carcinoma. | Kumar A, Yip YL, Smith B, Grenon P | Computers in biology and medicine | 16343472 | Comput Biol Med | 2006 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/16343472 |
| Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. | Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, Westerfield M | Journal of experimental zoology. Part B, Molecular and developmental evolution | 17599725 | J Exp Zool B Mol Dev Evol | 2007 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/17599725 |
| Investigating subsumption in SNOMED CT: an exploration into large description logic-based biomedical terminologies. | Bodenreider O, Smith B, Kumar A, Burgun A | Artificial intelligence in medicine | 17241777 | Artif Intell Med | 2007 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17241777 |
| The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. | Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M | Nucleic acids research | 17991680 | Nucleic Acids Res | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17991680 |
| ChEBI: a database and ontology for chemical entities of biological interest. | Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M | Nucleic acids research | 17932057 | Nucleic Acids Res | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17932057 |
| Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment. | Smith B, Brochhausen M | Studies in health technology and informatics | 18376049 | Stud Health Technol Inform | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18376049 |
| Gene Ontology annotations: what they mean and where they come from. | Hill DP, Smith B, McAndrews-Hill MS, Blake JA | BMC bioinformatics | 18460184 | BMC Bioinformatics | 2008 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/18460184 |
| Ontologies of cellular networks. | Arp R, Smith B | Science signaling | 19091693 | Sci Signal | 2008 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/19091693 |
| An improved ontological representation of dendritic cells as a paradigm for all cell types. | Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG | BMC bioinformatics | 19243617 | BMC Bioinformatics | 2009 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/19243617 |
| FMA-RadLex: An application ontology of radiological anatomy derived from the foundational model of anatomy reference ontology. | Mejino JL, Rubin DL, Brinkley JF | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18999035 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18999035 |
| Building a biomedical ontology recommender web service. | Jonquet C, Musen MA, Shah NH | Journal of biomedical semantics | 20626921 | J Biomed Semantics | 2010 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/20626921 |
| Towards a framework for developing semantic relatedness reference standards. | Pakhomov SV, Pedersen T, McInnes B, Melton GB, Ruggieri A, Chute CG | Journal of biomedical informatics | 21044697 | J Biomed Inform | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21044697 |
| Effectiveness of lexico-syntactic pattern matching for ontology enrichment with clinical documents. | Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS | Methods of information in medicine | 21057720 | Methods Inf Med | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21057720 |
| Linking human diseases to animal models using ontology-based phenotype annotation. | Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE | PLoS biology | 19956802 | PLoS Biol | 2009 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19956802 |
| Putting biomedical ontologies to work. | Smith B, Brochhausen M | Methods of information in medicine | 20135080 | Methods Inf Med | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20135080 |
| Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. | Ai J, Smith B, Wong DT | BMC bioinformatics | 20525291 | BMC Bioinformatics | 2010 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/20525291 |
| A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations. | Xu R, Musen MA, Shah NH | AMIA ... Annual Symposium proceedings. AMIA Symposium | 21347110 | AMIA Annu Symp Proc | 2010 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/21347110 |
| The open biomedical annotator. | Jonquet C, Shah NH, Musen MA | Summit on translational bioinformatics | 21347171 | Summit Transl Bioinform | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347171 |
| An ontology-neutral framework for enrichment analysis. | Tirrell R, Evani U, Berman AE, Mooney SD, Musen MA, Shah NH | AMIA ... Annual Symposium proceedings. AMIA Symposium | 21347088 | AMIA Annu Symp Proc | 2010 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/21347088 |
| Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing. | Quinn TA, Granite S, Allessie MA, Antzelevitch C, Bollensdorff C, Bub G, Burton RA, Cerbai E, Chen PS, Delmar M, Difrancesco D, Earm YE, Efimov IR, Egger M, Entcheva E, Fink M, Fischmeister R, Franz MR, Garny A, Giles WR, Hannes T, Harding SE, Hunter PJ, Iribe G, Jalife J, Johnson CR, Kass RS, Kodama I, Koren G, Lord P, Markhasin VS, Matsuoka S, McCulloch AD, Mirams GR, Morley GE, Nattel S, Noble D, Olesen SP, Panfilov AV, Trayanova NA, Ravens U, Richard S, Rosenbaum DS, Rudy Y, Sachs F, Sachse FB, Saint DA, Schotten U, Solovyova O, Taggart P, Tung L, Varró A, Volders PG, Wang K, Weiss JN, Wettwer E, White E, Wilders R, Winslow RL, Kohl P | Progress in biophysics and molecular biology | 21745496 | Prog Biophys Mol Biol | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21745496 |
| The representation of protein complexes in the Protein Ontology (PRO). | Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C | BMC bioinformatics | 21929785 | BMC Bioinformatics | 2011 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/21929785 |
| CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. | Tao C, Solbrig HR, Chute CG | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22211182 | AMIA Jt Summits Transl Sci Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22211182 |
| Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources. | Pathak J, Jiang G, Dwarkanath SO, Buntrock JD, Chute CG | Proceedings. IEEE International Conference on Semantic Computing | 21625412 | Proc IEEE Int Conf Semant Comput | 2008 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/21625412 |
| Informatics and standards for nanomedicine technology. | Thomas DG, Klaessig F, Harper SL, Fritts M, Hoover MD, Gaheen S, Stokes TH, Reznik-Zellen R, Freund ET, Klemm JD, Paik DS, Baker NA | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 21721140 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21721140 |
| Would SNOMED CT benefit from realism-based ontology evolution? | Ceusters WM, Spackman KA, Smith B | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18693807 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18693807 |
| Interpretation errors related to the GO annotation file format. | Moreira DA, Shah NH, Musen MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18693894 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18693894 |
| Functional organization and its implication in evolution of the human protein-protein interaction network. | Zhao Y, Mooney SD | BMC genomics | 22530615 | BMC Genomics | 2012 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/22530615 |
| Bioinformatics advances in saliva diagnostics. | Ai JY, Smith B, Wong DT | International journal of oral science | 22699264 | Int J Oral Sci | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22699264 |
| DEFOG: discrete enrichment of functionally organized genes. | Wittkop T, Berman AE, Fleisch KM, Mooney SD | Integrative biology : quantitative biosciences from nano to macro | 22706384 | Integr Biol (Camb) | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22706384 |
| Mining the pharmacogenomics literature--a survey of the state of the art. | Hahn U, Cohen KB, Garten Y, Shah NH | Briefings in bioinformatics | 22833496 | Brief Bioinform | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22833496 |
| Where to Publish and Find Ontologies? A Survey of Ontology Libraries. | d'Aquin M, Noy NF | Web semantics (Online) | 22408576 | Web Semant | 2012 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/22408576 |
| Using temporal patterns in medical records to discern adverse drug events from indications. | Liu Y, Lependu P, Iyer S, Shah NH | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22779050 | AMIA Jt Summits Transl Sci Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22779050 |
| Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes. | Lependu P, Iyer SV, Fairon C, Shah NH | Journal of biomedical semantics | 22541596 | J Biomed Semantics | 2012 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/22541596 |
| Comment on: "Zoo or savannah? Choice of training ground for evidence-based pharmacovigilance". | Harpaz R, DuMouchel W, Shah NH | Drug safety | 25432779 | Drug Saf | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25432779 |
| Functional evaluation of out-of-the-box text-mining tools for data-mining tasks. | Jung K, LePendu P, Iyer S, Bauer-Mehren A, Percha B, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 25336595 | J Am Med Inform Assoc | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25336595 |
| Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical records. | Lyalina S, Percha B, LePendu P, Iyer SV, Altman RB, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 23956017 | J Am Med Inform Assoc | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23956017 |
| Pharmacokinetics and pharmacodynamics of oral artesunate monotherapy in patients with uncomplicated Plasmodium falciparum malaria in western Cambodia. | Saunders D, Khemawoot P, Vanachayangkul P, Siripokasupkul R, Bethell D, Tyner S, Se Y, Rutvisuttinunt W, Sriwichai S, Chanthap L, Lin J, Timmermans A, Socheat D, Ringwald P, Noedl H, Smith B, Fukuda M, Teja-Isavadharm P | Antimicrobial agents and chemotherapy | 22869581 | Antimicrob Agents Chemother | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22869581 |
| Translational bioinformatics embraces big data. | Shah NH | Yearbook of medical informatics | 22890354 | Yearb Med Inform | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22890354 |
| Terminology representation guidelines for biomedical ontologies in the semantic web notations. | Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG | Journal of biomedical informatics | 23026232 | J Biomed Inform | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23026232 |
| NCBO Technology: Powering semantically aware applications. | Whetzel PL, NCBO Team | Journal of biomedical semantics | 23734708 | J Biomed Semantics | 2013 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/23734708 |
| Genome-wide DNA methylation changes with age in disease-free human skeletal muscle. | Zykovich A, Hubbard A, Flynn JM, Tarnopolsky M, Fraga MF, Kerksick C, Ogborn D, MacNeil L, Mooney SD, Melov S | Aging cell | 24304487 | Aging Cell | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24304487 |
| Mining the ultimate phenome repository. | Shah NH | Nature biotechnology | 24316646 | Nat Biotechnol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24316646 |
| Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. | Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, Bowers S, Buttigieg PL, Davies N, Endresen D, Gandolfo MA, Hanner R, Janning A, Krishtalka L, Matsunaga A, Midford P, Morrison N, Ó Tuama É, Schildhauer M, Smith B, Stucky BJ, Thomer A, Wieczorek J, Whitacre J, Wooley J | PloS one | 24595056 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24595056 |
| Network analysis of unstructured EHR data for clinical research. | Bauer-Mehren A, Lependu P, Iyer SV, Harpaz R, Leeper NJ, Shah NH | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 24303229 | AMIA Jt Summits Transl Sci Proc | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24303229 |
| A Linked Science Investigation: Enhancing Climate Change Data Discovery with Semantic Technologies. | Pouchard LC, Branstetter ML, Cook RB, Devarakonda R, Green J, Palanisamy G, Alexander P, Noy NF | Earth science informatics | 24416086 | Earth Sci Inform | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24416086 |
| Automated detection of off-label drug use. | Jung K, LePendu P, Chen WS, Iyer SV, Readhead B, Dudley JT, Shah NH | PloS one | 24586689 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24586689 |
| The automated function prediction SIG looks back at 2013 and prepares for 2014. | Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I | Bioinformatics (Oxford, England) | 24590444 | Bioinformatics | 2014 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/24590444 |
| A large-scale evaluation of computational protein function prediction. | Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I | Nature methods | 23353650 | Nat Methods | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23353650 |
| A genome-scale RNA-interference screen identifies RRAS signaling as a pathologic feature of Huntington's disease. | Miller JP, Yates BE, Al-Ramahi I, Berman AE, Sanhueza M, Kim E, de Haro M, DeGiacomo F, Torcassi C, Holcomb J, Gafni J, Mooney SD, Botas J, Ellerby LM, Hughes RE | PLoS genetics | 23209424 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23209424 |
| Ranking adverse drug reactions with crowdsourcing. | Gottlieb A, Hoehndorf R, Dumontier M, Altman RB | Journal of medical Internet research | 25800813 | J Med Internet Res | 2015 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/25800813 |
| Proton Pump Inhibitor Usage and the Risk of Myocardial Infarction in the General Population. | Shah NH, LePendu P, Bauer-Mehren A, Ghebremariam YT, Iyer SV, Marcus J, Nead KT, Cooke JP, Leeper NJ | PloS one | 26061035 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26061035 |
| Rapid identification of slow healing wounds. | Jung K, Covington S, Sen CK, Januszyk M, Kirsner RS, Gurtner GC, Shah NH | Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society | 26606167 | Wound Repair Regen | 2016 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/26606167 |
| A gene expression resource generated by genome-wide lacZ profiling in the mouse. | Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C, Green AL, Wardle-Jones H, Carragher DM, Karp NA, Smedley D, Adams NC, Sanger Institute Mouse Genetics Project, Bussell JN, Adams DJ, Ramírez-Solis R, Steel KP, Galli A, White JK | Disease models & mechanisms | 26398943 | Dis Model Mech | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26398943 |
| Comparing high-dimensional confounder control methods for rapid cohort studies from electronic health records. | Low YS, Gallego B, Shah NH | Journal of comparative effectiveness research | 26634383 | J Comp Eff Res | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26634383 |
| Genome wide in vivo mouse screen data from studies to assess host regulation of metastatic colonisation. | van der Weyden L, Karp NA, Swiatkowska A, Adams DJ, Speak AO | Scientific data | 28895944 | Sci Data | 2017 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/28895944 |
| Enabling enrichment analysis with the Human Disease Ontology. | LePendu P, Musen MA, Shah NH | Journal of biomedical informatics | 21550421 | J Biomed Inform | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21550421 |
| BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. | Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA | Nucleic acids research | 21672956 | Nucleic Acids Res | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21672956 |
| Modular Ontology Techniques and their Applications in the Biomedical Domain. | Pathak J, Johnson TM, Chute CG | Proceedings of the ... IEEE International Conference on Information Reuse and Integration. IEEE International Conference on Information Reuse and Integration | 21625409 | Proc IEEE Int Conf Inf Reuse Integr | 2008 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/21625409 |
| Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. | Kohane IS, Valtchinov VI | Bioinformatics (Oxford, England) | 22219206 | Bioinformatics | 2012 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/22219206 |
| Semantator: semantic annotator for converting biomedical text to linked data. | Tao C, Song D, Sharma D, Chute CG | Journal of biomedical informatics | 23867104 | J Biomed Inform | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23867104 |
| MicroRNA-centric measurement improves functional enrichment analysis of co-expressed and differentially expressed microRNA clusters. | Lee SY, Sohn KA, Kim JH | BMC genomics | 23281707 | BMC Genomics | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23281707 |
| Applications of ontology design patterns in biomedical ontologies. | Mortensen JM, Horridge M, Musen MA, Noy NF | AMIA ... Annual Symposium proceedings. AMIA Symposium | 23304337 | AMIA Annu Symp Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23304337 |
| STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. | Wittkop T, TerAvest E, Evani US, Fleisch KM, Berman AE, Powell C, Shah NH, Mooney SD | BMC bioinformatics | 23409969 | BMC Bioinformatics | 2013 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/23409969 |
| ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. | Thomas DG, Gaheen S, Harper SL, Fritts M, Klaessig F, Hahn-Dantona E, Paik D, Pan S, Stafford GA, Freund ET, Klemm JD, Baker NA | BMC biotechnology | 23311978 | BMC Biotechnol | 2013 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/23311978 |
| CLASSIFYING PROCESSES: AN ESSAY IN APPLIED ONTOLOGY. | Smith B | Ratio | 23888086 | Ratio (Oxf) | 2012 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/23888086 |
| Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II. | Lu Z, Hirschman L | Database : the journal of biological databases and curation | 23160416 | Database (Oxford) | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23160416 |
| Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. | Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, He Y | PloS one | 23209624 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23209624 |
| The plant ontology as a tool for comparative plant anatomy and genomic analyses. | Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P | Plant & cell physiology | 23220694 | Plant Cell Physiol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23220694 |
| Ontologies for cancer nanotechnology research. | Thomas DG, Pappu RV, Baker NA | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 19964619 | Annu Int Conf IEEE Eng Med Biol Soc | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19964619 |
| Creating mappings for ontologies in biomedicine: simple methods work. | Ghazvinian A, Noy NF, Musen MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 20351849 | AMIA Annu Symp Proc | 2009 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/20351849 |
| The Enterprise Data Trust at Mayo Clinic: a semantically integrated warehouse of biomedical data. | Chute CG, Beck SA, Fisk TB, Mohr DN | Journal of the American Medical Informatics Association : JAMIA | 20190054 | J Am Med Inform Assoc | 2010 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/20190054 |
| An evolutionary approach to the representation of adverse events. | Ceusters W, Capolupo M, Smith B, De Moor G | Studies in health technology and informatics | 19745369 | Stud Health Technol Inform | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19745369 |
| The National Center for Biomedical Ontology. | Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B, NCBO team | Journal of the American Medical Informatics Association : JAMIA | 22081220 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22081220 |
| Developing predictive molecular maps of human disease through community-based modeling. | Derry JM, Mangravite LM, Suver C, Furia MD, Henderson D, Schildwachter X, Bot B, Izant J, Sieberts SK, Kellen MR, Friend SH | Nature genetics | 22281773 | Nat Genet | 2012 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/22281773 |
| Using ontology-based annotation to profile disease research. | Liu Y, Coulet A, LePendu P, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 22494789 | J Am Med Inform Assoc | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22494789 |
| Analyzing patterns of drug use in clinical notes for patient safety. | Lependu P, Liu Y, Iyer S, Udell MR, Shah NH | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22779054 | AMIA Jt Summits Transl Sci Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22779054 |
| Ontologies as integrative tools for plant science. | Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW | American journal of botany | 22847540 | Am J Bot | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22847540 |
| Tor1 regulates protein solubility in Saccharomyces cerevisiae. | Peters TW, Rardin MJ, Czerwieniec G, Evani US, Reis-Rodrigues P, Lithgow GJ, Mooney SD, Gibson BW, Hughes RE | Molecular biology of the cell | 23097491 | Mol Biol Cell | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23097491 |
| Mining clinical text for signals of adverse drug-drug interactions. | Iyer SV, Harpaz R, LePendu P, Bauer-Mehren A, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 24158091 | J Am Med Inform Assoc | 2014 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/24158091 |
| A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. | Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A | Cell | 24074861 | Cell | 2013 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/24074861 |
| Automated chart review for asthma cohort identification using natural language processing: an exploratory study. | Wu ST, Sohn S, Ravikumar KE, Wagholikar K, Jonnalagadda SR, Liu H, Juhn YJ | Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology | 24125142 | Ann Allergy Asthma Immunol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24125142 |
| The neurological disease ontology. | Jensen M, Cox AP, Chaudhry N, Ng M, Sule D, Duncan W, Ray P, Weinstock-Guttman B, Smith B, Ruttenberg A, Szigeti K, Diehl AD | Journal of biomedical semantics | 24314207 | J Biomed Semantics | 2013 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/24314207 |
| In silico approaches and the role of ontologies in aging research. | Fuellen G, Boerries M, Busch H, de Grey A, Hahn U, Hiller T, Hoeflich A, Jansen L, Janssens GE, Kaleta C, Meinema AC, Schäuble S, Simm A, Schofield PN, Smith B, Sühnel J, Vera J, Wagner W, Wönne EC, Wuttke D | Rejuvenation research | 24188080 | Rejuvenation Res | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24188080 |
| Cross-domain targeted ontology subsets for annotation: the case of SNOMED CORE and RxNorm. | López-García P, Lependu P, Musen M, Illarramendi A | Journal of biomedical informatics | 24095962 | J Biomed Inform | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24095962 |
| Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for Clinical and Research Applications: recommendations of the International RDC/TMD Consortium Network* and Orofacial Pain Special Interest Group†. | Schiffman E, Ohrbach R, Truelove E, Look J, Anderson G, Goulet JP, List T, Svensson P, Gonzalez Y, Lobbezoo F, Michelotti A, Brooks SL, Ceusters W, Drangsholt M, Ettlin D, Gaul C, Goldberg LJ, Haythornthwaite JA, Hollender L, Jensen R, John MT, De Laat A, de Leeuw R, Maixner W, van der Meulen M, Murray GM, Nixdorf DR, Palla S, Petersson A, Pionchon P, Smith B, Visscher CM, Zakrzewska J, Dworkin SF, International RDC/TMD Consortium Network, International association for Dental Research, Orofacial Pain Special Interest Group, International Association for the Study of Pain | Journal of oral & facial pain and headache | 24482784 | J Oral Facial Pain Headache | 2014 Winter | https://www.ncbi.nlm.nih.gov/pubmed/24482784 |
| The EBI RDF platform: linked open data for the life sciences. | Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM | Bioinformatics (Oxford, England) | 24413672 | Bioinformatics | 2014 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/24413672 |
| The environment ontology: contextualising biological and biomedical entities. | Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE, ENVO Consortium | Journal of biomedical semantics | 24330602 | J Biomed Semantics | 2013 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/24330602 |
| What particulars are referred to in Electronic Health Record data? A case study in integrating Referent Tracking into an EHR application. | Rudnicki R, Ceusters W, Manzoor S, Smith B | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18693912 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18693912 |
| Comparison of ontology-based semantic-similarity measures. | Lee WN, Shah N, Sundlass K, Musen M | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18999312 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18999312 |
| TGF-beta signaling proteins and the Protein Ontology. | Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH | BMC bioinformatics | 19426460 | BMC Bioinformatics | 2009 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/19426460 |
| Automated semantic indexing of figure captions to improve radiology image retrieval. | Kahn CE Jr, Rubin DL | Journal of the American Medical Informatics Association : JAMIA | 19261938 | J Am Med Inform Assoc | 2009 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/19261938 |
| UMLS-Query: a perl module for querying the UMLS. | Shah NH, Muse MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18998805 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18998805 |
| Ontology-driven indexing of public datasets for translational bioinformatics. | Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA | BMC bioinformatics | 19208184 | BMC Bioinformatics | 2009 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/19208184 |
| The Stanford Tissue Microarray Database. | Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, van de Rijn M, Brown PO, Ball CA | Nucleic acids research | 17989087 | Nucleic Acids Res | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17989087 |
| The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. | Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S | Nature biotechnology | 17989687 | Nat Biotechnol | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17989687 |
| Framework for a protein ontology. | Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH | BMC bioinformatics | 18047702 | BMC Bioinformatics | 2007 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/18047702 |
| OBO to OWL: a protege OWL tab to read/save OBO ontologies. | Moreira DA, Musen MA | Bioinformatics (Oxford, England) | 17496317 | Bioinformatics | 2007 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/17496317 |
| The Release 5.1 annotation of Drosophila melanogaster heterochromatin. | Smith CD, Shu S, Mungall CJ, Karpen GH | Science (New York, N.Y.) | 17569856 | Science | 2007 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/17569856 |
| Informatics: the fuel for pharmacometric analysis. | Grasela TH, Fiedler-Kelly J, Cirincione B, Hitchcock D, Reitz K, Sardella S, Smith B | The AAPS journal | 17408238 | AAPS J | 2007 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/17408238 |
| Ontology and the future of dental research informatics. | Smith B, Goldberg LJ, Ruttenberg A, Glick M | Journal of the American Dental Association (1939) | 20884915 | J Am Dent Assoc | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20884915 |
| Concept Systems and Ontologies: Recommendations for Basic Terminology. | Klein GO, Smith B | Transactions of the Japanese Society for Artificial Intelligence = Jinko Chino Gakkai ronbunshi | 21308002 | Trans Jpn Soc Artif Intell | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/21308002 |
| User requirements for exploring a resource inventory for clinical research. | Mirel BR, Wright Z, Tenenbaum JD, Saxman P, Smith KA | Summit on translational bioinformatics | 21347144 | Summit Transl Bioinform | 2010 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347144 |
| An evolutionary approach to realism-based adverse event representations. | Ceusters W, Capolupo M, de Moor G, Devlies J, Smith B | Methods of information in medicine | 21057717 | Methods Inf Med | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21057717 |
| Genome-wide in vivo screen identifies novel host regulators of metastatic colonization. | van der Weyden L, Arends MJ, Campbell AD, Bald T, Wardle-Jones H, Griggs N, Velasco-Herrera MD, Tüting T, Sansom OJ, Karp NA, Clare S, Gleeson D, Ryder E, Galli A, Tuck E, Cambridge EL, Voet T, Macaulay IC, Wong K, Sanger Mouse Genetics Project, Spiegel S, Speak AO, Adams DJ | Nature | 28052056 | Nature | 2017 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/28052056 |
| Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud. | Kamdar MR, Musen MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 29854169 | AMIA Annu Symp Proc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29854169 |
| PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data. | Kamdar MR, Musen MA | Proceedings of the ... International World-Wide Web Conference. International WWW Conference | 29479581 | Proc Int World Wide Web Conf | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29479581 |
| Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. | Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM | Nucleic acids research | 25348409 | Nucleic Acids Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25348409 |
| ArrayExpress update--simplifying data submissions. | Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A | Nucleic acids research | 25361974 | Nucleic Acids Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25361974 |
| Implications of non-stationarity on predictive modeling using EHRs. | Jung K, Shah NH | Journal of biomedical informatics | 26483171 | J Biomed Inform | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26483171 |
| Androgen Deprivation Therapy and Future Alzheimer's Disease Risk. | Nead KT, Gaskin G, Chester C, Swisher-McClure S, Dudley JT, Leeper NJ, Shah NH | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 26644522 | J Clin Oncol | 2016 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/26644522 |
| Predictive modeling of risk factors and complications of cataract surgery. | Gaskin GL, Pershing S, Cole TS, Shah NH | European journal of ophthalmology | 26692059 | Eur J Ophthalmol | 2016 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/26692059 |
| An empirically derived taxonomy of errors in SNOMED CT. | Mortensen JM, Musen MA, Noy NF | AMIA ... Annual Symposium proceedings. AMIA Symposium | 25954397 | AMIA Annu Symp Proc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25954397 |
| Ten Simple Rules for Selecting a Bio-ontology. | Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C | PLoS computational biology | 26867217 | PLoS Comput Biol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26867217 |
| Referent tracking: the problem of negative findings. | Ceusters W, Elkin P, Smith B | Studies in health technology and informatics | 17108603 | Stud Health Technol Inform | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17108603 |
| Representing lexical components of medical terminologies in OWL. | Supekar K, Chute CG, Solbrig H | AMIA ... Annual Symposium proceedings. AMIA Symposium | 16779134 | AMIA Annu Symp Proc | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16779134 |
| Development of FuGO: an ontology for functional genomics investigations. | Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ Jr, Taylor C, White J, Wood A, FuGO Working Group | Omics : a journal of integrative biology | 16901226 | OMICS | 2006 Summer | https://www.ncbi.nlm.nih.gov/pubmed/16901226 |
| Quality control for terms and definitions in ontologies and taxonomies. | Köhler J, Munn K, Rüegg A, Skusa A, Smith B | BMC bioinformatics | 16623942 | BMC Bioinformatics | 2006 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/16623942 |
| Ontology-based annotation and query of tissue microarray data. | Shah NH, Rubin DL, Supekar KS, Musen MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 17238433 | AMIA Annu Symp Proc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17238433 |
| From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies. | Smith B | Journal of biomedical informatics | 16293444 | J Biomed Inform | 2006 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16293444 |
| Biomedical ontologies: a functional perspective. | Rubin DL, Shah NH, Noy NF | Briefings in bioinformatics | 18077472 | Brief Bioinform | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18077472 |
| Annotation and query of tissue microarray data using the NCI Thesaurus. | Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA | BMC bioinformatics | 17686183 | BMC Bioinformatics | 2007 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/17686183 |
| The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. | Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME | Neuroinformatics | 18975148 | Neuroinformatics | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18975148 |
| Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. | Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S | Nature biotechnology | 18688244 | Nat Biotechnol | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18688244 |
| Translating the Foundational Model of Anatomy into OWL. | Noy NF, Rubin DL | Web semantics (Online) | 18688289 | Web Semant | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18688289 |
| Information-theoretic classification of SNOMED improves the organization of context-sensitive excerpts from Cochrane reviews. | Sam L, Borlawsky T, Tao Y, Li J, Friedman C, Smith B, Lussier YA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18694197 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18694197 |
| Semantator: annotating clinical narratives with semantic web ontologies. | Song D, Chute CG, Tao C | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22779043 | AMIA Jt Summits Transl Sci Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22779043 |
| Comparative protein interactomics of neuroglobin and myoglobin. | Haines BA, Davis DA, Zykovich A, Peng B, Rao R, Mooney SD, Jin K, Greenberg DA | Journal of neurochemistry | 22816983 | J Neurochem | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22816983 |
| Collaborative software for traditional and translational research. | Berman AE, Barnett WK, Mooney SD | Human genomics | 23157911 | Hum Genomics | 2012 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/23157911 |
| Chapter 9: Analyses using disease ontologies. | Shah NH, Cole T, Musen MA | PLoS computational biology | 23300417 | PLoS Comput Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23300417 |
| An excess of deleterious variants in VEGF-A pathway genes in Down-syndrome-associated atrioventricular septal defects. | Ackerman C, Locke AE, Feingold E, Reshey B, Espana K, Thusberg J, Mooney S, Bean LJ, Dooley KJ, Cua CL, Reeves RH, Sherman SL, Maslen CL | American journal of human genetics | 23040494 | Am J Hum Genet | 2012 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/23040494 |
| Nanoinformatics: developing new computing applications for nanomedicine. | Maojo V, Fritts M, Martin-Sanchez F, De la Iglesia D, Cachau RE, Garcia-Remesal M, Crespo J, Mitchell JA, Anguita A, Baker N, Barreiro JM, Benitez SE, De la Calle G, Facelli JC, Ghazal P, Geissbuhler A, Gonzalez-Nilo F, Graf N, Grangeat P, Hermosilla I, Hussein R, Kern J, Koch S, Legre Y, Lopez-Alonso V, Lopez-Campos G, Milanesi L, Moustakis V, Munteanu C, Otero P, Pazos A, Perez-Rey D, Potamias G, Sanz F, Kulikowski C | Computing in science & engineering | 22942787 | Comput Sci Eng | 2012 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/22942787 |
| OntoMaton: a bioportal powered ontology widget for Google Spreadsheets. | Maguire E, González-Beltrán A, Whetzel PL, Sansone SA, Rocca-Serra P | Bioinformatics (Oxford, England) | 23267176 | Bioinformatics | 2013 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/23267176 |
| Discussion of "Biomedical informatics: we are what we publish". | Geissbuhler A, Hammond WE, Hasman A, Hussein R, Koppel R, Kulikowski CA, Maojo V, Martin-Sanchez F, Moorman PW, Moura LA, de Quirós FG, Schuemie MJ, Smith B, Talmon J | Methods of information in medicine | 24310397 | Methods Inf Med | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24310397 |
| Molecular testing of 163 patients with Morquio A (Mucopolysaccharidosis IVA) identifies 39 novel GALNS mutations. | Morrone A, Tylee KL, Al-Sayed M, Brusius-Facchin AC, Caciotti A, Church HJ, Coll MJ, Davidson K, Fietz MJ, Gort L, Hegde M, Kubaski F, Lacerda L, Laranjeira F, Leistner-Segal S, Mooney S, Pajares S, Pollard L, Ribeiro I, Wang RY, Miller N | Molecular genetics and metabolism | 24726177 | Mol Genet Metab | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24726177 |
| Crowdsourcing the verification of relationships in biomedical ontologies. | Mortensen JM, Musen MA, Noy NF | AMIA ... Annual Symposium proceedings. AMIA Symposium | 24551391 | AMIA Annu Symp Proc | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24551391 |
| MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. | Mort M, Sterne-Weiler T, Li B, Ball EV, Cooper DN, Radivojac P, Sanford JR, Mooney SD | Genome biology | 24451234 | Genome Biol | 2014 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/24451234 |
| Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research. | Cole TS, Frankovich J, Iyer S, Lependu P, Bauer-Mehren A, Shah NH | Pediatric rheumatology online journal | 24299016 | Pediatr Rheumatol Online J | 2013 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/24299016 |
| LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies. | Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG | CEUR workshop proceedings. | 21804785 | CEUR Workshop Proc | 2009 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/21804785 |
| Towards Semantic-Web Based Representation and Harmonization of Standard Meta-data Models for Clinical Studies. | Tao C, Jiang G, Wei W, Solbrig HR, Chute CG | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22211181 | AMIA Jt Summits Transl Sci Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22211181 |
| Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. | Wu ST, Liu H, Li D, Tao C, Musen MA, Chute CG, Shah NH | Journal of the American Medical Informatics Association : JAMIA | 22493050 | J Am Med Inform Assoc | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22493050 |
| Empowering industrial research with shared biomedical vocabularies. | Harland L, Larminie C, Sansone SA, Popa S, Marshall MS, Braxenthaler M, Cantor M, Filsell W, Forster MJ, Huang E, Matern A, Musen M, Saric J, Slater T, Wilson J, Lynch N, Wise J, Dix I | Drug discovery today | 21963522 | Drug Discov Today | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21963522 |
| Mapping between the OBO and OWL ontology languages. | Tirmizi SH, Aitken S, Moreira DA, Mungall C, Sequeda J, Shah NH, Miranker DP | Journal of biomedical semantics | 21388572 | J Biomed Semantics | 2011 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/21388572 |
| Creating a controlled vocabulary for the ethics of human research: towards a biomedical ethics ontology. | Koepsell D, Arp R, Fostel J, Smith B | Journal of empirical research on human research ethics : JERHRE | 19374479 | J Empir Res Hum Res Ethics | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19374479 |
| BioPortal: ontologies and integrated data resources at the click of a mouse. | Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA | Nucleic acids research | 19483092 | Nucleic Acids Res | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19483092 |
| Foundations for a realist ontology of mental disease. | Ceusters W, Smith B | Journal of biomedical semantics | 21143905 | J Biomed Semantics | 2010 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/21143905 |
| Recent progress in automatically extracting information from the pharmacogenomic literature. | Garten Y, Coulet A, Altman RB | Pharmacogenomics | 21047206 | Pharmacogenomics | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21047206 |
| Ontological realism: A methodology for coordinated evolution of scientific ontologies. | Smith B, Ceusters W | Applied ontology | 21637730 | Appl Ontol | 2010 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/21637730 |
| Integration and publication of heterogeneous text-mined relationships on the Semantic Web. | Coulet A, Garten Y, Dumontier M, Altman RB, Musen MA, Shah NH | Journal of biomedical semantics | 21624156 | J Biomed Semantics | 2011 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/21624156 |
| How orthogonal are the OBO Foundry ontologies? | Ghazvinian A, Noy NF, Musen MA | Journal of biomedical semantics | 21624157 | J Biomed Semantics | 2011 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/21624157 |
| HyQue: evaluating hypotheses using Semantic Web technologies. | Callahan A, Dumontier M, Shah NH | Journal of biomedical semantics | 21624158 | J Biomed Semantics | 2011 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/21624158 |
| CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. | Tao C, Wei WQ, Solbrig HR, Savova G, Chute CG | AMIA ... Annual Symposium proceedings. AMIA Symposium | 21347086 | AMIA Annu Symp Proc | 2010 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/21347086 |
| Ontologies for clinical and translational research: Introduction. | Smith B, Scheuermann RH | Journal of biomedical informatics | 21241822 | J Biomed Inform | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21241822 |
| Survey of modular ontology techniques and their applications in the biomedical domain. | Pathak J, Johnson TM, Chute CG | Integrated computer-aided engineering | 21686030 | Integr Comput Aided Eng | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21686030 |
| The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies. | Noy N, Tudorache T, Nyulas C, Musen M | AMIA ... Annual Symposium proceedings. AMIA Symposium | 21347039 | AMIA Annu Symp Proc | 2010 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/21347039 |
| The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies. | Parai GK, Jonquet C, Xu R, Musen MA, Shah NH | AMIA ... Annual Symposium proceedings. AMIA Symposium | 21347046 | AMIA Annu Symp Proc | 2010 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/21347046 |
| The role of ontologies for sustainable, semantically interoperable and trustworthy EHR solutions. | Blobel B, Kalra D, Koehn M, Lunn K, Pharow P, Ruotsalainen P, Schulz S, Smith B | Studies in health technology and informatics | 19745454 | Stud Health Technol Inform | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19745454 |
| Comparison of concept recognizers for building the Open Biomedical Annotator. | Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA | BMC bioinformatics | 19761568 | BMC Bioinformatics | 2009 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/19761568 |
| An interactive tool for visualizing design heterogeneity in clinical trials. | Hernandez ME, Carini S, Storey MA, Sim I | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18998925 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18998925 |
| BioPortal: ontologies and data resources with the click of a mouse. | Musen MA, Shah NH, Noy NF, Dai BY, Dorf M, Griffith N, Buntrok J, Jonquet C, Montegut MJ, Rubin DL | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18999306 | AMIA Annu Symp Proc | 2008 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/18999306 |
| Text mining for adverse drug events: the promise, challenges, and state of the art. | Harpaz R, Callahan A, Tamang S, Low Y, Odgers D, Finlayson S, Jung K, LePendu P, Shah NH | Drug safety | 25151493 | Drug Saf | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25151493 |
| Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT. | Mortensen JM, Minty EP, Januszyk M, Sweeney TE, Rector AL, Noy NF, Musen MA | Journal of the American Medical Informatics Association : JAMIA | 25342179 | J Am Med Inform Assoc | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25342179 |
| BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF. | Salvadores M, Alexander PR, Musen MA, Noy NF | Semantic web | 25214827 | Semant Web | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/25214827 |
| Using text to build semantic networks for pharmacogenomics. | Coulet A, Shah NH, Garten Y, Musen M, Altman RB | Journal of biomedical informatics | 20723615 | J Biomed Inform | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20723615 |
| A UIMA wrapper for the NCBO annotator. | Roeder C, Jonquet C, Shah NH, Baumgartner WA Jr, Verspoor K, Hunter L | Bioinformatics (Oxford, England) | 20505005 | Bioinformatics | 2010 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/20505005 |
| NanoParticle Ontology for cancer nanotechnology research. | Thomas DG, Pappu RV, Baker NA | Journal of biomedical informatics | 20211274 | J Biomed Inform | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20211274 |
| Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways. | Rardin MJ, Newman JC, Held JM, Cusack MP, Sorensen DJ, Li B, Schilling B, Mooney SD, Kahn CR, Verdin E, Gibson BW | Proceedings of the National Academy of Sciences of the United States of America | 23576753 | Proc Natl Acad Sci U S A | 2013 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/23576753 |
| Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. | Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL | Science translational medicine | 23596205 | Sci Transl Med | 2013 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/23596205 |
| Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. | Ochs C, He Z, Zheng L, Geller J, Perl Y, Hripcsak G, Musen MA | Journal of biomedical informatics | 26988001 | J Biomed Inform | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26988001 |
| Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. | Mortensen JM, Telis N, Hughey JJ, Fan-Minogue H, Van Auken K, Dumontier M, Musen MA | Journal of biomedical informatics | 26873781 | J Biomed Inform | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26873781 |
| Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants. | Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A | Nucleic acids research | 26481351 | Nucleic Acids Res | 2016 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/26481351 |
| The digital revolution in phenotyping. | Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M | Briefings in bioinformatics | 26420780 | Brief Bioinform | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26420780 |
| Analyzing search behavior of healthcare professionals for drug safety surveillance. | Odgers DJ, Harpaz R, Callahan A, Stiglic G, Shah NH | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 25592591 | Pac Symp Biocomput | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25592591 |
| Analyzing Information Seeking and Drug-Safety Alert Response by Health Care Professionals as New Methods for Surveillance. | Callahan A, Pernek I, Stiglic G, Leskovec J, Strasberg HR, Shah NH | Journal of medical Internet research | 26293444 | J Med Internet Res | 2015 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/26293444 |
| BiOnIC: A Catalog of User Interactions with Biomedical Ontologies. | Kamdar MR, Walk S, Tudorache T, Musen MA | The semantic Web--ISWC ... : ... International Semantic Web Conference ... proceedings. International Semantic Web Conference | 29637199 | Semant Web ISWC | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29637199 |
| Analyzing user interactions with biomedical ontologies: A visual perspective. | Kamdar MR, Walk S, Tudorache T, Musen MA | Web semantics (Online) | 29657560 | Web Semant | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29657560 |
| Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. | Martínez-Romero M, O'Connor MJ, Egyedi AL, Willrett D, Hardi J, Graybeal J, Musen MA | Database : the journal of biological databases and curation | 31210270 | Database (Oxford) | 2019 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/31210270 |
| Unleashing the value of Common Data Elements through the CEDAR Workbench. | O'Connor MJ, Warzel DB, Martínez-Romero M, Hardi J, Willrett D, Egyedi AL, Eftekhari A, Graybeal J, Musen MA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 32308863 | AMIA Annu Symp Proc | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/32308863 |
| The variable quality of metadata about biological samples used in biomedical experiments. | Gonçalves RS, Musen MA | Scientific data | 30778255 | Sci Data | 2019 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/30778255 |
| Dynamic simulation of articulated rigid bodies with contact and collision. | Weinstein R, Teran J, Fedkiw R | IEEE transactions on visualization and computer graphics | 16640250 | IEEE Trans Vis Comput Graph | 2006 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/16640250 |
| A model of the upper extremity for simulating musculoskeletal surgery and analyzing neuromuscular control. | Holzbaur KR, Murray WM, Delp SL | Annals of biomedical engineering | 16078622 | Ann Biomed Eng | 2005 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16078622 |
| Rectus femoris and vastus intermedius fiber excursions predicted by three-dimensional muscle models. | Blemker SS, Delp SL | Journal of biomechanics | 15972213 | J Biomech | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/15972213 |
| Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. | Eastman P, Pande VS | Journal of computational chemistry | 19847780 | J Comput Chem | 2010 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/19847780 |
| Multiscale dynamics of macromolecules using normal mode Langevin. | Izaguirre JA, Sweet CR, Pande VS | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 19908376 | Pac Symp Biocomput | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/19908376 |
| Muscle contributions to propulsion and support during running. | Hamner SR, Seth A, Delp SL | Journal of biomechanics | 20691972 | J Biomech | 2010 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/20691972 |
| Muscle contributions to support and progression during single-limb stance in crouch gait. | Steele KM, Seth A, Hicks JL, Schwartz MS, Delp SL | Journal of biomechanics | 20493489 | J Biomech | 2010 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/20493489 |
| Progress and challenges in the automated construction of Markov state models for full protein systems. | Bowman GR, Beauchamp KA, Boxer G, Pande VS | The Journal of chemical physics | 19791846 | J Chem Phys | 2009 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/19791846 |
| Network models for molecular kinetics and their initial applications to human health. | Bowman GR, Huang X, Pande VS | Cell research | 20421891 | Cell Res | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20421891 |
| Super-resolution biomolecular crystallography with low-resolution data. | Schröder GF, Levitt M, Brunger AT | Nature | 20376006 | Nature | 2010 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/20376006 |
| SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs. | Haque IS, Pande VS, Walters WP | Journal of chemical information and modeling | 20218693 | J Chem Inf Model | 2010 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/20218693 |
| RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription. | Huang X, Wang D, Weiss DR, Bushnell DA, Kornberg RD, Levitt M | Proceedings of the National Academy of Sciences of the United States of America | 20798057 | Proc Natl Acad Sci U S A | 2010 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/20798057 |
| Three-dimensional hemodynamics in the human pulmonary arteries under resting and exercise conditions. | Tang BT, Fonte TA, Chan FP, Tsao PS, Feinstein JA, Taylor CA | Annals of biomedical engineering | 20640512 | Ann Biomed Eng | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20640512 |
| Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. | Zheng W, Liao JC, Brooks BR, Doniach S | Proteins | 17373706 | Proteins | 2007 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/17373706 |
| Flattening the abdominal aortic tree for effective visualization. | Won JH, Rubin GD, Napel S | Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference | 17946176 | Conf Proc IEEE Eng Med Biol Soc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17946176 |
| Topological methods for exploring low-density states in biomolecular folding pathways. | Yao Y, Sun J, Huang X, Bowman GR, Singh G, Lesnick M, Guibas LJ, Pande VS, Carlsson G | The Journal of chemical physics | 19368437 | J Chem Phys | 2009 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/19368437 |
| Knee muscle forces during walking and running in patellofemoral pain patients and pain-free controls. | Besier TF, Fredericson M, Gold GE, Beaupré GS, Delp SL | Journal of biomechanics | 19268945 | J Biomech | 2009 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/19268945 |
| Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. | Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD | Science (New York, N.Y.) | 19478184 | Science | 2009 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/19478184 |
| Accelerating molecular dynamic simulation on graphics processing units. | Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, Legrand S, Beberg AL, Ensign DL, Bruns CM, Pande VS | Journal of computational chemistry | 19191337 | J Comput Chem | 2009 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/19191337 |
| Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. | Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB | Nature protocols | 18772866 | Nat Protoc | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18772866 |
| Muscle function may depend on model selection in forward simulation of normal walking. | Xiao M, Higginson JS | Journal of biomechanics | 18804767 | J Biomech | 2008 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/18804767 |
| Multiscale modeling in computational biomechanics. | Tawhai M, Bischoff J, Einstein D, Erdemir A, Guess T, Reinbolt J | IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society | 19457733 | IEEE Eng Med Biol Mag | 2009 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/19457733 |
| Can morphing methods predict intermediate structures? | Weiss DR, Levitt M | Journal of molecular biology | 18996395 | J Mol Biol | 2009 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/18996395 |
| Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI. | Spink BJ, Sivaramakrishnan S, Lipfert J, Doniach S, Spudich JA | Nature structural & molecular biology | 18511944 | Nat Struct Mol Biol | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18511944 |
| The influence of femoral internal and external rotation on cartilage stresses within the patellofemoral joint. | Besier TF, Gold GE, Delp SL, Fredericson M, Beaupré GS | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 18524000 | J Orthop Res | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18524000 |
| High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. | Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A | Nucleic acids research | 18477638 | Nucleic Acids Res | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18477638 |
| Contributions of muscles to terminal-swing knee motions vary with walking speed. | Arnold AS, Schwartz MH, Thelen DG, Delp SL | Journal of biomechanics | 17659289 | J Biomech | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17659289 |
| Using surface envelopes to constrain molecular modeling. | Dugan JM, Altman RB | Protein science : a publication of the Protein Society | 17586766 | Protein Sci | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17586766 |
| Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways. | Liao JC, Spudich JA, Parker D, Delp SL | Proceedings of the National Academy of Sciences of the United States of America | 17360624 | Proc Natl Acad Sci U S A | 2007 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/17360624 |
| Muscle contributions to support and progression over a range of walking speeds. | Liu MQ, Anderson FC, Schwartz MH, Delp SL | Journal of biomechanics | 18822415 | J Biomech | 2008 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/18822415 |
| Importance of preswing rectus femoris activity in stiff-knee gait. | Reinbolt JA, Fox MD, Arnold AS, Ounpuu S, Delp SL | Journal of biomechanics | 18617180 | J Biomech | 2008 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/18617180 |
| Molecular dynamics/order parameter extrapolation for bionanosystem simulations. | Miao Y, Ortoleva PJ | Journal of computational chemistry | 18636559 | J Comput Chem | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18636559 |
| Two-way coupled SPH and particle level set fluid simulation. | Losasso F, Talton J, Kwatra N, Fedkiw R | IEEE transactions on visualization and computer graphics | 18467755 | IEEE Trans Vis Comput Graph | 2008 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/18467755 |
| Combining molecular dynamics and machine learning to improve protein function recognition. | Glazer DS, Radmer RJ, Altman RB | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 18229697 | Pac Symp Biocomput | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18229697 |
| The three-dimensional micro- and nanostructure of the aortic medial lamellar unit measured using 3D confocal and electron microscopy imaging. | O'Connell MK, Murthy S, Phan S, Xu C, Buchanan J, Spilker R, Dalman RL, Zarins CK, Denk W, Taylor CA | Matrix biology : journal of the International Society for Matrix Biology | 18248974 | Matrix Biol | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18248974 |
| Structural inference of native and partially folded RNA by high-throughput contact mapping. | Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D | Proceedings of the National Academy of Sciences of the United States of America | 18322008 | Proc Natl Acad Sci U S A | 2008 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/18322008 |
| Cartilage imaging at 3.0T with gradient refocused acquisition in the steady-state (GRASS) and IDEAL fat-water separation. | Kijowski R, Tuite M, Passov L, Shimakawa A, Yu H, Reeder SB | Journal of magnetic resonance imaging : JMRI | 18581337 | J Magn Reson Imaging | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18581337 |
| Accelerating molecular dynamic simulation on the cell processor and Playstation 3. | Luttmann E, Ensign DL, Vaidyanathan V, Houston M, Rimon N, Øland J, Jayachandran G, Friedrichs M, Pande VS | Journal of computational chemistry | 18615421 | J Comput Chem | 2009 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/18615421 |
| Reconstruction Using Witness Complexes. | Guibas LJ, Oudot SY | Discrete & computational geometry | 21643440 | Discrete Comput Geom | 2008 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/21643440 |
| A package for exact kinetic data structures and sweepline algorithms. | Russel D, Karavelas MI, Guibas LJ | Computational geometry : theory and applications | 21165159 | Comput Geom | 2007 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/21165159 |
| Meshless Animation of Fracturing Solids. | Pauly M, Keiser R, Adams B, Dutré P, Gross M, Guibas LJ | ACM transactions on graphics | 21165160 | ACM Trans Graph | 2005 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/21165160 |
| Remote thioredoxin recognition using evolutionary conservation and structural dynamics. | Tang GW, Altman RB | Structure (London, England : 1993) | 21481770 | Structure | 2011 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/21481770 |
| Fibre operating lengths of human lower limb muscles during walking. | Arnold EM, Delp SL | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 21502124 | Philos Trans R Soc Lond B Biol Sci | 2011 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/21502124 |
| On the effect of prestrain and residual stress in thin biological membranes. | Rausch MK, Kuhl E | Journal of the mechanics and physics of solids | 23976792 | J Mech Phys Solids | 2013 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/23976792 |
| Meshless Modeling of Deformable Shapes and their Motion. | Adams B, Ovsjanikov M, Wand M, Seidel HP, Guibas LJ | Computer animation. ACM SIGGRAPH Symposium on Computer Animation | 24839614 | Comput Animat | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/24839614 |
| Computational modelling of electrocardiograms: repolarisation and T-wave polarity in the human heart. | Hurtado DE, Kuhl E | Computer methods in biomechanics and biomedical engineering | 23113842 | Comput Methods Biomech Biomed Engin | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/23113842 |
| A fully implicit finite element method for bidomain models of cardiac electromechanics. | Dal H, Göktepe S, Kaliske M, Kuhl E | Computer methods in applied mechanics and engineering | 23175588 | Comput Methods Appl Mech Eng | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23175588 |
| Muscle contributions to fore-aft and vertical body mass center accelerations over a range of running speeds. | Hamner SR, Delp SL | Journal of biomechanics | 23246045 | J Biomech | 2013 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/23246045 |
| How much muscle strength is required to walk in a crouch gait? | Steele KM, van der Krogt MM, Schwartz MH, Delp SL | Journal of biomechanics | 22959837 | J Biomech | 2012 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/22959837 |
| To milliseconds and beyond: challenges in the simulation of protein folding. | Lane TJ, Shukla D, Beauchamp KA, Pande VS | Current opinion in structural biology | 23237705 | Curr Opin Struct Biol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23237705 |
| A rolling constraint reproduces ground reaction forces and moments in dynamic simulations of walking, running, and crouch gait. | Hamner SR, Seth A, Steele KM, Delp SL | Journal of biomechanics | 23702045 | J Biomech | 2013 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/23702045 |
| Mechanical consequences of cell-wall turnover in the elongation of a Gram-positive bacterium. | Misra G, Rojas ER, Gopinathan A, Huang KC | Biophysical journal | 23746506 | Biophys J | 2013 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/23746506 |
| Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. | Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS | Nature chemistry | 24345941 | Nat Chem | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24345941 |
| SCISSORS: practical considerations. | Kearnes SM, Haque IS, Pande VS | Journal of chemical information and modeling | 24289274 | J Chem Inf Model | 2014 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/24289274 |
| Calculations of the electric fields in liquid solutions. | Fried SD, Wang LP, Boxer SG, Ren P, Pande VS | The journal of physical chemistry. B | 24304155 | J Phys Chem B | 2013 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/24304155 |
| Simbios: an NIH national center for physics-based simulation of biological structures. | Delp SL, Ku JP, Pande VS, Sherman MA, Altman RB | Journal of the American Medical Informatics Association : JAMIA | 22081222 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22081222 |
| Structure-based drug screening for G-protein-coupled receptors. | Shoichet BK, Kobilka BK | Trends in pharmacological sciences | 22503476 | Trends Pharmacol Sci | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22503476 |
| Growing skin: tissue expansion in pediatric forehead reconstruction. | Zöllner AM, Buganza Tepole A, Gosain AK, Kuhl E | Biomechanics and modeling in mechanobiology | 22052000 | Biomech Model Mechanobiol | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22052000 |
| Grand challenge competition to predict in vivo knee loads. | Fregly BJ, Besier TF, Lloyd DG, Delp SL, Banks SA, Pandy MG, D'Lima DD | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 22161745 | J Orthop Res | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22161745 |
| Patients with patellofemoral pain exhibit elevated bone metabolic activity at the patellofemoral joint. | Draper CE, Fredericson M, Gold GE, Besier TF, Delp SL, Beaupre GS, Quon A | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 21812024 | J Orthop Res | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21812024 |
| In vitro validation of finite-element model of AAA hemodynamics incorporating realistic outlet boundary conditions. | Kung EO, Les AS, Medina F, Wicker RB, McConnell MV, Taylor CA | Journal of biomechanical engineering | 21428677 | J Biomech Eng | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21428677 |
| Patient-Specific Airway Wall Remodeling in Chronic Lung Disease. | Eskandari M, Kuschner WG, Kuhl E | Annals of biomedical engineering | 25821112 | Ann Biomed Eng | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25821112 |
| WHAT IS A MOMENT ARM? CALCULATING MUSCLE EFFECTIVENESS IN BIOMECHANICAL MODELS USING GENERALIZED COORDINATES. | Sherman MA, Seth A, Delp SL | Proceedings of the ... ASME Design Engineering Technical Conferences. ASME Design Engineering Technical Conferences | 25905111 | Proc ASME Des Eng Tech Conf | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25905111 |
| Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species. | Miguel A, Hsin J, Liu T, Tang G, Altman RB, Huang KC | PLoS computational biology | 25811761 | PLoS Comput Biol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25811761 |
| Use it or lose it: multiscale skeletal muscle adaptation to mechanical stimuli. | Wisdom KM, Delp SL, Kuhl E | Biomechanics and modeling in mechanobiology | 25199941 | Biomech Model Mechanobiol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25199941 |
| The Living Heart Project: A robust and integrative simulator for human heart function. | Baillargeon B, Rebelo N, Fox DD, Taylor RL, Kuhl E | European journal of mechanics. A, Solids | 25267880 | Eur J Mech A Solids | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25267880 |
| Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. | Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ | Nature genetics | 26691984 | Nat Genet | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26691984 |
| Mechanical characterization of human brain tissue. | Budday S, Sommer G, Birkl C, Langkammer C, Haybaeck J, Kohnert J, Bauer M, Paulsen F, Steinmann P, Kuhl E, Holzapfel GA | Acta biomaterialia | 27989920 | Acta Biomater | 2017 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/27989920 |
| Simulating Ideal Assistive Devices to Reduce the Metabolic Cost of Running. | Uchida TK, Seth A, Pouya S, Dembia CL, Hicks JL, Delp SL | PloS one | 27656901 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27656901 |
| OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. | Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS | PLoS computational biology | 28746339 | PLoS Comput Biol | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28746339 |
| On the Role of Mechanics in Chronic Lung Disease. | Eskandari M, Pfaller MR, Kuhl E | Materials (Basel, Switzerland) | 28788414 | Materials (Basel) | 2013 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/28788414 |
| Conformational heterogeneity of the calmodulin binding interface. | Shukla D, Peck A, Pande VS | Nature communications | 27040077 | Nat Commun | 2016 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/27040077 |
| Building Force Fields: An Automatic, Systematic, and Reproducible Approach. | Wang LP, Martinez TJ, Pande VS | The journal of physical chemistry letters | 26273869 | J Phys Chem Lett | 2014 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/26273869 |
| Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. | Laederach A, Shcherbakova I, Liang MP, Brenowitz M, Altman RB | Journal of molecular biology | 16574145 | J Mol Biol | 2006 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/16574145 |
| Characterization of coherent structures in the cardiovascular system. | Shadden SC, Taylor CA | Annals of biomedical engineering | 18437573 | Ann Biomed Eng | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18437573 |
| Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. | Huang X, Bowman GR, Pande VS | The Journal of chemical physics | 18513049 | J Chem Phys | 2008 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/18513049 |
| How hydrophobic buckminsterfullerene affects surrounding water structure. | Weiss DR, Raschke TM, Levitt M | The journal of physical chemistry. B | 18275178 | J Phys Chem B | 2008 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/18275178 |
| Feasibility of using real-time MRI to measure joint kinematics in 1.5T and open-bore 0.5T systems. | Draper CE, Santos JM, Kourtis LC, Besier TF, Fredericson M, Beaupre GS, Gold GE, Delp SL | Journal of magnetic resonance imaging : JMRI | 18581329 | J Magn Reson Imaging | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18581329 |
| Structural insight into RNA hairpin folding intermediates. | Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ, Pande VS | Journal of the American Chemical Society | 18593120 | J Am Chem Soc | 2008 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/18593120 |
| Can conformational change be described by only a few normal modes? | Petrone P, Pande VS | Biophysical journal | 16361336 | Biophys J | 2006 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/16361336 |
| The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. | Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, Herschlag D | Journal of molecular biology | 16963081 | J Mol Biol | 2006 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/16963081 |
| CT colonography: influence of 3D viewing and polyp candidate features on interpretation with computer-aided detection. | Shi R, Schraedley-Desmond P, Napel S, Olcott EW, Jeffrey RB Jr, Yee J, Zalis ME, Margolis D, Paik DS, Sherbondy AJ, Sundaram P, Beaulieu CF | Radiology | 16714460 | Radiology | 2006 Jun | https://www.ncbi.nlm.nih.gov/pubmed/16714460 |
| Increased anterior abdominal aortic wall motion: possible role in aneurysm pathogenesis and design of endovascular devices. | Goergen CJ, Johnson BL, Greve JM, Taylor CA, Zarins CK | Journal of endovascular therapy : an official journal of the International Society of Endovascular Specialists | 17696635 | J Endovasc Ther | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17696635 |
| Image-based musculoskeletal modeling: applications, advances, and future opportunities. | Blemker SS, Asakawa DS, Gold GE, Delp SL | Journal of magnetic resonance imaging : JMRI | 17260405 | J Magn Reson Imaging | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17260405 |
| Efficient algorithms to explore conformation spaces of flexible protein loops. | Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin-Landsberg I, Altman RB | IEEE/ACM transactions on computational biology and bioinformatics | 18989041 | IEEE/ACM Trans Comput Biol Bioinform | 2008 Oct-Dec | https://www.ncbi.nlm.nih.gov/pubmed/18989041 |
| Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach. | Kelley NW, Vishal V, Krafft GA, Pande VS | The Journal of chemical physics | 19063575 | J Chem Phys | 2008 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/19063575 |
| Rapid equilibrium sampling initiated from nonequilibrium data. | Huang X, Bowman GR, Bacallado S, Pande VS | Proceedings of the National Academy of Sciences of the United States of America | 19805023 | Proc Natl Acad Sci U S A | 2009 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/19805023 |
| Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. | Jonikas MA, Radmer RJ, Altman RB | Bioinformatics (Oxford, England) | 19812110 | Bioinformatics | 2009 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/19812110 |
| The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. | Ensign DL, Pande VS | Biophysical journal | 19383445 | Biophys J | 2009 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/19383445 |
| Predicting outcomes of rectus femoris transfer surgery. | Reinbolt JA, Fox MD, Schwartz MH, Delp SL | Gait & posture | 19411175 | Gait Posture | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19411175 |
| Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding. | Liu T, Altman RB | PLoS computational biology | 22219723 | PLoS Comput Biol | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22219723 |
| Stabilisation of walking by intrinsic muscle properties revealed in a three-dimensional muscle-driven simulation. | John CT, Anderson FC, Higginson JS, Delp SL | Computer methods in biomechanics and biomedical engineering | 22224406 | Comput Methods Biomech Biomed Engin | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22224406 |
| Crouched posture maximizes ground reaction forces generated by muscles. | Hoang HX, Reinbolt JA | Gait & posture | 22542242 | Gait Posture | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22542242 |
| Predicting the metabolic cost of incline walking from muscle activity and walking mechanics. | Silder A, Besier T, Delp SL | Journal of biomechanics | 22578744 | J Biomech | 2012 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/22578744 |
| On the biomechanics and mechanobiology of growing skin. | Zöllner AM, Buganza Tepole A, Kuhl E | Journal of theoretical biology | 22227432 | J Theor Biol | 2012 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/22227432 |
| Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. | Beauchamp KA, Ensign DL, Das R, Pande VS | Proceedings of the National Academy of Sciences of the United States of America | 21768345 | Proc Natl Acad Sci U S A | 2011 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/21768345 |
| Fast flexible modeling of RNA structure using internal coordinates. | Flores SC, Sherman MA, Bruns CM, Eastman P, Altman RB | IEEE/ACM transactions on computational biology and bioinformatics | 21778523 | IEEE/ACM Trans Comput Biol Bioinform | 2011 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/21778523 |
| Multiscale computational models for optogenetic control of cardiac function. | Abilez OJ, Wong J, Prakash R, Deisseroth K, Zarins CK, Kuhl E | Biophysical journal | 21943413 | Biophys J | 2011 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/21943413 |
| Non-bulk-like solvent behavior in the ribosome exit tunnel. | Lucent D, Snow CD, Aitken CE, Pande VS | PLoS computational biology | 20975935 | PLoS Comput Biol | 2010 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/20975935 |
| Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. | Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS | The Journal of chemical physics | 21721612 | J Chem Phys | 2011 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/21721612 |
| MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures. | Saha M, Levitt M, Chiu W | Bioinformatics (Oxford, England) | 20529921 | Bioinformatics | 2010 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/20529921 |
| The Simbios National Center: Systems Biology in Motion. | Schmidt JP, Delp SL, Sherman MA, Taylor CA, Pande VS, Altman RB | Proceedings of the IEEE. Institute of Electrical and Electronics Engineers | 20107615 | Proc IEEE Inst Electr Electron Eng | 2008 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/20107615 |
| Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. | Wu S, Liu T, Altman RB | BMC structural biology | 20122268 | BMC Struct Biol | 2010 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/20122268 |
| Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). | Voelz VA, Bowman GR, Beauchamp K, Pande VS | Journal of the American Chemical Society | 20070076 | J Am Chem Soc | 2010 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/20070076 |
| Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. | Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB | RNA (New York, N.Y.) | 19144906 | RNA | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19144906 |
| Robust high-resolution cloth using parallelism, history-based collisions, and accurate friction. | Selle A, Su J, Irving G, Fedkiw R | IEEE transactions on visualization and computer graphics | 19147895 | IEEE Trans Vis Comput Graph | 2009 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/19147895 |
| Methods for quantifying three-dimensional deformation of arteries due to pulsatile and nonpulsatile forces: implications for the design of stents and stent grafts. | Choi G, Cheng CP, Wilson NM, Taylor CA | Annals of biomedical engineering | 19002584 | Ann Biomed Eng | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19002584 |
| Variation of hamstrings lengths and velocities with walking speed. | Agarwal-Harding KJ, Schwartz MH, Delp SL | Journal of biomechanics | 20381047 | J Biomech | 2010 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/20381047 |
| Tracking Knee Joint Functional Axes through Tikhonov Filtering and Plűcker Coordinates. | Kim W, Kim YH, Veloso AP, Kohles SS | Journal of novel physiotherapies | 23720709 | J Nov Physiother | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23720709 |
| Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB. | Colavin A, Hsin J, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 24550504 | Proc Natl Acad Sci U S A | 2014 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/24550504 |
| SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery. | Novick PA, Ortiz OF, Poelman J, Abdulhay AY, Pande VS | PloS one | 24223973 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24223973 |
| Minimal formulation of joint motion for biomechanisms. | Seth A, Sherman M, Eastman P, Delp S | Nonlinear dynamics | 21170173 | Nonlinear Dyn | 2010 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/21170173 |
| Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation. | Stumpe MC, Blinov N, Wishart D, Kovalenko A, Pande VS | The journal of physical chemistry. B | 21174421 | J Phys Chem B | 2011 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/21174421 |
| Muscle contributions to vertical and fore-aft accelerations are altered in subjects with crouch gait. | Steele KM, Seth A, Hicks JL, Schwartz MH, Delp SL | Gait & posture | 23200083 | Gait Posture | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23200083 |
| On the mechanics of continua with boundary energies and growing surfaces. | Papastavrou A, Steinmann P, Kuhl E | Journal of the mechanics and physics of solids | 23606760 | J Mech Phys Solids | 2013 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/23606760 |
| Contributions of muscles to mediolateral ground reaction force over a range of walking speeds. | John CT, Seth A, Schwartz MH, Delp SL | Journal of biomechanics | 22884038 | J Biomech | 2012 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/22884038 |
| 3D finite element models of shoulder muscles for computing lines of actions and moment arms. | Webb JD, Blemker SS, Delp SL | Computer methods in biomechanics and biomedical engineering | 22994141 | Comput Methods Biomech Biomed Engin | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/22994141 |
| Systems-based approaches toward wound healing. | Buganza Tepole A, Kuhl E | Pediatric research | 23314298 | Pediatr Res | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23314298 |
| OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. | Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, Pande VS | Journal of chemical theory and computation | 23316124 | J Chem Theory Comput | 2013 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/23316124 |
| Human Cardiac Function Simulator for the Optimal Design of a Novel Annuloplasty Ring with a Sub-valvular Element for Correction of Ischemic Mitral Regurgitation. | Baillargeon B, Costa I, Leach JR, Lee LC, Genet M, Toutain A, Wenk JF, Rausch MK, Rebelo N, Acevedo-Bolton G, Kuhl E, Navia JL, Guccione JM | Cardiovascular engineering and technology | 25984248 | Cardiovasc Eng Technol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25984248 |
| Differences in muscle activity between natural forefoot and rearfoot strikers during running. | Yong JR, Silder A, Delp SL | Journal of biomechanics | 25458201 | J Biomech | 2014 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/25458201 |
| On the mechanics of growing thin biological membranes. | Rausch MK, Kuhl E | Journal of the mechanics and physics of solids | 24563551 | J Mech Phys Solids | 2014 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/24563551 |
| Discovering chemistry with an ab initio nanoreactor. | Wang LP, Titov A, McGibbon R, Liu F, Pande VS, Martínez TJ | Nature chemistry | 25411881 | Nat Chem | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25411881 |
| Development of A Physical Windkessel Module to Re-Create In-Vivo Vascular Flow Impedance for In-Vitro Experiments. | Kung EO, Taylor CA | Cardiovascular engineering and technology | 26316899 | Cardiovasc Eng Technol | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26316899 |
| Generating Purkinje networks in the human heart. | Sahli Costabal F, Hurtado DE, Kuhl E | Journal of biomechanics | 26748729 | J Biomech | 2016 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/26748729 |
| A Biomechanical Model of the Scapulothoracic Joint to Accurately Capture Scapular Kinematics during Shoulder Movements. | Seth A, Matias R, Veloso AP, Delp SL | PloS one | 26734761 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26734761 |
| A network of molecular switches controls the activation of the two-component response regulator NtrC. | Vanatta DK, Shukla D, Lawrenz M, Pande VS | Nature communications | 26073186 | Nat Commun | 2015 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/26073186 |
| Optimizing Locomotion Controllers Using Biologically-Based Actuators and Objectives. | Wang JM, Hamner SR, Delp SL, Koltun V | ACM transactions on graphics | 26251560 | ACM Trans Graph | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26251560 |
| Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. | Liu T, Altman RB | Journal of chemical information and modeling | 26121262 | J Chem Inf Model | 2015 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/26121262 |
| United polarizable multipole water model for molecular mechanics simulation. | Qi R, Wang LP, Wang Q, Pande VS, Ren P | The Journal of chemical physics | 26156485 | J Chem Phys | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26156485 |
| Knowledge-based fragment binding prediction. | Tang GW, Altman RB | PLoS computational biology | 24762971 | PLoS Comput Biol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24762971 |
| High precision prediction of functional sites in protein structures. | Buturovic L, Wong M, Tang GW, Altman RB, Petkovic D | PloS one | 24632601 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24632601 |
| Making a meaningful impact: modelling simultaneous frictional collisions in spatial multibody systems. | Uchida TK, Sherman MA, Delp SL | Proceedings. Mathematical, physical, and engineering sciences | 27547093 | Proc Math Phys Eng Sci | 2015 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/27547093 |
| Partial LVAD restores ventricular outputs and normalizes LV but not RV stress distributions in the acutely failing heart in silico. | Sack KL, Baillargeon B, Acevedo-Bolton G, Genet M, Rebelo N, Kuhl E, Klein L, Weiselthaler GM, Burkhoff D, Franz T, Guccione JM | The International journal of artificial organs | 27646633 | Int J Artif Organs | 2016 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/27646633 |
| Stretching Your Energetic Budget: How Tendon Compliance Affects the Metabolic Cost of Running. | Uchida TK, Hicks JL, Dembia CL, Delp SL | PloS one | 26930416 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26930416 |
| Simulating ideal assistive devices to reduce the metabolic cost of walking with heavy loads. | Dembia CL, Silder A, Uchida TK, Hicks JL, Delp SL | PloS one | 28700630 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28700630 |
| OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement. | Seth A, Hicks JL, Uchida TK, Habib A, Dembia CL, Dunne JJ, Ong CF, DeMers MS, Rajagopal A, Millard M, Hamner SR, Arnold EM, Yong JR, Lakshmikanth SK, Sherman MA, Ku JP, Delp SL | PLoS computational biology | 30048444 | PLoS Comput Biol | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30048444 |
| The outer membrane is an essential load-bearing element in Gram-negative bacteria. | Rojas ER, Billings G, Odermatt PD, Auer GK, Zhu L, Miguel A, Chang F, Weibel DB, Theriot JA, Huang KC | Nature | 30022160 | Nature | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30022160 |
| Homeostatic Cell Growth Is Accomplished Mechanically through Membrane Tension Inhibition of Cell-Wall Synthesis. | Rojas ER, Huang KC, Theriot JA | Cell systems | 29203279 | Cell Syst | 2017 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/29203279 |
| Preparatory co-activation of the ankle muscles may prevent ankle inversion injuries. | DeMers MS, Hicks JL, Delp SL | Journal of biomechanics | 28057351 | J Biomech | 2017 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/28057351 |
| Can biomechanical variables predict improvement in crouch gait? | Hicks JL, Delp SL, Schwartz MH | Gait & posture | 21616666 | Gait Posture | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21616666 |
| Computational modeling of bone density profiles in response to gait: a subject-specific approach. | Pang H, Shiwalkar AP, Madormo CM, Taylor RE, Andriacchi TP, Kuhl E | Biomechanics and modeling in mechanobiology | 21604146 | Biomech Model Mechanobiol | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21604146 |
| CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms. | Kohlhoff KJ, Sosnick MH, Hsu WT, Pande VS, Altman RB | Bioinformatics (Oxford, England) | 21712246 | Bioinformatics | 2011 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/21712246 |
| RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. | Mitra S, Laederach A, Golden BL, Altman RB, Brenowitz M | RNA (New York, N.Y.) | 21712400 | RNA | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21712400 |
| Turning limited experimental information into 3D models of RNA. | Flores SC, Altman RB | RNA (New York, N.Y.) | 20651028 | RNA | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20651028 |
| Ballistocardiography--a method worth revisiting. | Giovangrandi L, Inan OT, Wiard RM, Etemadi M, Kovacs GT | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255285 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22255285 |
| Growth on demand: reviewing the mechanobiology of stretched skin. | Zöllner AM, Holland MA, Honda KS, Gosain AK, Kuhl E | Journal of the mechanical behavior of biomedical materials | 23623569 | J Mech Behav Biomed Mater | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23623569 |
| Enhanced modeling via network theory: Adaptive sampling of Markov state models. | Bowman GR, Ensign DL, Pande VS | Journal of chemical theory and computation | 23626502 | J Chem Theory Comput | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/23626502 |
| Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins. | Kiss G, Pande VS, Houk KN | Methods in enzymology | 23422429 | Methods Enzymol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23422429 |
| Insights into diseases of human telomerase from dynamical modeling. | Flores SC, Zemora G, Waldsich C | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 23424125 | Pac Symp Biocomput | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23424125 |
| An informational framework to predict reaction of constraints using a reciprocally connected knee model. | Kim W, Veloso AP, Araújo D, Vleck V, João F | Computer methods in biomechanics and biomedical engineering | 23528152 | Comput Methods Biomech Biomed Engin | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/23528152 |
| Flexing computational muscle: modeling and simulation of musculotendon dynamics. | Millard M, Uchida T, Seth A, Delp SL | Journal of biomechanical engineering | 23445050 | J Biomech Eng | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23445050 |
| Systematic improvement of a classical molecular model of water. | Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS | The journal of physical chemistry. B | 23750713 | J Phys Chem B | 2013 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/23750713 |
| Computational modeling of chemo-electro-mechanical coupling: a novel implicit monolithic finite element approach. | Wong J, Göktepe S, Kuhl E | International journal for numerical methods in biomedical engineering | 23798328 | Int J Numer Method Biomed Eng | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23798328 |
| Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes. | Andrews LD, Fenn TD, Herschlag D | PLoS biology | 23843744 | PLoS Biol | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23843744 |
| The stationary configuration of the knee. | Kim W, Veloso AP, Vleck VE, Andrade C, Kohles SS | Journal of the American Podiatric Medical Association | 23536503 | J Am Podiatr Med Assoc | 2013 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/23536503 |
| Six-week gait retraining program reduces knee adduction moment, reduces pain, and improves function for individuals with medial compartment knee osteoarthritis. | Shull PB, Silder A, Shultz R, Dragoo JL, Besier TF, Delp SL, Cutkosky MR | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 23494804 | J Orthop Res | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23494804 |
| Patellar maltracking is prevalent among patellofemoral pain subjects with patella alta: an upright, weightbearing MRI study. | Pal S, Besier TF, Beaupre GS, Fredericson M, Delp SL, Gold GE | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 23165335 | J Orthop Res | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23165335 |
| Generating fibre orientation maps in human heart models using Poisson interpolation. | Wong J, Kuhl E | Computer methods in biomechanics and biomedical engineering | 23210529 | Comput Methods Biomech Biomed Engin | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/23210529 |
| Predicting RNA structure by multiple template homology modeling. | Flores SC, Wan Y, Russell R, Altman RB | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 19908374 | Pac Symp Biocomput | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/19908374 |
| Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms. | Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, Pande VS | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 19908375 | Pac Symp Biocomput | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/19908375 |
| A model of the lower limb for analysis of human movement. | Arnold EM, Ward SR, Lieber RL, Delp SL | Annals of biomedical engineering | 19957039 | Ann Biomed Eng | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19957039 |
| Estimation of central aortic forces in the ballistocardiogram under rest and exercise conditions. | Wiard RM, Kim HJ, Figueroa C, Kovacs GT, Taylor CA, Giovangrandi L | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 19964271 | Annu Int Conf IEEE Eng Med Biol Soc | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19964271 |
| Prediction of calcium-binding sites by combining loop-modeling with machine learning. | Liu T, Altman RB | BMC structural biology | 20003365 | BMC Struct Biol | 2009 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/20003365 |
| Robotics-based synthesis of human motion. | Khatib O, Demircan E, De Sapio V, Sentis L, Besier T, Delp S | Journal of physiology, Paris | 19665552 | J Physiol Paris | 2009 Sep-Dec | https://www.ncbi.nlm.nih.gov/pubmed/19665552 |
| New resource for the computation of cartilage biphasic material properties with the interpolant response surface method. | Keenan KE, Kourtis LC, Besier TF, Lindsey DP, Gold GE, Delp SL, Beaupre GS | Computer methods in biomechanics and biomedical engineering | 19675978 | Comput Methods Biomech Biomed Engin | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19675978 |
| Improving structure-based function prediction using molecular dynamics. | Glazer DS, Radmer RJ, Altman RB | Structure (London, England : 1993) | 19604472 | Structure | 2009 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/19604472 |
| Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics. | Parker D, Bryant Z, Delp SL | Cellular and molecular bioengineering | 20428469 | Cell Mol Bioeng | 2009 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/20428469 |
| Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. | Voelz VA, Singh VR, Wedemeyer WJ, Lapidus LJ, Pande VS | Journal of the American Chemical Society | 20218718 | J Am Chem Soc | 2010 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/20218718 |
| Reconstruction and EMG-informed control, simulation and analysis of human movement for athletics: performance improvement and injury prevention. | Demircan E, Khatib O, Wheeler J, Delp S | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 19964175 | Annu Int Conf IEEE Eng Med Biol Soc | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19964175 |
| A Computational Framework for Fluid-Solid-Growth Modeling in Cardiovascular Simulations. | Figueroa CA, Baek S, Taylor CA, Humphrey JD | Computer methods in applied mechanics and engineering | 20160923 | Comput Methods Appl Mech Eng | 2009 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/20160923 |
| Engineered myosin VI motors reveal minimal structural determinants of directionality and processivity. | Liao JC, Elting MW, Delp SL, Spudich JA, Bryant Z | Journal of molecular biology | 19631216 | J Mol Biol | 2009 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/19631216 |
| Compressive tibiofemoral force during crouch gait. | Steele KM, Demers MS, Schwartz MH, Delp SL | Gait & posture | 22206783 | Gait Posture | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22206783 |
| Characteristics associated with improved knee extension after strength training for individuals with cerebral palsy and crouch gait. | Steele KM, Damiano DL, Eek MN, Unger M, Delp SL | Journal of pediatric rehabilitation medicine | 22699100 | J Pediatr Rehabil Med | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22699100 |
| Changes in in vivo knee contact forces through gait modification. | Kinney AL, Besier TF, Silder A, Delp SL, D'Lima DD, Fregly BJ | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 23027590 | J Orthop Res | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23027590 |
| How robust is human gait to muscle weakness? | van der Krogt MM, Delp SL, Schwartz MH | Gait & posture | 22386624 | Gait Posture | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22386624 |
| Computational Optogenetics: A Novel Continuum Framework for the Photoelectrochemistry of Living Systems. | Wong J, Abilez OJ, Kuhl E | Journal of the mechanics and physics of solids | 22773861 | J Mech Phys Solids | 2012 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/22773861 |
| Mathematical modeling of collagen turnover in biological tissue. | Sáez P, Peña E, Ángel Martínez M, Kuhl E | Journal of mathematical biology | 23129392 | J Math Biol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23129392 |
| Comparison of MRI and ¹⁸F-NaF PET/CT in patients with patellofemoral pain. | Draper CE, Quon A, Fredericson M, Besier TF, Delp SL, Beaupre GS, Gold GE | Journal of magnetic resonance imaging : JMRI | 22549985 | J Magn Reson Imaging | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22549985 |
| Growing matter: a review of growth in living systems. | Kuhl E | Journal of the mechanical behavior of biomedical materials | 24239171 | J Mech Behav Biomed Mater | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24239171 |
| A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel. | Voelz VA, Petrone P, Pande VS | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 19209713 | Pac Symp Biocomput | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19209713 |
| Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin. | Kasson PM, Pande VS | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 19209725 | Pac Symp Biocomput | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19209725 |
| Optimal estimation of dynamically consistent kinematics and kinetics for forward dynamic simulation of gait. | Remy CD, Thelen DG | Journal of biomechanical engineering | 19154064 | J Biomech Eng | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19154064 |
| The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. | Kelley NW, Huang X, Tam S, Spiess C, Frydman J, Pande VS | Journal of molecular biology | 19361448 | J Mol Biol | 2009 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/19361448 |
| Chemical denaturants inhibit the onset of dewetting. | England JL, Pande VS, Haran G | Journal of the American Chemical Society | 18707183 | J Am Chem Soc | 2008 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/18707183 |
| ConTrack: finding the most likely pathways between brain regions using diffusion tractography. | Sherbondy AJ, Dougherty RF, Ben-Shachar M, Napel S, Wandell BA | Journal of vision | 18831651 | J Vis | 2008 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/18831651 |
| The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. | Halperin I, Glazer DS, Wu S, Altman RB | BMC genomics | 18831785 | BMC Genomics | 2008 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/18831785 |
| Side-chain recognition and gating in the ribosome exit tunnel. | Petrone PM, Snow CD, Lucent D, Pande VS | Proceedings of the National Academy of Sciences of the United States of America | 18946046 | Proc Natl Acad Sci U S A | 2008 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/18946046 |
| Using generalized ensemble simulations and Markov state models to identify conformational states. | Bowman GR, Huang X, Pande VS | Methods (San Diego, Calif.) | 19410002 | Methods | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19410002 |
| Mechanisms of improved knee flexion after rectus femoris transfer surgery. | Fox MD, Reinbolt JA, Ounpuu S, Delp SL | Journal of biomechanics | 19217109 | J Biomech | 2009 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/19217109 |
| Normal mode partitioning of Langevin dynamics for biomolecules. | Sweet CR, Petrone P, Pande VS, Izaguirre JA | The Journal of chemical physics | 18412479 | J Chem Phys | 2008 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/18412479 |
| Using real-time MRI to quantify altered joint kinematics in subjects with patellofemoral pain and to evaluate the effects of a patellar brace or sleeve on joint motion. | Draper CE, Besier TF, Santos JM, Jennings F, Fredericson M, Gold GE, Beaupre GS, Delp SL | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 18985690 | J Orthop Res | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/18985690 |
| Impulse-based control of joints and muscles. | Weinstein R, Guendelman E, Fedkiw R | IEEE transactions on visualization and computer graphics | 17993700 | IEEE Trans Vis Comput Graph | 2008 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/17993700 |
| OpenSim: open-source software to create and analyze dynamic simulations of movement. | Delp SL, Anderson FC, Arnold AS, Loan P, Habib A, John CT, Guendelman E, Thelen DG | IEEE transactions on bio-medical engineering | 18018689 | IEEE Trans Biomed Eng | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18018689 |
| Crouched postures reduce the capacity of muscles to extend the hip and knee during the single-limb stance phase of gait. | Hicks JL, Schwartz MH, Arnold AS, Delp SL | Journal of biomechanics | 18291404 | J Biomech | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18291404 |
| Persistent voids: a new structural metric for membrane fusion. | Kasson PM, Zomorodian A, Park S, Singhal N, Guibas LJ, Pande VS | Bioinformatics (Oxford, England) | 17488753 | Bioinformatics | 2007 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/17488753 |
| Coplanar and coaxial orientations of RNA bases and helices. | Laederach A, Chan JM, Schwartzman A, Willgohs E, Altman RB | RNA (New York, N.Y.) | 17339576 | RNA | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17339576 |
| HingeMaster: normal mode hinge prediction approach and integration of complementary predictors. | Flores SC, Keating KS, Painter J, Morcos F, Nguyen K, Merritt EA, Kuhn LA, Gerstein MB | Proteins | 18433058 | Proteins | 2008 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/18433058 |
| Informatics challenges in structured RNA. | Laederach A | Briefings in bioinformatics | 17611237 | Brief Bioinform | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17611237 |
| Predicting allosteric communication in myosin via a pathway of conserved residues. | Tang S, Liao JC, Dunn AR, Altman RB, Spudich JA, Schmidt JP | Journal of molecular biology | 17900617 | J Mol Biol | 2007 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/17900617 |
| Colon polyp detection using smoothed shape operators: preliminary results. | Sundaram P, Zomorodian A, Beaulieu C, Napel S | Medical image analysis | 17910934 | Med Image Anal | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17910934 |
| Molecular dynamics simulations of the full triple helical region of collagen type I provide an atomic scale view of the protein's regional heterogeneity. | Bodian DL, Radmer RJ, Holbert S, Klein TE | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 21121047 | Pac Symp Biocomput | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21121047 |
| Structural insights into pre-translocation ribosome motions. | Flores SC, Altman R | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 21121048 | Pac Symp Biocomput | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21121048 |
| Deformable spanners and applications. | Gao J, Guibas LJ, Nguyen A | Computational geometry : theory and applications | 21165161 | Comput Geom | 2006 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/21165161 |
| Computational modeling of growth: systemic and pulmonary hypertension in the heart. | Rausch MK, Dam A, Göktepe S, Abilez OJ, Kuhl E | Biomechanics and modeling in mechanobiology | 21188611 | Biomech Model Mechanobiol | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21188611 |
| Discovering Structural Regularity in 3D Geometry. | Pauly M, Mitra NJ, Wallner J, Pottmann H, Guibas LJ | ACM transactions on graphics | 21170292 | ACM Trans Graph | 2008 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/21170292 |
| Differences in patellofemoral kinematics between weight-bearing and non-weight-bearing conditions in patients with patellofemoral pain. | Draper CE, Besier TF, Fredericson M, Santos JM, Beaupre GS, Delp SL, Gold GE | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 20949442 | J Orthop Res | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20949442 |
| Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules. | Fenn TD, Schnieders MJ, Brunger AT, Pande VS | Biophysical journal | 20550911 | Biophys J | 2010 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/20550911 |
| CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations. | Eastman P, Pande VS | Journal of chemical theory and computation | 20563234 | J Chem Theory Comput | 2010 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/20563234 |
| Biological and functional relevance of CASP predictions. | Liu T, Ish-Shalom S, Torng W, Lafita A, Bock C, Mort M, Cooper DN, Bliven S, Capitani G, Mooney SD, Altman RB | Proteins | 28975675 | Proteins | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28975675 |
| Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2. | Schwantes CR, Shukla D, Pande VS | Biophysical journal | 27119632 | Biophys J | 2016 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/27119632 |
| Modeling and Simulation of Viscous Electro-Active Polymers. | Vogel F, Göktepe S, Steinmann P, Kuhl E | European journal of mechanics. A, Solids | 25267881 | Eur J Mech A Solids | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25267881 |
| The Generalized Hill Model: A Kinematic Approach Towards Active Muscle Contraction. | Göktepe S, Menzel A, Kuhl E | Journal of the mechanics and physics of solids | 25221354 | J Mech Phys Solids | 2014 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/25221354 |
| Predictive simulation generates human adaptations during loaded and inclined walking. | Dorn TW, Wang JM, Hicks JL, Delp SL | PloS one | 25830913 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25830913 |
| A mechanical model predicts morphological abnormalities in the developing human brain. | Budday S, Raybaud C, Kuhl E | Scientific reports | 25008163 | Sci Rep | 2014 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/25008163 |
| Characterization of living skin using multi-view stereo and isogeometric analysis. | Tepole AB, Gart M, Gosain AK, Kuhl E | Acta biomaterialia | 25016279 | Acta Biomater | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25016279 |
| Complex pathways in folding of protein G explored by simulation and experiment. | Lapidus LJ, Acharya S, Schwantes CR, Wu L, Shukla D, King M, DeCamp SJ, Pande VS | Biophysical journal | 25140430 | Biophys J | 2014 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/25140430 |
| Millisecond dynamics of RNA polymerase II translocation at atomic resolution. | Silva DA, Weiss DR, Pardo Avila F, Da LT, Levitt M, Wang D, Huang X | Proceedings of the National Academy of Sciences of the United States of America | 24753580 | Proc Natl Acad Sci U S A | 2014 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/24753580 |
| Bayesian energy landscape tilting: towards concordant models of molecular ensembles. | Beauchamp KA, Pande VS, Das R | Biophysical journal | 24655513 | Biophys J | 2014 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/24655513 |
| An Informational Algorithm as the Basis for Perception-Action Control of the Instantaneous Axes of the Knee. | Kim W, Espanha MM, Veloso AP, Araújo D, João F, Carrão L, Kohles SS | Journal of novel physiotherapies | 24932433 | J Nov Physiother | 2013 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/24932433 |
| Application of finite element modeling to optimize flap design with tissue expansion. | Buganza-Tepole A, Steinberg JP, Kuhl E, Gosain AK | Plastic and reconstructive surgery | 24945952 | Plast Reconstr Surg | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24945952 |
| Open Knee: Open Source Modeling and Simulation in Knee Biomechanics. | Erdemir A | The journal of knee surgery | 26444849 | J Knee Surg | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26444849 |
| OpenSim: a musculoskeletal modeling and simulation framework for in silico investigations and exchange. | Seth A, Sherman M, Reinbolt JA, Delp SL | Procedia IUTAM | 25893160 | Procedia IUTAM | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/25893160 |
| Bacterial division. Mechanical crack propagation drives millisecond daughter cell separation in Staphylococcus aureus. | Zhou X, Halladin DK, Rojas ER, Koslover EF, Lee TK, Huang KC, Theriot JA | Science (New York, N.Y.) | 25931560 | Science | 2015 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/25931560 |
| Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches. | Shukla D, Lawrenz M, Pande VS | Methods in enzymology | 25950981 | Methods Enzymol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25950981 |
| Is my model good enough? Best practices for verification and validation of musculoskeletal models and simulations of movement. | Hicks JL, Uchida TK, Seth A, Rajagopal A, Delp SL | Journal of biomechanical engineering | 25474098 | J Biomech Eng | 2015 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/25474098 |
| Fracturing rigid materials. | Bao Z, Hong JM, Teran J, Fedkiw R | IEEE transactions on visualization and computer graphics | 17218752 | IEEE Trans Vis Comput Graph | 2007 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/17218752 |
| Local RNA structural changes induced by crystallization are revealed by SHAPE. | Vicens Q, Gooding AR, Laederach A, Cech TR | RNA (New York, N.Y.) | 17299128 | RNA | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17299128 |
| Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. | Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M | Proceedings of the National Academy of Sciences of the United States of America | 17438287 | Proc Natl Acad Sci U S A | 2007 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/17438287 |
| The effect of excessive tibial torsion on the capacity of muscles to extend the hip and knee during single-limb stance. | Hicks J, Arnold A, Anderson F, Schwartz M, Delp S | Gait & posture | 17229573 | Gait Posture | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17229573 |
| Determining the Mg2+ stoichiometry for folding an RNA metal ion core. | Das R, Travers KJ, Bai Y, Herschlag D | Journal of the American Chemical Society | 15941246 | J Am Chem Soc | 2005 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/15941246 |
| Transparent rendering of intraluminal contrast for 3D polyp visualization at CT colonography. | Shi R, Napel S, Rosenberg JK, Shin LK, Walsh CF, Mogensen MA, Joshi AJ, Pankhudi P, Beaulieu CF | Journal of computer assisted tomography | 17895791 | J Comput Assist Tomogr | 2007 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/17895791 |
| Muscular coordination of knee motion during the terminal-swing phase of normal gait. | Arnold AS, Thelen DG, Schwartz MH, Anderson FC, Delp SL | Journal of biomechanics | 17572431 | J Biomech | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17572431 |
| Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. | Schröder GF, Brunger AT, Levitt M | Structure (London, England : 1993) | 18073112 | Structure | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18073112 |
| Intracranial and abdominal aortic aneurysms: similarities, differences, and need for a new class of computational models. | Humphrey JD, Taylor CA | Annual review of biomedical engineering | 18647115 | Annu Rev Biomed Eng | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18647115 |
| Toe-in gait reduces the first peak knee adduction moment in patients with medial compartment knee osteoarthritis. | Shull PB, Shultz R, Silder A, Dragoo JL, Besier TF, Cutkosky MR, Delp SL | Journal of biomechanics | 23146322 | J Biomech | 2013 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/23146322 |
| Stretching skeletal muscle: chronic muscle lengthening through sarcomerogenesis. | Zöllner AM, Abilez OJ, Böl M, Kuhl E | PloS one | 23049683 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23049683 |
| Frontiers in growth and remodeling. | Menzel A, Kuhl E | Mechanics research communications | 22919118 | Mech Res Commun | 2012 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/22919118 |
| Bioinformatics and variability in drug response: a protein structural perspective. | Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB | Journal of the Royal Society, Interface | 22552919 | J R Soc Interface | 2012 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/22552919 |
| Response of Escherichia coli growth rate to osmotic shock. | Rojas E, Theriot JA, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 24821776 | Proc Natl Acad Sci U S A | 2014 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/24821776 |
| Changes in tibiofemoral forces due to variations in muscle activity during walking. | Demers MS, Pal S, Delp SL | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 24615885 | J Orthop Res | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24615885 |
| A novel strategy to identify the critical conditions for growth-induced instabilities. | Javili A, Steinmann P, Kuhl E | Journal of the mechanical behavior of biomedical materials | 24041754 | J Mech Behav Biomed Mater | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24041754 |
| Anatomy of high-performance 2D similarity calculations. | Haque IS, Pande VS, Walters WP | Journal of chemical information and modeling | 21854053 | J Chem Inf Model | 2011 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/21854053 |
| A platform for dynamic simulation and control of movement based on OpenSim and MATLAB. | Mansouri M, Reinbolt JA | Journal of biomechanics | 22464351 | J Biomech | 2012 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/22464351 |
| Growing skin: A computational model for skin expansion in reconstructive surgery. | Tepole AB, Ploch CJ, Wong J, Gosain AK, Kuhl E | Journal of the mechanics and physics of solids | 22081726 | J Mech Phys Solids | 2011 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/22081726 |
| Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. | Mysinger MM, Weiss DR, Ziarek JJ, Gravel S, Doak AK, Karpiak J, Heveker N, Shoichet BK, Volkman BF | Proceedings of the National Academy of Sciences of the United States of America | 22431600 | Proc Natl Acad Sci U S A | 2012 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/22431600 |
| Error bounds on the SCISSORS approximation method. | Haque IS, Pande VS | Journal of chemical information and modeling | 21851122 | J Chem Inf Model | 2011 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/21851122 |
| Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes. | Bray JK, Weiss DR, Levitt M | Biophysical journal | 22208195 | Biophys J | 2011 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/22208195 |
| In vitro validation of finite element analysis of blood flow in deformable models. | Kung EO, Les AS, Figueroa CA, Medina F, Arcaute K, Wicker RB, McConnell MV, Taylor CA | Annals of biomedical engineering | 21404126 | Ann Biomed Eng | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21404126 |
| Circumferential and longitudinal cyclic strain of the human thoracic aorta: age-related changes. | Morrison TM, Choi G, Zarins CK, Taylor CA | Journal of vascular surgery | 19341890 | J Vasc Surg | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19341890 |
| In vivo deformation of the human abdominal aorta and common iliac arteries with hip and knee flexion: implications for the design of stent-grafts. | Choi G, Shin LK, Taylor CA, Cheng CP | Journal of endovascular therapy : an official journal of the International Society of Endovascular Specialists | 19842734 | J Endovasc Ther | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19842734 |
| 2010 translational bioinformatics year in review. | Altman RB, Miller KS | Journal of the American Medical Informatics Association : JAMIA | 21672905 | J Am Med Inform Assoc | 2011 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/21672905 |
| StoneHinge: hinge prediction by network analysis of individual protein structures. | Keating KS, Flores SC, Gerstein MB, Kuhn LA | Protein science : a publication of the Protein Society | 19180449 | Protein Sci | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19180449 |
| Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation. | Voelz VA, Luttmann E, Bowman GR, Pande VS | International journal of molecular sciences | 19399235 | Int J Mol Sci | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19399235 |
| Patient-specific modeling of cardiovascular mechanics. | Taylor CA, Figueroa CA | Annual review of biomedical engineering | 19400706 | Annu Rev Biomed Eng | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19400706 |
| Computational modeling of skin: Using stress profiles as predictor for tissue necrosis in reconstructive surgery. | Tepole AB, Gosain AK, Kuhl E | Computers & structures | 25225454 | Comput Struct | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/25225454 |
| Running with a load increases leg stiffness. | Silder A, Besier T, Delp SL | Journal of biomechanics | 25728581 | J Biomech | 2015 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/25728581 |
| Simbody: multibody dynamics for biomedical research. | Sherman MA, Seth A, Delp SL | Procedia IUTAM | 25866705 | Procedia IUTAM | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/25866705 |
| The role of mechanics during brain development. | Budday S, Steinmann P, Kuhl E | Journal of the mechanics and physics of solids | 25202162 | J Mech Phys Solids | 2014 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/25202162 |
| Cloud computing approaches for prediction of ligand binding poses and pathways. | Lawrenz M, Shukla D, Pande VS | Scientific reports | 25608737 | Sci Rep | 2015 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/25608737 |
| Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. | Laury ML, Wang LP, Pande VS, Head-Gordon T, Ponder JW | The journal of physical chemistry. B | 25683601 | J Phys Chem B | 2015 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/25683601 |
| Contributions of muscles and passive dynamics to swing initiation over a range of walking speeds. | Fox MD, Delp SL | Journal of biomechanics | 20236644 | J Biomech | 2010 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/20236644 |
| Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework. | England JL, Pande VS | Biochemistry and cell biology = Biochimie et biologie cellulaire | 20453936 | Biochem Cell Biol | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20453936 |
| Image-based modeling of blood flow and vessel wall dynamics: applications, methods and future directions: Sixth International Bio-Fluid Mechanics Symposium and Workshop, March 28-30, 2008 Pasadena, California. | Taylor CA, Steinman DA | Annals of biomedical engineering | 20087775 | Ann Biomed Eng | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20087775 |
| Quantification of hemodynamics in abdominal aortic aneurysms during rest and exercise using magnetic resonance imaging and computational fluid dynamics. | Les AS, Shadden SC, Figueroa CA, Park JM, Tedesco MM, Herfkens RJ, Dalman RL, Taylor CA | Annals of biomedical engineering | 20143263 | Ann Biomed Eng | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20143263 |
| Open Problems in Computational Vascular Biomechanics: Hemodynamics and Arterial Wall Mechanics. | Taylor CA, Humphrey JD | Computer methods in applied mechanics and engineering | 20161129 | Comput Methods Appl Mech Eng | 2009 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/20161129 |
| How muscle fiber lengths and velocities affect muscle force generation as humans walk and run at different speeds. | Arnold EM, Hamner SR, Seth A, Millard M, Delp SL | The Journal of experimental biology | 23470656 | J Exp Biol | 2013 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/23470656 |
| Stretching skin: The physiological limit and beyond. | Tepole AB, Gosain AK, Kuhl E | International journal of non-linear mechanics | 23459410 | Int J Non Linear Mech | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23459410 |
| Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. | Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK | ACS chemical biology | 23485065 | ACS Chem Biol | 2013 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/23485065 |
| OpenMM: A Hardware Independent Framework for Molecular Simulations. | Eastman P, Pande VS | Computing in science & engineering | 26146490 | Comput Sci Eng | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/26146490 |
| Computational modeling of hypertensive growth in the human carotid artery. | Sáez P, Peña E, Martínez MA, Kuhl E | Computational mechanics | 25342868 | Comput Mech | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25342868 |
| Transition path theory analysis of c-Src kinase activation. | Meng Y, Shukla D, Pande VS, Roux B | Proceedings of the National Academy of Sciences of the United States of America | 27482115 | Proc Natl Acad Sci U S A | 2016 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/27482115 |
| Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. | Liu T, Oprea T, Ursu O, Hasselgren C, Altman RB | Clinical and translational science | 27736015 | Clin Transl Sci | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27736015 |
| Full-Body Musculoskeletal Model for Muscle-Driven Simulation of Human Gait. | Rajagopal A, Dembia CL, DeMers MS, Delp DD, Hicks JL, Delp SL | IEEE transactions on bio-medical engineering | 27392337 | IEEE Trans Biomed Eng | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27392337 |
| Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models. | Dodani SC, Kiss G, Cahn JK, Su Y, Pande VS, Arnold FH | Nature chemistry | 27102675 | Nat Chem | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27102675 |
| Affordance-Based Surgical Design Methods Considering Biomechanical Artifacts. | Kim W, Araujo D, Kohles SS, Kim SG, Alvarez Sanchez HH | Ecological psychology : a publication of the International Society for Ecological Psychology | 37123457 | Ecol Psychol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/37123457 |
| White matter alterations in cerebral amyloid angiopathy measured by diffusion tensor imaging. | Salat DH, Smith EE, Tuch DS, Benner T, Pappu V, Schwab KM, Gurol ME, Rosas HD, Rosand J, Greenberg SM | Stroke | 16763176 | Stroke | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16763176 |
| Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis. | Corouge I, Fletcher PT, Joshi S, Gilmore JH, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685838 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685838 |
| A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. | Pichon E, Westin CF, Tannenbaum AR | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685844 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685844 |
| Regional brain atrophy in cognitively intact adults with a single APOE epsilon4 allele. | Wishart HA, Saykin AJ, McAllister TW, Rabin LA, McDonald BC, Flashman LA, Roth RM, Mamourian AC, Tsongalis GJ, Rhodes CH | Neurology | 17030756 | Neurology | 2006 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/17030756 |
| Choice reaction time performance correlates with diffusion anisotropy in white matter pathways supporting visuospatial attention. | Tuch DS, Salat DH, Wisco JJ, Zaleta AK, Hevelone ND, Rosas HD | Proceedings of the National Academy of Sciences of the United States of America | 16103359 | Proc Natl Acad Sci U S A | 2005 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/16103359 |
| Single nucleotide RNA choreography. | Hsiao C, Mohan S, Hershkovitz E, Tannenbaum A, Williams LD | Nucleic acids research | 16531589 | Nucleic Acids Res | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16531589 |
| Flattening maps for the visualization of multibranched vessels. | Zhu L, Haker S, Tannenbaum A | IEEE transactions on medical imaging | 15707245 | IEEE Trans Med Imaging | 2005 Feb | https://www.ncbi.nlm.nih.gov/pubmed/15707245 |
| MRI signal intensity based B-spline nonrigid registration for pre- and intraoperative imaging during prostate brachytherapy. | Oguro S, Tokuda J, Elhawary H, Haker S, Kikinis R, Tempany CM, Hata N | Journal of magnetic resonance imaging : JMRI | 19856437 | J Magn Reson Imaging | 2009 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19856437 |
| STATISTICAL SHAPE ANALYSIS OF BRAIN STRUCTURES USING SPHERICAL WAVELETS. | Nain D, Styner M, Niethammer M, Levitt JJ, Shenton ME, Gerig G, Bobick A, Tannenbaum A | Proceedings. IEEE International Symposium on Biomedical Imaging | 19888446 | Proc IEEE Int Symp Biomed Imaging | 2007 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/19888446 |
| Reduced task-related suppression during semantic repetition priming in schizophrenia. | Jeong B, Kubicki M | Psychiatry research | 20083395 | Psychiatry Res | 2010 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/20083395 |
| Multimodal functional imaging using fMRI-informed regional EEG/MEG source estimation. | Ou W, Nummenmaa A, Golland P, Hamalainen MS | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 19964568 | Annu Int Conf IEEE Eng Med Biol Soc | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19964568 |
| Microstructural connectivity of the arcuate fasciculus in adolescents with high-functioning autism. | Fletcher PT, Whitaker RT, Tao R, DuBray MB, Froehlich A, Ravichandran C, Alexander AL, Bigler ED, Lange N, Lainhart JE | NeuroImage | 20132894 | Neuroimage | 2010 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/20132894 |
| Open core control software for surgical robots. | Arata J, Kozuka H, Kim HW, Takesue N, Vladimirov B, Sakaguchi M, Tokuda J, Hata N, Chinzei K, Fujimoto H | International journal of computer assisted radiology and surgery | 20033506 | Int J Comput Assist Radiol Surg | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20033506 |
| Age-associated alterations in cortical gray and white matter signal intensity and gray to white matter contrast. | Salat DH, Lee SY, van der Kouwe AJ, Greve DN, Fischl B, Rosas HD | NeuroImage | 19580876 | Neuroimage | 2009 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/19580876 |
| Genetic and environmental influences on the size of specific brain regions in midlife: the VETSA MRI study. | Kremen WS, Prom-Wormley E, Panizzon MS, Eyler LT, Fischl B, Neale MC, Franz CE, Lyons MJ, Pacheco J, Perry ME, Stevens A, Schmitt JE, Grant MD, Seidman LJ, Thermenos HW, Tsuang MT, Eisen SA, Dale AM, Fennema-Notestine C | NeuroImage | 19786105 | Neuroimage | 2010 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/19786105 |
| Cortical gray matter atrophy in healthy aging cannot be explained by undetected incipient cognitive disorders: a comment on Burgmans et al. (2009). | Fjell AM, Westlye LT, Espeseth T, Reinvang I, Dale AM, Holland D, Walhovd KB | Neuropsychology | 20230119 | Neuropsychology | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20230119 |
| Diffusion tensor tractography findings in schizophrenia across the adult lifespan. | Voineskos AN, Lobaugh NJ, Bouix S, Rajji TK, Miranda D, Kennedy JL, Mulsant BH, Pollock BG, Shenton ME | Brain : a journal of neurology | 20237131 | Brain | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20237131 |
| FRATS: Functional Regression Analysis of DTI Tract Statistics. | Zhu H, Styner M, Tang N, Liu Z, Lin W, Gilmore JH | IEEE transactions on medical imaging | 20335089 | IEEE Trans Med Imaging | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20335089 |
| Salivary cortisol and prefrontal cortical thickness in middle-aged men: A twin study. | Kremen WS, O'Brien RC, Panizzon MS, Prom-Wormley E, Eaves LJ, Eisen SA, Eyler LT, Hauger RL, Fennema-Notestine C, Fischl B, Grant MD, Hellhammer DH, Jak AJ, Jacobson KC, Jernigan TL, Lupien SJ, Lyons MJ, Mendoza SP, Neale MC, Seidman LJ, Thermenos HW, Tsuang MT, Dale AM, Franz CE | NeuroImage | 20156572 | Neuroimage | 2010 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/20156572 |
| Cranial base superimposition for 3-dimensional evaluation of soft-tissue changes. | Cevidanes LH, Motta A, Proffit WR, Ackerman JL, Styner M | American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics | 20381752 | Am J Orthod Dentofacial Orthop | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20381752 |
| Comparison of actual surgical outcomes and 3-dimensional surgical simulations. | Tucker S, Cevidanes LH, Styner M, Kim H, Reyes M, Proffit W, Turvey T | Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons | 20591553 | J Oral Maxillofac Surg | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20591553 |
| A variational image-based approach to the correction of susceptibility artifacts in the alignment of diffusion weighted and structural MRI. | Tao R, Fletcher PT, Gerber S, Whitaker RT | Information processing in medical imaging : proceedings of the ... conference | 19694302 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694302 |
| Color Stroop and negative priming in schizophrenia: an fMRI study. | Ungar L, Nestor PG, Niznikiewicz MA, Wible CG, Kubicki M | Psychiatry research | 19963356 | Psychiatry Res | 2010 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/19963356 |
| Evaluation of volume-based and surface-based brain image registration methods. | Klein A, Ghosh SS, Avants B, Yeo BT, Fischl B, Ardekani B, Gee JC, Mann JJ, Parsey RV | NeuroImage | 20123029 | Neuroimage | 2010 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/20123029 |
| Joint segmentation of image ensembles via latent atlases. | Raviv TR, Van Leemput K, Wells WM 3rd, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20425997 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20425997 |
| Spatiotemporal atlas estimation for developmental delay detection in longitudinal datasets. | Durrleman S, Pennec X, Trouvé A, Gerig G, Ayache N | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426000 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426000 |
| Modeling adaptation effects in fMRI analysis. | Ou W, Raij T, Lin FH, Golland P, Hämäläinen M | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426087 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426087 |
| On diffusion tensor estimation. | Niethammer M, Estepar RS, Bouix S, Shenton M, Westin CF | Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference | 17959492 | Conf Proc IEEE Eng Med Biol Soc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17959492 |
| Characterization of the "deqi" response in acupuncture. | Hui KK, Nixon EE, Vangel MG, Liu J, Marina O, Napadow V, Hodge SM, Rosen BR, Makris N, Kennedy DN | BMC complementary and alternative medicine | 17973984 | BMC Complement Altern Med | 2007 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/17973984 |
| A generic framework for tracking using particle filter with dynamic shape prior. | Rathi Y, Vaswani N, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 17491466 | IEEE Trans Image Process | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17491466 |
| Event-related functional magnetic resonance imaging of response inhibition in obsessive-compulsive disorder. | Roth RM, Saykin AJ, Flashman LA, Pixley HS, West JD, Mamourian AC | Biological psychiatry | 17511967 | Biol Psychiatry | 2007 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/17511967 |
| Lowering the barriers inherent in translating advances in neuroimage analysis to clinical research applications. | Pujol S, Kikinis R, Gollub R | Academic radiology | 18078914 | Acad Radiol | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18078914 |
| Finsler tractography for white matter connectivity analysis of the cingulum bundle. | Melonakos J, Mohan V, Niethammer M, Smith K, Kubicki M, Tannenbaum A | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051041 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051041 |
| Boosting the sampling efficiency of q-Ball imaging using multiple wavevector fusion. | Khachaturian MH, Wisco JJ, Tuch DS | Magnetic resonance in medicine | 17260358 | Magn Reson Med | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17260358 |
| Altered orbitofrontal sulcogyral pattern in schizophrenia. | Nakamura M, Nestor PG, McCarley RW, Levitt JJ, Hsu L, Kawashima T, Niznikiewicz M, Shenton ME | Brain : a journal of neurology | 17347256 | Brain | 2007 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17347256 |
| Diffusion tensor imaging detects abnormalities in the corticospinal tracts of neonates with infantile Krabbe disease. | Escolar ML, Poe MD, Smith JK, Gilmore JH, Kurtzberg J, Lin W, Styner M | AJNR. American journal of neuroradiology | 19386732 | AJNR Am J Neuroradiol | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19386732 |
| Widespread reductions of cortical thickness in schizophrenia and spectrum disorders and evidence of heritability. | Goldman AL, Pezawas L, Mattay VS, Fischl B, Verchinski BA, Chen Q, Weinberger DR, Meyer-Lindenberg A | Archives of general psychiatry | 19414706 | Arch Gen Psychiatry | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19414706 |
| 3D nonrigid registration via optimal mass transport on the GPU. | Ur Rehman T, Haber E, Pryor G, Melonakos J, Tannenbaum A | Medical image analysis | 19135403 | Med Image Anal | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19135403 |
| Distribution Metrics and Image Segmentation. | Georgiou T, Michailovich O, Rathi Y, Malcolm J, Tannenbaum A | Linear algebra and its applications | 18769529 | Linear Algebra Appl | 2007 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/18769529 |
| Range of motion after computed tomography-based simulation of intertrochanteric corrective osteotomy in cases of slipped capital femoral epiphysis: comparison of uniplanar flexion osteotomy and multiplanar flexion, valgisation, and rotational osteotomies. | Mamisch TC, Kim YJ, Richolt J, Zilkens C, Kikinis R, Millis M, Kordelle J | Journal of pediatric orthopedics | 19461373 | J Pediatr Orthop | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19461373 |
| Image-driven population analysis through mixture modeling. | Sabuncu MR, Balci SK, Shenton ME, Golland P | IEEE transactions on medical imaging | 19336293 | IEEE Trans Med Imaging | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19336293 |
| White matter pathology isolates the hippocampal formation in Alzheimer's disease. | Salat DH, Tuch DS, van der Kouwe AJ, Greve DN, Pappu V, Lee SY, Hevelone ND, Zaleta AK, Growdon JH, Corkin S, Fischl B, Rosas HD | Neurobiology of aging | 18455835 | Neurobiol Aging | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18455835 |
| Shape modeling and analysis with entropy-based particle systems. | Cates J, Fletcher PT, Styner M, Shenton M, Whitaker R | Information processing in medical imaging : proceedings of the ... conference | 17633711 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633711 |
| A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI. | Fletcher PT, Tao R, Jeong WK, Whitaker RT | Information processing in medical imaging : proceedings of the ... conference | 17633712 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633712 |
| Quantifying metabolic asymmetry modulo structure in Alzheimer's disease. | Fletcher PT, Powell S, Foster NL, Joshi SC | Information processing in medical imaging : proceedings of the ... conference | 17633720 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633720 |
| Occipital lobe gray matter volume in male patients with chronic schizophrenia: A quantitative MRI study. | Onitsuka T, McCarley RW, Kuroki N, Dickey CC, Kubicki M, Demeo SS, Frumin M, Kikinis R, Jolesz FA, Shenton ME | Schizophrenia research | 17350226 | Schizophr Res | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17350226 |
| A nonparametric bayesian approach to detecting spatial activation patterns in fMRI data. | Kim S, Smyth P, Stern H | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354775 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354775 |
| Shape-driven 3D segmentation using spherical wavelets. | Nain D, Haker S, Bobick A, Tannenbaum A | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354875 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354875 |
| Geometrically accurate topology-correction of cortical surfaces using nonseparating loops. | Ségonne F, Pacheco J, Fischl B | IEEE transactions on medical imaging | 17427739 | IEEE Trans Med Imaging | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17427739 |
| Multiscale 3-D shape representation and segmentation using spherical wavelets. | Nain D, Haker S, Bobick A, Tannenbaum A | IEEE transactions on medical imaging | 17427745 | IEEE Trans Med Imaging | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17427745 |
| Candidate mechanisms for chemotherapy-induced cognitive changes. | Ahles TA, Saykin AJ | Nature reviews. Cancer | 17318212 | Nat Rev Cancer | 2007 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17318212 |
| Adjusted exponentially tilted likelihood with applications to brain morphology. | Zhu H, Zhou H, Chen J, Li Y, Lieberman J, Styner M | Biometrics | 18945269 | Biometrics | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/18945269 |
| A distributed spatio-temporal EEG/MEG inverse solver. | Ou W, Golland P, Hämäläinen M | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979728 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979728 |
| Assessment of reliability of multi-site neuroimaging via traveling phantom study. | Gouttard S, Styner M, Prastawa M, Piven J, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18982614 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18982614 |
| Effects of registration regularization and atlas sharpness on segmentation accuracy. | Yeo BT, Sabuncu MR, Desikan R, Fischl B, Golland P | Medical image analysis | 18667352 | Med Image Anal | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18667352 |
| Brain morphometry with multiecho MPRAGE. | van der Kouwe AJW, Benner T, Salat DH, Fischl B | NeuroImage | 18242102 | Neuroimage | 2008 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/18242102 |
| Probabilistic white matter fiber tracking using particle filtering and von Mises-Fisher sampling. | Zhang F, Hancock ER, Goodlett C, Gerig G | Medical image analysis | 18602332 | Med Image Anal | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18602332 |
| Discovering structure in the space of activation profiles in fMRI. | Lashkari D, Vul E, Kanwisher N, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979845 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979845 |
| Software strategy for robotic transperineal prostate therapy in closed-bore MRI. | Tokuda J, Fischer GS, Csoma C, DiMaio SP, Gobbi DG, Fichtinger G, Tempany CM, Hata N | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18982666 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18982666 |
| Regional gray matter correlates of perceived emotional intelligence. | Koven NS, Roth RM, Garlinghouse MA, Flashman LA, Saykin AJ | Social cognitive and affective neuroscience | 20934987 | Soc Cogn Affect Neurosci | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20934987 |
| Nonparametric Mixture Models for Supervised Image Parcellation. | Sabuncu MR, Yeo BT, Van Leemput K, Fischl B, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20814584 | Med Image Comput Comput Assist Interv | 2009 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/20814584 |
| Morphology-guided graph search for untangling objects: C. elegans analysis. | Raviv TR, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, Wählby C | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879454 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879454 |
| Spatially regularized compressed sensing for high angular resolution diffusion imaging. | Michailovich O, Rathi Y, Dolui S | IEEE transactions on medical imaging | 21536524 | IEEE Trans Med Imaging | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21536524 |
| Brain structure correlates of individual differences in the acquisition and inhibition of conditioned fear. | Hartley CA, Fischl B, Phelps EA | Cerebral cortex (New York, N.Y. : 1991) | 21263037 | Cereb Cortex | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21263037 |
| Automatic Prediction of Conversion from Mild Cognitive Impairment to Probable Alzheimer's Disease using Structural Magnetic Resonance Imaging. | Nho K, Shen L, Kim S, Risacher SL, West JD, Foroud T, Jack CR, Weiner MW, Saykin AJ | AMIA ... Annual Symposium proceedings. AMIA Symposium | 21347037 | AMIA Annu Symp Proc | 2010 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/21347037 |
| XCEDE: an extensible schema for biomedical data. | Gadde S, Aucoin N, Grethe JS, Keator DB, Marcus DS, Pieper S, FBIRN, MBIRN, BIRN-CC | Neuroinformatics | 21479735 | Neuroinformatics | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21479735 |
| Object tracking and target reacquisition based on 3-D range data for moving vehicles. | Lee J, Lankton S, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 21486717 | IEEE Trans Image Process | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21486717 |
| In vivo evidence of disseminated subpial T2* signal changes in multiple sclerosis at 7 T: a surface-based analysis. | Cohen-Adad J, Benner T, Greve D, Kinkel RP, Radding A, Fischl B, Rosen BR, Mainero C | NeuroImage | 21511042 | Neuroimage | 2011 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/21511042 |
| Anisotropy of transcallosal motor fibres indicates functional impairment in children with periventricular leukomalacia. | Koerte I, Pelavin P, Kirmess B, Fuchs T, Berweck S, Laubender RP, Borggraefe I, Schroeder S, Danek A, Rummeny C, Reiser M, Kubicki M, Shenton ME, Ertl-Wagner B, Heinen F | Developmental medicine and child neurology | 21121906 | Dev Med Child Neurol | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21121906 |
| Voxel-based morphometry (VBM) studies in schizophrenia-can white matter changes be reliably detected with VBM? | Melonakos ED, Shenton ME, Rathi Y, Terry DP, Bouix S, Kubicki M | Psychiatry research | 21684124 | Psychiatry Res | 2011 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/21684124 |
| Optical flow estimation for flame detection in videos. | Mueller M, Karasev P, Kolesov I, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 23613042 | IEEE Trans Image Process | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23613042 |
| GBM volumetry using the 3D Slicer medical image computing platform. | Egger J, Kapur T, Fedorov A, Pieper S, Miller JV, Veeraraghavan H, Freisleben B, Golby AJ, Nimsky C, Kikinis R | Scientific reports | 23455483 | Sci Rep | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23455483 |
| A Graph Cut Approach to Image Segmentation in Tensor Space. | Malcolm J, Rathi Y, Tannenbaum A | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 23680693 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/23680693 |
| A New Distance Measure Based on Generalized Image Normalized Cross-Correlation for Robust Video Tracking and Image Recognition. | Nakhmani A, Tannenbaum A | Pattern recognition letters | 23503649 | Pattern Recognit Lett | 2013 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/23503649 |
| ENTROPY BASED DTI QUALITY CONTROL VIA REGIONAL ORIENTATION DISTRIBUTION. | Farzinfar M, Dietrich C, Smith R, Li Y, Gupta A, Liu Z, Styner M | Proceedings. IEEE International Symposium on Biomedical Imaging | 23595508 | Proc IEEE Int Symp Biomed Imaging | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23595508 |
| STATISTICAL GROWTH MODELING OF LONGITUDINAL DT-MRI FOR REGIONAL CHARACTERIZATION OF EARLY BRAIN DEVELOPMENT. | Sadeghi N, Prastawa M, Fletcher PT, Gilmore JH, Lin W, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 23999084 | Proc IEEE Int Symp Biomed Imaging | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23999084 |
| Combined SPHARM-PDM and entropy-based particle systems shape analysis framework. | Paniagua B, Bompard L, Cates J, Whitaker R, Datar M, Vachet C, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24027625 | Proc SPIE Int Soc Opt Eng | 2012 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/24027625 |
| A longitudinal functional analysis framework for analysis of white matter tract statistics. | Yuan Y, Gilmore JH, Geng X, Styner MA, Chen K, Wang JL, Zhu H | Information processing in medical imaging : proceedings of the ... conference | 24683971 | Inf Process Med Imaging | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24683971 |
| Systematic network lesioning reveals the core white matter scaffold of the human brain. | Irimia A, Van Horn JD | Frontiers in human neuroscience | 24574993 | Front Hum Neurosci | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24574993 |
| A complete system for automatic extraction of left ventricular myocardium from CT images using shape segmentation and contour evolution. | Liangjia Zhu, Yi Gao, Appia V, Yezzi A, Arepalli C, Faber T, Stillman A, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 24723531 | IEEE Trans Image Process | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24723531 |
| Errors in Quantitative Image Analysis due to Platform-Dependent Image Scaling. | Chenevert TL, Malyarenko DI, Newitt D, Li X, Jayatilake M, Tudorica A, Fedorov A, Kikinis R, Liu TT, Muzi M, Oborski MJ, Laymon CM, Li X, Thomas Y, Jayashree KC, Mountz JM, Kinahan PE, Rubin DL, Fennessy F, Huang W, Hylton N, Ross BD | Translational oncology | 24772209 | Transl Oncol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24772209 |
| Automatic segmentation of head and neck CT images for radiotherapy treatment planning using multiple atlases, statistical appearance models, and geodesic active contours. | Fritscher KD, Peroni M, Zaffino P, Spadea MF, Schubert R, Sharp G | Medical physics | 24784389 | Med Phys | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24784389 |
| Coping with confounds in multivoxel pattern analysis: what should we do about reaction time differences? A comment on Todd, Nystrom & Cohen 2013. | Woolgar A, Golland P, Bode S | NeuroImage | 24793832 | Neuroimage | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24793832 |
| Neuroinformatics challenges to the structural, connectomic, functional and electrophysiological multimodal imaging of human traumatic brain injury. | Goh SY, Irimia A, Torgerson CM, Horn JD | Frontiers in neuroinformatics | 24616696 | Front Neuroinform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24616696 |
| Structural and connectomic neuroimaging for the personalized study of longitudinal alterations in cortical shape, thickness and connectivity after traumatic brain injury. | Irimia A, Goh SY, Torgerson CM, Vespa P, Van Horn JD | Journal of neurosurgical sciences | 24844173 | J Neurosurg Sci | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24844173 |
| Multi-Channel neurodegenerative pattern analysis and its application in Alzheimer's disease characterization. | Liu S, Cai W, Wen L, Feng DD, Pujol S, Kikinis R, Fulham MJ, Eberl S, ADNI | Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society | 24933011 | Comput Med Imaging Graph | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24933011 |
| Differences in subcortical structures in young adolescents at familial risk for schizophrenia: a preliminary study. | Dougherty MK, Gu H, Bizzell J, Ramsey S, Gerig G, Perkins DO, Belger A | Psychiatry research | 23146250 | Psychiatry Res | 2012 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/23146250 |
| Toward an understanding of the short bone phenotype associated with multiple osteochondromas. | Jones KB, Datar M, Ravichandran S, Jin H, Jurrus E, Whitaker R, Capecchi MR | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 23192691 | J Orthop Res | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23192691 |
| Brain volume findings in 6-month-old infants at high familial risk for autism. | Hazlett HC, Gu H, McKinstry RC, Shaw DW, Botteron KN, Dager SR, Styner M, Vachet C, Gerig G, Paterson SJ, Schultz RT, Estes AM, Evans AC, Piven J, IBIS Network | The American journal of psychiatry | 22684595 | Am J Psychiatry | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22684595 |
| Endoscopic image analysis in semantic space. | Kwitt R, Vasconcelos N, Rasiwasia N, Uhl A, Davis B, Häfner M, Wrba F | Medical image analysis | 22717411 | Med Image Anal | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22717411 |
| Semiparametric Bayesian local functional models for diffusion tensor tract statistics. | Hua Z, Dunson DB, Gilmore JH, Styner MA, Zhu H | NeuroImage | 22732565 | Neuroimage | 2012 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/22732565 |
| Automated dispersion and orientation analysis for carbon nanotube reinforced polymer composites. | Gao Y, Li Z, Lin Z, Zhu L, Tannenbaum A, Bouix S, Wong CP | Nanotechnology | 23060008 | Nanotechnology | 2012 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/23060008 |
| A 3D interactive multi-object segmentation tool using local robust statistics driven active contours. | Gao Y, Kikinis R, Bouix S, Shenton M, Tannenbaum A | Medical image analysis | 22831773 | Med Image Anal | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22831773 |
| Template-cut: a pattern-based segmentation paradigm. | Egger J, Freisleben B, Nimsky C, Kapur T | Scientific reports | 22639728 | Sci Rep | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22639728 |
| From brain connectivity models to identifying foci of a neurological disorder. | Venkataraman A, Kubicki M, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23285615 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23285615 |
| Metamorphic geodesic regression. | Hong Y, Joshi S, Sanchez M, Styner M, Niethammer M | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286131 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286131 |
| In-bore setup and software for 3T MRI-guided transperineal prostate biopsy. | Tokuda J, Tuncali K, Iordachita I, Song SE, Fedorov A, Oguro S, Lasso A, Fennessy FM, Tempany CM, Hata N | Physics in medicine and biology | 22951350 | Phys Med Biol | 2012 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/22951350 |
| On removing interpolation and resampling artifacts in rigid image registration. | Aganj I, Yeo BT, Sabuncu MR, Fischl B | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 23076044 | IEEE Trans Image Process | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23076044 |
| Spectral label fusion. | Wachinger C, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286157 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286157 |
| MULTIVARIATE VARYING COEFFICIENT MODEL FOR FUNCTIONAL RESPONSES. | Zhu H, Li R, Kong L | Annals of statistics | 23645942 | Ann Stat | 2012 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/23645942 |
| Surgery, virtual reality, and the future. | Vosburgh KG, Golby A, Pieper SD | Studies in health technology and informatics | 23653952 | Stud Health Technol Inform | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23653952 |
| Human middle longitudinal fascicle: segregation and behavioral-clinical implications of two distinct fiber connections linking temporal pole and superior temporal gyrus with the angular gyrus or superior parietal lobule using multi-tensor tractography. | Makris N, Preti MG, Wassermann D, Rathi Y, Papadimitriou GM, Yergatian C, Dickerson BC, Shenton ME, Kubicki M | Brain imaging and behavior | 23686576 | Brain Imaging Behav | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23686576 |
| Circular representation of human cortical networks for subject and population-level connectomic visualization. | Irimia A, Chambers MC, Torgerson CM, Van Horn JD | NeuroImage | 22305988 | Neuroimage | 2012 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/22305988 |
| Locally-Constrained Region-Based Methods for DW-MRI Segmentation. | Melonakos J, Niethammer M, Mohan V, Kubicki M, Miller JV, Tannenbaum A | Proceedings. IEEE International Conference on Computer Vision | 23857521 | Proc IEEE Int Conf Comput Vis | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/23857521 |
| Automatic delineation of the myocardial wall from CT images via shape segmentation and variational region growing. | Zhu L, Gao Y, Appia V, Yezzi A, Arepalli C, Faber T, Stillman A, Tannenbaum A | IEEE transactions on bio-medical engineering | 23744658 | IEEE Trans Biomed Eng | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23744658 |
| Cortical Correspondence via Sulcal Curve-Constrained Spherical Registration with Application to Macaque Studies. | Lyu I, Kim SH, Seong JK, Yoo SW, Evans AC, Shi Y, Sanchez M, Niethammer M, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24357916 | Proc SPIE Int Soc Opt Eng | 2013 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24357916 |
| Tissue Tracking: Applications for Brain MRI Classification. | Melonakos J, Gao Y, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 24392193 | Proc SPIE Int Soc Opt Eng | 2007 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/24392193 |
| Quality Control of Diffusion Weighted Images. | Liu Z, Wang Y, Gerig G, Gouttard S, Tao R, Fletcher T, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24353379 | Proc SPIE Int Soc Opt Eng | 2010 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/24353379 |
| More accurate neuronavigation data provided by biomechanical modeling instead of rigid registration. | Garlapati RR, Roy A, Joldes GR, Wittek A, Mostayed A, Doyle B, Warfield SK, Kikinis R, Knuckey N, Bunt S, Miller K | Journal of neurosurgery | 24460486 | J Neurosurg | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24460486 |
| Semi-Automatic Parcellation of the Corpus Striatum. | Al-Hakim R, Nain D, Levitt J, Shenton M, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 24511366 | Proc SPIE Int Soc Opt Eng | 2007 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/24511366 |
| VARYING COEFFICIENT MODEL FOR MODELING DIFFUSION TENSORS ALONG WHITE MATTER TRACTS. | Yuan Y, Zhu H, Styner M, Gilmore JH, Marron JS | The annals of applied statistics | 24533040 | Ann Appl Stat | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24533040 |
| Long-term 3-dimensional stability of mandibular advancement surgery. | Franco AA, Cevidanes LH, Phillips C, Rossouw PE, Turvey TA, Carvalho Fde A, Paula LK, Quintão CC, Almeida MA | Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons | 23769460 | J Oral Maxillofac Surg | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23769460 |
| Intrinsic Regression Models for Medial Representation of Subcortical Structures. | Shi X, Zhu H, Ibrahim JG, Liang F, Lieberman J, Styner M | Journal of the American Statistical Association | 23794769 | J Am Stat Assoc | 2012 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23794769 |
| A generative approach for image-based modeling of tumor growth. | Menze BH, Van Leemput K, Honkela A, Konukoglu E, Weber MA, Ayache N, Golland P | Information processing in medical imaging : proceedings of the ... conference | 21761700 | Inf Process Med Imaging | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21761700 |
| Nonparametric Hierarchical Bayesian Model for Functional Brain Parcellation. | Lashkari D, Sridharan R, Vul E, Hsieh PJ, Kanwisher N, Golland P | Conference on Computer Vision and Pattern Recognition Workshops. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops | 21841977 | Conf Comput Vis Pattern Recognit Workshops | 2010 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/21841977 |
| Deformable Image Registration of Sliding Organs Using Anisotropic Diffusive Regularization. | Pace DF, Enquobahrie A, Yang H, Aylward SR, Niethammer M | Proceedings. IEEE International Symposium on Biomedical Imaging | 21785755 | Proc IEEE Int Symp Biomed Imaging | 2011 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/21785755 |
| Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM. | Styner M, Oguz I, Xu S, Brechbühler C, Pantazis D, Levitt JJ, Shenton ME, Gerig G | The insight journal | 21941375 | Insight J | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/21941375 |
| Efficient Probabilistic and Geometric Anatomical Mapping Using Particle Mesh Approximation on GPUs. | Ha L, Prastawa M, Gerig G, Gilmore JH, Silva CT, Joshi S | International journal of biomedical imaging | 21941523 | Int J Biomed Imaging | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21941523 |
| Search for patterns of functional specificity in the brain: a nonparametric hierarchical Bayesian model for group fMRI data. | Lashkari D, Sridharan R, Vul E, Hsieh PJ, Kanwisher N, Golland P | NeuroImage | 21884803 | Neuroimage | 2012 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/21884803 |
| Morphometric analysis of subcortical structures in progressive supranuclear palsy: In vivo evidence of neostriatal and mesencephalic atrophy. | Looi JC, Macfarlane MD, Walterfang M, Styner M, Velakoulis D, Lätt J, van Westen D, Nilsson C | Psychiatry research | 21899988 | Psychiatry Res | 2011 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/21899988 |
| Iterative refinement of point correspondences for 3D statistical shape models. | Seshamani S, Chintalapani G, Taylor R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 21995056 | Med Image Comput Comput Assist Interv | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21995056 |
| 3D quantification of mandibular asymmetry using the SPHARM-PDM tool box. | Alhadidi A, Cevidanes LH, Paniagua B, Cook R, Festy F, Tyndall D | International journal of computer assisted radiology and surgery | 22089896 | Int J Comput Assist Radiol Surg | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22089896 |
| Atlas-guided segmentation of vervet monkey brain MRI. | Fedorov A, Li X, Pohl KM, Bouix S, Styner M, Addicott M, Wyatt C, Daunais JB, Wells WM, Kikinis R | The open neuroimaging journal | 22253661 | Open Neuroimag J | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22253661 |
| Segmentation of nerve bundles and ganglia in spine MRI using particle filters. | Dalca A, Danagoulian G, Kikinis R, Schmidt E, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 22003741 | Med Image Comput Comput Assist Interv | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22003741 |
| Anterior limb of the internal capsule in schizophrenia: a diffusion tensor tractography study. | Rosenberger G, Nestor PG, Oh JS, Levitt JJ, Kindleman G, Bouix S, Fitzsimmons J, Niznikiewicz M, Westin CF, Kikinis R, McCarley RW, Shenton ME, Kubicki M | Brain imaging and behavior | 22415192 | Brain Imaging Behav | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22415192 |
| Spherical Topic Models for Imaging Phenotype Discovery in Genetic Studies. | Batmanghelich KN, Cho M, Jose RS, Golland P | Bayesian and grAphical models for biomedical imaging : first International Workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers. BAMBI (Workshop) (1st : 2014 : Cambridge, Mass.) | 25717477 | Bayesian Graph Models Biomed Imaging (2014) | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25717477 |
| Comparison of Twin and Extended Pedigree Designs for Obtaining Heritability Estimates. | Docherty AR, Kremen WS, Panizzon MS, Prom-Wormley EC, Franz CE, Lyons MJ, Eaves LJ, Neale MC | Behavior genetics | 25894926 | Behav Genet | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25894926 |
| Subject-Motion Correction in HARDI Acquisitions: Choices and Consequences. | Elhabian S, Gur Y, Vachet C, Piven J, Styner M, Leppert IR, Pike GB, Gerig G | Frontiers in neurology | 25538672 | Front Neurol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25538672 |
| BrainPrint: a discriminative characterization of brain morphology. | Wachinger C, Golland P, Kremen W, Fischl B, Reuter M, Alzheimer's Disease Neuroimaging Initiative | NeuroImage | 25613439 | Neuroimage | 2015 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/25613439 |
| Quantification and Analysis of Large Multimodal Clinical Image Studies: Application to Stroke. | Sridharan R, Dalca AV, Fitzpatrick KM, Cloonan L, Kanakis A, Wu O, Furie KL, Rosand J, Rost NS, Golland P | Multimodal brain image analysis : third International Workshop, MBIA 2013, held in conjunction with MICCAI 2013, Nagoya, Japan, September 22, 2013 : proceedings. MBIA (Workshop) (3rd : 2013 : Nagoya-shi, Japan) | 25632408 | Multimodal Brain Image Anal (2013) | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/25632408 |
| Decoupling function and anatomy in atlases of functional connectivity patterns: language mapping in tumor patients. | Langs G, Sweet A, Lashkari D, Tie Y, Rigolo L, Golby AJ, Golland P | NeuroImage | 25172207 | Neuroimage | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25172207 |
| PARAMETRIC REGRESSION SCHEME FOR DISTRIBUTIONS: ANALYSIS OF DTI FIBER TRACT DIFFUSION CHANGES IN EARLY BRAIN DEVELOPMENT. | Sharma A, Fletcher PT, Gilmore JH, Escolar ML, Gupta A, Styner M, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 25356194 | Proc IEEE Int Symp Biomed Imaging | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25356194 |
| A JOINT FRAMEWORK FOR 4D SEGMENTATION AND ESTIMATION OF SMOOTH TEMPORAL APPEARANCE CHANGES. | Gao Y, Prastawa M, Styner M, Piven J, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 25356196 | Proc IEEE Int Symp Biomed Imaging | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25356196 |
| Cingulum bundle integrity associated with delusions of control in schizophrenia: Preliminary evidence from diffusion-tensor tractography. | Whitford TJ, Kubicki M, Pelavin PE, Lucia D, Schneiderman JS, Pantelis C, McCarley RW, Shenton ME | Schizophrenia research | 25311780 | Schizophr Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25311780 |
| Multi-modal robust inverse-consistent linear registration. | Wachinger C, Golland P, Magnain C, Fischl B, Reuter M | Human brain mapping | 25470798 | Hum Brain Mapp | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25470798 |
| Medial frontal white and gray matter contributions to general intelligence. | Ohtani T, Nestor PG, Bouix S, Saito Y, Hosokawa T, Kubicki M | PloS one | 25551572 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25551572 |
| Robust estimation of group-wise cortical correspondence with an application to macaque and human neuroimaging studies. | Lyu I, Kim SH, Seong JK, Yoo SW, Evans A, Shi Y, Sanchez M, Niethammer M, Styner MA | Frontiers in neuroscience | 26113807 | Front Neurosci | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26113807 |
| Pairwise Latent Semantic Association for Similarity Computation in Medical Imaging. | Zhang F, Song Y, Cai W, Liu S, Liu S, Pujol S, Kikinis R, Xia Y, Fulham MJ, Feng DD, Alzheimers Disease Neuroimaging Initiative | IEEE transactions on bio-medical engineering | 26372117 | IEEE Trans Biomed Eng | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26372117 |
| Characterizing growth patterns in longitudinal MRI using image contrast. | Vardhan A, Prastawa M, Vachet C, Piven J, Gerig G | Proceedings of SPIE--the International Society for Optical Engineering | 25309699 | Proc SPIE Int Soc Opt Eng | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/25309699 |
| BrainPrint: identifying subjects by their brain. | Wachinger C, Golland P, Reuter M | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 25320780 | Med Image Comput Comput Assist Interv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25320780 |
| ShapeCut: Bayesian surface estimation using shape-driven graph. | Veni G, Elhabian SY, Whitaker RT | Medical image analysis | 28582702 | Med Image Anal | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28582702 |
| MONITORING SLOWLY EVOLVING TUMORS. | Konukoglu E, Wells WM, Novellas S, Ayache N, Kikinis R, Black PM, Pohl KM | Proceedings. IEEE International Symposium on Biomedical Imaging | 28593030 | Proc IEEE Int Symp Biomed Imaging | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/28593030 |
| Longitudinal diffusion changes in prodromal and early HD: Evidence of white-matter tract deterioration. | Shaffer JJ, Ghayoor A, Long JD, Kim RE, Lourens S, O'Donnell LJ, Westin CF, Rathi Y, Magnotta V, Paulsen JS, Johnson HJ | Human brain mapping | 28045213 | Hum Brain Mapp | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28045213 |
| A Generative Probabilistic Model and Discriminative Extensions for Brain Lesion Segmentation--With Application to Tumor and Stroke. | Menze BH, Van Leemput K, Lashkari D, Riklin-Raviv T, Geremia E, Alberts E, Gruber P, Wegener S, Weber MA, Szekely G, Ayache N, Golland P | IEEE transactions on medical imaging | 26599702 | IEEE Trans Med Imaging | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26599702 |
| Compressive Sensing Based Q-Space Resampling for Handling Fast Bulk Motion in Hardi Acquisitions. | Elhabian S, Vachet C, Piven J, for IBIS, Styner M, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 29492184 | Proc IEEE Int Symp Biomed Imaging | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/29492184 |
| Common 3-dimensional coordinate system for assessment of directional changes. | Ruellas AC, Tonello C, Gomes LR, Yatabe MS, Macron L, Lopinto J, Goncalves JR, Garib Carreira DG, Alonso N, Souki BQ, Coqueiro Rda S, Cevidanes LH | American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics | 27131246 | Am J Orthod Dentofacial Orthop | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27131246 |
| Linear Models Based on Noisy Data and the Frisch Scheme. | Ning L, Georgiou TT, Tannenbaum A, Boyd SP | SIAM review. Society for Industrial and Applied Mathematics | 27168672 | SIAM Rev Soc Ind Appl Math | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/27168672 |
| EXPLORING FUNCTIONAL CONNECTIVITY IN FMRI VIA CLUSTERING. | Venkataraman A, Van Dijk KR, Buckner RL, Golland P | Proceedings of the ... IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP (Conference) | 26028993 | Proc IEEE Int Conf Acoust Speech Signal Process | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26028993 |
| Affine Registration of label maps in Label Space. | Rathi Y, Malcolm J, Bouix S, Tannenbaum A, Shenton ME | Journal of computing | 26029473 | J Comput | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26029473 |
| Tobacco Smoking and the Resting Maternal Brain: A Preliminary Study of Frontal EEG. | Wilbanks HE, Von Mohr M, Potenza MN, Mayes LC, Rutherford HJ | The Yale journal of biology and medicine | 27354838 | Yale J Biol Med | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27354838 |
| Twin-singleton developmental study of brain white matter anatomy. | Sadeghi N, Gilmore JH, Gerig G | Human brain mapping | 27739634 | Hum Brain Mapp | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27739634 |
| Exploring the neural substrates of attentional control and human intelligence: Diffusion tensor imaging of prefrontal white matter tractography in healthy cognition. | Ohtani T, Nestor PG, Bouix S, Newell D, Melonakos ED, McCarley RW, Shenton ME, Kubicki M | Neuroscience | 27840231 | Neuroscience | 2017 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/27840231 |
| Trajectories from Distribution-valued Functional Curves: A Unified Wasserstein Framework(★). | Sharma A, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 36108328 | Med Image Comput Comput Assist Interv | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36108328 |
| White matter development and language abilities during infancy in autism spectrum disorder. | McFayden TC, Rutsohn J, Cetin G, Forsen E, Swanson MR, Meera SS, Wolff JJ, Elison JT, Shen MD, Botteron K, Dager SR, Estes A, Gerig G, McKinstry RC, Pandey J, Schultz R, St John T, Styner M, Truong Y, Zwaigenbaum L, Hazlett HC, Piven J, Girault JB, IBIS Network | Molecular psychiatry | 38383768 | Mol Psychiatry | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38383768 |
| Infants who develop autism show smaller inventories of deictic and symbolic gestures at 12 months of age. | Wu D, Wolff JJ, Ravi S, Elison JT, Estes A, Paterson S, St John T, Abdi H, Moraglia LE, Piven J, Swanson MR, IBIS Network | Autism research : official journal of the International Society for Autism Research | 38204321 | Autism Res | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38204321 |
| Detection of entorhinal layer II using 7Tesla [corrected] magnetic resonance imaging. | Augustinack JC, van der Kouwe AJ, Blackwell ML, Salat DH, Wiggins CJ, Frosch MP, Wiggins GC, Potthast A, Wald LL, Fischl BR | Annals of neurology | 15786476 | Ann Neurol | 2005 Apr | https://www.ncbi.nlm.nih.gov/pubmed/15786476 |
| Fornix integrity and hippocampal volume in male schizophrenic patients. | Kuroki N, Kubicki M, Nestor PG, Salisbury DF, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, McCarley RW, Shenton ME | Biological psychiatry | 16406249 | Biol Psychiatry | 2006 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/16406249 |
| Imaging phenotypes and genotypes in schizophrenia. | Turner JA, Smyth P, Macciardi F, Fallon JH, Kennedy JL, Potkin SG | Neuroinformatics | 16595857 | Neuroinformatics | 2006 Winter | https://www.ncbi.nlm.nih.gov/pubmed/16595857 |
| Scaling aspects of block co-polymer adsorption on curved surfaces from nonselective solvents. | Hershkovits E, Tannenbaum A, Tannenbaum R | The journal of physical chemistry. B | 18399678 | J Phys Chem B | 2008 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/18399678 |
| Interactive visualization of volumetric white matter connectivity in DT-MRI using a parallel-hardware Hamilton-Jacobi solver. | Jeong WK, Fletcher PT, Tao R, Whitaker R | IEEE transactions on visualization and computer graphics | 17968100 | IEEE Trans Vis Comput Graph | 2007 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/17968100 |
| Image segmentation using active contours driven by the Bhattacharyya gradient flow. | Michailovich O, Rathi Y, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 17990755 | IEEE Trans Image Process | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/17990755 |
| Tract-based morphometry. | O'Donnell LJ, Westin CF, Golby AJ | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18044565 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18044565 |
| Sources of variability in MEG. | Ou W, Golland P, Hämäläinen M | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18044636 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18044636 |
| Quantification of measurement error in DTI: theoretical predictions and validation. | Goodlett C, Fletcher PT, Lin W, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051038 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051038 |
| Detection of spatial activation patterns as unsupervised segmentation of fMRI data. | Golland P, Golland Y, Malach R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051050 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051050 |
| Outlier rejection for diffusion weighted imaging. | Niethammer M, Bouix S, Aja-Fernández S, Westin CF, Shenton ME | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051055 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051055 |
| The intrinsic shape of human and macaque primary visual cortex. | Hinds O, Polimeni JR, Rajendran N, Balasubramanian M, Wald LL, Augustinack JC, Wiggins G, Rosas HD, Fischl B, Schwartz EL | Cerebral cortex (New York, N.Y. : 1991) | 18308709 | Cereb Cortex | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18308709 |
| Neuropsychological disturbance in schizophrenia: a diffusion tensor imaging study. | Nestor PG, Kubicki M, Niznikiewicz M, Gurrera RJ, McCarley RW, Shenton ME | Neuropsychology | 18331167 | Neuropsychology | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18331167 |
| Blind deconvolution of medical ultrasound images: a parametric inverse filtering approach. | Michailovich O, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 18092599 | IEEE Trans Image Process | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18092599 |
| A Bayesian model for joint segmentation and registration. | Pohl KM, Fisher J, Grimson WE, Kikinis R, Wells WM | NeuroImage | 16466677 | Neuroimage | 2006 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/16466677 |
| Statistical analysis of RNA backbone. | Hershkovitz E, Sapiro G, Tannenbaum A, Williams LD | IEEE/ACM transactions on computational biology and bioinformatics | 17048391 | IEEE/ACM Trans Comput Biol Bioinform | 2006 Jan-Mar | https://www.ncbi.nlm.nih.gov/pubmed/17048391 |
| The uncinate fasciculus and extraversion in schizotypal personality disorder: a diffusion tensor imaging study. | Gurrera RJ, Nakamura M, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, McCarley RW, Shenton ME, Westin CF, Maier SE, Seidman LJ | Schizophrenia research | 17126532 | Schizophr Res | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17126532 |
| On the detection of simple points in higher dimensions using cubical homology. | Niethammer M, Kalies WD, Mischaikow K, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 16900699 | IEEE Trans Image Process | 2006 Aug | https://www.ncbi.nlm.nih.gov/pubmed/16900699 |
| Automated atlas-based clustering of white matter fiber tracts from DTMRI. | Maddah M, Mewes AU, Haker S, Grimson WE, Warfield SK | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685845 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685845 |
| A method for clustering white matter fiber tracts. | O'Donnell LJ, Kubicki M, Shenton ME, Dreusicke MH, Grimson WE, Westin CF | AJNR. American journal of neuroradiology | 16687538 | AJNR Am J Neuroradiol | 2006 May | https://www.ncbi.nlm.nih.gov/pubmed/16687538 |
| From spatial regularization to anatomical priors in fMRI analysis. | Ou W, Golland P | Information processing in medical imaging : proceedings of the ... conference | 17354687 | Inf Process Med Imaging | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/17354687 |
| Segmentation of thalamic nuclei from DTI using spectral clustering. | Ziyan U, Tuch D, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354847 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354847 |
| 3D histological reconstruction of fiber tracts and direct comparison with diffusion tensor MRI tractography. | Dauguet J, Peled S, Berezovskii V, Delzescaux T, Warfield SK, Born R, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354880 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354880 |
| Atlas stratification. | Blezek DJ, Miller JV | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354953 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354953 |
| Cortical surface shape analysis based on spherical wavelets. | Yu P, Grant PE, Qi Y, Han X, Ségonne F, Pienaar R, Busa E, Pacheco J, Makris N, Buckner RL, Golland P, Fischl B | IEEE transactions on medical imaging | 17427744 | IEEE Trans Med Imaging | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17427744 |
| Using the wild bootstrap to quantify uncertainty in diffusion tensor imaging. | Whitcher B, Tuch DS, Wisco JJ, Sorensen AG, Wang L | Human brain mapping | 17455199 | Hum Brain Mapp | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17455199 |
| Abnormal cortical folding patterns within Broca's area in schizophrenia: evidence from structural MRI. | Wisco JJ, Kuperberg G, Manoach D, Quinn BT, Busa E, Fischl B, Heckers S, Sorensen AG | Schizophrenia research | 17490861 | Schizophr Res | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17490861 |
| Volumetric cerebral characteristics of children exposed to opiates and other substances in utero. | Walhovd KB, Moe V, Slinning K, Due-Tønnessen P, Bjørnerud A, Dale AM, van der Kouwe A, Quinn BT, Kosofsky B, Greve D, Fischl B | NeuroImage | 17513131 | Neuroimage | 2007 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/17513131 |
| Tracking deforming objects using particle filtering for geometric active contours. | Rathi Y, Vaswani N, Tannenbaum A, Yezzi A | IEEE transactions on pattern analysis and machine intelligence | 17568149 | IEEE Trans Pattern Anal Mach Intell | 2007 Aug | https://www.ncbi.nlm.nih.gov/pubmed/17568149 |
| Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain. | Dauguet J, Peled S, Berezovskii V, Delzescaux T, Warfield SK, Born R, Westin CF | NeuroImage | 17604650 | Neuroimage | 2007 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/17604650 |
| Challenges in image-guided therapy system design. | Dimaio S, Kapur T, Cleary K, Aylward S, Kazanzides P, Vosburgh K, Ellis R, Duncan J, Farahani K, Lemke H, Peters T, Lorensen WB, Gobbi D, Haller J, Clarke LL, Pizer S, Taylor R, Galloway R Jr, Fichtinger G, Hata N, Lawson K, Tempany C, Kikinis R, Jolesz F | NeuroImage | 17644360 | Neuroimage | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17644360 |
| Using the logarithm of odds to define a vector space on probabilistic atlases. | Pohl KM, Fisher J, Bouix S, Shenton M, McCarley RW, Grimson WE, Kikinis R, Wells WM | Medical image analysis | 17698403 | Med Image Anal | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17698403 |
| A hierarchical algorithm for MR brain image parcellation. | Pohl KM, Bouix S, Nakamura M, Rohlfing T, McCarley RW, Kikinis R, Grimson WE, Shenton ME, Wells WM | IEEE transactions on medical imaging | 17896593 | IEEE Trans Med Imaging | 2007 Sep | https://www.ncbi.nlm.nih.gov/pubmed/17896593 |
| 3D modeling of patient-specific geometries of portal veins using MR images. | Yang Y, George S, Martin DR, Tannenbaum AR, Giddens DP | Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference | 17946691 | Conf Proc IEEE Eng Med Biol Soc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17946691 |
| Cavum septum pellucidum in schizophrenia: clinical and neuropsychological correlates. | Flashman LA, Roth RM, Pixley HS, Cleavinger HB, McAllister TW, Vidaver R, Saykin AJ | Psychiatry research | 17291728 | Psychiatry Res | 2007 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/17291728 |
| White matter abnormalities in dystonia normalize after botulinum toxin treatment. | Blood AJ, Tuch DS, Makris N, Makhlouf ML, Sudarsky LR, Sharma N | Neuroreport | 16951564 | Neuroreport | 2006 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/16951564 |
| Image-guided neurosurgery at Brigham and Women's Hospital. | Dimaio SP, Archip N, Hata N, Talos IF, Warfield SK, Majumdar A, Mcdannold N, Hynynen K, Morrison PR, Wells WM 3rd, Kacher DF, Ellis RE, Golby AJ, Black PM, Jolesz FA, Kikinis R | IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society | 17020201 | IEEE Eng Med Biol Mag | 2006 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/17020201 |
| A role for self-gravity at multiple length scales in the process of star formation. | Goodman AA, Rosolowsky EW, Borkin MA, Foster JB, Halle M, Kauffmann J, Pineda JE | Nature | 19122636 | Nature | 2009 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19122636 |
| Reliability of MRI-derived cortical and subcortical morphometric measures: effects of pulse sequence, voxel geometry, and parallel imaging. | Wonderlick JS, Ziegler DA, Hosseini-Varnamkhasti P, Locascio JJ, Bakkour A, van der Kouwe A, Triantafyllou C, Corkin S, Dickerson BC | NeuroImage | 19038349 | Neuroimage | 2009 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/19038349 |
| Diffusion tractography of the fornix in schizophrenia. | Fitzsimmons J, Kubicki M, Smith K, Bushell G, Estepar RS, Westin CF, Nestor PG, Niznikiewicz MA, Kikinis R, McCarley RW, Shenton ME | Schizophrenia research | 19046624 | Schizophr Res | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19046624 |
| Discovering modes of an image population through mixture modeling. | Sabuncu MR, Balci SK, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18982628 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18982628 |
| Collaborative computational anatomy: an MRI morphometry study of the human brain via diffeomorphic metric mapping. | Miller MI, Priebe CE, Qiu A, Fischl B, Kolasny A, Brown T, Park Y, Ratnanather JT, Busa E, Jovicich J, Yu P, Dickerson BC, Buckner RL, Morphometry BIRN | Human brain mapping | 18781592 | Hum Brain Mapp | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18781592 |
| Accurate and robust brain image alignment using boundary-based registration. | Greve DN, Fischl B | NeuroImage | 19573611 | Neuroimage | 2009 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/19573611 |
| Exploratory fMRI analysis without spatial normalization. | Lashkari D, Golland P | Information processing in medical imaging : proceedings of the ... conference | 19694280 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694280 |
| Integrated navigation and control software system for MRI-guided robotic prostate interventions. | Tokuda J, Fischer GS, DiMaio SP, Gobbi DG, Csoma C, Mewes PW, Fichtinger G, Tempany CM, Hata N | Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society | 19699057 | Comput Med Imaging Graph | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19699057 |
| Spherical demons: fast diffeomorphic landmark-free surface registration. | Yeo BT, Sabuncu MR, Vercauteren T, Ayache N, Fischl B, Golland P | IEEE transactions on medical imaging | 19709963 | IEEE Trans Med Imaging | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19709963 |
| Perk Station--Percutaneous surgery training and performance measurement platform. | Vikal S, U-Thainual P, Carrino JA, Iordachita I, Fischer GS, Fichtinger G | Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society | 19539446 | Comput Med Imaging Graph | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19539446 |
| Adsorption of poly(methyl methacrylate) on concave Al2O3 surfaces in nanoporous membranes. | Nunnery G, Hershkovits E, Tannenbaum A, Tannenbaum R | Langmuir : the ACS journal of surfaces and colloids | 19415910 | Langmuir | 2009 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/19415910 |
| Anterior cruciate ligament reconstruction in the skeletally immature: an anatomical study utilizing 3-dimensional magnetic resonance imaging reconstructions. | Kercher J, Xerogeanes J, Tannenbaum A, Al-Hakim R, Black JC, Zhao J | Journal of pediatric orthopedics | 19352236 | J Pediatr Orthop | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19352236 |
| Particle-based shape analysis of multi-object complexes. | Cates J, Fletcher PT, Styner M, Hazlett HC, Whitaker R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979781 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979781 |
| Directional functions for orientation distribution estimation. | Rathi Y, Michailovich O, Shenton ME, Bouix S | Medical image analysis | 19269242 | Med Image Anal | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19269242 |
| Automated segmentation of hippocampal subfields from ultra-high resolution in vivo MRI. | Van Leemput K, Bakkour A, Benner T, Wiggins G, Wald LL, Augustinack J, Dickerson BC, Golland P, Fischl B | Hippocampus | 19405131 | Hippocampus | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19405131 |
| Uncinate fasciculus abnormalities in recent onset schizophrenia and affective psychosis: a diffusion tensor imaging study. | Kawashima T, Nakamura M, Bouix S, Kubicki M, Salisbury DF, Westin CF, McCarley RW, Shenton ME | Schizophrenia research | 19328656 | Schizophr Res | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19328656 |
| Multiscale 3D shape representation and segmentation with applications to hippocampal/caudate extraction from brain MRI. | Gao Y, Corn B, Schifter D, Tannenbaum A | Medical image analysis | 22119491 | Med Image Anal | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22119491 |
| Size and shape of the caudate nucleus in individuals with bipolar affective disorder. | Ong D, Walterfang M, Malhi GS, Styner M, Velakoulis D, Pantelis C | The Australian and New Zealand journal of psychiatry | 22368240 | Aust N Z J Psychiatry | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22368240 |
| A review of magnetic resonance imaging and diffusion tensor imaging findings in mild traumatic brain injury. | Shenton ME, Hamoda HM, Schneiderman JS, Bouix S, Pasternak O, Rathi Y, Vu MA, Purohit MP, Helmer K, Koerte I, Lin AP, Westin CF, Kikinis R, Kubicki M, Stern RA, Zafonte R | Brain imaging and behavior | 22438191 | Brain Imaging Behav | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22438191 |
| TwinMARM: two-stage multiscale adaptive regression methods for twin neuroimaging data. | Li Y, Gilmore JH, Wang J, Styner M, Lin W, Zhu H | IEEE transactions on medical imaging | 22287236 | IEEE Trans Med Imaging | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22287236 |
| Comparison of two methods for quantitative assessment of mandibular asymmetry using cone beam computed tomography image volumes. | AlHadidi A, Cevidanes LH, Mol A, Ludlow J, Styner M | Dento maxillo facial radiology | 21831974 | Dentomaxillofac Radiol | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21831974 |
| Asymmetric bias in user guided segmentations of brain structures. | Maltbie E, Bhatt K, Paniagua B, Smith RG, Graves MM, Mosconi MW, Peterson S, White S, Blocher J, El-Sayed M, Hazlett HC, Styner MA | NeuroImage | 21889995 | Neuroimage | 2012 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/21889995 |
| Geometric correspondence for ensembles of nonregular shapes. | Datar M, Gur Y, Paniagua B, Styner M, Whitaker R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 21995050 | Med Image Comput Comput Assist Interv | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21995050 |
| A compressive sensing approach for glioma margin delineation using mass spectrometry. | Gholami B, Agar NY, Jolesz FA, Haddad WM, Tannenbaum AR | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255629 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22255629 |
| 3D Slicer as a tool for interactive brain tumor segmentation. | Kikinis R, Pieper S | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255945 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22255945 |
| Assessment of mandibular advancement surgery with 3D CBCT models superimposition. | Motta AT, de Assis Ribeiro Carvalho F, Cevidanes LH, de Oliveira Almeida MA | Dental press journal of orthodontics | 21738889 | Dental Press J Orthod | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21738889 |
| White matter bundle registration and population analysis based on Gaussian processes. | Wassermann D, Rathi Y, Bouix S, Kubicki M, Kikinis R, Shenton M, Westin CF | Information processing in medical imaging : proceedings of the ... conference | 21761667 | Inf Process Med Imaging | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21761667 |
| Comparison of acute and chronic traumatic brain injury using semi-automatic multimodal segmentation of MR volumes. | Irimia A, Chambers MC, Alger JR, Filippou M, Prastawa MW, Wang B, Hovda DA, Gerig G, Toga AW, Kikinis R, Vespa PM, Van Horn JD | Journal of neurotrauma | 21787171 | J Neurotrauma | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21787171 |
| Superimposition of 3D cone-beam CT models in orthognathic surgery. | da Motta AT, de Assis Ribeiro Carvalho F, Oliveira AE, Cevidanes LH, de Oliveira Almeida MA | Dental press journal of orthodontics | 21814624 | Dental Press J Orthod | 2010 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21814624 |
| Impact of nonrigid motion correction technique on pixel-wise pharmacokinetic analysis of free-breathing pulmonary dynamic contrast-enhanced MR imaging. | Tokuda J, Mamata H, Gill RR, Hata N, Kikinis R, Padera RF Jr, Lenkinski RE, Sugarbaker DJ, Hatabu H | Journal of magnetic resonance imaging : JMRI | 21448965 | J Magn Reson Imaging | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21448965 |
| Clinical application of 3D imaging for assessment of treatment outcomes. | Cevidanes LH, Oliveira AE, Grauer D, Styner M, Proffit WR | Seminars in orthodontics | 21516170 | Semin Orthod | 2011 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21516170 |
| Early brain overgrowth in autism associated with an increase in cortical surface area before age 2 years. | Hazlett HC, Poe MD, Gerig G, Styner M, Chappell C, Smith RG, Vachet C, Piven J | Archives of general psychiatry | 21536976 | Arch Gen Psychiatry | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21536976 |
| Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age. | Ghosh SS, Kakunoori S, Augustinack J, Nieto-Castanon A, Kovelman I, Gaab N, Christodoulou JA, Triantafyllou C, Gabrieli JD, Fischl B | NeuroImage | 20621657 | Neuroimage | 2010 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/20621657 |
| Detecting stable distributed patterns of brain activation using Gini contrast. | Langs G, Menze BH, Lashkari D, Golland P | NeuroImage | 20709176 | Neuroimage | 2011 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/20709176 |
| Point set registration via particle filtering and stochastic dynamics. | Sandhu R, Dambreville S, Tannenbaum A | IEEE transactions on pattern analysis and machine intelligence | 20558877 | IEEE Trans Pattern Anal Mach Intell | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20558877 |
| Multivariate varying coefficient models for DTI tract statistics. | Zhu H, Styner M, Li Y, Kong L, Shi Y, Lin W, Coe C, Gilmore JH | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879291 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879291 |
| A generative model for brain tumor segmentation in multi-modal images. | Menze BH, Van Leemput K, Lashkari D, Weber MA, Ayache N, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879310 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879310 |
| Summarizing and visualizing uncertainty in non-rigid registration. | Risholm P, Pieper S, Samset E, Wells WM 3rd | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879359 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879359 |
| Multimodality non-rigid image registration for planning, targeting and monitoring during CT-guided percutaneous liver tumor cryoablation. | Elhawary H, Oguro S, Tuncali K, Morrison PR, Tatli S, Shyn PB, Silverman SG, Hata N | Academic radiology | 20817574 | Acad Radiol | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20817574 |
| Interactive diffusion tensor tractography visualization for neurosurgical planning. | Golby AJ, Kindlmann G, Norton I, Yarmarkovich A, Pieper S, Kikinis R | Neurosurgery | 21135713 | Neurosurgery | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21135713 |
| Gray matter volume reduction in rostral middle frontal gyrus in patients with chronic schizophrenia. | Kikinis Z, Fallon JH, Niznikiewicz M, Nestor P, Davidson C, Bobrow L, Pelavin PE, Fischl B, Yendiki A, McCarley RW, Kikinis R, Kubicki M, Shenton ME | Schizophrenia research | 20822884 | Schizophr Res | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20822884 |
| Thickness of the human cerebral cortex is associated with metrics of cerebrovascular health in a normative sample of community dwelling older adults. | Leritz EC, Salat DH, Williams VJ, Schnyer DM, Rudolph JL, Lipsitz L, Fischl B, McGlinchey RE, Milberg WP | NeuroImage | 21035552 | Neuroimage | 2011 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/21035552 |
| DTI registration in atlas based fiber analysis of infantile Krabbe disease. | Wang Y, Gupta A, Liu Z, Zhang H, Escolar ML, Gilmore JH, Gouttard S, Fillard P, Maltbie E, Gerig G, Styner M | NeuroImage | 21256236 | Neuroimage | 2011 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/21256236 |
| Statistical analysis of fiber bundles using multi-tensor tractography: application to first-episode schizophrenia. | Rathi Y, Kubicki M, Bouix S, Westin CF, Goldstein J, Seidman L, Mesholam-Gately R, McCarley RW, Shenton ME | Magnetic resonance imaging | 21277725 | Magn Reson Imaging | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21277725 |
| AN EFFICIENT NUMERICAL METHOD FOR THE SOLUTION OF THE L(2) OPTIMAL MASS TRANSFER PROBLEM. | Haber E, Rehman T, Tannenbaum A | SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics | 21278828 | SIAM J Sci Comput | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21278828 |
| Texture mapping via optimal mass transport. | Dominitz A, Tannenbaum A | IEEE transactions on visualization and computer graphics | 20224137 | IEEE Trans Vis Comput Graph | 2010 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/20224137 |
| Consistency Clustering: A Robust Algorithm for Group-wise Registration, Segmentation and Automatic Atlas Construction in Diffusion MRI. | Ziyan U, Sabuncu MR, Grimson WE, Westin CF | International journal of computer vision | 20442792 | Int J Comput Vis | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20442792 |
| Mining the mind research network: a novel framework for exploring large scale, heterogeneous translational neuroscience research data sources. | Bockholt HJ, Scully M, Courtney W, Rachakonda S, Scott A, Caprihan A, Fries J, Kalyanam R, Segall JM, de la Garza R, Lane S, Calhoun VD | Frontiers in neuroinformatics | 20461147 | Front Neuroinform | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20461147 |
| Age-related changes in the corpus callosum in early-onset bipolar disorder assessed using volumetric and cross-sectional measurements. | Lopez-Larson M, Breeze JL, Kennedy DN, Hodge SM, Tang L, Moore C, Giuliano AJ, Makris N, Caviness VS, Frazier JA | Brain imaging and behavior | 20686873 | Brain Imaging Behav | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20686873 |
| Ssecrett and NeuroTrace: interactive visualization and analysis tools for large-scale neuroscience data sets. | Jeong WK, Beyer J, Hadwiger M, Blue R, Law C, Vazquez-Reina A, Reid RC, Lichtman J, Pfister H | IEEE computer graphics and applications | 20650718 | IEEE Comput Graph Appl | 2010 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/20650718 |
| A nonrigid kernel-based framework for 2D-3D pose estimation and 2D image segmentation. | Sandhu R, Dambreville S, Yezzi A, Tannenbaum A | IEEE transactions on pattern analysis and machine intelligence | 20733218 | IEEE Trans Pattern Anal Mach Intell | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20733218 |
| Filtered multitensor tractography. | Malcolm JG, Shenton ME, Rathi Y | IEEE transactions on medical imaging | 20805043 | IEEE Trans Med Imaging | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20805043 |
| A generative model for image segmentation based on label fusion. | Sabuncu MR, Yeo BT, Van Leemput K, Fischl B, Golland P | IEEE transactions on medical imaging | 20562040 | IEEE Trans Med Imaging | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20562040 |
| Tensor kernels for simultaneous fiber model estimation and tractography. | Rathi Y, Malcolm JG, Michailovich O, Westin CF, Shenton ME, Bouix S | Magnetic resonance in medicine | 20572129 | Magn Reson Med | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20572129 |
| Manifold modeling for brain population analysis. | Gerber S, Tasdizen T, Thomas Fletcher P, Joshi S, Whitaker R, Alzheimers Disease Neuroimaging Initiative (ADNI) | Medical image analysis | 20579930 | Med Image Anal | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20579930 |
| Segmentation of image ensembles via latent atlases. | Riklin-Raviv T, Van Leemput K, Menze BH, Wells WM 3rd, Golland P | Medical image analysis | 20580305 | Med Image Anal | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20580305 |
| Two-tensor tractography using a constrained filter. | Malcolm JG, Shenton ME, Rathi Y | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426073 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426073 |
| Supervised nonparametric image parcellation. | Sabuncu MR, Yeo BT, Van Leemput K, Fischl B, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426218 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426218 |
| Heritability of brain ventricle volume: converging evidence from inconsistent results. | Kremen WS, Panizzon MS, Neale MC, Fennema-Notestine C, Prom-Wormley E, Eyler LT, Stevens A, Franz CE, Lyons MJ, Grant MD, Jak AJ, Jernigan TL, Xian H, Fischl B, Thermenos HW, Seidman LJ, Tsuang MT, Dale AM | Neurobiology of aging | 20363053 | Neurobiol Aging | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20363053 |
| Relevance vector machine learning for neonate pain intensity assessment using digital imaging. | Gholami B, Haddad WM, Tannenbaum AR | IEEE transactions on bio-medical engineering | 20172803 | IEEE Trans Biomed Eng | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20172803 |
| Comparison of manual and automated determination of hippocampal volumes in MCI and early AD. | Shen L, Saykin AJ, Kim S, Firpi HA, West JD, Risacher SL, McDonald BC, McHugh TL, Wishart HA, Flashman LA | Brain imaging and behavior | 20454594 | Brain Imaging Behav | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20454594 |
| On approximation of smooth functions from samples of partial derivatives with application to phase unwrapping. | Michailovich O, Tannenbaum A | Signal processing | 20046803 | Signal Processing | 2008 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/20046803 |
| MRI-based anatomical model of the human head for specific absorption rate mapping. | Makris N, Angelone L, Tulloch S, Sorg S, Kaiser J, Kennedy D, Bonmassar G | Medical & biological engineering & computing | 18985401 | Med Biol Eng Comput | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18985401 |
| An Automated Method for Segmenting White Matter Lesions through Multi-Level Morphometric Feature Classification with Application to Lupus. | Scully M, Anderson B, Lane T, Gasparovic C, Magnotta V, Sibbitt W, Roldan C, Kikinis R, Bockholt HJ | Frontiers in human neuroscience | 20428508 | Front Hum Neurosci | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20428508 |
| A locally adaptive regularization based on anisotropic diffusion for deformable image registration of sliding organs. | Pace DF, Aylward SR, Niethammer M | IEEE transactions on medical imaging | 23899632 | IEEE Trans Med Imaging | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23899632 |
| Polymer Adsorption on Curved Surfaces: A Geometric Approach. | Hershkovits E, Tannenbaum A, Tannenbaum R | The journal of physical chemistry. C, Nanomaterials and interfaces | 23710263 | J Phys Chem C Nanomater Interfaces | 2007 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/23710263 |
| Multimodal deformable registration of traumatic brain injury MR volumes via the Bhattacharyya distance. | Lou Y, Irimia A, Vela PA, Chambers MC, Van Horn JD, Vespa PM, Tannenbaum AR | IEEE transactions on bio-medical engineering | 23962986 | IEEE Trans Biomed Eng | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23962986 |
| Biomechanical model as a registration tool for image-guided neurosurgery: evaluation against BSpline registration. | Mostayed A, Garlapati RR, Joldes GR, Wittek A, Roy A, Kikinis R, Warfield SK, Miller K | Annals of biomedical engineering | 23771299 | Ann Biomed Eng | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23771299 |
| Decreased axial diffusivity within language connections: a possible biomarker of schizophrenia risk. | Kubicki M, Shenton ME, Maciejewski PK, Pelavin PE, Hawley KJ, Ballinger T, Swisher T, Jabbar GA, Thermenos HW, Keshavan MS, Seidman LJ, Delisi LE | Schizophrenia research | 23800617 | Schizophr Res | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23800617 |
| DTIPrep: quality control of diffusion-weighted images. | Oguz I, Farzinfar M, Matsui J, Budin F, Liu Z, Gerig G, Johnson HJ, Styner M | Frontiers in neuroinformatics | 24523693 | Front Neuroinform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24523693 |
| Fiber feature map based landmark initialization for highly deformable DTI registration. | Gupta A, Toews M, Janardhana R, Rathi Y, Gilmore J, Escolar M, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24353392 | Proc SPIE Int Soc Opt Eng | 2013 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24353392 |
| Regional 3D superimposition to assess temporomandibular joint condylar morphology. | Schilling J, Gomes LC, Benavides E, Nguyen T, Paniagua B, Styner M, Boen V, Gonçalves JR, Cevidanes LH | Dento maxillo facial radiology | 24170802 | Dentomaxillofac Radiol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24170802 |
| Reviewing the ketamine model for schizophrenia. | Frohlich J, Van Horn JD | Journal of psychopharmacology (Oxford, England) | 24257811 | J Psychopharmacol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24257811 |
| Software-based Diffusion MR Human Brain Phantom for Evaluating Fiber-tracking Algorithms. | Shi Y, Roger G, Vachet C, Budin F, Maltbie E, Verde A, Hoogstoel M, Berger JB, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24357914 | Proc SPIE Int Soc Opt Eng | 2013 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24357914 |
| Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI. | McGann C, Akoum N, Patel A, Kholmovski E, Revelo P, Damal K, Wilson B, Cates J, Harrison A, Ranjan R, Burgon NS, Greene T, Kim D, Dibella EV, Parker D, Macleod RS, Marrouche NF | Circulation. Arrhythmia and electrophysiology | 24363354 | Circ Arrhythm Electrophysiol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24363354 |
| 3D of Brain Shape and Volume After Cranial Vault Remodeling Surgery for Craniosynostosis Correction in Infants. | Paniagua B, Emodi O, Hill J, Fishbaugh J, Pimenta LA, Aylward SR, Andinet E, Gerig G, Gilmore J, van Aalst JA, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24465118 | Proc SPIE Int Soc Opt Eng | 2013 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/24465118 |
| Fast approximate surface evolution in arbitrary dimension. | Malcolm J, Rathi Y, Yezzi A, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 24392194 | Proc SPIE Int Soc Opt Eng | 2008 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/24392194 |
| Particle-guided image registration. | Lee J, Lyu I, Oğuz I, Styner MA | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 24505762 | Med Image Comput Comput Assist Interv | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24505762 |
| Contour-driven regression for label inference in atlas-based segmentation. | Wachinger C, Sharp GC, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 24505763 | Med Image Comput Comput Assist Interv | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24505763 |
| MANDIBULAR ASYMMETRY CHARACTERIZATION USING GENERALIZED TENSOR-BASED MORPHOMETRY. | Paniagua B, Alhadidi A, Cevidanes L, Styner M, Oguz I | Proceedings. IEEE International Symposium on Biomedical Imaging | 24443671 | Proc IEEE Int Symp Biomed Imaging | 2011 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/24443671 |
| LONGITUDINAL GROWTH MODELING OF DISCRETE-TIME FUNCTIONS WITH APPLICATION TO DTI TRACT EVOLUTION IN EARLY NEURODEVELOPMENT. | Sharma A, Durrleman S, Gilmore JH, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 24443681 | Proc IEEE Int Symp Biomed Imaging | 2013 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/24443681 |
| ANALYZING IMAGING BIOMARKERS FOR TRAUMATIC BRAIN INJURY USING 4D MODELING OF LONGITUDINAL MRI. | Wang B, Prastawa M, Irimia A, Chambers MC, Sadeghi N, Vespa PM, van Horn JD, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 24443697 | Proc IEEE Int Symp Biomed Imaging | 2013 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/24443697 |
| Three-dimensional analysis of maxillary changes associated with facemask and rapid maxillary expansion compared with bone anchored maxillary protraction. | Hino CT, Cevidanes LH, Nguyen TT, De Clerck HJ, Franchi L, McNamara JA Jr | American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics | 24182587 | Am J Orthod Dentofacial Orthop | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24182587 |
| Improved segmentation of white matter tracts with adaptive Riemannian metrics. | Hao X, Zygmunt K, Whitaker RT, Fletcher PT | Medical image analysis | 24211814 | Med Image Anal | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24211814 |
| Interactive medical image segmentation using PDE control of active contours. | Karasev P, Kolesov I, Fritscher K, Vela P, Mitchell P, Tannenbaum A | IEEE transactions on medical imaging | 23893712 | IEEE Trans Med Imaging | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23893712 |
| Toward a comprehensive framework for the spatiotemporal statistical analysis of longitudinal shape data. | Durrleman S, Pennec X, Trouvé A, Braga J, Gerig G, Ayache N | International journal of computer vision | 23956495 | Int J Comput Vis | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23956495 |
| Outcome quantification using SPHARM-PDM toolbox in orthognathic surgery. | Paniagua B, Cevidanes L, Zhu H, Styner M | International journal of computer assisted radiology and surgery | 21161693 | Int J Comput Assist Radiol Surg | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21161693 |
| A new metric for detecting change in slowly evolving brain tumors: validation in meningioma patients. | Pohl KM, Konukoglu E, Novellas S, Ayache N, Fedorov A, Talos IF, Golby A, Wells WM, Kikinis R, Black PM | Neurosurgery | 21206318 | Neurosurgery | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21206318 |
| A 4-channel 3 Tesla phased array receive coil for awake rhesus monkey fMRI and diffusion MRI experiments. | Khachaturian MH | Journal of biomedical science and engineering | 21243106 | J Biomed Sci Eng | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/21243106 |
| FADTTS: functional analysis of diffusion tensor tract statistics. | Zhu H, Kong L, Li R, Styner M, Gerig G, Lin W, Gilmore JH | NeuroImage | 21335092 | Neuroimage | 2011 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/21335092 |
| Shape alterations in the striatum in chorea-acanthocytosis. | Walterfang M, Looi JC, Styner M, Walker RH, Danek A, Niethammer M, Evans A, Kotschet K, Rodrigues GR, Hughes A, Velakoulis D | Psychiatry research | 21377843 | Psychiatry Res | 2011 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/21377843 |
| RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS. | Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, Carpenter AE | Proceedings. IEEE International Symposium on Biomedical Imaging | 21383863 | Proc IEEE Int Symp Biomed Imaging | 2010 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/21383863 |
| Abnormalities of middle longitudinal fascicle and disorganization in patients with schizophrenia. | Asami T, Saito Y, Whitford TJ, Makris N, Niznikiewicz M, McCarley RW, Shenton ME, Kubicki M | Schizophrenia research | 23290607 | Schizophr Res | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23290607 |
| TRACKING THROUGH CHANGES IN SCALE. | Lankton S, Malcolm J, Nakhmani A, Tannenbaum A | Proceedings. International Conference on Image Processing | 23645076 | Proc Int Conf Image Proc | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/23645076 |
| MATHEMATICAL METHODS IN MEDICAL IMAGE PROCESSING. | Angenent S, Pichon E, Tannenbaum A | Bulletin (new series) of the American Mathematical Society | 23645963 | Bull New Ser Am Math Soc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/23645963 |
| KERNEL-BASED HIGH-DIMENSIONAL HISTOGRAM ESTIMATION FOR VISUAL TRACKING. | Karasev P, Malcolm J, Tannenbaum A | Proceedings. International Conference on Image Processing | 23666258 | Proc Int Conf Image Proc | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/23666258 |
| Diffusion weighted imaging of prefrontal cortex in prodromal Huntington's disease. | Matsui JT, Vaidya JG, Johnson HJ, Magnotta VA, Long JD, Mills JA, Lowe MJ, Sakaie KE, Rao SM, Smith MM, Paulsen JS | Human brain mapping | 23568433 | Hum Brain Mapp | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23568433 |
| Imaging patients with psychosis and a mouse model establishes a spreading pattern of hippocampal dysfunction and implicates glutamate as a driver. | Schobel SA, Chaudhury NH, Khan UA, Paniagua B, Styner MA, Asllani I, Inbar BP, Corcoran CM, Lieberman JA, Moore H, Small SA | Neuron | 23583108 | Neuron | 2013 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/23583108 |
| Clinical Decision Support and Closed-Loop Control for Cardiopulmonary Management and Intensive Care Unit Sedation Using Expert Systems. | Gholami B, Bailey JM, Haddad WM, Tannenbaum AR | IEEE transactions on control systems technology : a publication of the IEEE Control Systems Society | 23620646 | IEEE Trans Control Syst Technol | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23620646 |
| Reduced fractional anisotropy and axial diffusivity in white matter in 22q11.2 deletion syndrome: a pilot study. | Kikinis Z, Asami T, Bouix S, Finn CT, Ballinger T, Tworog-Dube E, Kucherlapati R, Kikinis R, Shenton ME, Kubicki M | Schizophrenia research | 22863550 | Schizophr Res | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22863550 |
| Extended Broca's area in the functional connectome of language in adults: combined cortical and subcortical single-subject analysis using fMRI and DTI tractography. | Lemaire JJ, Golby A, Wells WM 3rd, Pujol S, Tie Y, Rigolo L, Yarmarkovich A, Pieper S, Westin CF, Jolesz F, Kikinis R | Brain topography | 23001727 | Brain Topogr | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23001727 |
| Associations between white matter microstructure and infants' working memory. | Short SJ, Elison JT, Goldman BD, Styner M, Gu H, Connelly M, Maltbie E, Woolson S, Lin W, Gerig G, Reznick JS, Gilmore JH | NeuroImage | 22989623 | Neuroimage | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/22989623 |
| The structural, connectomic and network covariance of the human brain. | Irimia A, Van Horn JD | NeuroImage | 23116816 | Neuroimage | 2013 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/23116816 |
| Anisotropic conductivity of magnetic carbon nanotubes embedded in epoxy matrices. | Kim IT, Tannenbaum A, Tannenbaum R | Carbon | 23019381 | Carbon N Y | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23019381 |
| Imaging nigral pathology and clinical progression in Parkinson's disease. | Du G, Lewis MM, Sen S, Wang J, Shaffer ML, Styner M, Yang QX, Huang X | Movement disorders : official journal of the Movement Disorder Society | 23008179 | Mov Disord | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23008179 |
| Recursive feature elimination for brain tumor classification using desorption electrospray ionization mass spectrometry imaging. | Gholami B, Norton I, Tannenbaum AR, Agar NY | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 23367115 | Annu Int Conf IEEE Eng Med Biol Soc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23367115 |
| Analysis of longitudinal shape variability via subject specific growth modeling. | Fishbaugh J, Prastawa M, Durrleman S, Piven J, Gerig G, IBIS Network | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23285617 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23285617 |
| Group analysis of resting-state fMRI by hierarchical Markov random fields. | Liu W, Awate SP, Fletcher PT | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286130 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286130 |
| Learning a reliable estimate of the number of fiber directions in diffusion MRI. | Schultz T | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286167 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286167 |
| Pituitary adenoma volumetry with 3D Slicer. | Egger J, Kapur T, Nimsky C, Kikinis R | PloS one | 23240062 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23240062 |
| Multiscale adaptive generalized estimating equations for longitudinal neuroimaging data. | Li Y, Gilmore JH, Shen D, Styner M, Lin W, Zhu H | NeuroImage | 23357075 | Neuroimage | 2013 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/23357075 |
| Sexually dimorphic white matter geometry abnormalities in adolescent onset schizophrenia. | Savadjiev P, Whitford TJ, Hough ME, Clemm von Hohenberg C, Bouix S, Westin CF, Shenton ME, Crow TJ, James AC, Kubicki M | Cerebral cortex (New York, N.Y. : 1991) | 23307635 | Cereb Cortex | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/23307635 |
| Modeling 4D Changes in Pathological Anatomy using Domain Adaptation: Analysis of TBI Imaging using a Tumor Database. | Wang B, Prastawa M, Saha A, Awate SP, Irimia A, Chambers MC, Vespa PM, Van Horn JD, Pascucci V, Gerig G | Multimodal brain image analysis : third International Workshop, MBIA 2013, held in conjunction with MICCAI 2013, Nagoya, Japan, September 22, 2013 : proceedings. MBIA (Workshop) (3rd : 2013 : Nagoya-shi, Japan) | 25346953 | Multimodal Brain Image Anal (2013) | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/25346953 |
| MRI Brain Tumor Segmentation and Necrosis Detection Using Adaptive Sobolev Snakes. | Nakhmani A, Kikinis R, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 25302005 | Proc SPIE Int Soc Opt Eng | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/25302005 |
| Reconstruction and Feature Selection for Desorption Electrospray Ionization Mass Spectroscopy Imagery. | Gao Y, Zhu L, Norton I, Agar NY, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 25302009 | Proc SPIE Int Soc Opt Eng | 2014 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/25302009 |
| Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality. | Bronson JR, Levine JA, Whitaker RT | Proceedings. International Meshing Roundtable | 25309969 | Proc Int Meshing Roundtable | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/25309969 |
| Statistical estimation of physiological brain age as a descriptor of senescence rate during adulthood. | Irimia A, Torgerson CM, Goh SY, Van Horn JD | Brain imaging and behavior | 25376330 | Brain Imaging Behav | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25376330 |
| Spatio-Temporal Analysis of Early Brain Development. | Sadeghi N, Prastawa M, Gilmore JH, Lin W, Gerig G | Conference record. Asilomar Conference on Signals, Systems & Computers | 25328368 | Conf Rec Asilomar Conf Signals Syst Comput | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/25328368 |
| T1ρ imaging in premanifest Huntington disease reveals changes associated with disease progression. | Wassef SN, Wemmie J, Johnson CP, Johnson H, Paulsen JS, Long JD, Magnotta VA | Movement disorders : official journal of the Movement Disorder Society | 25820773 | Mov Disord | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25820773 |
| Neuroinformatics and the The Insight ToolKit. | Avants BB, Johnson HJ, Tustison NJ | Frontiers in neuroinformatics | 25859213 | Front Neuroinform | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25859213 |
| Towards Effcient Label Fusion by Pre-Alignment of Training Data. | Depa M, Holmvang G, Schmidt EJ, Golland P, Sabuncu MR | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 24660167 | Med Image Comput Comput Assist Interv | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/24660167 |
| Group-wise cortical correspondence via sulcal curve-constrained entropy minimization. | Lyu I, Kim SH, Seong JK, Yoo SW, Evans AC, Shi Y, Sanchez M, Niethammer M, Styner MA | Information processing in medical imaging : proceedings of the ... conference | 24683983 | Inf Process Med Imaging | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24683983 |
| Bayesian segmentation of atrium wall using globally-optimal graph cuts on 3D meshes. | Veni G, Fu Z, Awate SP, Whitaker RT | Information processing in medical imaging : proceedings of the ... conference | 24684007 | Inf Process Med Imaging | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24684007 |
| Multivariate longitudinal shape analysis of human lateral ventricles during the first twenty-four months of life. | Bompard L, Xu S, Styner M, Paniagua B, Ahn M, Yuan Y, Jewells V, Gao W, Shen D, Zhu H, Lin W | PloS one | 25265017 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25265017 |
| Transperineal in-bore 3-T MR imaging-guided prostate biopsy: a prospective clinical observational study. | Penzkofer T, Tuncali K, Fedorov A, Song SE, Tokuda J, Fennessy FM, Vangel MG, Kibel AS, Mulkern RV, Wells WM, Hata N, Tempany CM | Radiology | 25222067 | Radiology | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25222067 |
| Bayesian Generalized Low Rank Regression Models for Neuroimaging Phenotypes and Genetic Markers. | Zhu H, Khondker Z, Lu Z, Ibrahim JG, Alzheimer's Disease Neuroimaging Initiative | Journal of the American Statistical Association | 25349462 | J Am Stat Assoc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25349462 |
| GEODESIC REGRESSION OF IMAGE AND SHAPE DATA FOR IMPROVED MODELING OF 4D TRAJECTORIES. | Fishbaugh J, Prastawa M, Gerig G, Durrleman S | Proceedings. IEEE International Symposium on Biomedical Imaging | 25356192 | Proc IEEE Int Symp Biomed Imaging | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25356192 |
| Atlas-based under-segmentation. | Wachinger C, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 25333133 | Med Image Comput Comput Assist Interv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25333133 |
| Segmentation of cerebrovascular pathologies in stroke patients with spatial and shape priors. | Dalca AV, Sridharan R, Cloonan L, Fitzpatrick KM, Kanakis A, Furie KL, Rosand J, Wu O, Sabuncu M, Rost NS, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 25485450 | Med Image Comput Comput Assist Interv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25485450 |
| Fitting Nonlinear Ordinary Differential Equation Models with Random Effects and Unknown Initial Conditions Using the Stochastic Approximation Expectation-Maximization (SAEM) Algorithm. | Chow SM, Lu Z, Sherwood A, Zhu H | Psychometrika | 25416456 | Psychometrika | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25416456 |
| Splenium development and early spoken language in human infants. | Swanson MR, Wolff JJ, Elison JT, Gu H, Hazlett HC, Botteron K, Styner M, Paterson S, Gerig G, Constantino J, Dager S, Estes A, Vachet C, Piven J, IBIS Network | Developmental science | 26490257 | Dev Sci | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26490257 |
| Interactive Whole-Heart Segmentation in Congenital Heart Disease. | Pace DF, Dalca AV, Geva T, Powell AJ, Moghari MH, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 26889498 | Med Image Comput Comput Assist Interv | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26889498 |
| Automatic Sulcal Curve Extraction on the Human Cortical Surface. | Lyu I, Kim SH, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 26028801 | Proc SPIE Int Soc Opt Eng | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26028801 |
| Shape index distribution based local surface complexity applied to the human cortex. | Kim SH, Fonov V, Collins DL, Gerig G, IBIS Network, Styner MA | Proceedings of SPIE--the International Society for Optical Engineering | 26028803 | Proc SPIE Int Soc Opt Eng | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26028803 |
| A diffusion tensor MRI atlas of the postmortem rhesus macaque brain. | Calabrese E, Badea A, Coe CL, Lubach GR, Shi Y, Styner MA, Johnson GA | NeuroImage | 26037056 | Neuroimage | 2015 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/26037056 |
| Sampling from Determinantal Point Processes for Scalable Manifold Learning. | Wachinger C, Golland P | Information processing in medical imaging : proceedings of the ... conference | 26221713 | Inf Process Med Imaging | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26221713 |
| Geodesic distances to landmarks for dense correspondence on ensembles of complex shapes. | Datar M, Lyu I, Kim S, Cates J, Styner MA, Whitaker R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 24579119 | Med Image Comput Comput Assist Interv | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24579119 |
| Interactive MRI Segmentation with Controlled Active Vision. | Karasev P, Kolesov I, Chudy K, Muller G, Xerogeanes J, Tannenbaum A | Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control | 24584213 | Proc IEEE Conf Decis Control | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/24584213 |
| Functional Geometry Alignment and Localization of Brain Areas. | Langs G, Golland P, Tie Y, Rigolo L, Golby AJ | Advances in neural information processing systems | 24808719 | Adv Neural Inf Process Syst | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/24808719 |
| Categories and Functional Units: An Infinite Hierarchical Model for Brain Activations. | Lashkari D, Sridharan R, Golland P | Advances in neural information processing systems | 24839377 | Adv Neural Inf Process Syst | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/24839377 |
| Localized abnormalities in the cingulum bundle in patients with schizophrenia: a Diffusion Tensor tractography study. | Whitford TJ, Lee SW, Oh JS, de Luis-Garcia R, Savadjiev P, Alvarado JL, Westin CF, Niznikiewicz M, Nestor PG, McCarley RW, Kubicki M, Shenton ME | NeuroImage. Clinical | 25003032 | Neuroimage Clin | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25003032 |
| EM-Navigated Catheter Placement for Gynecologic Brachytherapy: An Accuracy Study. | Mehrtash A, Damato A, Pernelle G, Barber L, Farhat N, Viswanathan A, Cormack R, Kapur T | Proceedings of SPIE--the International Society for Optical Engineering | 25076828 | Proc SPIE Int Soc Opt Eng | 2014 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/25076828 |
| Multi-atlas segmentation with particle-based group-wise image registration. | Lee J, Lyu I, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 25075158 | Proc SPIE Int Soc Opt Eng | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/25075158 |
| Antenatal depression, treatment with selective serotonin reuptake inhibitors, and neonatal brain structure: A propensity-matched cohort study. | Jha SC, Meltzer-Brody S, Steiner RJ, Cornea E, Woolson S, Ahn M, Verde AR, Hamer RM, Zhu H, Styner M, Gilmore JH, Knickmeyer RC | Psychiatry research. Neuroimaging | 27254086 | Psychiatry Res Neuroimaging | 2016 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/27254086 |
| Multimodal neuroimaging computing: a review of the applications in neuropsychiatric disorders. | Liu S, Cai W, Liu S, Zhang F, Fulham M, Feng D, Pujol S, Kikinis R | Brain informatics | 27747507 | Brain Inform | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27747507 |
| Multimodal neuroimaging computing: the workflows, methods, and platforms. | Liu S, Cai W, Liu S, Zhang F, Fulham M, Feng D, Pujol S, Kikinis R | Brain informatics | 27747508 | Brain Inform | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27747508 |
| Reinforced Angle-based Multicategory Support Vector Machines. | Zhang C, Liu Y, Wang J, Zhu H | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 27891045 | J Comput Graph Stat | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27891045 |
| Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience. | Kapur T, Pieper S, Fedorov A, Fillion-Robin JC, Halle M, O'Donnell L, Lasso A, Ungi T, Pinter C, Finet J, Pujol S, Jagadeesan J, Tokuda J, Norton I, Estepar RSJ, Gering D, Aerts HJWL, Jakab M, Hata N, Ibanez L, Blezek D, Miller J, Aylward S, Grimson WEL, Fichtinger G, Wells WM, Lorensen WE, Schroeder W, Kikinis R | Medical image analysis | 27498015 | Med Image Anal | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27498015 |
| Modeling 4D Pathological Changes by Leveraging Normative Models. | Wang B, Prastawa M, Irimia A, Saha A, Liu W, Goh SY, Vespa PM, Van Horn JD, Gerig G | Computer vision and image understanding : CVIU | 27818606 | Comput Vis Image Underst | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27818606 |
| Development of White Matter Circuitry in Infants With Fragile X Syndrome. | Swanson MR, Wolff JJ, Shen MD, Styner M, Estes A, Gerig G, McKinstry RC, Botteron KN, Piven J, Hazlett HC, Infant Brain Imaging Study (IBIS) Network | JAMA psychiatry | 29617515 | JAMA Psychiatry | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29617515 |
| 4D CONTINUOUS MEDIAL REPRESENTATION BY GEODESIC SHAPE REGRESSION. | Hong S, Fishbaugh J, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 29973975 | Proc IEEE Int Symp Biomed Imaging | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29973975 |
| Investigating the association between parity and the maternal neural response to infant cues. | Maupin AN, Rutherford HJV, Landi N, Potenza MN, Mayes LC | Social neuroscience | 29291661 | Soc Neurosci | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29291661 |
| Early brain development in infants at high risk for autism spectrum disorder. | Hazlett HC, Gu H, Munsell BC, Kim SH, Styner M, Wolff JJ, Elison JT, Swanson MR, Zhu H, Botteron KN, Collins DL, Constantino JN, Dager SR, Estes AM, Evans AC, Fonov VS, Gerig G, Kostopoulos P, McKinstry RC, Pandey J, Paterson S, Pruett JR, Schultz RT, Shaw DW, Zwaigenbaum L, Piven J, IBIS Network, Clinical Sites, Data Coordinating Center, Image Processing Core, Statistical Analysis | Nature | 28202961 | Nature | 2017 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/28202961 |
| OPTIMAL PARAMETER MAP ESTIMATION FOR SHAPE REPRESENTATION: A GENERATIVE APPROACH. | Elhabian SY, Agrawal P, Whitaker RT | Proceedings. IEEE International Symposium on Biomedical Imaging | 28090247 | Proc IEEE Int Symp Biomed Imaging | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28090247 |
| Geodesic shape regression with multiple geometries and sparse parameters. | Fishbaugh J, Durrleman S, Prastawa M, Gerig G | Medical image analysis | 28399476 | Med Image Anal | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28399476 |
| Subject-Specific Longitudinal Shape Analysis by Coupling Spatiotemporal Shape Modeling with Medial Analysis. | Hong S, Fishbaugh J, Rezanejad M, Siddiqi K, Johnson H, Paulsen J, Kim EY, Gerig G | Proceedings of SPIE--the International Society for Optical Engineering | 28966430 | Proc SPIE Int Soc Opt Eng | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28966430 |
| Traumatic Brain Injury Severity, Neuropathophysiology, and Clinical Outcome: Insights from Multimodal Neuroimaging. | Irimia A, Goh SM, Wade AC, Patel K, Vespa PM, Van Horn JD | Frontiers in neurology | 29051745 | Front Neurol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29051745 |
| Neural circuitry at age 6 months associated with later repetitive behavior and sensory responsiveness in autism. | Wolff JJ, Swanson MR, Elison JT, Gerig G, Pruett JR Jr, Styner MA, Vachet C, Botteron KN, Dager SR, Estes AM, Hazlett HC, Schultz RT, Shen MD, Zwaigenbaum L, Piven J, IBIS Network | Molecular autism | 28316772 | Mol Autism | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28316772 |
| Single-index varying coefficient model for functional responses. | Luo X, Zhu L, Zhu H | Biometrics | 27061414 | Biometrics | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27061414 |
| Influence of APOE Genotype on Hippocampal Atrophy over Time - An N=1925 Surface-Based ADNI Study. | Li B, Shi J, Gutman BA, Baxter LC, Thompson PM, Caselli RJ, Wang Y, Alzheimer’s Disease Neuroimaging Initiative | PloS one | 27065111 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27065111 |
| Multimodal Registration of White Matter Brain Data via Optimal Mass Transport. | Rehman T, Haber E, Pohl KM, Haker S, Halle M, Talos F, Wald LL, Kikinis R, Tannenbaum A | MIDAS journal | 28626844 | Midas J | 2008 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28626844 |
| Impact of aeration change and beam arrangement on the robustness of proton plans. | Shusharina N, Fullerton B, Adams JA, Sharp GC, Chan AW | Journal of applied clinical medical physics | 30756466 | J Appl Clin Med Phys | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30756466 |
| SlicerDMRI: Diffusion MRI and Tractography Research Software for Brain Cancer Surgery Planning and Visualization. | Zhang F, Noh T, Juvekar P, Frisken SF, Rigolo L, Norton I, Kapur T, Pujol S, Wells W 3rd, Yarmarkovich A, Kindlmann G, Wassermann D, San Jose Estepar R, Rathi Y, Kikinis R, Johnson HJ, Westin CF, Pieper S, Golby AJ, O'Donnell LJ | JCO clinical cancer informatics | 32216636 | JCO Clin Cancer Inform | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32216636 |
| Are early social communication skills a harbinger for language development in infants later diagnosed autistic?-A longitudinal study using a standardized social communication assessment. | Ravi S, Bradshaw A, Abdi H, Meera SS, Parish-Morris J, Yankowitz L, Paterson S, Dager SR, Burrows CA, Chappell C, St John T, Estes AM, Piven J, Swanson MR, IBIS Network | Frontiers in communication | 37168581 | Front Commun (Lausanne) | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37168581 |
| Adaptive Riemannian metrics for improved geodesic tracking of white matter. | Hao X, Whitaker RT, Fletcher PT | Information processing in medical imaging : proceedings of the ... conference | 21761642 | Inf Process Med Imaging | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21761642 |
| Diffusion tensor imaging of anterior commissural fibers in patients with schizophrenia. | Choi H, Kubicki M, Whitford TJ, Alvarado JL, Terry DP, Niznikiewicz M, McCarley RW, Kwon JS, Shenton ME | Schizophrenia research | 21561738 | Schizophr Res | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21561738 |
| Three-dimensional quantification of mandibular asymmetry through cone-beam computerized tomography. | Cevidanes LH, Alhadidi A, Paniagua B, Styner M, Ludlow J, Mol A, Turvey T, Proffit WR, Rossouw PE | Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics | 21497527 | Oral Surg Oral Med Oral Pathol Oral Radiol Endod | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21497527 |
| Estimation of smooth growth trajectories with controlled acceleration from time series shape data. | Fishbaugh J, Durrleman S, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 21995054 | Med Image Comput Comput Assist Interv | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21995054 |
| Clinical application of pharmacokinetic analysis as a biomarker of solitary pulmonary nodules: dynamic contrast-enhanced MR imaging. | Mamata H, Tokuda J, Gill RR, Padera RF, Lenkinski RE, Sugarbaker DJ, Butler JP, Hatabu H | Magnetic resonance in medicine | 22231729 | Magn Reson Med | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22231729 |
| Classification of astrocytomas and oligodendrogliomas from mass spectrometry data using sparse kernel machines. | Huang J, Gholami B, Agar NY, Norton I, Haddad WM, Tannenbaum AR | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22256188 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22256188 |
| Estimation of Myocardial Volume at Risk from CT Angiography. | Zhu L, Gao Y, Mohan V, Stillman A, Faber T, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 21572535 | Proc SPIE Int Soc Opt Eng | 2011 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/21572535 |
| Robust Feature Selection in Resting-State fMRI Connectivity Based on Population Studies. | Venkataraman A, Kubicki M, Westin CF, Golland P | Conference on Computer Vision and Pattern Recognition Workshops. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops | 21660131 | Conf Comput Vis Pattern Recognit Workshops | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21660131 |
| Lateral ventricle morphology analysis via mean latitude axis. | Paniagua B, Lyall A, Berger JB, Vachet C, Hamer RM, Woolson S, Lin W, Gilmore J, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 23606800 | Proc SPIE Int Soc Opt Eng | 2013 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/23606800 |
| Localized Statistics for DW-MRI Fiber Bundle Segmentation. | Lankton S, Melonakos J, Malcolm J, Dambreville S, Tannenbaum A | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 23652079 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/23652079 |
| Shape-Based Approach to Robust Image Segmentation using Kernel PCA. | Dambreville S, Rathi Y, Tannenbaum A | Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition | 23685633 | Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/23685633 |
| Morse-Smale Regression. | Gerber S, Rübel O, Bremer PT, Pascucci V, Whitaker RT | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 23687424 | J Comput Graph Stat | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23687424 |
| Joint CT/CBCT deformable registration and CBCT enhancement for cancer radiotherapy. | Lou Y, Niu T, Jia X, Vela PA, Zhu L, Tannenbaum AR | Medical image analysis | 23433756 | Med Image Anal | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23433756 |
| Dynamic Active Contours for Visual Tracking. | Niethammer M, Tannenbaum A, Angenent S | IEEE transactions on automatic control | 23729836 | IEEE Trans Automat Contr | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/23729836 |
| Increased gray matter diffusion anisotropy in patients with persistent post-concussive symptoms following mild traumatic brain injury. | Bouix S, Pasternak O, Rathi Y, Pelavin PE, Zafonte R, Shenton ME | PloS one | 23776631 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23776631 |
| Sparse texture active contour. | Gao Y, Bouix S, Shenton M, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 23799695 | IEEE Trans Image Process | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23799695 |
| Statistical shape modeling of cam femoroacetabular impingement. | Harris MD, Datar M, Whitaker RT, Jurrus ER, Peters CL, Anderson AE | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 23832798 | J Orthop Res | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23832798 |
| DTI Quality Control Assessment via Error Estimation From Monte Carlo Simulations. | Farzinfar M, Li Y, Verde AR, Oguz I, Gerig G, Styner MA | Proceedings of SPIE--the International Society for Optical Engineering | 23833547 | Proc SPIE Int Soc Opt Eng | 2013 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/23833547 |
| Localized differences in caudate and hippocampal shape are associated with schizophrenia but not antipsychotic type. | McClure RK, Styner M, Maltbie E, Lieberman JA, Gouttard S, Gerig G, Shi X, Zhu H | Psychiatry research | 23142194 | Psychiatry Res | 2013 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/23142194 |
| One-year assessment of surgical outcomes in Class III patients using cone beam computed tomography. | de Paula LK, Ruellas AC, Paniagua B, Styner M, Turvey T, Zhu H, Wang J, Cevidanes LH | International journal of oral and maxillofacial surgery | 23403336 | Int J Oral Maxillofac Surg | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23403336 |
| Common variants in psychiatric risk genes predict brain structure at birth. | Knickmeyer RC, Wang J, Zhu H, Geng X, Woolson S, Hamer RM, Konneker T, Lin W, Styner M, Gilmore JH | Cerebral cortex (New York, N.Y. : 1991) | 23283688 | Cereb Cortex | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/23283688 |
| A feature-based developmental model of the infant brain in structural MRI. | Toews M, Wells WM 3rd, Zöllei L | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286050 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286050 |
| Longitudinal image registration with non-uniform appearance change. | Csapo I, Davis B, Shi Y, Sanchez M, Styner M, Niethammer M | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286141 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286141 |
| Localizing the human primary auditory cortex in vivo using structural MRI. | Wasserthal C, Brechmann A, Stadler J, Fischl B, Engel K | NeuroImage | 23891882 | Neuroimage | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23891882 |
| Magnetic resonance microscopy-based analyses of the neuroanatomical effects of gestational day 9 ethanol exposure in mice. | Parnell SE, Holloway HT, O'Leary-Moore SK, Dehart DB, Paniaqua B, Oguz I, Budin F, Styner MA, Johnson GA, Sulik KK | Neurotoxicology and teratology | 23911654 | Neurotoxicol Teratol | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/23911654 |
| Shape abnormalities of the caudate nucleus correlate with poorer gait and balance: results from a subset of the LADIS study. | Macfarlane MD, Looi JC, Walterfang M, Spulber G, Velakoulis D, Styner M, Crisby M, Orndahl E, Erkinjuntti T, Waldemar G, Garde E, Hennerici MG, Bäzner H, Blahak C, Wallin A, Wahlund LO, LADIS Study Group | The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry | 23916546 | Am J Geriatr Psychiatry | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23916546 |
| Despeckling of medical ultrasound images. | Michailovich OV, Tannenbaum A | IEEE transactions on ultrasonics, ferroelectrics, and frequency control | 16471433 | IEEE Trans Ultrason Ferroelectr Freq Control | 2006 Jan | https://www.ncbi.nlm.nih.gov/pubmed/16471433 |
| Flux driven automatic centerline extraction. | Bouix S, Siddiqi K, Tannenbaum A | Medical image analysis | 15854842 | Med Image Anal | 2005 Jun | https://www.ncbi.nlm.nih.gov/pubmed/15854842 |
| Local white matter geometry from diffusion tensor gradients. | Savadjiev P, Kindlmann GL, Bouix S, Shenton ME, Westin CF | NeuroImage | 19896542 | Neuroimage | 2010 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/19896542 |
| Deform PF-MT: particle filter with mode tracker for tracking nonaffine contour deformations. | Vaswani N, Rathi Y, Yezzi A, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 19933014 | IEEE Trans Image Process | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19933014 |
| Genetic and environmental contributions to neonatal brain structure: A twin study. | Gilmore JH, Schmitt JE, Knickmeyer RC, Smith JK, Lin W, Styner M, Gerig G, Neale MC | Human brain mapping | 20063301 | Hum Brain Mapp | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20063301 |
| DT-REFinD: diffusion tensor registration with exact finite-strain differential. | Yeo BT, Vercauteren T, Fillard P, Peyrat JM, Pennec X, Golland P, Ayache N, Clatz O | IEEE transactions on medical imaging | 19556193 | IEEE Trans Med Imaging | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19556193 |
| Functional and anatomical connectivity abnormalities in left inferior frontal gyrus in schizophrenia. | Jeong B, Wible CG, Hashimoto R, Kubicki M | Human brain mapping | 19569073 | Hum Brain Mapp | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19569073 |
| A Bayesian mixture approach to modeling spatial activation patterns in multisite fMRI data. | Kim S, Smyth P, Stern H | IEEE transactions on medical imaging | 20304727 | IEEE Trans Med Imaging | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20304727 |
| VARIABLE SELECTION FOR REGRESSION MODELS WITH MISSING DATA. | Garcia RI, Ibrahim JG, Zhu H | Statistica Sinica | 20336190 | Stat Sin | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20336190 |
| Combining spatial priors and anatomical information for fMRI detection. | Ou W, Wells WM 3rd, Golland P | Medical image analysis | 20362488 | Med Image Anal | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20362488 |
| Age-related decline in white matter tract integrity and cognitive performance: a DTI tractography and structural equation modeling study. | Voineskos AN, Rajji TK, Lobaugh NJ, Miranda D, Shenton ME, Kennedy JL, Pollock BG, Mulsant BH | Neurobiology of aging | 20363050 | Neurobiol Aging | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20363050 |
| Three-dimensional assessment of mandibular advancement 1 year after surgery. | Carvalho Fde A, Cevidanes LH, da Motta AT, Almeida MA, Phillips C | American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics | 20381760 | Am J Orthod Dentofacial Orthop | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20381760 |
| Atlas-based improved prediction of magnetic field inhomogeneity for distortion correction of EPI data. | Poynton C, Jenkinson M, Wells W 3rd | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426203 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426203 |
| Cortical correspondence with probabilistic fiber connectivity. | Oguz I, Niethammer M, Cates J, Whitaker R, Fletcher T, Vachet C, Styner M | Information processing in medical imaging : proceedings of the ... conference | 19694301 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694301 |
| Improved tractography alignment using combined volumetric and surface registration. | Zöllei L, Stevens A, Huber K, Kakunoori S, Fischl B | NeuroImage | 20153833 | Neuroimage | 2010 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/20153833 |
| Trajectory control of PbSe-gamma-Fe2O3 nanoplatforms under viscous flow and an external magnetic field. | Etgar L, Nakhmani A, Tannenbaum A, Lifshitz E, Tannenbaum R | Nanotechnology | 20368678 | Nanotechnology | 2010 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/20368678 |
| Quantification of condylar resorption in temporomandibular joint osteoarthritis. | Cevidanes LH, Hajati AK, Paniagua B, Lim PF, Walker DG, Palconet G, Nackley AG, Styner M, Ludlow JB, Zhu H, Phillips C | Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics | 20382043 | Oral Surg Oral Med Oral Pathol Oral Radiol Endod | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20382043 |
| Imaging of meningioma progression by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. | Agar NY, Malcolm JG, Mohan V, Yang HW, Johnson MD, Tannenbaum A, Agar JN, Black PM | Analytical chemistry | 20196536 | Anal Chem | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20196536 |
| Multimodal functional imaging using fMRI-informed regional EEG/MEG source estimation. | Ou W, Nummenmaa A, Ahveninen J, Belliveau JW, Hämäläinen MS, Golland P | NeuroImage | 20211266 | Neuroimage | 2010 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/20211266 |
| Agitation and pain assessment using digital imaging. | Gholami B, Haddad WM, Tannenbaum AR | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 19963539 | Annu Int Conf IEEE Eng Med Biol Soc | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19963539 |
| The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis. | Kapur T, Pieper S, Whitaker R, Aylward S, Jakab M, Schroeder W, Kikinis R | Journal of the American Medical Informatics Association : JAMIA | 22081219 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22081219 |
| Fast shape-based nearest-neighbor search for brain MRIs using hierarchical feature matching. | Zhu P, Awate SP, Gerber S, Whitaker R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 21995064 | Med Image Comput Comput Assist Interv | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21995064 |
| FreeSurfer. | Fischl B | NeuroImage | 22248573 | Neuroimage | 2012 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/22248573 |
| Ranking of stopping criteria for log domain diffeomorphic demons application in clinical radiation therapy. | Peroni M, Golland P, Sharp GC, Baroni G | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255433 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22255433 |
| 3-T MR-guided brachytherapy for gynecologic malignancies. | Kapur T, Egger J, Damato A, Schmidt EJ, Viswanathan AN | Magnetic resonance imaging | 22898699 | Magn Reson Imaging | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22898699 |
| Differences in white matter fiber tract development present from 6 to 24 months in infants with autism. | Wolff JJ, Gu H, Gerig G, Elison JT, Styner M, Gouttard S, Botteron KN, Dager SR, Dawson G, Estes AM, Evans AC, Hazlett HC, Kostopoulos P, McKinstry RC, Paterson SJ, Schultz RT, Zwaigenbaum L, Piven J, IBIS Network | The American journal of psychiatry | 22362397 | Am J Psychiatry | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22362397 |
| Self-crossing detection and location for parametric active contours. | Nakhmani A, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 22374361 | IEEE Trans Image Process | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22374361 |
| Prenatal isolated mild ventriculomegaly is associated with persistent ventricle enlargement at ages 1 and 2. | Lyall AE, Woolson S, Wolfe HM, Goldman BD, Reznick JS, Hamer RM, Lin W, Styner M, Gerig G, Gilmore JH | Early human development | 22445211 | Early Hum Dev | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22445211 |
| An image analysis toolbox for high-throughput C. elegans assays. | Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O'Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE | Nature methods | 22522656 | Nat Methods | 2012 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/22522656 |
| Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury. | Irimia A, Chambers MC, Torgerson CM, Filippou M, Hovda DA, Alger JR, Gerig G, Toga AW, Vespa PM, Kikinis R, Van Horn JD | Frontiers in neurology | 22363313 | Front Neurol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22363313 |
| Integration of the OpenIGTLink network protocol for image-guided therapy with the medical platform MeVisLab. | Egger J, Tokuda J, Chauvin L, Freisleben B, Nimsky C, Kapur T, Wells W | The international journal of medical robotics + computer assisted surgery : MRCAS | 22374845 | Int J Med Robot | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22374845 |
| Filtering in the diffeomorphism group and the registration of point sets. | Gao Y, Rathi Y, Bouix S, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 22752129 | IEEE Trans Image Process | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22752129 |
| 3D Slicer as an image computing platform for the Quantitative Imaging Network. | Fedorov A, Beichel R, Kalpathy-Cramer J, Finet J, Fillion-Robin JC, Pujol S, Bauer C, Jennings D, Fennessy F, Sonka M, Buatti J, Aylward S, Miller JV, Pieper S, Kikinis R | Magnetic resonance imaging | 22770690 | Magn Reson Imaging | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22770690 |
| Adaptive prior probability and spatial temporal intensity change estimation for segmentation of the one-year-old human brain. | Kim SH, Fonov VS, Dietrich C, Vachet C, Hazlett HC, Smith RG, Graves MM, Piven J, Gilmore JH, Dager SR, McKinstry RC, Paterson S, Evans AC, Collins DL, Gerig G, Styner MA, IBIS network | Journal of neuroscience methods | 23032117 | J Neurosci Methods | 2013 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/23032117 |
| Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline. | Wang J, Vachet C, Rumple A, Gouttard S, Ouziel C, Perrot E, Du G, Huang X, Gerig G, Styner M | Frontiers in neuroinformatics | 24567717 | Front Neuroinform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24567717 |
| Joint modeling of imaging and genetics. | Batmanghelich NK, Dalca AV, Sabuncu MR, Polina G, ADNI | Information processing in medical imaging : proceedings of the ... conference | 24684016 | Inf Process Med Imaging | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24684016 |
| Stable Atlas-based Mapped Prior (STAMP) machine-learning segmentation for multicenter large-scale MRI data. | Kim EY, Magnotta VA, Liu D, Johnson HJ | Magnetic resonance imaging | 24818817 | Magn Reson Imaging | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24818817 |
| FMEM: functional mixed effects modeling for the analysis of longitudinal white matter Tract data. | Yuan Y, Gilmore JH, Geng X, Martin S, Chen K, Wang JL, Zhu H | NeuroImage | 24076225 | Neuroimage | 2014 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/24076225 |
| Automated skin segmentation in ultrasonic evaluation of skin toxicity in breast cancer radiotherapy. | Gao Y, Tannenbaum A, Chen H, Torres M, Yoshida E, Yang X, Wang Y, Curran W, Liu T | Ultrasound in medicine & biology | 23993172 | Ultrasound Med Biol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23993172 |
| A Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury. | Wang B, Prastawa M, Irimia A, Chambers MC, Vespa PM, Van Horn JD, Gerig G | Proceedings of SPIE--the International Society for Optical Engineering | 24465115 | Proc SPIE Int Soc Opt Eng | 2012 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/24465115 |
| Towards Analysis of Growth Trajectory through Multi-modal Longitudinal MR Imaging. | Sadeghi N, Prastawa M, Gilmore JH, Lin W, Gerig G | Proceedings of SPIE--the International Society for Optical Engineering | 24353376 | Proc SPIE Int Soc Opt Eng | 2010 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/24353376 |
| Particle Filters and Occlusion Handling for Rigid 2D-3D Pose Tracking. | Lee J, Sandhu R, Tannenbaum A | Computer vision and image understanding : CVIU | 24058277 | Comput Vis Image Underst | 2013 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/24058277 |
| Electroencephalographic inverse localization of brain activity in acute traumatic brain injury as a guide to surgery, monitoring and treatment. | Irimia A, Goh SY, Torgerson CM, Stein NR, Chambers MC, Vespa PM, Van Horn JD | Clinical neurology and neurosurgery | 24011495 | Clin Neurol Neurosurg | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24011495 |
| UNC-Utah NA-MIC DTI framework: Atlas Based Fiber Tract Analysis with Application to a Study of Nicotine Smoking Addiction. | Verde AR, Berger JB, Gupta A, Farzinfar M, Kaiser A, Chanon VW, Boettiger C, Goodlett C, Shi Y, Zhu H, Gerig G, Gouttard S, Vachet C, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24386543 | Proc SPIE Int Soc Opt Eng | 2013 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24386543 |
| UNC-Utah NA-MIC framework for DTI fiber tract analysis. | Verde AR, Budin F, Berger JB, Gupta A, Farzinfar M, Kaiser A, Ahn M, Johnson H, Matsui J, Hazlett HC, Sharma A, Goodlett C, Shi Y, Gouttard S, Vachet C, Piven J, Zhu H, Gerig G, Styner M | Frontiers in neuroinformatics | 24409141 | Front Neuroinform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24409141 |
| Evaluation of DTI Property Maps as Basis of DTI Atlas Building. | Liu Z, Goodlett C, Gerig G, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24353377 | Proc SPIE Int Soc Opt Eng | 2010 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/24353377 |
| Changes of MR and DTI appearance in early human brain development. | Marc C, Vachet C, Gerig G, Blocher J, Gilmore J, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 24353378 | Proc SPIE Int Soc Opt Eng | 2010 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/24353378 |
| Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. | Hershkovitz E, Tannenbaum E, Howerton SB, Sheth A, Tannenbaum A, Williams LD | Nucleic acids research | 14576313 | Nucleic Acids Res | 2003 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/14576313 |
| Model-based segmentation of hippocampal subfields in ultra-high resolution in vivo MRI. | Van Leemput K, Bakkour A, Benner T, Wiggins G, Wald LL, Augustinack J, Dickerson BC, Golland P, Fischl B | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979753 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979753 |
| Spherical demons: fast surface registration. | Yeo BT, Sabuncu M, Vercauteren T, Ayache N, Fischl B, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979813 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979813 |
| Introduction to the special section on computer vision for intravascular and intracardiac imaging. | Unal G, Slabaugh G, Kakadiaris IA, Tannenbaum A | IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society | 18693494 | IEEE Trans Inf Technol Biomed | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18693494 |
| Near-tubular fiber bundle segmentation for diffusion weighted imaging: segmentation through frame reorientation. | Niethammer M, Zach C, Melonakos J, Tannenbaum A | NeuroImage | 19101640 | Neuroimage | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19101640 |
| Choice of in vivo versus idealized velocity boundary conditions influences physiologically relevant flow patterns in a subject-specific simulation of flow in the human carotid bifurcation. | Wake AK, Oshinski JN, Tannenbaum AR, Giddens DP | Journal of biomechanical engineering | 19102572 | J Biomech Eng | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19102572 |
| Tract-based morphometry for white matter group analysis. | O'Donnell LJ, Westin CF, Golby AJ | NeuroImage | 19154790 | Neuroimage | 2009 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/19154790 |
| Group analysis of DTI fiber tract statistics with application to neurodevelopment. | Goodlett CB, Fletcher PT, Gilmore JH, Gerig G | NeuroImage | 19059345 | Neuroimage | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19059345 |
| Shape abnormalities of caudate nucleus in schizotypal personality disorder. | Levitt JJ, Styner M, Niethammer M, Bouix S, Koo MS, Voglmaier MM, Dickey CC, Niznikiewicz MA, Kikinis R, McCarley RW, Shenton ME | Schizophrenia research | 19328654 | Schizophr Res | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19328654 |
| Focal reversible deactivation of cerebral metabolism affects water diffusion. | Khachaturian MH, Arsenault J, Ekstrom LB, Tuch DS, Vanduffel W | Magnetic resonance in medicine | 18958855 | Magn Reson Med | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18958855 |
| An integrated system for planning, navigation and robotic assistance for skull base surgery. | Xia T, Baird C, Jallo G, Hayes K, Nakajima N, Hata N, Kazanzides P | The international journal of medical robotics + computer assisted surgery : MRCAS | 18803337 | Int J Med Robot | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18803337 |
| Shape analysis with overcomplete spherical wavelets. | Yeo BT, Yu P, Grant PE, Fischl B, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979780 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979780 |
| Group statistics of DTI fiber bundles using spatial functions of tensor measures. | Goodlett CB, Fletcher PT, Gilmore JH, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979851 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979851 |
| Predicting the location of entorhinal cortex from MRI. | Fischl B, Stevens AA, Rajendran N, Yeo BT, Greve DN, Van Leemput K, Polimeni JR, Kakunoori S, Buckner RL, Pacheco J, Salat DH, Melcher J, Frosch MP, Hyman BT, Grant PE, Rosen BR, van der Kouwe AJ, Wiggins GC, Wald LL, Augustinack JC | NeuroImage | 19376238 | Neuroimage | 2009 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/19376238 |
| Target-specific contrast agents for magnetic resonance microscopy. | Blackwell ML, Farrar CT, Fischl B, Rosen BR | NeuroImage | 19385012 | Neuroimage | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19385012 |
| A cooperatively-controlled image guided robot system for skull base surgery. | Kazanzides P, Xia T, Baird C, Jallo G, Hayes K, Nakajima N, Hata N | Studies in health technology and informatics | 18391286 | Stud Health Technol Inform | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18391286 |
| Segmentation of tracking sequences using dynamically updated adaptive learning. | Michailovich O, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 19004712 | IEEE Trans Image Process | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19004712 |
| Joint segmentation of thalamic nuclei from a population of diffusion tensor MR images. | Ziyan U, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979758 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979758 |
| Findings in schizophrenia by tract-oriented DT-MRI analysis. | Maddah M, Kubicki M, Wells WM, Westin CF, Shenton ME, Grimson WE | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18979833 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18979833 |
| Label space: a coupled multi-shape representation. | Malcolm J, Rathi Y, Shenton ME, Tannenbaum A | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18982632 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18982632 |
| Feasibility of multi-site clinical structural neuroimaging studies of aging using legacy data. | Fennema-Notestine C, Gamst AC, Quinn BT, Pacheco J, Jernigan TL, Thal L, Buckner R, Killiany R, Blacker D, Dale AM, Fischl B, Dickerson B, Gollub RL | Neuroinformatics | 17999200 | Neuroinformatics | 2007 Winter | https://www.ncbi.nlm.nih.gov/pubmed/17999200 |
| Accurate prediction of V1 location from cortical folds in a surface coordinate system. | Hinds OP, Rajendran N, Polimeni JR, Augustinack JC, Wiggins G, Wald LL, Diana Rosas H, Potthast A, Schwartz EL, Fischl B | NeuroImage | 18055222 | Neuroimage | 2008 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/18055222 |
| On the construction of invertible filter banks on the 2-sphere. | Yeo BT, Ou W, Golland P | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 18270119 | IEEE Trans Image Process | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18270119 |
| Fiber bundle estimation and parameterization. | Niethammer M, Bouix S, Westin CF, Shenton ME | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354779 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354779 |
| Improved correspondence for DTI population studies via unbiased atlas building. | Goodlett C, Davis B, Jean R, Gilmore J, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354780 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354780 |
| A method for registering diffusion weighted magnetic resonance images. | Tao X, Miller JV | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354821 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354821 |
| Interictal alterations of the trigeminal somatosensory pathway and periaqueductal gray matter in migraine. | DaSilva AF, Granziera C, Tuch DS, Snyder J, Vincent M, Hadjikhani N | Neuroreport | 17435592 | Neuroreport | 2007 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/17435592 |
| An MRI-based method for measuring volume, thickness and surface area of entorhinal, perirhinal, and posterior parahippocampal cortex. | Feczko E, Augustinack JC, Fischl B, Dickerson BC | Neurobiology of aging | 17850926 | Neurobiol Aging | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17850926 |
| Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area. | Dickerson BC, Feczko E, Augustinack JC, Pacheco J, Morris JC, Fischl B, Buckner RL | Neurobiology of aging | 17869384 | Neurobiol Aging | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/17869384 |
| Apathy and the processing of novelty in schizophrenia. | Roth RM, Koven NS, Pendergrass JC, Flashman LA, McAllister TW, Saykin AJ | Schizophrenia research | 17884352 | Schizophr Res | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17884352 |
| Early postnatal development of corpus callosum and corticospinal white matter assessed with quantitative tractography. | Gilmore JH, Lin W, Corouge I, Vetsa YS, Smith JK, Kang C, Gu H, Hamer RM, Lieberman JA, Gerig G | AJNR. American journal of neuroradiology | 17923457 | AJNR Am J Neuroradiol | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17923457 |
| Phase maps reveal cortical architecture. | Fischl B, Wald LL | Proceedings of the National Academy of Sciences of the United States of America | 17609374 | Proc Natl Acad Sci U S A | 2007 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/17609374 |
| Heritability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study. | Goldman AL, Pezawas L, Mattay VS, Fischl B, Verchinski BA, Zoltick B, Weinberger DR, Meyer-Lindenberg A | Biological psychiatry | 17727823 | Biol Psychiatry | 2008 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/17727823 |
| Atlas stratification. | Blezek DJ, Miller JV | Medical image analysis | 17765003 | Med Image Anal | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17765003 |
| Cortical folding patterns and predicting cytoarchitecture. | Fischl B, Rajendran N, Busa E, Augustinack J, Hinds O, Yeo BT, Mohlberg H, Amunts K, Zilles K | Cerebral cortex (New York, N.Y. : 1991) | 18079129 | Cereb Cortex | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18079129 |
| Finsler active contours. | Melonakos J, Pichon E, Angenent S, Tannenbaum A | IEEE transactions on pattern analysis and machine intelligence | 18195436 | IEEE Trans Pattern Anal Mach Intell | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18195436 |
| On diffusion tensor estimation. | Niethammer M, San Jose Estepar R, Bouix S, Shenton M, Westin CF | Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference | 17946125 | Conf Proc IEEE Eng Med Biol Soc | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17946125 |
| Active mean fields: solving the mean field approximation in the level set framework. | Pohl KM, Kikinis R, Wells WM | Information processing in medical imaging : proceedings of the ... conference | 17633686 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633686 |
| Nonlinear registration of diffusion MR images based on fiber bundles. | Ziyan U, Sabuncu MR, O'Donnell LJ, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051078 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051078 |
| MR-guided prostate interventions. | Tempany C, Straus S, Hata N, Haker S | Journal of magnetic resonance imaging : JMRI | 18219689 | J Magn Reson Imaging | 2008 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18219689 |
| Two methods for validating brain tissue classifiers. | Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685885 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685885 |
| Mass preserving registration for heart MR images. | Zhu L, Haker S, Tannenbaum A | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685954 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685954 |
| Middle and inferior temporal gyrus gray matter volume abnormalities in first-episode schizophrenia: an MRI study. | Kuroki N, Shenton ME, Salisbury DF, Hirayasu Y, Onitsuka T, Ersner-Hershfield H, Yurgelun-Todd D, Kikinis R, Jolesz FA, McCarley RW | The American journal of psychiatry | 17151161 | Am J Psychiatry | 2006 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17151161 |
| Longitudinal in vivo reproducibility of cartilage volume and surface in osteoarthritis of the knee. | Brem MH, Pauser J, Yoshioka H, Brenning A, Stratmann J, Hennig FF, Kikinis R, Duryea J, Winalski CS, Lang P | Skeletal radiology | 17219231 | Skeletal Radiol | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17219231 |
| Rician noise removal in diffusion tensor MRI. | Basu S, Fletcher T, Whitaker R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354881 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354881 |
| Hippocampal volume and shape analysis in an older adult population. | McHugh TL, Saykin AJ, Wishart HA, Flashman LA, Cleavinger HB, Rabin LA, Mamourian AC, Shen L | The Clinical neuropsychologist | 17366281 | Clin Neuropsychol | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17366281 |
| Statistical group comparison of diffusion tensors via multivariate hypothesis testing. | Whitcher B, Wisco JJ, Hadjikhani N, Tuch DS | Magnetic resonance in medicine | 17534902 | Magn Reson Med | 2007 Jun | https://www.ncbi.nlm.nih.gov/pubmed/17534902 |
| Frontal connections and cognitive changes in normal aging rhesus monkeys: a DTI study. | Makris N, Papadimitriou GM, van der Kouwe A, Kennedy DN, Hodge SM, Dale AM, Benner T, Wald LL, Wu O, Tuch DS, Caviness VS, Moore TL, Killiany RJ, Moss MB, Rosene DL | Neurobiology of aging | 16962214 | Neurobiol Aging | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/16962214 |
| Hippocampal degeneration is associated with temporal and limbic gray matter/white matter tissue contrast in Alzheimer's disease. | Salat DH, Chen JJ, van der Kouwe AJ, Greve DN, Fischl B, Rosas HD | NeuroImage | 20965261 | Neuroimage | 2011 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/20965261 |
| Visual exploration of high dimensional scalar functions. | Gerber S, Bremer PT, Pascucci V, Whitaker R | IEEE transactions on visualization and computer graphics | 20975167 | IEEE Trans Vis Comput Graph | 2010 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/20975167 |
| Three-dimensional surgical simulation. | Cevidanes LH, Tucker S, Styner M, Kim H, Chapuis J, Reyes M, Proffit W, Turvey T, Jaskolka M | American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics | 20816308 | Am J Orthod Dentofacial Orthop | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20816308 |
| Joint generative model for fMRI/DWI and its application to population studies. | Venkataraman A, Rathi Y, Kubicki M, Westin CF, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879231 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879231 |
| Biomarkers for identifying first-episode schizophrenia patients using diffusion weighted imaging. | Rathi Y, Malcolm J, Michailovich O, Goldstein J, Seidman L, McCarley RW, Westin CF, Shenton ME | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879287 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879287 |
| A geometry-based particle filtering approach to white matter tractography. | Savadjiev P, Rathi Y, Malcolm JG, Shenton ME, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879320 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879320 |
| Image registration driven by combined probabilistic and geometric descriptors. | Ha L, Prastawa M, Gerig G, Gilmore JH, Silva CT, Joshi S | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879365 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879365 |
| A Geometric Approach to Joint 2D Region-Based Segmentation and 3D Pose Estimation Using a 3D Shape Prior. | Dambreville S, Sandhu R, Yezzi A, Tannenbaum A | SIAM journal on imaging sciences | 20613886 | SIAM J Imaging Sci | 2010 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/20613886 |
| Soft tissue response to mandibular advancement using 3D CBCT scanning. | Almeida RC, Cevidanes LH, Carvalho FA, Motta AT, Almeida MA, Styner M, Turvey T, Proffit WR, Phillips C | International journal of oral and maxillofacial surgery | 21208782 | Int J Oral Maxillofac Surg | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21208782 |
| Structural neuroimaging in schizophrenia: from methods to insights to treatments. | Shenton ME, Whitford TJ, Kubicki M | Dialogues in clinical neuroscience | 20954428 | Dialogues Clin Neurosci | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20954428 |
| Image registration of pre-procedural MRI and intra-procedural CT images to aid CT-guided percutaneous cryoablation of renal tumors. | Oguro S, Tuncali K, Elhawary H, Morrison PR, Hata N, Silverman SG | International journal of computer assisted radiology and surgery | 20499194 | Int J Comput Assist Radiol Surg | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20499194 |
| Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. | Destrieux C, Fischl B, Dale A, Halgren E | NeuroImage | 20547229 | Neuroimage | 2010 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/20547229 |
| Robust automated constellation-based landmark detection in human brain imaging. | Ghayoor A, Vaidya JG, Johnson HJ | NeuroImage | 28392490 | Neuroimage | 2018 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/28392490 |
| SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. | Norton I, Essayed W, Zhang F, Pujol S, Yarmarkovich A, Golby AJ, Kindlmann G, Wassermann D, Estepar RSJ, Rathi Y, Pieper S, Kikinis R, Johnson HJ, Westin CF, O'Donnell LJ | Cancer research | 29092950 | Cancer Res | 2017 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/29092950 |
| Transformations Based on Continuous Piecewise-Affine Velocity Fields. | Freifeld O, Hauberg S, Batmanghelich K, Fisher JW | IEEE transactions on pattern analysis and machine intelligence | 28092517 | IEEE Trans Pattern Anal Mach Intell | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28092517 |
| A Likelihood-Free Approach for Characterizing Heterogeneous Diseases in Large-Scale Studies. | Schabdach J, Wells WM 3rd, Cho M, Batmanghelich KN | Information processing in medical imaging : proceedings of the ... conference | 29129964 | Inf Process Med Imaging | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29129964 |
| Shape Based Segmentation of Anatomical Structures in Magnetic Resonance Images. | Pohl KM, Fisher J, Kikinis R, Grimson WEL, Wells WM | Computer vision for biomedical image applications : first international workshop, CVBIA 2005, Beijing, China, October 21, 2005 : proceedings. CVBIA 2005 (2005 : Beijing, China) | 28664197 | Comput Vis Biomed Image Appl (2005) | 2005 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28664197 |
| UNC-Emory Infant Atlases for Macaque Brain Image Analysis: Postnatal Brain Development through 12 Months. | Shi Y, Budin F, Yapuncich E, Rumple A, Young JT, Payne C, Zhang X, Hu X, Godfrey J, Howell B, Sanchez MM, Styner MA | Frontiers in neuroscience | 28119564 | Front Neurosci | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28119564 |
| Dictionary Pruning with Visual Word Significance for Medical Image Retrieval. | Zhang F, Song Y, Cai W, Hauptmann AG, Liu S, Pujol S, Kikinis R, Fulham MJ, Feng DD, Chen M | Neurocomputing | 27688597 | Neurocomputing (Amst) | 2016 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/27688597 |
| Group-wise Shape Correspondence of Variable and Complex Objects. | Lyu I, Perdomo J, Yapuncich GS, Paniagua B, Boyer DM, Styner MA | Proceedings of SPIE--the International Society for Optical Engineering | 30381780 | Proc SPIE Int Soc Opt Eng | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30381780 |
| Cross-View Neuroimage Pattern Analysis in Alzheimer's Disease Staging. | Liu S, Cai W, Pujol S, Kikinis R, Feng DD, Alzheimer's Disease Neuroimaging Initiative | Frontiers in aging neuroscience | 26941639 | Front Aging Neurosci | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26941639 |
| Non-Euclidean classification of medically imaged objects via s-reps. | Hong J, Vicory J, Schulz J, Styner M, Marron JS, Pizer SM | Medical image analysis | 26963609 | Med Image Anal | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26963609 |
| 3T MR-guided in-bore transperineal prostate biopsy: A comparison of robotic and manual needle-guidance templates. | Tilak G, Tuncali K, Song SE, Tokuda J, Olubiyi O, Fennessy F, Fedorov A, Penzkofer T, Tempany C, Hata N | Journal of magnetic resonance imaging : JMRI | 25263213 | J Magn Reson Imaging | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25263213 |
| A Framework for Joint Image-and-Shape Analysis. | Gao Y, Tannenbaum A, Bouix S | Proceedings of SPIE--the International Society for Optical Engineering | 25302006 | Proc SPIE Int Soc Opt Eng | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/25302006 |
| Gaussian process interpolation for uncertainty estimation in image registration. | Wachinger C, Golland P, Reuter M, Wells W | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 25333127 | Med Image Comput Comput Assist Interv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25333127 |
| Preliminary analysis using multi-atlas labeling algorithms for tracing longitudinal change. | Kim RE, Lourens S, Long JD, Paulsen JS, Johnson HJ | Frontiers in neuroscience | 26236182 | Front Neurosci | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26236182 |
| Robust Atlas-Based Segmentation of Highly Variable Anatomy: Left Atrium Segmentation. | Depa M, Sabuncu MR, Holmvang G, Nezafat R, Schmidt EJ, Golland P | Statistical atlases and computational models of the heart. STACOM (Workshop) | 26090522 | Stat Atlases Comput Models Heart | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/26090522 |
| Generative Method to Discover Genetically Driven Image Biomarkers. | Batmanghelich NK, Saeedi A, Cho M, Estepar RS, Golland P | Information processing in medical imaging : proceedings of the ... conference | 26221665 | Inf Process Med Imaging | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26221665 |
| Prenatal cocaine effects on brain structure in early infancy. | Grewen K, Burchinal M, Vachet C, Gouttard S, Gilmore JH, Lin W, Johns J, Elam M, Gerig G | NeuroImage | 24999039 | Neuroimage | 2014 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/24999039 |
| A framework for longitudinal data analysis via shape regression. | Fishbaugh J, Durrleman S, Piven J, Gerig G | Proceedings of SPIE--the International Society for Optical Engineering | 24392201 | Proc SPIE Int Soc Opt Eng | 2012 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/24392201 |
| Detecting epileptic regions based on global brain connectivity patterns. | Sweet A, Venkataraman A, Stufflebeam SM, Liu H, Tanaka N, Madsen J, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 24505654 | Med Image Comput Comput Assist Interv | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24505654 |
| Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. | Pernelle G, Mehrtash A, Barber L, Damato A, Wang W, Seethamraju RT, Schmidt E, Cormack RA, Wells W, Viswanathan A, Kapur T | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 24505784 | Med Image Comput Comput Assist Interv | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24505784 |
| A PRELIMINARY STUDY ON THE EFFECT OF MOTION CORRECTION ON HARDI RECONSTRUCTION. | Elhabian S, Gur Y, Vachet C, Piven J, Styner M, Leppert I, Pike GB, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 25356195 | Proc IEEE Int Symp Biomed Imaging | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25356195 |
| Diffeomorphic shape trajectories for improved longitudinal segmentation and statistics. | Muralidharan P, Fishbaugh J, Johnson HJ, Durrleman S, Paulsen JS, Gerig G, Fletcher PT | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 25320781 | Med Image Comput Comput Assist Interv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25320781 |
| OpenIGTLink interface for state control and visualisation of a robot for image-guided therapy systems. | Tauscher S, Tokuda J, Schreiber G, Neff T, Hata N, Ortmaier T | International journal of computer assisted radiology and surgery | 24923473 | Int J Comput Assist Radiol Surg | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24923473 |
| Social subordination alters estradiol-induced changes in cortico-limbic brain volumes in adult female rhesus monkeys. | Reding KM, Styner MM, Wilson ME, Toufexis D, Sanchez MM | Psychoneuroendocrinology | 32023501 | Psychoneuroendocrinology | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32023501 |
| SPReM: Sparse Projection Regression Model For High-dimensional Linear Regression. | Sun Q, Zhu H, Liu Y, Ibrahim JG, Alzheimer’;s Disease Neuroimaging Initiative | Journal of the American Statistical Association | 26527844 | J Am Stat Assoc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26527844 |
| Using 3D Modeling Techniques to Enhance Teaching of Difficult Anatomical Concepts. | Pujol S, Baldwin M, Nassiri J, Kikinis R, Shaffer K | Academic radiology | 26897601 | Acad Radiol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26897601 |
| Apathy Is Associated With Ventral Striatum Volume in Schizophrenia Spectrum Disorder. | Roth RM, Garlinghouse MA, Flashman LA, Koven NS, Pendergrass JC, Ford JC, McAllister TW, Saykin AJ | The Journal of neuropsychiatry and clinical neurosciences | 26900738 | J Neuropsychiatry Clin Neurosci | 2016 Summer | https://www.ncbi.nlm.nih.gov/pubmed/26900738 |
| Parental reflective functioning and the neural correlates of processing infant affective cues. | Rutherford HJV, Maupin AN, Landi N, Potenza MN, Mayes LC | Social neuroscience | 27253222 | Soc Neurosci | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27253222 |
| Epileptogenic focus localization in treatment-resistant post-traumatic epilepsy. | Irimia A, Van Horn JD | Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia | 25542591 | J Clin Neurosci | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25542591 |
| The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS). | Menze BH, Jakab A, Bauer S, Kalpathy-Cramer J, Farahani K, Kirby J, Burren Y, Porz N, Slotboom J, Wiest R, Lanczi L, Gerstner E, Weber MA, Arbel T, Avants BB, Ayache N, Buendia P, Collins DL, Cordier N, Corso JJ, Criminisi A, Das T, Delingette H, Demiralp Ç, Durst CR, Dojat M, Doyle S, Festa J, Forbes F, Geremia E, Glocker B, Golland P, Guo X, Hamamci A, Iftekharuddin KM, Jena R, John NM, Konukoglu E, Lashkari D, Mariz JA, Meier R, Pereira S, Precup D, Price SJ, Raviv TR, Reza SM, Ryan M, Sarikaya D, Schwartz L, Shin HC, Shotton J, Silva CA, Sousa N, Subbanna NK, Szekely G, Taylor TJ, Thomas OM, Tustison NJ, Unal G, Vasseur F, Wintermark M, Ye DH, Zhao L, Zhao B, Zikic D, Prastawa M, Reyes M, Van Leemput K | IEEE transactions on medical imaging | 25494501 | IEEE Trans Med Imaging | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25494501 |
| Attentional Control and Intelligence: MRI Orbital Frontal Gray Matter and Neuropsychological Correlates. | Nestor PG, Nakamura M, Niznikiewicz M, Levitt JJ, Newell DT, Shenton ME, McCarley RW | Behavioural neurology | 26101457 | Behav Neurol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26101457 |
| Towards measuring neuroimage misalignment. | Garlapati RR, Mostayed A, Joldes GR, Wittek A, Doyle B, Miller K | Computers in biology and medicine | 26112607 | Comput Biol Med | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26112607 |
| Convex Clustering with Exemplar-Based Models. | Lashkari D, Golland P | Advances in neural information processing systems | 26140013 | Adv Neural Inf Process Syst | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/26140013 |
| Bayesian Case-deletion Model Complexity and Information Criterion. | Zhu H, Ibrahim JG, Chen Q | Statistics and its interface | 26180578 | Stat Interface | 2014 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/26180578 |
| Contour-Driven Atlas-Based Segmentation. | Wachinger C, Fritscher K, Sharp G, Golland P | IEEE transactions on medical imaging | 26068202 | IEEE Trans Med Imaging | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26068202 |
| Spatial Patterns and Functional Profiles for Discovering Structure in fMRI Data. | Golland P, Lashkari D, Venkataraman A | Conference record. Asilomar Conference on Signals, Systems & Computers | 26082607 | Conf Rec Asilomar Conf Signals Syst Comput | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26082607 |
| What Data to Co-register for Computing Atlases. | Yeo BT, Sabuncu M, Mohlberg H, Amunts K, Zilles K, Golland P, Fischl B | Proceedings. IEEE International Conference on Computer Vision | 26082678 | Proc IEEE Int Conf Comput Vis | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26082678 |
| Automatic Tissue Segmentation of Neonate Brain MR Images with Subject-specific Atlases. | Cherel M, Budin F, Prastawa M, Gerig G, Lee K, Buss C, Lyall A, Consing KZ, Styner M | Proceedings of SPIE--the International Society for Optical Engineering | 26089584 | Proc SPIE Int Soc Opt Eng | 2015 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/26089584 |
| A Stochastic Approach to Diffeomorphic Point Set Registration with Landmark Constraints. | Kolesov I, Lee J, Sharp G, Vela P, Tannenbaum A | IEEE transactions on pattern analysis and machine intelligence | 26761731 | IEEE Trans Pattern Anal Mach Intell | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26761731 |
| Longitudinal modeling of appearance and shape and its potential for clinical use. | Gerig G, Fishbaugh J, Sadeghi N | Medical image analysis | 27344938 | Med Image Anal | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27344938 |
| General anaesthesia during infancy reduces white matter micro-organisation in developing rhesus monkeys. | Young JT, Vlasova RM, Howell BR, Knickmeyer RC, Morin E, Kuitchoua KI, Lubach GR, Noel J, Hu X, Shi Y, Caudill G, Alexander AL, Niethammer M, Paule MG, Coe CL, Sanchez M, Styner M | British journal of anaesthesia | 33549320 | Br J Anaesth | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33549320 |
| Impact of Eating a Carbohydrate-Restricted Diet on Cortical Atrophy in a Cross-Section of Amyloid Positive Patients with Alzheimer's Disease: A Small Sample Study. | Bramen JE, Siddarth P, Popa ES, Kress GT, Rapozo MK, Hodes JF, Ganapathi AS, Slyapich CB, Glatt RM, Pierce K, Porter VR, Wong C, Kim M, Dye RV, Panos S, Bookheimer T, Togashi T, Loong S, Raji CA, Bookheimer SY, Roach JC, Merrill DA | Journal of Alzheimer's disease : JAD | 37742646 | J Alzheimers Dis | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37742646 |
| Optimal data-driven sparse parameterization of diffeomorphisms for population analysis. | Durrleman S, Prastawa M, Gerig G, Joshi S | Information processing in medical imaging : proceedings of the ... conference | 21761651 | Inf Process Med Imaging | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21761651 |
| Learning an atlas of a cognitive process in its functional geometry. | Langs G, Lashkari D, Sweet A, Tie Y, Rigolo L, Golby AJ, Golland P | Information processing in medical imaging : proceedings of the ... conference | 21761652 | Inf Process Med Imaging | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21761652 |
| Source cancellation profiles of electroencephalography and magnetoencephalography. | Irimia A, Van Horn JD, Halgren E | NeuroImage | 21959078 | Neuroimage | 2012 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/21959078 |
| Fiber geometry in the corpus callosum in schizophrenia: evidence for transcallosal misconnection. | Whitford TJ, Savadjiev P, Kubicki M, O'Donnell LJ, Terry DP, Bouix S, Westin CF, Schneiderman JS, Bobrow L, Rausch AC, Niznikiewicz M, Nestor PG, Pantelis C, Wood SJ, McCarley RW, Shenton ME | Schizophrenia research | 21831601 | Schizophr Res | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21831601 |
| Mapping human cortical areas in vivo based on myelin content as revealed by T1- and T2-weighted MRI. | Glasser MF, Van Essen DC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 21832190 | J Neurosci | 2011 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/21832190 |
| Joint modeling of anatomical and functional connectivity for population studies. | Venkataraman A, Rathi Y, Kubicki M, Westin CF, Golland P | IEEE transactions on medical imaging | 21878411 | IEEE Trans Med Imaging | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21878411 |
| Genetic contributions to changes of fiber tracts of ventral visual stream in 22q11.2 deletion syndrome. | Kikinis Z, Makris N, Finn CT, Bouix S, Lucia D, Coleman MJ, Tworog-Dube E, Kikinis R, Kucherlapati R, Shenton ME, Kubicki M | Brain imaging and behavior | 23612843 | Brain Imaging Behav | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23612843 |
| Diffusion imaging quality control via entropy of principal direction distribution. | Farzinfar M, Oguz I, Smith RG, Verde AR, Dietrich C, Gupta A, Escolar ML, Piven J, Pujol S, Vachet C, Gouttard S, Gerig G, Dager S, McKinstry RC, Paterson S, Evans AC, IBIS network, Styner MA | NeuroImage | 23684874 | Neuroimage | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/23684874 |
| COMBINING ATLAS AND ACTIVE CONTOUR FOR AUTOMATIC 3D MEDICAL IMAGE SEGMENTATION. | Gao Y, Tannenbaum A | Proceedings. IEEE International Symposium on Biomedical Imaging | 23685464 | Proc IEEE Int Symp Biomed Imaging | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/23685464 |
| Building Spatiotemporal Anatomical Models using Joint 4-D Segmentation, Registration, and Subject-Specific Atlas Estimation. | Prastawa M, Awate SP, Gerig G | Proceedings. Workshop on Mathematical Methods in Biomedical Image Analysis | 23568185 | Proc Workshop Math Methods Biomed Image Analysis | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23568185 |
| Towards improved ultrasound-based analysis and 3D visualization of the fetal brain using the 3D Slicer. | Oyama R, Jakab M, Kikuchi A, Sugiyama T, Kikinis R, Pujol S | Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology | 23576282 | Ultrasound Obstet Gynecol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23576282 |
| Fiber tractography based on diffusion tensor imaging compared with high-angular-resolution diffusion imaging with compressed sensing: initial experience. | Kuhnt D, Bauer MH, Egger J, Richter M, Kapur T, Sommer J, Merhof D, Nimsky C | Neurosurgery | 23254805 | Neurosurgery | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23254805 |
| Tissue plasminogen activator prevents mortality from sulfur mustard analog-induced airway obstruction. | Veress LA, Hendry-Hofer TB, Loader JE, Rioux JS, Garlick RB, White CW | American journal of respiratory cell and molecular biology | 23258228 | Am J Respir Cell Mol Biol | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23258228 |
| Analytic regularization of uniform cubic B-spline deformation fields. | Shackleford JA, Yang Q, Lourenço AM, Shusharina N, Kandasamy N, Sharp GC | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286040 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286040 |
| Topology preserving atlas construction from shape data without correspondence using sparse parameters. | Durrleman S, Prastawa M, Korenberg JR, Joshi S, Trouvé A, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 23286134 | Med Image Comput Comput Assist Interv | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23286134 |
| Automatic segmentation of the left atrium from MRI images using salient feature and contour evolution. | Zhu L, Gao Y, Yezzi A, MacLeod R, Cates J, Tannenbaum A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 23366609 | Annu Int Conf IEEE Eng Med Biol Soc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23366609 |
| Longitudinal image registration with temporally-dependent image similarity measure. | Csapo I, Davis B, Shi Y, Sanchez M, Styner M, Niethammer M | IEEE transactions on medical imaging | 23846465 | IEEE Trans Med Imaging | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23846465 |
| From connectivity models to region labels: identifying foci of a neurological disorder. | Venkataraman A, Kubicki M, Golland P | IEEE transactions on medical imaging | 23864168 | IEEE Trans Med Imaging | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23864168 |
| VOXEL-WISE GROUP ANALYSIS OF DTI. | Liu Z, Zhu H, Marks BL, Katz LM, Goodlett CB, Gerig G, Styner M | Proceedings. IEEE International Symposium on Biomedical Imaging | 23703686 | Proc IEEE Int Symp Biomed Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/23703686 |
| TEMPORAL REGISTRATION OF PARTIAL DATA USING PARTICLE FILTERING. | Nir G, Tannenbaum A | Proceedings. International Conference on Image Processing | 23744132 | Proc Int Conf Image Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/23744132 |
| Forward and inverse electroencephalographic modeling in health and in acute traumatic brain injury. | Irimia A, Goh SY, Torgerson CM, Chambers MC, Kikinis R, Van Horn JD | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 23746499 | Clin Neurophysiol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23746499 |
| White matter microstructure and atypical visual orienting in 7-month-olds at risk for autism. | Elison JT, Paterson SJ, Wolff JJ, Reznick JS, Sasson NJ, Gu H, Botteron KN, Dager SR, Estes AM, Evans AC, Gerig G, Hazlett HC, Schultz RT, Styner M, Zwaigenbaum L, Piven J, IBIS Network | The American journal of psychiatry | 23511344 | Am J Psychiatry | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23511344 |
| Regionally selective atrophy of subcortical structures in prodromal HD as revealed by statistical shape analysis. | Younes L, Ratnanather JT, Brown T, Aylward E, Nopoulos P, Johnson H, Magnotta VA, Paulsen JS, Margolis RL, Albin RL, Miller MI, Ross CA, PREDICT-HD Investigators and Coordinators of the Huntington Study Group | Human brain mapping | 23281100 | Hum Brain Mapp | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23281100 |
| White matter fractional anisotropy is inversely related to anxious symptoms in older adults with atherosclerosis. | Bijanki KR, Stillman AN, Arndt S, Magnotta VA, Fiedorowicz JG, Haynes WG, Matsui JT, Johnson HJ, Moser DJ | International journal of geriatric psychiatry | 23348834 | Int J Geriatr Psychiatry | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23348834 |
| Regional characterization of longitudinal DT-MRI to study white matter maturation of the early developing brain. | Sadeghi N, Prastawa M, Fletcher PT, Wolff J, Gilmore JH, Gerig G | NeuroImage | 23235270 | Neuroimage | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23235270 |
| Impact of sex and gonadal steroids on neonatal brain structure. | Knickmeyer RC, Wang J, Zhu H, Geng X, Woolson S, Hamer RM, Konneker T, Styner M, Gilmore JH | Cerebral cortex (New York, N.Y. : 1991) | 23689636 | Cereb Cortex | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23689636 |
| A NEW FRAMEWORK FOR ANALYZING WHITE MATTER MATURATION IN EARLY BRAIN DEVELOPMENT. | Prastawa M, Sadeghi N, Gilmore JH, Lin W, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 23959442 | Proc IEEE Int Symp Biomed Imaging | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/23959442 |
| MULTIVARIATE MODELING OF LONGITUDINAL MRI IN EARLY BRAIN DEVELOPMENT WITH CONFIDENCE MEASURES. | Sadeghi N, Prastawa M, Fletcher PT, Vachet C, Wang B, Gilmore J, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 23959506 | Proc IEEE Int Symp Biomed Imaging | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23959506 |
| Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis. | Corouge I, Fletcher PT, Joshi S, Gouttard S, Gerig G | Medical image analysis | 16926104 | Med Image Anal | 2006 Oct | https://www.ncbi.nlm.nih.gov/pubmed/16926104 |
| White matter tract clustering and correspondence in populations. | O'Donnell L, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685839 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685839 |
| A unifying approach to registration, segmentation, and intensity correction. | Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WE, Wells WM | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685860 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685860 |
| Parametric response surface models for analysis of multi-site fMRI data. | Kim S, Smyth P, Stern H, Turner J | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685865 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685865 |
| Harmonic skeleton guided evaluation of stenoses in human coronary arteries. | Yang Y, Zhu L, Haker S, Tannenbaum AR, Giddens DP | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685882 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685882 |
| Multiscale 3D shape analysis using spherical wavelets. | Nain D, Haker S, Bobick A, Tannenbaum AR | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 16685992 | Med Image Comput Comput Assist Interv | 2005 | https://www.ncbi.nlm.nih.gov/pubmed/16685992 |
| High-dimensional white matter atlas generation and group analysis. | O'Donnell L, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354778 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354778 |
| Logarithm odds maps for shape representation. | Pohl KM, Fisher J, Shenton M, McCarley RW, Grimson WE, Kikinis R, Wells WM | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 17354865 | Med Image Comput Comput Assist Interv | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/17354865 |
| Atlas renormalization for improved brain MR image segmentation across scanner platforms. | Han X, Fischl B | IEEE transactions on medical imaging | 17427735 | IEEE Trans Med Imaging | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17427735 |
| On evaluating brain tissue classifiers without a ground truth. | Bouix S, Martin-Fernandez M, Ungar L, Nakamura M, Koo MS, McCarley RW, Shenton ME | NeuroImage | 17532646 | Neuroimage | 2007 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/17532646 |
| Diffusion tensor analysis with invariant gradients and rotation tangents. | Kindlmann G, Ennis DB, Whitaker RT, Westin CF | IEEE transactions on medical imaging | 18041264 | IEEE Trans Med Imaging | 2007 Nov | https://www.ncbi.nlm.nih.gov/pubmed/18041264 |
| Application of open source image guided therapy software in MR-guided therapies. | Hata N, Piper S, Jolesz FA, Tempany CM, Black PM, Morikawa S, Iseki H, Hashizume M, Kikinis R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051095 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051095 |
| A unified framework for clustering and quantitative analysis of white matter fiber tracts. | Maddah M, Grimson WE, Warfield SK, Wells WM | Medical image analysis | 18180197 | Med Image Anal | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18180197 |
| The effect of early human diet on caudate volumes and IQ. | Isaacs EB, Gadian DG, Sabatini S, Chong WK, Quinn BT, Fischl BR, Lucas A | Pediatric research | 18287970 | Pediatr Res | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18287970 |
| Probabilistic clustering and quantitative analysis of white matter fiber tracts. | Maddah M, Wells WM 3rd, Warfield SK, Westin CF, Grimson WE | Information processing in medical imaging : proceedings of the ... conference | 17633714 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633714 |
| Geometry driven volumetric registration. | Postelnicu G, Zollei L, Desikan R, Fischl B | Information processing in medical imaging : proceedings of the ... conference | 17633739 | Inf Process Med Imaging | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17633739 |
| MCMC curve sampling for image segmentation. | Fan AC, Fisher JW 3rd, Wells WM 3rd, Levitt JJ, Willsky AS | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18044603 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18044603 |
| Effects of registration regularization and atlas sharpness on segmentation accuracy. | Yeo BT, Sabuncu MR, Desikan R, Fischl B, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051118 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051118 |
| Global medical shape analysis using the Laplace-Beltrami spectrum. | Niethammer M, Reuter M, Wolter FE, Bouix S, Peinecke N, Koo MS, Shenton ME | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18051138 | Med Image Comput Comput Assist Interv | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/18051138 |
| SEGMENTATION OF SERIAL MRI OF TBI PATIENTS USING PERSONALIZED ATLAS CONSTRUCTION AND TOPOLOGICAL CHANGE ESTIMATION. | Wang B, Prastawa M, Awate SP, Irimia A, Chambers MC, Vespa PM, van Horn JD, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 23999192 | Proc IEEE Int Symp Biomed Imaging | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23999192 |
| Stopping Criteria for Log-Domain Diffeomorphic Demons Registration: An Experimental Survey for Radiotherapy Application. | Peroni M, Golland P, Sharp GC, Baroni G | Technology in cancer research & treatment | 24000996 | Technol Cancer Res Treat | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24000996 |
| Temporomandibular joint condylar changes following maxillomandibular advancement and articular disc repositioning. | Goncalves JR, Wolford LM, Cassano DS, da Porciuncula G, Paniagua B, Cevidanes LH | Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons | 24040949 | J Oral Maxillofac Surg | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24040949 |
| SGPP: spatial Gaussian predictive process models for neuroimaging data. | Hyun JW, Li Y, Gilmore JH, Lu Z, Styner M, Zhu H | NeuroImage | 24269800 | Neuroimage | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24269800 |
| A midas plugin to enable construction of reproducible web-based image processing pipelines. | Grauer M, Reynolds P, Hoogstoel M, Budin F, Styner MA, Oguz I | Frontiers in neuroinformatics | 24416016 | Front Neuroinform | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24416016 |
| Three-dimensional treatment outcomes in Class II patients treated with the Herbst appliance: a pilot study. | LeCornu M, Cevidanes LH, Zhu H, Wu CD, Larson B, Nguyen T | American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics | 24286905 | Am J Orthod Dentofacial Orthop | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24286905 |
| SPATIOTEMPORAL MODELING OF DISCRETE-TIME DISTRIBUTION-VALUED DATA APPLIED TO DTI TRACT EVOLUTION IN INFANT NEURODEVELOPMENT. | Sharma A, Fletcher PT, Gilmore JH, Escolar ML, Gupta A, Styner M, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 24443688 | Proc IEEE Int Symp Biomed Imaging | 2013 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/24443688 |
| PROPER ORDERED MESHING OF COMPLEX SHAPES AND OPTIMAL GRAPH CUTS APPLIED TO ATRIAL-WALL SEGMENTATION FROM DE-MRI. | Veni G, Fu Z, Awate SP, Whitaker RT | Proceedings. IEEE International Symposium on Biomedical Imaging | 24443695 | Proc IEEE Int Symp Biomed Imaging | 2013 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/24443695 |
| Sparse projections of medical images onto manifolds. | Chen GH, Wachinger C, Golland P | Information processing in medical imaging : proceedings of the ... conference | 24683977 | Inf Process Med Imaging | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24683977 |
| Geodesic shape regression in the framework of currents. | Fishbaugh J, Prastawa M, Gerig G, Durrleman S | Information processing in medical imaging : proceedings of the ... conference | 24684012 | Inf Process Med Imaging | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24684012 |
| Variations of dynamic contrast-enhanced magnetic resonance imaging in evaluation of breast cancer therapy response: a multicenter data analysis challenge. | Huang W, Li X, Chen Y, Li X, Chang MC, Oborski MJ, Malyarenko DI, Muzi M, Jajamovich GH, Fedorov A, Tudorica A, Gupta SN, Laymon CM, Marro KI, Dyvorne HA, Miller JV, Barbodiak DP, Chenevert TL, Yankeelov TE, Mountz JM, Kinahan PE, Kikinis R, Taouli B, Fennessy F, Kalpathy-Cramer J | Translational oncology | 24772219 | Transl Oncol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24772219 |
| Efficient inverse isoparametric mapping algorithm for whole-body computed tomography registration using deformations predicted by nonlinear finite element modeling. | Li M, Wittek A, Miller K | Journal of biomechanical engineering | 24828796 | J Biomech Eng | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24828796 |
| Automatic segmentation of the left atrium from MR images via variational region growing with a moments-based shape prior. | Zhu L, Gao Y, Yezzi A, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 24058026 | IEEE Trans Image Process | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24058026 |
| Instrumentation bias in the use and evaluation of scientific software: recommendations for reproducible practices in the computational sciences. | Tustison NJ, Johnson HJ, Rohlfing T, Klein A, Ghosh SS, Ibanez L, Avants BB | Frontiers in neuroscience | 24058331 | Front Neurosci | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24058331 |
| Neural encoding of acupuncture needling sensations: evidence from a FMRI study. | Wang X, Chan ST, Fang J, Nixon EE, Liu J, Kwong KK, Rosen BR, Hui KK | Evidence-based complementary and alternative medicine : eCAM | 24062782 | Evid Based Complement Alternat Med | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24062782 |
| Neuroimaging of structural pathology and connectomics in traumatic brain injury: Toward personalized outcome prediction. | Irimia A, Wang B, Aylward SR, Prastawa MW, Pace DF, Gerig G, Hovda DA, Kikinis R, Vespa PM, Van Horn JD | NeuroImage. Clinical | 24179732 | Neuroimage Clin | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/24179732 |
| Localized Sparse Code Gradient in Alzheimer's disease staging. | Liu S, Cai W, Song Y, Pujol S, Kikinis R, Wen L, Feng DD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 24110956 | Annu Int Conf IEEE Eng Med Biol Soc | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24110956 |
| Prostate cancer detection and diagnosis: the role of MR and its comparison with other diagnostic modalities--a radiologist's perspective. | Penzkofer T, Tempany-Afdhal CM | NMR in biomedicine | 24000133 | NMR Biomed | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24000133 |
| Faceted visualization of three dimensional neuroanatomy by combining ontology with faceted search. | Veeraraghavan H, Miller JV | Neuroinformatics | 24006207 | Neuroinformatics | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24006207 |
| Application of tolerance limits to the characterization of image registration performance. | Fedorov A, Wells WM, Kikinis R, Tempany CM, Vangel MG | IEEE transactions on medical imaging | 24759985 | IEEE Trans Med Imaging | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24759985 |
| Vision 20/20: perspectives on automated image segmentation for radiotherapy. | Sharp G, Fritscher KD, Pekar V, Peroni M, Shusharina N, Veeraraghavan H, Yang J | Medical physics | 24784366 | Med Phys | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24784366 |
| Multifold Bayesian kernelization in Alzheimer's diagnosis. | Liu S, Song Y, Cai W, Pujol S, Kikinis R, Wang X, Feng D | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 24579154 | Med Image Comput Comput Assist Interv | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24579154 |
| Multiatlas segmentation as nonparametric regression. | Awate SP, Whitaker RT | IEEE transactions on medical imaging | 24802528 | IEEE Trans Med Imaging | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24802528 |
| Stochastic Image Registration with User Constraints. | Kolesov I, Lee J, Vela P, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 24357915 | Proc SPIE Int Soc Opt Eng | 2013 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24357915 |
| MODELING LONGITUDINAL MRI CHANGES IN POPULATIONS USING A LOCALIZED, INFORMATION-THEORETIC MEASURE OF CONTRAST. | Vardhan A, Prastawa M, Sharma A, Piven J, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 24443698 | Proc IEEE Int Symp Biomed Imaging | 2013 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/24443698 |
| Mutual information as a measure of image quality for 3D dynamic lung imaging with EIT. | Crabb MG, Davidson JL, Little R, Wright P, Morgan AR, Miller CA, Naish JH, Parker GJ, Kikinis R, McCann H, Lionheart WR | Physiological measurement | 24710978 | Physiol Meas | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24710978 |
| Measures for Validation of DTI Tractography. | Gouttard S, Goodlett CB, Kubicki M, Gerig G | Proceedings of SPIE--the International Society for Optical Engineering | 24353381 | Proc SPIE Int Soc Opt Eng | 2012 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/24353381 |
| Clinical application of SPHARM-PDM to quantify temporomandibular joint osteoarthritis. | Paniagua B, Cevidanes L, Walker D, Zhu H, Guo R, Styner M | Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society | 21185694 | Comput Med Imaging Graph | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21185694 |
| Adsorption of Block Copolymers from Selective Solvents on Curved Surfaces. | Hershkovits E, Tannenbaum A, Tannenbaum R | Macromolecules | 20976029 | Macromolecules | 2008 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/20976029 |
| Data Synthesis and Tool Development for Exploring Imaging Genomic Patterns. | Kim S, Shen L, Saykin AJ, West JD | IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology proceedings. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology | 21461341 | IEEE Symp Comput Intell Bioinforma Comput Biol Proc | 2009 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/21461341 |
| Geometric metamorphosis. | Niethammer M, Hart GL, Pace DF, Vespa PM, Irimia A, Van Horn JD, Aylward SR | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 21995083 | Med Image Comput Comput Assist Interv | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21995083 |
| Dark regions of no-reflow on late gadolinium enhancement magnetic resonance imaging result in scar formation after atrial fibrillation ablation. | McGann C, Kholmovski E, Blauer J, Vijayakumar S, Haslam T, Cates J, DiBella E, Burgon N, Wilson B, Alexander A, Prastawa M, Daccarett M, Vergara G, Akoum N, Parker D, MacLeod R, Marrouche N | Journal of the American College of Cardiology | 21718914 | J Am Coll Cardiol | 2011 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/21718914 |
| Robust Radiomics feature quantification using semiautomatic volumetric segmentation. | Parmar C, Rios Velazquez E, Leijenaar R, Jermoumi M, Carvalho S, Mak RH, Mitra S, Shankar BU, Kikinis R, Haibe-Kains B, Lambin P, Aerts HJ | PloS one | 25025374 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25025374 |
| Square-cut: a segmentation algorithm on the basis of a rectangle shape. | Egger J, Kapur T, Dukatz T, Kolodziej M, Zukić D, Freisleben B, Nimsky C | PloS one | 22363547 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22363547 |
| Analytic regularization for landmark-based image registration. | Shusharina N, Sharp G | Physics in medicine and biology | 22390947 | Phys Med Biol | 2012 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/22390947 |
| Diffusion tensor imaging-based characterization of brain neurodevelopment in primates. | Shi Y, Short SJ, Knickmeyer RC, Wang J, Coe CL, Niethammer M, Gilmore JH, Zhu H, Styner MA | Cerebral cortex (New York, N.Y. : 1991) | 22275483 | Cereb Cortex | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22275483 |
| Quantitative tract-based white matter development from birth to age 2years. | Geng X, Gouttard S, Sharma A, Gu H, Styner M, Lin W, Gerig G, Gilmore JH | NeuroImage | 22510254 | Neuroimage | 2012 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/22510254 |
| The effect of reference panels and software tools on genotype imputation. | Nho K, Shen L, Kim S, Swaminathan S, Risacher SL, Saykin AJ, Alzheimer’s Disease Neuroimaging Initiative (ADNI) | AMIA ... Annual Symposium proceedings. AMIA Symposium | 22195161 | AMIA Annu Symp Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22195161 |
| Hippocampal shape analysis in Alzheimer's disease and frontotemporal lobar degeneration subtypes. | Lindberg O, Walterfang M, Looi JC, Malykhin N, Ostberg P, Zandbelt B, Styner M, Paniagua B, Velakoulis D, Orndahl E, Wahlund LO | Journal of Alzheimer's disease : JAD | 22414571 | J Alzheimers Dis | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22414571 |
| Particle Filtering with Region-based Matching for Tracking of Partially Occluded and Scaled Targets. | Nakhmani A, Tannenbaum A | SIAM journal on imaging sciences | 22506088 | SIAM J Imaging Sci | 2011 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/22506088 |
| In search of the functional neuroanatomy of sociality: MRI subdivisions of orbital frontal cortex and social cognition. | Nestor PG, Nakamura M, Niznikiewicz M, Thompson E, Levitt JJ, Choate V, Shenton ME, McCarley RW | Social cognitive and affective neuroscience | 22345366 | Soc Cogn Affect Neurosci | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22345366 |
| How to measure cortical folding from MR images: a step-by-step tutorial to compute local gyrification index. | Schaer M, Cuadra MB, Schmansky N, Fischl B, Thiran JP, Eliez S | Journal of visualized experiments : JoVE | 22230945 | J Vis Exp | 2012 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/22230945 |
| Bayesian lasso for semiparametric structural equation models. | Guo R, Zhu H, Chow SM, Ibrahim JG | Biometrics | 22376150 | Biometrics | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22376150 |
| Nonparametric clustering for studying RNA conformations. | Le Faucheur X, Hershkovits E, Tannenbaum R, Tannenbaum A | IEEE/ACM transactions on computational biology and bioinformatics | 21173460 | IEEE/ACM Trans Comput Biol Bioinform | 2011 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/21173460 |
| Combined volumetric and surface registration. | Postelnicu G, Zollei L, Fischl B | IEEE transactions on medical imaging | 19273000 | IEEE Trans Med Imaging | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19273000 |
| Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. | Shen L, Firpi HA, Saykin AJ, West JD | Hippocampus | 19405146 | Hippocampus | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19405146 |
| Increased sensitivity to effects of normal aging and Alzheimer's disease on cortical thickness by adjustment for local variability in gray/white contrast: a multi-sample MRI study. | Westlye LT, Walhovd KB, Dale AM, Espeseth T, Reinvang I, Raz N, Agartz I, Greve DN, Fischl B, Fjell AM | NeuroImage | 19501655 | Neuroimage | 2009 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/19501655 |
| Structural integrity of the uncinate fasciculus in geriatric depression: Relationship with age of onset. | Taylor WD, MacFall JR, Gerig G, Krishnan RR | Neuropsychiatric disease and treatment | 19300596 | Neuropsychiatr Dis Treat | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/19300596 |
| Intrinsic Regression Models for Manifold-Valued Data. | Shi X, Styner M, Lieberman J, Ibrahim JG, Lin W, Zhu H | Journal of the American Statistical Association | 19960103 | J Am Stat Assoc | 2009 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19960103 |
| A METHODOLOGY FOR ANALYZING CURVATURE IN THE DEVELOPING BRAIN FROM PRETERM TO ADULT. | Pienaar R, Fischl B, Caviness V, Makris N, Grant PE | International journal of imaging systems and technology | 19936261 | Int J Imaging Syst Technol | 2008 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/19936261 |
| Impact of breast milk on intelligence quotient, brain size, and white matter development. | Isaacs EB, Fischl BR, Quinn BT, Chong WK, Gadian DG, Lucas A | Pediatric research | 20035247 | Pediatr Res | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20035247 |
| Modeling of Anatomical Information in Clustering of White Matter Fiber Trajectories Using Dirichlet Distribution. | Maddah M, Zöllei L, Grimson WE, Wells WM | Proceedings. Workshop on Mathematical Methods in Biomedical Image Analysis | 21625356 | Proc Workshop Math Methods Biomed Image Analysis | 2008 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/21625356 |
| Three-dimensional regional displacements after mandibular advancement surgery: one year of follow-up. | Motta AT, Cevidanes LH, Carvalho FA, Almeida MA, Phillips C | Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons | 21256643 | J Oral Maxillofac Surg | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21256643 |
| Stochastic tractography study of Inferior Frontal Gyrus anatomical connectivity in schizophrenia. | Kubicki M, Alvarado JL, Westin CF, Tate DF, Markant D, Terry DP, Whitford TJ, De Siebenthal J, Bouix S, McCarley RW, Kikinis R, Shenton ME | NeuroImage | 21256966 | Neuroimage | 2011 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/21256966 |
| Tubular surface segmentation for extracting anatomical structures from medical imagery. | Mohan V, Sundaramoorthi G, Tannenbaum A | IEEE transactions on medical imaging | 21118754 | IEEE Trans Med Imaging | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21118754 |
| Development of stereotactic mass spectrometry for brain tumor surgery. | Agar NY, Golby AJ, Ligon KL, Norton I, Mohan V, Wiseman JM, Tannenbaum A, Jolesz FA | Neurosurgery | 21135749 | Neurosurgery | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21135749 |
| A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI Analysis. | Maddah M, Zöllei L, Grimson WE, Westin CF, Wells WM | Proceedings. IEEE International Symposium on Biomedical Imaging | 19212449 | Proc IEEE Int Symp Biomed Imaging | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/19212449 |
| Quantitative examination of a novel clustering method using magnetic resonance diffusion tensor tractography. | Voineskos AN, O'Donnell LJ, Lobaugh NJ, Markant D, Ameis SH, Niethammer M, Mulsant BH, Pollock BG, Kennedy JL, Westin CF, Shenton ME | NeuroImage | 19159690 | Neuroimage | 2009 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/19159690 |
| A unified framework for MR based disease classification. | Pohl KM, Sabuncu MR | Information processing in medical imaging : proceedings of the ... conference | 19694272 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694272 |
| Minute effects of sex on the aging brain: a multisample magnetic resonance imaging study of healthy aging and Alzheimer's disease. | Fjell AM, Westlye LT, Amlien I, Espeseth T, Reinvang I, Raz N, Agartz I, Salat DH, Greve DN, Fischl B, Dale AM, Walhovd KB | The Journal of neuroscience : the official journal of the Society for Neuroscience | 19587284 | J Neurosci | 2009 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/19587284 |
| Anatomical atlas-guided diffuse optical tomography of brain activation. | Custo A, Boas DA, Tsuzuki D, Dan I, Mesquita R, Fischl B, Grimson WE, Wells W 3rd | NeuroImage | 19643185 | Neuroimage | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19643185 |
| High consistency of regional cortical thinning in aging across multiple samples. | Fjell AM, Westlye LT, Amlien I, Espeseth T, Reinvang I, Raz N, Agartz I, Salat DH, Greve DN, Fischl B, Dale AM, Walhovd KB | Cerebral cortex (New York, N.Y. : 1991) | 19150922 | Cereb Cortex | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19150922 |
| Encoding probabilistic brain atlases using Bayesian inference. | Van Leemput K | IEEE transactions on medical imaging | 19068424 | IEEE Trans Med Imaging | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19068424 |
| Increased diffusivity in superior temporal gyrus in patients with schizophrenia: a Diffusion Tensor Imaging study. | Lee K, Yoshida T, Kubicki M, Bouix S, Westin CF, Kindlmann G, Niznikiewicz M, Cohen A, McCarley RW, Shenton ME | Schizophrenia research | 19135872 | Schizophr Res | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19135872 |
| Multimodal functional imaging using fMRI-informed regional EEG/MEG source estimation. | Oun W, Numënmaa A, Hämäläinen M, Golland P | Information processing in medical imaging : proceedings of the ... conference | 19694255 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694255 |
| Tractography segmentation using a hierarchical Dirichlet processes mixture model. | Wang X, Grimson WE, Westin CF | Information processing in medical imaging : proceedings of the ... conference | 19694256 | Inf Process Med Imaging | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19694256 |
| Lack of relationship between psychological denial and unawareness of illness in schizophrenia-spectrum disorders. | Kruck CL, Flashman LA, Roth RM, Koven NS, McAllister TW, Saykin AJ | Psychiatry research | 19616309 | Psychiatry Res | 2009 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/19616309 |
| OpenIGTLink: an open network protocol for image-guided therapy environment. | Tokuda J, Fischer GS, Papademetris X, Yaniv Z, Ibanez L, Cheng P, Liu H, Blevins J, Arata J, Golby AJ, Kapur T, Pieper S, Burdette EC, Fichtinger G, Tempany CM, Hata N | The international journal of medical robotics + computer assisted surgery : MRCAS | 19621334 | Int J Med Robot | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19621334 |
| The DTI connectivity of the human claustrum. | Torgerson CM, Irimia A, Goh SY, Van Horn JD | Human brain mapping | 25339630 | Hum Brain Mapp | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25339630 |
| 3D osteoarthritic changes in TMJ condylar morphology correlates with specific systemic and local biomarkers of disease. | Cevidanes LH, Walker D, Schilling J, Sugai J, Giannobile W, Paniagua B, Benavides E, Zhu H, Marron JS, Jung BT, Baranowski D, Rhodes J, Nackley A, Lim PF, Ludlow JB, Nguyen T, Goncalves JR, Wolford L, Kapila S, Styner M | Osteoarthritis and cartilage | 25278075 | Osteoarthritis Cartilage | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25278075 |
| Geodesic image regression with a sparse parameterization of diffeomorphisms. | Fishbaugh J, Prastawa M, Gerig G, Durrleman S | Geometric science of information : first international conference, GSI 2013, Paris, France, August 28-30, 2013 : proceedings. Geometric Science of Information (1st : 2013 : Paris, France) | 25664349 | Geom Sci Inf (2013) | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/25664349 |
| Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy. | Datar M, Muralidharan P, Kumar A, Gouttard S, Piven J, for the IBIS Network, Gerig G, Whitaker R, Fletcher PT | Spatio-temporal image analysis for longitudinal and time-series image data : Second International Workshop, STIA 2012, held in conjunction with MICCAI 2012, Nice, France, October 1, 2012, proceedings. STIA (Conference) (2nd : 2012 : Nic... | 25506622 | Spatiotemporal Image Anal Longitud Time Ser Image Data (2012) | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25506622 |
| Patient-specific biomechanical model as whole-body CT image registration tool. | Li M, Miller K, Joldes GR, Doyle B, Garlapati RR, Kikinis R, Wittek A | Medical image analysis | 25721296 | Med Image Anal | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25721296 |
| Hierarchical bayesian modeling, estimation, and sampling for multigroup shape analysis. | Yu YY, Fletcher PT, Awate SP | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 25320776 | Med Image Comput Comput Assist Interv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25320776 |
| Subject-specific prediction using nonlinear population modeling: application to early brain maturation from DTI. | Sadeghi N, Fletcher PT, Prastawa M, Gilmore JH, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 25320779 | Med Image Comput Comput Assist Interv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25320779 |
| Longitudinal quantification and visualization of intracerebral haemorrhage using multimodal magnetic resonance and diffusion tensor imaging. | Goh SY, Irimia A, Torgerson CM, Tubi MA, Real CR, Hanley DF, Martin NA, Vespa PM, Van Horn JD | Brain injury | 25518865 | Brain Inj | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25518865 |
| Subjective rating of working memory is associated with frontal lobe volume in schizophrenia. | Garlinghouse MA, Roth RM, Isquith PK, Flashman LA, Saykin AJ | Schizophrenia research | 20303715 | Schizophr Res | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20303715 |
| Constrained data decomposition and regression for analyzing healthy aging from fiber tract diffusion properties. | Gouttard S, Prastawa M, Bullitt E, Lin W, Goodlett C, Gerig G | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426003 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426003 |
| Local white matter geometry indices from diffusion tensor gradients. | Savadjiev P, Kindlmann G, Bouix S, Shenton ME, Westin CF | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426006 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426006 |
| Task-optimal registration cost functions. | Yeo BT, Sabuncu M, Golland P, Fischl B | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426037 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426037 |
| Particle based shape regression of open surfaces with applications to developmental neuroimaging. | Datar M, Cates J, Fletcher PT, Gouttard S, Gerig G, Whitaker R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426109 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426109 |
| Genetic pathway-based hierarchical clustering analysis of older adults with cognitive complaints and amnestic mild cognitive impairment using clinical and neuroimaging phenotypes. | Sloan CD, Shen L, West JD, Wishart HA, Flashman LA, Rabin LA, Santulli RB, Guerin SJ, Rhodes CH, Tsongalis GJ, McAllister TW, Ahles TA, Lee SL, Moore JH, Saykin AJ | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 20468060 | Am J Med Genet B Neuropsychiatr Genet | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20468060 |
| Tractography segmentation using a hierarchical Dirichlet processes mixture model. | Wang X, Grimson WE, Westin CF | NeuroImage | 20678578 | Neuroimage | 2011 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/20678578 |
| Nonclinical obsessive-compulsive symptoms and executive functions in schizophrenia. | Kumbhani SR, Roth RM, Kruck CL, Flashman LA, McAllister TW | The Journal of neuropsychiatry and clinical neurosciences | 20686137 | J Neuropsychiatry Clin Neurosci | 2010 Summer | https://www.ncbi.nlm.nih.gov/pubmed/20686137 |
| Discovering structure in the space of fMRI selectivity profiles. | Lashkari D, Vul E, Kanwisher N, Golland P | NeuroImage | 20053382 | Neuroimage | 2010 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/20053382 |
| Atlas generation for subcortical and ventricular structures with its applications in shape analysis. | Qiu A, Brown T, Fischl B, Ma J, Miller MI | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 20129863 | IEEE Trans Image Process | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20129863 |
| Prediction of Successful Memory Encoding from fMRI Data. | Balci SK, Sabuncu MR, Yoo J, Ghosh SS, Whitfield-Gabrieli S, Gabrieli JD, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20401334 | Med Image Comput Comput Assist Interv | 2008 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/20401334 |
| On the manifold structure of the space of brain images. | Gerber S, Tasdizen T, Joshi S, Whitaker R | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426001 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426001 |
| Asymmetric image-template registration. | Sabuncu MR, Yeo BT, Van Leemput K, Vercauteren T, Golland P | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426033 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426033 |
| Intrinsic regression models for manifold-valued data. | Shi X, Styner M, Lieberman J, Ibrahim JG, Lin W, Zhu H | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20426112 | Med Image Comput Comput Assist Interv | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20426112 |
| Laplace-Beltrami Eigenvalues and Topological Features of Eigenfunctions for Statistical Shape Analysis. | Reuter M, Wolter FE, Shenton M, Niethammer M | Computer aided design | 20161035 | Comput Aided Des | 2009 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/20161035 |
| WebParc: a tool for analysis of the topography and volume of stroke from MRI. | Kennedy DN, Haselgrove C, Makris N, Goldin DM, Lev MH, Caplan D, Caviness VS | Medical & biological engineering & computing | 20077026 | Med Biol Eng Comput | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20077026 |
| Editorial. | Rueckert D, Hawkes D, Gerig G, Yang GZ | Medical image analysis | 20627174 | Med Image Anal | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20627174 |
| Corpus callosum abnormalities and their association with psychotic symptoms in patients with schizophrenia. | Whitford TJ, Kubicki M, Schneiderman JS, O'Donnell LJ, King R, Alvarado JL, Khan U, Markant D, Nestor PG, Niznikiewicz M, McCarley RW, Westin CF, Shenton ME | Biological psychiatry | 20494336 | Biol Psychiatry | 2010 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/20494336 |
| Scalable and interactive segmentation and visualization of neural processes in EM datasets. | Jeong WK, Beyer J, Hadwiger M, Vazquez A, Pfister H, Whitaker RT | IEEE transactions on visualization and computer graphics | 19834227 | IEEE Trans Vis Comput Graph | 2009 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/19834227 |
| Efficient Descriptor-Based Segmentation of Parotid Glands With Nonlocal Means. | Wachinger C, Brennan M, Sharp GC, Golland P | IEEE transactions on bio-medical engineering | 28113224 | IEEE Trans Biomed Eng | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28113224 |
| Naturalistic Language Recordings Reveal "Hypervocal" Infants at High Familial Risk for Autism. | Swanson MR, Shen MD, Wolff JJ, Boyd B, Clements M, Rehg J, Elison JT, Paterson S, Parish-Morris J, Chappell JC, Hazlett HC, Emerson RW, Botteron K, Pandey J, Schultz RT, Dager SR, Zwaigenbaum L, Estes AM, Piven J, IBIS Network | Child development | 28295208 | Child Dev | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28295208 |
| Genome-wide association analysis identifies common variants influencing infant brain volumes. | Xia K, Zhang J, Ahn M, Jha S, Crowley JJ, Szatkiewicz J, Li T, Zou F, Zhu H, Hibar D, Thompson P, ENIGMA Consortium, Sullivan PF, Styner M, Gilmore JH, Knickmeyer RC | Translational psychiatry | 28763065 | Transl Psychiatry | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/28763065 |
| Altered corpus callosum morphology associated with autism over the first 2 years of life. | Wolff JJ, Gerig G, Lewis JD, Soda T, Styner MA, Vachet C, Botteron KN, Elison JT, Dager SR, Estes AM, Hazlett HC, Schultz RT, Zwaigenbaum L, Piven J, IBIS Network | Brain : a journal of neurology | 25937563 | Brain | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25937563 |
| Prefrontal cortex white matter tracts in prodromal Huntington disease. | Matsui JT, Vaidya JG, Wassermann D, Kim RE, Magnotta VA, Johnson HJ, Paulsen JS, PREDICT-HD Investigators and Coordinators of the Huntington Study Group | Human brain mapping | 26179962 | Hum Brain Mapp | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26179962 |
| Keypoint Transfer Segmentation. | Wachinger C, Toews M, Langs G, Wells W, Golland P | Information processing in medical imaging : proceedings of the ... conference | 26221677 | Inf Process Med Imaging | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26221677 |
| Depressive symptoms related to low fractional anisotropy of white matter underlying the right ventral anterior cingulate in older adults with atherosclerotic vascular disease. | Bijanki KR, Matsui JT, Mayberg HS, Magnotta VA, Arndt S, Johnson HJ, Nopoulos P, Paradiso S, McCormick LM, Fiedorowicz JG, Epping EA, Moser DJ | Frontiers in human neuroscience | 26236221 | Front Hum Neurosci | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26236221 |
| Cortical Folding Development Study based on Over-Complete Spherical Wavelets. | Yu P, Yeo BT, Grant PE, Fischl B, Golland P | Proceedings. IEEE International Conference on Computer Vision | 26082677 | Proc IEEE Int Conf Comput Vis | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26082677 |
| Biomechanical model for computing deformations for whole-body image registration: A meshless approach. | Li M, Miller K, Joldes GR, Kikinis R, Wittek A | International journal for numerical methods in biomedical engineering | 26791945 | Int J Numer Method Biomed Eng | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26791945 |
| Entropy-based particle correspondence for shape populations. | Oguz I, Cates J, Datar M, Paniagua B, Fletcher T, Vachet C, Styner M, Whitaker R | International journal of computer assisted radiology and surgery | 26646417 | Int J Comput Assist Radiol Surg | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26646417 |
| Probabilistic Modeling of Imaging, Genetics and Diagnosis. | Batmanghelich NK, Dalca A, Quon G, Sabuncu M, Golland P | IEEE transactions on medical imaging | 26886973 | IEEE Trans Med Imaging | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26886973 |
| BFLCRM: A BAYESIAN FUNCTIONAL LINEAR COX REGRESSION MODEL FOR PREDICTING TIME TO CONVERSION TO ALZHEIMER'S DISEASE. | Lee E, Zhu H, Kong D, Wang Y, Giovanello KS, Ibrahim JG | The annals of applied statistics | 26900412 | Ann Appl Stat | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26900412 |
| Three-dimensional regional displacement after surgical-orthodontic correction of Class III malocclusion. | Koerich L, Ruellas AC, Paniagua B, Styner M, Turvey T, Cevidanes LH | Orthodontics & craniofacial research | 26521755 | Orthod Craniofac Res | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26521755 |
| XNAT Central: Open sourcing imaging research data. | Herrick R, Horton W, Olsen T, McKay M, Archie KA, Marcus DS | NeuroImage | 26143202 | Neuroimage | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26143202 |
| LOGISMOS-B for Primates: Primate Cortical Surface Reconstruction and Thickness Measurement. | Oguz I, Styner M, Sanchez M, Shi Y, Sonka M | Proceedings of SPIE--the International Society for Optical Engineering | 26028802 | Proc SPIE Int Soc Opt Eng | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26028802 |
| Cortical Surface Shape Analysis Based on Spherical Wavelet Transformation. | Yu P, Han X, Ségonne F, Pienaar R, Buckner RL, Golland P, Grant PE, Fischl B | Conference on Computer Vision and Pattern Recognition Workshops. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops | 26082947 | Conf Comput Vis Pattern Recognit Workshops | 2006 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26082947 |
| 4D ACTIVE CUT: AN INTERACTIVE TOOL FOR PATHOLOGICAL ANATOMY MODELING. | Wang B, Liu W, Prastawa M, Irimia A, Vespa PM, van Horn JD, Fletcher PT, Gerig G | Proceedings. IEEE International Symposium on Biomedical Imaging | 25356193 | Proc IEEE Int Symp Biomed Imaging | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25356193 |
| Interpolation of Longitudinal Shape and Image Data via Optimal Mass Transport. | Gao Y, Zhu LJ, Bouix S, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 25302008 | Proc SPIE Int Soc Opt Eng | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/25302008 |
| Multimodal neuroimaging feature learning for multiclass diagnosis of Alzheimer's disease. | Liu S, Liu S, Cai W, Che H, Pujol S, Kikinis R, Feng D, Fulham MJ, ADNI | IEEE transactions on bio-medical engineering | 25423647 | IEEE Trans Biomed Eng | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25423647 |
| Investigating Maternal Brain Structure and its Relationship to Substance Use and Motivational Systems. | Rutherford HJ, Gerig G, Gouttard S, Potenza MN, Mayes LC | The Yale journal of biology and medicine | 26339203 | Yale J Biol Med | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26339203 |
| The DTI Challenge: Toward Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery. | Pujol S, Wells W, Pierpaoli C, Brun C, Gee J, Cheng G, Vemuri B, Commowick O, Prima S, Stamm A, Goubran M, Khan A, Peters T, Neher P, Maier-Hein KH, Shi Y, Tristan-Vega A, Veni G, Whitaker R, Styner M, Westin CF, Gouttard S, Norton I, Chauvin L, Mamata H, Gerig G, Nabavi A, Golby A, Kikinis R | Journal of neuroimaging : official journal of the American Society of Neuroimaging | 26259925 | J Neuroimaging | 2015 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/26259925 |
| Abnormal white matter connections between medial frontal regions predict symptoms in patients with first episode schizophrenia. | Ohtani T, Bouix S, Lyall AE, Hosokawa T, Saito Y, Melonakos E, Westin CF, Seidman LJ, Goldstein J, Mesholam-Gately R, Petryshen T, Wojcik J, Kubicki M | Cortex; a journal devoted to the study of the nervous system and behavior | 26277547 | Cortex | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26277547 |
| Subcortical Brain and Behavior Phenotypes Differentiate Infants With Autism Versus Language Delay. | Swanson MR, Shen MD, Wolff JJ, Elison JT, Emerson RW, Styner MA, Hazlett HC, Truong K, Watson LR, Paterson S, Marrus N, Botteron KN, Pandey J, Schultz RT, Dager SR, Zwaigenbaum L, Estes AM, Piven J, IBIS Network | Biological psychiatry. Cognitive neuroscience and neuroimaging | 29560900 | Biol Psychiatry Cogn Neurosci Neuroimaging | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29560900 |
| 3D Mandibular Superimposition: Comparison of Regions of Reference for Voxel-Based Registration. | Ruellas AC, Yatabe MS, Souki BQ, Benavides E, Nguyen T, Luiz RR, Franchi L, Cevidanes LH | PloS one | 27336366 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27336366 |
| Keypoint Transfer for Fast Whole-Body Segmentation. | Wachinger C, Toews M, Langs G, Wells W, Golland P | IEEE transactions on medical imaging | 29994670 | IEEE Trans Med Imaging | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29994670 |
| Quantitative tract-based white matter heritability in 1- and 2-year-old twins. | Lee SJ, Zhang J, Neale MC, Styner M, Zhu H, Gilmore JH | Human brain mapping | 30368980 | Hum Brain Mapp | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30368980 |
| Early language exposure supports later language skills in infants with and without autism. | Swanson MR, Donovan K, Paterson S, Wolff JJ, Parish-Morris J, Meera SS, Watson LR, Estes AM, Marrus N, Elison JT, Shen MD, McNeilly HB, MacIntyre L, Zwaigenbaum L, St John T, Botteron K, Dager S, Piven J, IBIS Network | Autism research : official journal of the International Society for Autism Research | 31254329 | Autism Res | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31254329 |
| Sex differences associated with corpus callosum development in human infants: A longitudinal multimodal imaging study. | Schmied A, Soda T, Gerig G, Styner M, Swanson MR, Elison JT, Shen MD, McKinstry RC, Pruett JR Jr, Botteron KN, Estes AM, Dager SR, Hazlett HC, Schultz RT, Piven J, Wolff JJ, IBIS Network | NeuroImage | 32276067 | Neuroimage | 2020 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/32276067 |
| ACTIVE LEARNING GUIDED INTERACTIONS FOR CONSISTENT IMAGE SEGMENTATION WITH REDUCED USER INTERACTIONS. | Veeraraghavan H, Miller JV | Proceedings. IEEE International Symposium on Biomedical Imaging | 30881602 | Proc IEEE Int Symp Biomed Imaging | 2011 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/30881602 |
| Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells. | Tu LC, Yan X, Hood L, Lin B | Molecular & cellular proteomics : MCP | 17220478 | Mol Cell Proteomics | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17220478 |
| Strategies for plasma proteomic profiling of cancers. | Omenn GS | Proteomics | 16991194 | Proteomics | 2006 Oct | https://www.ncbi.nlm.nih.gov/pubmed/16991194 |
| Systematic comparison of the human saliva and plasma proteomes. | Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT | Proteomics. Clinical applications | 19898684 | Proteomics Clin Appl | 2009 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19898684 |
| Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge. | Saxena R, Hivert MF, Langenberg C, Tanaka T, Pankow JS, Vollenweider P, Lyssenko V, Bouatia-Naji N, Dupuis J, Jackson AU, Kao WH, Li M, Glazer NL, Manning AK, Luan J, Stringham HM, Prokopenko I, Johnson T, Grarup N, Boesgaard TW, Lecoeur C, Shrader P, O'Connell J, Ingelsson E, Couper DJ, Rice K, Song K, Andreasen CH, Dina C, Köttgen A, Le Bacquer O, Pattou F, Taneera J, Steinthorsdottir V, Rybin D, Ardlie K, Sampson M, Qi L, van Hoek M, Weedon MN, Aulchenko YS, Voight BF, Grallert H, Balkau B, Bergman RN, Bielinski SJ, Bonnefond A, Bonnycastle LL, Borch-Johnsen K, Böttcher Y, Brunner E, Buchanan TA, Bumpstead SJ, Cavalcanti-Proença C, Charpentier G, Chen YD, Chines PS, Collins FS, Cornelis M, J Crawford G, Delplanque J, Doney A, Egan JM, Erdos MR, Firmann M, Forouhi NG, Fox CS, Goodarzi MO, Graessler J, Hingorani A, Isomaa B, Jørgensen T, Kivimaki M, Kovacs P, Krohn K, Kumari M, Lauritzen T, Lévy-Marchal C, Mayor V, McAteer JB, Meyre D, Mitchell BD, Mohlke KL, Morken MA, Narisu N, Palmer CN, Pakyz R, Pascoe L, Payne F, Pearson D, Rathmann W, Sandbaek A, Sayer AA, Scott LJ, Sharp SJ, Sijbrands E, Singleton A, Siscovick DS, Smith NL, Sparsø T, Swift AJ, Syddall H, Thorleifsson G, Tönjes A, Tuomi T, Tuomilehto J, Valle TT, Waeber G, Walley A, Waterworth DM, Zeggini E, Zhao JH, GIANT consortium, MAGIC investigators, Illig T, Wichmann HE, Wilson JF, van Duijn C, Hu FB, Morris AD, Frayling TM, Hattersley AT, Thorsteinsdottir U, Stefansson K, Nilsson P, Syvänen AC, Shuldiner AR, Walker M, Bornstein SR, Schwarz P, Williams GH, Nathan DM, Kuusisto J, Laakso M, Cooper C, Marmot M, Ferrucci L, Mooser V, Stumvoll M, Loos RJ, Altshuler D, Psaty BM, Rotter JI, Boerwinkle E, Hansen T, Pedersen O, Florez JC, McCarthy MI, Boehnke M, Barroso I, Sladek R, Froguel P, Meigs JB, Groop L, Wareham NJ, Watanabe RM | Nature genetics | 20081857 | Nat Genet | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20081857 |
| Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder. | McEachin RC, Saccone NL, Saccone SF, Kleyman-Smith YD, Kar T, Kare RK, Ade AS, Sartor MA, Cavalcoli JD, McInnis MG | BMC medical genetics | 20102619 | BMC Med Genet | 2010 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/20102619 |
| Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. | Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney AS, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PR, Jørgensen T, Kao WH, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JR, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CN, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI, MAGIC investigators, GIANT Consortium | Nature genetics | 20581827 | Nat Genet | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20581827 |
| Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. | Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, Ramnarayanan K, Shankar S, Han B, Cao Q, Cao X, Suleman K, Kumar-Sinha C, Dhanasekaran SM, Chen YB, Esgueva R, Banerjee S, LaFargue CJ, Siddiqui J, Demichelis F, Moeller P, Bismar TA, Kuefer R, Fullen DR, Johnson TM, Greenson JK, Giordano TJ, Tan P, Tomlins SA, Varambally S, Rubin MA, Maher CA, Chinnaiyan AM | Nature medicine | 20526349 | Nat Med | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20526349 |
| Network analysis of genes regulated in renal diseases: implications for a molecular-based classification. | Bhavnani SK, Eichinger F, Martini S, Saxman P, Jagadish HV, Kretzler M | BMC bioinformatics | 19761573 | BMC Bioinformatics | 2009 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/19761573 |
| A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. | Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, Erdos MR, Stringham HM, Chines PS, Jackson AU, Prokunina-Olsson L, Ding CJ, Swift AJ, Narisu N, Hu T, Pruim R, Xiao R, Li XY, Conneely KN, Riebow NL, Sprau AG, Tong M, White PP, Hetrick KN, Barnhart MW, Bark CW, Goldstein JL, Watkins L, Xiang F, Saramies J, Buchanan TA, Watanabe RM, Valle TT, Kinnunen L, Abecasis GR, Pugh EW, Doheny KF, Bergman RN, Tuomilehto J, Collins FS, Boehnke M | Science (New York, N.Y.) | 17463248 | Science | 2007 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/17463248 |
| Supercomputing with toys: harnessing the power of NVIDIA 8800GTX and playstation 3 for bioinformatics problem. | Wilson J, Dai M, Jakupovic E, Watson S, Meng F | Computational systems bioinformatics. Computational Systems Bioinformatics Conference | 17951841 | Comput Syst Bioinformatics Conf | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17951841 |
| Elevated triglycerides correlate with progression of diabetic neuropathy. | Wiggin TD, Sullivan KA, Pop-Busui R, Amato A, Sima AA, Feldman EL | Diabetes | 19411614 | Diabetes | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19411614 |
| MicroRNA expression changes in lymphoblastoid cell lines in response to lithium treatment. | Chen H, Wang N, Burmeister M, McInnis MG | The international journal of neuropsychopharmacology | 19254429 | Int J Neuropsychopharmacol | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19254429 |
| Open Biomedical Ontology-based Medline exploration. | Xuan W, Dai M, Mirel B, Song J, Athey B, Watson SJ, Meng F | BMC bioinformatics | 19426463 | BMC Bioinformatics | 2009 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/19426463 |
| Prioritizing Disease Genes by Analysis of Common Elements (PDG-ACE). | McEachin RC, Keller BJ, Zandi PP, Almani M, McInnis MG | AMIA ... Annual Symposium proceedings. AMIA Symposium | 18694166 | AMIA Annu Symp Proc | 2007 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/18694166 |
| SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. | Hur J, Schuyler AD, States DJ, Feldman EL | Bioinformatics (Oxford, England) | 19188191 | Bioinformatics | 2009 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/19188191 |
| Targeting stem cells-clinical implications for cancer therapy. | Tu LC, Foltz G, Lin E, Hood L, Tian Q | Current stem cell research & therapy | 19442199 | Curr Stem Cell Res Ther | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19442199 |
| ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. | Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM | Bioinformatics (Oxford, England) | 19351619 | Bioinformatics | 2009 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/19351619 |
| MiSearch adaptive pubMed search tool. | States DJ, Ade AS, Wright ZC, Bookvich AV, Athey BD | Bioinformatics (Oxford, England) | 18326507 | Bioinformatics | 2009 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/18326507 |
| Web-based GeneChip analysis system for large-scale collaborative projects. | Dai M, Wang P, Jakupovic E, Watson SJ, Meng F | Bioinformatics (Oxford, England) | 17586830 | Bioinformatics | 2007 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/17586830 |
| Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function. | Chen Y, Blackwell TW, Chen J, Gao J, Lee AW, States DJ | PLoS computational biology | 17411336 | PLoS Comput Biol | 2007 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/17411336 |
| A gel-based proteomic comparison of human cerebrospinal fluid between inflicted and non-inflicted pediatric traumatic brain injury. | Gao WM, Chadha MS, Berger RP, Omenn GS, Allen DL, Pisano M, Adelson PD, Clark RS, Jenkins LW, Kochanek PM | Journal of neurotrauma | 17263669 | J Neurotrauma | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17263669 |
| Modeling gene-by-environment interaction in comorbid depression with alcohol use disorders via an integrated bioinformatics approach. | McEachin RC, Keller BJ, Saunders EF, McInnis MG | BioData mining | 18822146 | BioData Min | 2008 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/18822146 |
| A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer. | Laxman B, Morris DS, Yu J, Siddiqui J, Cao J, Mehra R, Lonigro RJ, Tsodikov A, Wei JT, Tomlins SA, Chinnaiyan AM | Cancer research | 18245462 | Cancer Res | 2008 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/18245462 |
| Literature-based discovery of diabetes- and ROS-related targets. | Hur J, Sullivan KA, Schuyler AD, Hong Y, Pande M, States DJ, Jagadish HV, Feldman EL | BMC medical genomics | 20979611 | BMC Med Genomics | 2010 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/20979611 |
| A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. | Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R | Molecular & cellular proteomics : MCP | 21632744 | Mol Cell Proteomics | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21632744 |
| A diagram editor for efficient biomedical knowledge capture and integration. | Yu B, Jakupovic E, Wilson J, Dai M, Xuan W, Mirel B, Athey B, Watson S, Meng F | Summit on translational bioinformatics | 21347131 | Summit Transl Bioinform | 2008 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347131 |
| GLay: community structure analysis of biological networks. | Su G, Kuchinsky A, Morris JH, States DJ, Meng F | Bioinformatics (Oxford, England) | 21123224 | Bioinformatics | 2010 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/21123224 |
| Cross-domain neurobiology data integration and exploration. | Xuan W, Dai M, Buckner J, Mirel B, Song J, Athey B, Watson SJ, Meng F | BMC genomics | 21143788 | BMC Genomics | 2010 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/21143788 |
| Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. | Omenn GS, Menon R, Zhang Y | Journal of proteomics | 23603631 | J Proteomics | 2013 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/23603631 |
| Identification of Functional Regulatory Residues of the β -Lactam Inducible Penicillin Binding Protein in Methicillin-Resistant Staphylococcus aureus. | Mbah AN, Isokpehi RD | Chemotherapy research and practice | 23984067 | Chemother Res Pract | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23984067 |
| Formal concept analysis of disease similarity. | Keller BJ, Eichinger F, Kretzler M | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22779049 | AMIA Jt Summits Transl Sci Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22779049 |
| SRM targeted proteomics in search for biomarkers of HCV-induced progression of fibrosis to cirrhosis in HALT-C patients. | Qin S, Zhou Y, Lok AS, Tsodikov A, Yan X, Gray L, Yuan M, Moritz RL, Galas D, Omenn GS, Hood L | Proteomics | 22577025 | Proteomics | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22577025 |
| Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. | Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, Wu SL, Hancock WS | Journal of proteome research | 23647160 | J Proteome Res | 2013 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/23647160 |
| Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. | Hur J, Xiang Z, Feldman EL, He Y | BMC immunology | 21871085 | BMC Immunol | 2011 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/21871085 |
| The identification of gene expression profiles associated with progression of human diabetic neuropathy. | Hur J, Sullivan KA, Pande M, Hong Y, Sima AA, Jagadish HV, Kretzler M, Feldman EL | Brain : a journal of neurology | 21926103 | Brain | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21926103 |
| Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. | Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS | Bioinformatics (Oxford, England) | 22135418 | Bioinformatics | 2012 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/22135418 |
| Spatio-temporal Structure of US Critical Care Transfer Network. | Unnikrishnan KP, Patnaik D, Iwashyna TJ | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 22211183 | AMIA Jt Summits Transl Sci Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22211183 |
| Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. | Menon R, Roy A, Mukherjee S, Belkin S, Zhang Y, Omenn GS | Journal of proteome research | 22003824 | J Proteome Res | 2011 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/22003824 |
| Characterization of KRAS rearrangements in metastatic prostate cancer. | Wang XS, Shankar S, Dhanasekaran SM, Ateeq B, Sasaki AT, Jing X, Robinson D, Cao Q, Prensner JR, Yocum AK, Wang R, Fries DF, Han B, Asangani IA, Cao X, Li Y, Omenn GS, Pflueger D, Gopalan A, Reuter VE, Kahoud ER, Cantley LC, Rubin MA, Palanisamy N, Varambally S, Chinnaiyan AM | Cancer discovery | 22140652 | Cancer Discov | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22140652 |
| Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors. | Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR | Drug safety | 27003817 | Drug Saf | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27003817 |
| The peroxisome proliferator-activated receptor-gamma2 Pro12A1a variant: association with type 2 diabetes and trait differences. | Douglas JA, Erdos MR, Watanabe RM, Braun A, Johnston CL, Oeth P, Mohlke KL, Valle TT, Ehnholm C, Buchanan TA, Bergman RN, Collins FS, Boehnke M, Tuomilehto J | Diabetes | 11289057 | Diabetes | 2001 Apr | https://www.ncbi.nlm.nih.gov/pubmed/11289057 |
| Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. | Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ | Genome biology | 16646984 | Genome Biol | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16646984 |
| Damage to the human cerebellum from prenatal alcohol exposure: the anatomy of a simple biometrical explanation. | Bookstein FL, Streissguth AP, Connor PD, Sampson PD | Anatomical record. Part B, New anatomist | 16955499 | Anat Rec B New Anat | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16955499 |
| A framework for protein structure classification and identification of novel protein structures. | Kim YJ, Patel JM | BMC bioinformatics | 17042958 | BMC Bioinformatics | 2006 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/17042958 |
| SNP Function Portal: a web database for exploring the function implication of SNP alleles. | Wang P, Dai M, Xuan W, McEachin RC, Jackson AU, Scott LJ, Athey B, Watson SJ, Meng F | Bioinformatics (Oxford, England) | 16873516 | Bioinformatics | 2006 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/16873516 |
| Mouse models of diabetic neuropathy. | Sullivan KA, Hayes JM, Wiggin TD, Backus C, Su Oh S, Lentz SI, Brosius F 3rd, Feldman EL | Neurobiology of disease | 17804249 | Neurobiol Dis | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17804249 |
| Automated learning of generative models for subcellular location: building blocks for systems biology. | Zhao T, Murphy RF | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 17972315 | Cytometry A | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17972315 |
| A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival. | Yu J, Yu J, Cordero KE, Johnson MD, Ghosh D, Rae JM, Chinnaiyan AM, Lippman ME | Neoplasia (New York, N.Y.) | 18231641 | Neoplasia | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18231641 |
| Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. | Rhodes DR, Kalyana-Sundaram S, Tomlins SA, Mahavisno V, Kasper N, Varambally R, Barrette TR, Ghosh D, Varambally S, Chinnaiyan AM | Neoplasia (New York, N.Y.) | 17534450 | Neoplasia | 2007 May | https://www.ncbi.nlm.nih.gov/pubmed/17534450 |
| Humoral response profiling reveals pathways to prostate cancer progression. | Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A | Molecular & cellular proteomics : MCP | 18077443 | Mol Cell Proteomics | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18077443 |
| Medline search engine for finding genetic markers with biological significance. | Xuan W, Wang P, Watson SJ, Meng F | Bioinformatics (Oxford, England) | 17823133 | Bioinformatics | 2007 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/17823133 |
| An active visual search interface for Medline. | Xuan W, Dai M, Mirel B, Wilson J, Athey B, Watson SJ, Meng F | Computational systems bioinformatics. Computational Systems Bioinformatics Conference | 17951838 | Comput Syst Bioinformatics Conf | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17951838 |
| miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. | Xiang Z, Minter RM, Bi X, Woolf PJ, He Y | Bioinformatics (Oxford, England) | 17644819 | Bioinformatics | 2007 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/17644819 |
| Automated image analysis of protein localization in budding yeast. | Chen SC, Zhao T, Gordon GJ, Murphy RF | Bioinformatics (Oxford, England) | 17646347 | Bioinformatics | 2007 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/17646347 |
| poolHiTS: a shifted transversal design based pooling strategy for high-throughput drug screening. | Kainkaryam RM, Woolf PJ | BMC bioinformatics | 18513431 | BMC Bioinformatics | 2008 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/18513431 |
| Rosiglitazone treatment reduces diabetic neuropathy in streptozotocin-treated DBA/2J mice. | Wiggin TD, Kretzler M, Pennathur S, Sullivan KA, Brosius FC, Feldman EL | Endocrinology | 18583417 | Endocrinology | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18583417 |
| Identifying gene-disease associations using centrality on a literature mined gene-interaction network. | Ozgür A, Vu T, Erkan G, Radev DR | Bioinformatics (Oxford, England) | 18586725 | Bioinformatics | 2008 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/18586725 |
| Michigan molecular interactions r2: from interacting proteins to pathways. | Tarcea VG, Weymouth T, Ade A, Bookvich A, Gao J, Mahavisno V, Wright Z, Chapman A, Jayapandian M, Ozgür A, Tian Y, Cavalcoli J, Mirel B, Patel J, Radev D, Athey B, States D, Jagadish HV | Nucleic acids research | 18978014 | Nucleic Acids Res | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18978014 |
| Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. | Luo W, Hankenson KD, Woolf PJ | BMC bioinformatics | 18980677 | BMC Bioinformatics | 2008 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/18980677 |
| Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge. | Martini S, Eichinger F, Nair V, Kretzler M | Reviews in endocrine & metabolic disorders | 18704688 | Rev Endocr Metab Disord | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18704688 |
| Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. | Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ | Cancer research | 19118015 | Cancer Res | 2009 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19118015 |
| Genome-wide association study identifies eight loci associated with blood pressure. | Newton-Cheh C, Johnson T, Gateva V, Tobin MD, Bochud M, Coin L, Najjar SS, Zhao JH, Heath SC, Eyheramendy S, Papadakis K, Voight BF, Scott LJ, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers JC, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee DE, Onland-Moret NC, Bots ML, Wain LV, Elliott KS, Teumer A, Luan J, Lucas G, Kuusisto J, Burton PR, Hadley D, McArdle WL, Wellcome Trust Case Control Consortium, Brown M, Dominiczak A, Newhouse SJ, Samani NJ, Webster J, Zeggini E, Beckmann JS, Bergmann S, Lim N, Song K, Vollenweider P, Waeber G, Waterworth DM, Yuan X, Groop L, Orho-Melander M, Allione A, Di Gregorio A, Guarrera S, Panico S, Ricceri F, Romanazzi V, Sacerdote C, Vineis P, Barroso I, Sandhu MS, Luben RN, Crawford GJ, Jousilahti P, Perola M, Boehnke M, Bonnycastle LL, Collins FS, Jackson AU, Mohlke KL, Stringham HM, Valle TT, Willer CJ, Bergman RN, Morken MA, Döring A, Gieger C, Illig T, Meitinger T, Org E, Pfeufer A, Wichmann HE, Kathiresan S, Marrugat J, O'Donnell CJ, Schwartz SM, Siscovick DS, Subirana I, Freimer NB, Hartikainen AL, McCarthy MI, O'Reilly PF, Peltonen L, Pouta A, de Jong PE, Snieder H, van Gilst WH, Clarke R, Goel A, Hamsten A, Peden JF, Seedorf U, Syvänen AC, Tognoni G, Lakatta EG, Sanna S, Scheet P, Schlessinger D, Scuteri A, Dörr M, Ernst F, Felix SB, Homuth G, Lorbeer R, Reffelmann T, Rettig R, Völker U, Galan P, Gut IG, Hercberg S, Lathrop GM, Zelenika D, Deloukas P, Soranzo N, Williams FM, Zhai G, Salomaa V, Laakso M, Elosua R, Forouhi NG, Völzke H, Uiterwaal CS, van der Schouw YT, Numans ME, Matullo G, Navis G, Berglund G, Bingham SA, Kooner JS, Connell JM, Bandinelli S, Ferrucci L, Watkins H, Spector TD, Tuomilehto J, Altshuler D, Strachan DP, Laan M, Meneton P, Wareham NJ, Uda M, Jarvelin MR, Mooser V, Melander O, Loos RJ, Elliott P, Abecasis GR, Caulfield M, Munroe PB | Nature genetics | 19430483 | Nat Genet | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19430483 |
| Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data. | Shah A, Woolf P | Journal of machine learning research : JMLR | 20161541 | J Mach Learn Res | 2009 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/20161541 |
| Bayesian network expansion identifies new ROS and biofilm regulators. | Hodges AP, Dai D, Xiang Z, Woolf P, Xi C, He Y | PloS one | 20209085 | PLoS One | 2010 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/20209085 |
| AUTOMATED COMPARISON OF PROTEIN SUBCELLULAR LOCATION PATTERNS BETWEEN IMAGES OF NORMAL AND CANCEROUS TISSUES. | Glory E, Newberg J, Murphy RF | Proceedings. IEEE International Symposium on Biomedical Imaging | 20628549 | Proc IEEE Int Symp Biomed Imaging | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/20628549 |
| Experimental approaches to the human renal transcriptome. | Hodgin JB, Cohen CD | Seminars in nephrology | 21044757 | Semin Nephrol | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21044757 |
| Using mechanistic Bayesian networks to identify downstream targets of the sonic hedgehog pathway. | Shah A, Tenzen T, McMahon AP, Woolf PJ | BMC bioinformatics | 20021670 | BMC Bioinformatics | 2009 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/20021670 |
| ConceptGen: a gene set enrichment and gene set relation mapping tool. | Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS | Bioinformatics (Oxford, England) | 20007254 | Bioinformatics | 2010 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/20007254 |
| WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. | Mo F, Mo Q, Chen Y, Goodlett DR, Hood L, Omenn GS, Li S, Lin B | BMC bioinformatics | 20429928 | BMC Bioinformatics | 2010 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/20429928 |
| RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples. | Alvarez A, Woolf PJ | BMC bioinformatics | 21682879 | BMC Bioinformatics | 2011 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/21682879 |
| Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. | Luo W, Friedman MS, Hankenson KD, Woolf PJ | BMC systems biology | 21605425 | BMC Syst Biol | 2011 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/21605425 |
| GSearcher: agile attribute querying for biological networks. | Su G, Athey BD, Meng F | Bioinformatics (Oxford, England) | 21088028 | Bioinformatics | 2010 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/21088028 |
| A mechanistic model of PCR for accurate quantification of quantitative PCR data. | Boggy GJ, Woolf PJ | PloS one | 20814578 | PLoS One | 2010 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/20814578 |
| Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks. | Alvarez A, Woolf PJ | BMC systems biology | 21619639 | BMC Syst Biol | 2011 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/21619639 |
| Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. | Vellaichamy A, Sreekumar A, Strahler JR, Rajendiran T, Yu J, Varambally S, Li Y, Omenn GS, Chinnaiyan AM, Nesvizhskii AI | PloS one | 19763266 | PLoS One | 2009 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/19763266 |
| Gene regulatory networks in embryonic stem cells and brain development. | Ghosh D, Yan X, Tian Q | Birth defects research. Part C, Embryo today : reviews | 19530135 | Birth Defects Res C Embryo Today | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19530135 |
| Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. | Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L | PloS one | 19668381 | PLoS One | 2009 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/19668381 |
| Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. | Yang CY, Sun H, Chen J, Nikolovska-Coleska Z, Wang S | Journal of the American Chemical Society | 19736924 | J Am Chem Soc | 2009 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/19736924 |
| GAGE: generally applicable gene set enrichment for pathway analysis. | Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ | BMC bioinformatics | 19473525 | BMC Bioinformatics | 2009 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/19473525 |
| Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription. | Chen Y, Lin G, Huo JS, Barney D, Wang Z, Livshiz T, States DJ, Qin ZS, Schwartz J | Endocrinology | 19406940 | Endocrinology | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19406940 |
| The University of Michigan Honest Broker: a Web-based service for clinical and translational research and practice. | Boyd AD, Saxman PR, Hunscher DA, Smith KA, Morris TD, Kaston M, Bayoff F, Rogers B, Hayes P, Rajeev N, Kline-Rogers E, Eagle K, Clauw D, Greden JF, Green LA, Athey BD | Journal of the American Medical Informatics Association : JAMIA | 19717803 | J Am Med Inform Assoc | 2009 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/19717803 |
| Integrating and annotating the interactome using the MiMI plugin for cytoscape. | Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ | Bioinformatics (Oxford, England) | 18812364 | Bioinformatics | 2009 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/18812364 |
| Metab2MeSH: annotating compounds with medical subject headings. | Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B, Karnovsky A | Bioinformatics (Oxford, England) | 22492643 | Bioinformatics | 2012 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/22492643 |
| Central nervous system endoplasmic reticulum stress in a murine model of type 2 diabetes. | Sims-Robinson C, Zhao S, Hur J, Feldman EL | Diabetologia | 22581041 | Diabetologia | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22581041 |
| Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity. | Dimas AS, Lagou V, Barker A, Knowles JW, Mägi R, Hivert MF, Benazzo A, Rybin D, Jackson AU, Stringham HM, Song C, Fischer-Rosinsky A, Boesgaard TW, Grarup N, Abbasi FA, Assimes TL, Hao K, Yang X, Lecoeur C, Barroso I, Bonnycastle LL, Böttcher Y, Bumpstead S, Chines PS, Erdos MR, Graessler J, Kovacs P, Morken MA, Narisu N, Payne F, Stancakova A, Swift AJ, Tönjes A, Bornstein SR, Cauchi S, Froguel P, Meyre D, Schwarz PE, Häring HU, Smith U, Boehnke M, Bergman RN, Collins FS, Mohlke KL, Tuomilehto J, Quertemous T, Lind L, Hansen T, Pedersen O, Walker M, Pfeiffer AF, Spranger J, Stumvoll M, Meigs JB, Wareham NJ, Kuusisto J, Laakso M, Langenberg C, Dupuis J, Watanabe RM, Florez JC, Ingelsson E, McCarthy MI, Prokopenko I, MAGIC Investigators | Diabetes | 24296717 | Diabetes | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24296717 |
| Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes. | Isokpehi RD, Udensi UK, Anyanwu MN, Mbah AN, Johnson MO, Edusei K, Bauer MA, Hall RA, Awofolu OR | Biomarker insights | 23115478 | Biomark Insights | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23115478 |
| Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. | Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M, Hu M, Sam L, Grasso C, Maher CA, Palanisamy N, Mehra R, Kominsky HD, Siddiqui J, Yu J, Qin ZS, Chinnaiyan AM | Genome research | 21724842 | Genome Res | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21724842 |
| Aberrantly Expressed Genes in HaCaT Keratinocytes Chronically Exposed to Arsenic Trioxide. | Udensi UK, Cohly HH, Graham-Evans BE, Ndebele K, Garcia-Reyero N, Nanduri B, Tchounwou PB, Isokpehi RD | Biomarker insights | 21461292 | Biomark Insights | 2011 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/21461292 |
| Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. | Ozgür A, Xiang Z, Radev DR, He Y | Journal of biomedicine & biotechnology | 20625487 | J Biomed Biotechnol | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20625487 |
| HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. | Contreras-Galindo R, Kaplan MH, He S, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Kappes F, Dube D, Chan SM, Robinson D, Meng F, Dai M, Gitlin SD, Chinnaiyan AM, Omenn GS, Markovitz DM | Genome research | 23657884 | Genome Res | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23657884 |
| Inferences on the biochemical and environmental regulation of universal stress proteins from Schistosomiasis parasites. | Mbah AN, Mahmud O, Awofolu OR, Isokpehi RD | Advances and applications in bioinformatics and chemistry : AABC | 23696708 | Adv Appl Bioinform Chem | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23696708 |
| N-glycoproteome of E14.Tg2a mouse embryonic stem cells. | Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L, Tian Q, Hood L | PloS one | 23405203 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23405203 |
| From single nucleotide polymorphism to transcriptional mechanism: a model for FRMD3 in diabetic nephropathy. | Martini S, Nair V, Patel SR, Eichinger F, Nelson RG, Weil EJ, Pezzolesi MG, Krolewski AS, Randolph A, Keller BJ, Werner T, Kretzler M | Diabetes | 23434934 | Diabetes | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23434934 |
| Gene expression alterations in bipolar disorder postmortem brains. | Chen H, Wang N, Zhao X, Ross CA, O'Shea KS, McInnis MG | Bipolar disorders | 23360497 | Bipolar Disord | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23360497 |
| Drug Target Exploitable Structural Features of Adenylyl Cyclase Activity in Schistosoma mansoni. | Mbah AN, Kamga HL, Awofolu OR, Isokpehi RD | Drug target insights | 23133313 | Drug Target Insights | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23133313 |
| Broadening instructional scope with network visualization. | Brandenburg MD, Song J | Journal of the Medical Library Association : JMLA | 23133334 | J Med Libr Assoc | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23133334 |
| The gputools package enables GPU computing in R. | Buckner J, Wilson J, Seligman M, Athey B, Watson S, Meng F | Bioinformatics (Oxford, England) | 19850754 | Bioinformatics | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/19850754 |
| BatchGenAna: a batch platform for large-scale genomic analysis of mammalian small RNAs. | Ying X, Kim YJ, Mao Y, Liu M, Hou Y, Li H, Wang X, Zhao Y, Zhao D, Patel JM, Li W | Bioinformation | 19707298 | Bioinformation | 2009 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/19707298 |
| Unified translation repression mechanism for microRNAs and upstream AUGs. | Ajay SS, Athey BD, Lee I | BMC genomics | 20205738 | BMC Genomics | 2010 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/20205738 |
| Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. | Menon R, Omenn GS | Cancer research | 20388783 | Cancer Res | 2010 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/20388783 |
| The NIH National Center for Integrative Biomedical Informatics (NCIBI). | Athey BD, Cavalcoli JD, Jagadish HV, Omenn GS, Mirel B, Kretzler M, Burant C, Isokpehi RD, DeLisi C, NCIBI faculty, trainees, and staff | Journal of the American Medical Informatics Association : JAMIA | 22101971 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22101971 |
| Evolutionary molecular medicine. | Nesse RM, Ganten D, Gregory TR, Omenn GS | Journal of molecular medicine (Berlin, Germany) | 22544168 | J Mol Med (Berl) | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22544168 |
| A graph algebra for scalable visual analytics. | Shaverdian AA, Zhou H, Michailidis G, Jagadish HV | IEEE computer graphics and applications | 24806630 | IEEE Comput Graph Appl | 2012 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/24806630 |
| State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. | Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL | Journal of proteome research | 24261998 | J Proteome Res | 2014 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/24261998 |
| Studying PubMed usages in the field for complex problem solving: Implications for tool design. | Mirel B, Song J, Tonks JS, Meng F, Xuan W, Ameziane R | Journal of the American Society for Information Science and Technology : JASIST | 24376375 | J Am Soc Inf Sci Technol | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/24376375 |
| Introducing meta-services for biomedical information extraction. | Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A | Genome biology | 18834497 | Genome Biol | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18834497 |
| A bioinformatics analysis of the cell line nomenclature. | Sarntivijai S, Ade AS, Athey BD, States DJ | Bioinformatics (Oxford, England) | 18849319 | Bioinformatics | 2008 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/18849319 |
| How to build a tight but permeable glomerular junction. | Martini S, Kretzler M | Journal of the American Society of Nephrology : JASN | 19520750 | J Am Soc Nephrol | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19520750 |
| Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. | Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, de Bakker PI, Abecasis GR, Almgren P, Andersen G, Ardlie K, Boström KB, Bergman RN, Bonnycastle LL, Borch-Johnsen K, Burtt NP, Chen H, Chines PS, Daly MJ, Deodhar P, Ding CJ, Doney AS, Duren WL, Elliott KS, Erdos MR, Frayling TM, Freathy RM, Gianniny L, Grallert H, Grarup N, Groves CJ, Guiducci C, Hansen T, Herder C, Hitman GA, Hughes TE, Isomaa B, Jackson AU, Jørgensen T, Kong A, Kubalanza K, Kuruvilla FG, Kuusisto J, Langenberg C, Lango H, Lauritzen T, Li Y, Lindgren CM, Lyssenko V, Marvelle AF, Meisinger C, Midthjell K, Mohlke KL, Morken MA, Morris AD, Narisu N, Nilsson P, Owen KR, Palmer CN, Payne F, Perry JR, Pettersen E, Platou C, Prokopenko I, Qi L, Qin L, Rayner NW, Rees M, Roix JJ, Sandbaek A, Shields B, Sjögren M, Steinthorsdottir V, Stringham HM, Swift AJ, Thorleifsson G, Thorsteinsdottir U, Timpson NJ, Tuomi T, Tuomilehto J, Walker M, Watanabe RM, Weedon MN, Willer CJ, Wellcome Trust Case Control Consortium, Illig T, Hveem K, Hu FB, Laakso M, Stefansson K, Pedersen O, Wareham NJ, Barroso I, Hattersley AT, Collins FS, Groop L, McCarthy MI, Boehnke M, Altshuler D | Nature genetics | 18372903 | Nat Genet | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18372903 |
| Identifying hypothetical genetic influences on complex disease phenotypes. | Keller BJ, McEachin RC | BMC bioinformatics | 19208188 | BMC Bioinformatics | 2009 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/19208188 |
| Feature selection and molecular classification of cancer using genetic programming. | Yu J, Yu J, Almal AA, Dhanasekaran SM, Ghosh D, Worzel WP, Chinnaiyan AM | Neoplasia (New York, N.Y.) | 17460773 | Neoplasia | 2007 Apr | https://www.ncbi.nlm.nih.gov/pubmed/17460773 |
| Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels. | Chen WM, Erdos MR, Jackson AU, Saxena R, Sanna S, Silver KD, Timpson NJ, Hansen T, Orrù M, Grazia Piras M, Bonnycastle LL, Willer CJ, Lyssenko V, Shen H, Kuusisto J, Ebrahim S, Sestu N, Duren WL, Spada MC, Stringham HM, Scott LJ, Olla N, Swift AJ, Najjar S, Mitchell BD, Lawlor DA, Smith GD, Ben-Shlomo Y, Andersen G, Borch-Johnsen K, Jørgensen T, Saramies J, Valle TT, Buchanan TA, Shuldiner AR, Lakatta E, Bergman RN, Uda M, Tuomilehto J, Pedersen O, Cao A, Groop L, Mohlke KL, Laakso M, Schlessinger D, Collins FS, Altshuler D, Abecasis GR, Boehnke M, Scuteri A, Watanabe RM | The Journal of clinical investigation | 18521185 | J Clin Invest | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18521185 |
| The role of SPINK1 in ETS rearrangement-negative prostate cancers. | Tomlins SA, Rhodes DR, Yu J, Varambally S, Mehra R, Perner S, Demichelis F, Helgeson BE, Laxman B, Morris DS, Cao Q, Cao X, Andrén O, Fall K, Johnson L, Wei JT, Shah RB, Al-Ahmadie H, Eastham JA, Eggener SE, Fine SW, Hotakainen K, Stenman UH, Tsodikov A, Gerald WL, Lilja H, Reuter VE, Kantoff PW, Scardino PT, Rubin MA, Bjartell AS, Chinnaiyan AM | Cancer cell | 18538735 | Cancer Cell | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18538735 |
| A framework for the automated analysis of subcellular patterns in human protein atlas images. | Newberg J, Murphy RF | Journal of proteome research | 18435555 | J Proteome Res | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18435555 |
| Evidence of interaction between PPARG2 and HNF4A contributing to variation in insulin sensitivity in Mexican Americans. | Black MH, Fingerlin TE, Allayee H, Zhang W, Xiang AH, Trigo E, Hartiala J, Lehtinen AB, Haffner SM, Bergman RN, McEachin RC, Kjos SL, Lawrence JM, Buchanan TA, Watanabe RM | Diabetes | 18162503 | Diabetes | 2008 Apr | https://www.ncbi.nlm.nih.gov/pubmed/18162503 |
| Family-based SNP association study on 8q24 in bipolar disorder. | Zandi PP, Zöllner S, Avramopoulos D, Willour VL, Chen Y, Qin ZS, Burmeister M, Miao K, Gopalakrishnan S, McEachin R, Potash JB, Depaulo JR Jr, McInnis MG | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 18163389 | Am J Med Genet B Neuropsychiatr Genet | 2008 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/18163389 |
| Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). | Lee I, Ajay SS, Chen H, Maruyama A, Wang N, McInnis MG, Athey BD | Nucleic acids research | 18208839 | Nucleic Acids Res | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18208839 |
| Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. | Sun B, Ranish JA, Utleg AG, White JT, Yan X, Lin B, Hood L | Molecular & cellular proteomics : MCP | 17074749 | Mol Cell Proteomics | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17074749 |
| SAGA: a subgraph matching tool for biological graphs. | Tian Y, McEachin RC, Santos C, States DJ, Patel JM | Bioinformatics (Oxford, England) | 17110368 | Bioinformatics | 2007 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/17110368 |
| Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. | Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV | Nucleic acids research | 17130145 | Nucleic Acids Res | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17130145 |
| Of mice and men: cancer gene discovery using comparative oncogenomics. | Tomlins SA, Chinnaiyan AM | Cancer cell | 16843259 | Cancer Cell | 2006 Jul | https://www.ncbi.nlm.nih.gov/pubmed/16843259 |
| Evolutionary-conserved gene expression response profiles across mammalian tissues. | Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, States DJ | Omics : a journal of integrative biology | 17411398 | OMICS | 2007 Spring | https://www.ncbi.nlm.nih.gov/pubmed/17411398 |
| NGSQC: cross-platform quality analysis pipeline for deep sequencing data. | Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F | BMC genomics | 21143816 | BMC Genomics | 2010 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/21143816 |
| BN+1 Bayesian network expansion for identifying molecular pathway elements. | Hodges AP, Woolf P, He Y | Communicative & integrative biology | 21331236 | Commun Integr Biol | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21331236 |
| A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. | Yan X, Ma L, Yi D, Yoon JG, Diercks A, Foltz G, Price ND, Hood LE, Tian Q | Proceedings of the National Academy of Sciences of the United States of America | 21220328 | Proc Natl Acad Sci U S A | 2011 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/21220328 |
| Comorbidity of bipolar disorder with substance abuse: selection of prioritized genes for translational research. | Isokpehi RD, Lewis SA, Oyeleye TO, Ayensu WK, Gerald TM | Summit on translational bioinformatics | 21347170 | Summit Transl Bioinform | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347170 |
| Integrating automated workflows, human intelligence and collaboration. | Mirel B, Eichinger F, Nair V, Kretzler M | Summit on translational bioinformatics | 21347175 | Summit Transl Bioinform | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347175 |
| Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. | Lin B, White JT, Wu J, Lele S, Old LJ, Hood L, Odunsi K | Proteomics. Clinical applications | 20559449 | Proteomics Clin Appl | 2009 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/20559449 |
| Integrative biology identifies shared transcriptional networks in CKD. | Martini S, Nair V, Keller BJ, Eichinger F, Hawkins JJ, Randolph A, Böger CA, Gadegbeku CA, Fox CS, Cohen CD, Kretzler M, European Renal cDNA Bank, C-PROBE Cohort, CKDGen Consortium | Journal of the American Society of Nephrology : JASN | 24925724 | J Am Soc Nephrol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24925724 |
| Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein. | Gonzalez-Hernandez MJ, Cavalcoli JD, Sartor MA, Contreras-Galindo R, Meng F, Dai M, Dube D, Saha AK, Gitlin SD, Omenn GS, Kaplan MH, Markovitz DM | Journal of virology | 24872592 | J Virol | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24872592 |
| Integrating biomedical knowledge to model pathways of prostate cancer progression. | Morris DS, Tomlins SA, Rhodes DR, Mehra R, Shah RB, Chinnaiyan AM | Cell cycle (Georgetown, Tex.) | 17495538 | Cell Cycle | 2007 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/17495538 |
| Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. | Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM | Neoplasia (New York, N.Y.) | 17356713 | Neoplasia | 2007 Feb | https://www.ncbi.nlm.nih.gov/pubmed/17356713 |
| Integrative molecular concept modeling of prostate cancer progression. | Tomlins SA, Mehra R, Rhodes DR, Cao X, Wang L, Dhanasekaran SM, Kalyana-Sundaram S, Wei JT, Rubin MA, Pienta KJ, Shah RB, Chinnaiyan AM | Nature genetics | 17173048 | Nat Genet | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17173048 |
| Standards for plasma and serum proteomics in early cancer detection: a needs assessment report from the national institute of standards and technology--National Cancer Institute Standards, Methods, Assays, Reagents and Technologies Workshop, August 18-19, 2005. | Barker PE, Wagner PD, Stein SE, Bunk DM, Srivastava S, Omenn GS | Clinical chemistry | 16840585 | Clin Chem | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16840585 |
| Association of transcription factor 7-like 2 (TCF7L2) variants with type 2 diabetes in a Finnish sample. | Scott LJ, Bonnycastle LL, Willer CJ, Sprau AG, Jackson AU, Narisu N, Duren WL, Chines PS, Stringham HM, Erdos MR, Valle TT, Tuomilehto J, Bergman RN, Mohlke KL, Collins FS, Boehnke M | Diabetes | 16936217 | Diabetes | 2006 Sep | https://www.ncbi.nlm.nih.gov/pubmed/16936217 |
| Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. | Qian Y, Murphy RF | Bioinformatics (Oxford, England) | 18033795 | Bioinformatics | 2008 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/18033795 |
| Cytoscape ESP: simple search of complex biological networks. | Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ | Bioinformatics (Oxford, England) | 18445605 | Bioinformatics | 2008 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/18445605 |
| An IR-aided machine learning framework for the BioCreative II.5 Challenge. | Cao Y, Li Z, Liu F, Agarwal S, Zhang Q, Yu H | IEEE/ACM transactions on computational biology and bioinformatics | 20671317 | IEEE/ACM Trans Comput Biol Bioinform | 2010 Jul-Sep | https://www.ncbi.nlm.nih.gov/pubmed/20671317 |
| LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types. | Kim JH, Karnovsky A, Mahavisno V, Weymouth T, Pande M, Dolinoy DC, Rozek LS, Sartor MA | BMC genomics | 23033966 | BMC Genomics | 2012 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/23033966 |
| A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. | Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, Lundberg E, Mias G, Menon R, Mu Z, Nice E, Paik YK, Uhlen M, Wells L, Wu SL, Yan F, Zhang F, Zhang Y, Snyder M, Omenn GS, Beavis RC, Hancock WS | Journal of proteome research | 23259914 | J Proteome Res | 2013 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/23259914 |
| Tissue-specific profiling reveals transcriptome alterations in Arabidopsis mutants lacking morphological phenotypes. | Simon M, Bruex A, Kainkaryam RM, Zheng X, Huang L, Woolf PJ, Schiefelbein J | The Plant cell | 24014549 | Plant Cell | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24014549 |
| The genetics of insulin resistance: Where's Waldo? | Watanabe RM | Current diabetes reports | 20820957 | Curr Diab Rep | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20820957 |
| A molecular profile of focal segmental glomerulosclerosis from formalin-fixed, paraffin-embedded tissue. | Hodgin JB, Borczuk AC, Nasr SH, Markowitz GS, Nair V, Martini S, Eichinger F, Vining C, Berthier CC, Kretzler M, D'Agati VD | The American journal of pathology | 20847290 | Am J Pathol | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20847290 |
| THINK Back: KNowledge-based Interpretation of High Throughput data. | Farfán F, Ma J, Sartor MA, Michailidis G, Jagadish HV | BMC bioinformatics | 22536867 | BMC Bioinformatics | 2012 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/22536867 |
| Functional Annotation Analytics of Rhodopseudomonas palustris Genomes. | Simmons SS, Isokpehi RD, Brown SD, McAllister DL, Hall CC, McDuffy WM, Medley TL, Udensi UK, Rajnarayanan RV, Ayensu WK, Cohly HH | Bioinformatics and biology insights | 22084572 | Bioinform Biol Insights | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22084572 |
| U-Compare bio-event meta-service: compatible BioNLP event extraction services. | Kano Y, Björne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen KB, Verspoor K, Roeder C, Hunter LE, Kilicoglu H, Bergler S, Van Landeghem S, Van Parys T, Van de Peer Y, Miwa M, Ananiadou S, Neves M, Pascual-Montano A, Özgür A, Radev DR, Riedel S, Sætre R, Chun HW, Kim JD, Pyysalo S, Ohta T, Tsujii J | BMC bioinformatics | 22177292 | BMC Bioinformatics | 2011 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/22177292 |
| A systems view of genetics in chronic kidney disease. | Keller BJ, Martini S, Sedor JR, Kretzler M | Kidney international | 22012128 | Kidney Int | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22012128 |
| Ratcheting up cancer potency estimates. | Crouch EA, Omenn GS | Environmental science & technology | 22296526 | Environ Sci Technol | 2012 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/22296526 |
| Appearance frequency modulated gene set enrichment testing. | Ma J, Sartor MA, Jagadish HV | BMC bioinformatics | 21418606 | BMC Bioinformatics | 2011 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/21418606 |
| Transcriptional profiling of diabetic neuropathy in the BKS db/db mouse: a model of type 2 diabetes. | Pande M, Hur J, Hong Y, Backus C, Hayes JM, Oh SS, Kretzler M, Feldman EL | Diabetes | 21617178 | Diabetes | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21617178 |
| Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. | Moll AG, Lindenmeyer MT, Kretzler M, Nelson PJ, Zimmer R, Cohen CD | PloS one | 19277110 | PLoS One | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19277110 |
| New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites. | Lee I, Ajay SS, Yook JI, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, Athey BD | Genome research | 19336450 | Genome Res | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19336450 |
| An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. | Wang XS, Prensner JR, Chen G, Cao Q, Han B, Dhanasekaran SM, Ponnala R, Cao X, Varambally S, Thomas DG, Giordano TJ, Beer DG, Palanisamy N, Sartor MA, Omenn GS, Chinnaiyan AM | Nature biotechnology | 19881495 | Nat Biotechnol | 2009 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19881495 |
| A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder. | McEachin RC, Chen H, Sartor MA, Saccone SF, Keller BJ, Prossin AR, Cavalcoli JD, McInnis MG | BMC systems biology | 21092101 | BMC Syst Biol | 2010 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/21092101 |
| A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. | Mo F, Hong X, Gao F, Du L, Wang J, Omenn GS, Lin B | BMC bioinformatics | 19087293 | BMC Bioinformatics | 2008 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/19087293 |
| Loss of myotubularin function results in T-tubule disorganization in zebrafish and human myotubular myopathy. | Dowling JJ, Vreede AP, Low SE, Gibbs EM, Kuwada JY, Bonnemann CG, Feldman EL | PLoS genetics | 19197364 | PLoS Genet | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19197364 |
| Disorders of cranial nerves IX and X. | Erman AB, Kejner AE, Hogikyan ND, Feldman EL | Seminars in neurology | 19214937 | Semin Neurol | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19214937 |
| Chimeric transcript discovery by paired-end transcriptome sequencing. | Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu J, Lonigro RJ, Schroth G, Kumar-Sinha C, Chinnaiyan AM | Proceedings of the National Academy of Sciences of the United States of America | 19592507 | Proc Natl Acad Sci U S A | 2009 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/19592507 |
| Variants in MTNR1B influence fasting glucose levels. | Prokopenko I, Langenberg C, Florez JC, Saxena R, Soranzo N, Thorleifsson G, Loos RJ, Manning AK, Jackson AU, Aulchenko Y, Potter SC, Erdos MR, Sanna S, Hottenga JJ, Wheeler E, Kaakinen M, Lyssenko V, Chen WM, Ahmadi K, Beckmann JS, Bergman RN, Bochud M, Bonnycastle LL, Buchanan TA, Cao A, Cervino A, Coin L, Collins FS, Crisponi L, de Geus EJ, Dehghan A, Deloukas P, Doney AS, Elliott P, Freimer N, Gateva V, Herder C, Hofman A, Hughes TE, Hunt S, Illig T, Inouye M, Isomaa B, Johnson T, Kong A, Krestyaninova M, Kuusisto J, Laakso M, Lim N, Lindblad U, Lindgren CM, McCann OT, Mohlke KL, Morris AD, Naitza S, Orrù M, Palmer CN, Pouta A, Randall J, Rathmann W, Saramies J, Scheet P, Scott LJ, Scuteri A, Sharp S, Sijbrands E, Smit JH, Song K, Steinthorsdottir V, Stringham HM, Tuomi T, Tuomilehto J, Uitterlinden AG, Voight BF, Waterworth D, Wichmann HE, Willemsen G, Witteman JC, Yuan X, Zhao JH, Zeggini E, Schlessinger D, Sandhu M, Boomsma DI, Uda M, Spector TD, Penninx BW, Altshuler D, Vollenweider P, Jarvelin MR, Lakatta E, Waeber G, Fox CS, Peltonen L, Groop LC, Mooser V, Cupples LA, Thorsteinsdottir U, Boehnke M, Barroso I, Van Duijn C, Dupuis J, Watanabe RM, Stefansson K, McCarthy MI, Wareham NJ, Meigs JB, Abecasis GR | Nature genetics | 19060907 | Nat Genet | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/19060907 |
| Pooling in high-throughput drug screening. | Kainkaryam RM, Woolf PJ | Current opinion in drug discovery & development | 19396735 | Curr Opin Drug Discov Devel | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19396735 |
| Transcriptome sequencing to detect gene fusions in cancer. | Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM | Nature | 19136943 | Nature | 2009 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/19136943 |
| Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. | Gao J, Tarcea VG, Karnovsky A, Mirel BR, Weymouth TE, Beecher CW, Cavalcoli JD, Athey BD, Omenn GS, Burant CF, Jagadish HV | Bioinformatics (Oxford, England) | 20139469 | Bioinformatics | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20139469 |
| ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository. | Hill JA, Smith BE, Papoulias PG, Andrews PC | Journal of proteome research | 20356086 | J Proteome Res | 2010 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/20356086 |
| Linking variants from genome-wide association analysis to function via transcriptional network analysis. | Keller B, Martini S, Sedor J, Kretzler M | Seminars in nephrology | 20347646 | Semin Nephrol | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20347646 |
| Genetic evidence that raised sex hormone binding globulin (SHBG) levels reduce the risk of type 2 diabetes. | Perry JR, Weedon MN, Langenberg C, Jackson AU, Lyssenko V, Sparsø T, Thorleifsson G, Grallert H, Ferrucci L, Maggio M, Paolisso G, Walker M, Palmer CN, Payne F, Young E, Herder C, Narisu N, Morken MA, Bonnycastle LL, Owen KR, Shields B, Knight B, Bennett A, Groves CJ, Ruokonen A, Jarvelin MR, Pearson E, Pascoe L, Ferrannini E, Bornstein SR, Stringham HM, Scott LJ, Kuusisto J, Nilsson P, Neptin M, Gjesing AP, Pisinger C, Lauritzen T, Sandbaek A, Sampson M, MAGIC, Zeggini E, Lindgren CM, Steinthorsdottir V, Thorsteinsdottir U, Hansen T, Schwarz P, Illig T, Laakso M, Stefansson K, Morris AD, Groop L, Pedersen O, Boehnke M, Barroso I, Wareham NJ, Hattersley AT, McCarthy MI, Frayling TM | Human molecular genetics | 19933169 | Hum Mol Genet | 2010 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/19933169 |
| Application of universal stress proteins in probing the dynamics of potent degraders in complex terephthalate metagenome. | Mbah AN, Isokpehi RD | BioMed research international | 24151583 | Biomed Res Int | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24151583 |
| Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. | Menon R, Im H, Zhang EY, Wu SL, Chen R, Snyder M, Hancock WS, Omenn GS | Journal of proteome research | 24111759 | J Proteome Res | 2014 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/24111759 |
| Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences. | Contreras-Galindo R, Kaplan MH, Dube D, Gonzalez-Hernandez MJ, Chan S, Meng F, Dai M, Omenn GS, Gitlin SD, Markovitz DM | Journal of virology | 25926654 | J Virol | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25926654 |
| Bayesian network analysis of multi-compartmentalized immune responses in a murine model of sepsis and direct lung injury. | Nemzek JA, Hodges AP, He Y | BMC research notes | 26423575 | BMC Res Notes | 2015 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/26423575 |
| Computational approaches to phenotyping: high-throughput phenomics. | Lussier YA, Liu Y | Proceedings of the American Thoracic Society | 17202287 | Proc Am Thorac Soc | 2007 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17202287 |
| European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. | Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I | European journal of human genetics : EJHG | 19844264 | Eur J Hum Genet | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19844264 |
| Looking at cerebellar malformations through text-mined interactomes of mice and humans. | Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A | PLoS computational biology | 19893633 | PLoS Comput Biol | 2009 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19893633 |
| Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. | Katsamba P, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price S, Jessell TM, Ben-Shaul A, Shapiro L, Honig BH | Proceedings of the National Academy of Sciences of the United States of America | 19553217 | Proc Natl Acad Sci U S A | 2009 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/19553217 |
| Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. | Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A | Nature biotechnology | 19741643 | Nat Biotechnol | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19741643 |
| Electrostatic interactions between arginines and the minor groove in the nucleosome. | West SM, Rohs R, Mann RS, Honig B | Journal of biomolecular structure & dynamics | 20232938 | J Biomol Struct Dyn | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20232938 |
| T-cadherin structures reveal a novel adhesive binding mechanism. | Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison OJ, Brasch J, Jin X, Posy S, Vendome J, Ranscht B, Jessell TM, Honig B, Shapiro L | Nature structural & molecular biology | 20190755 | Nat Struct Mol Biol | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20190755 |
| Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. | Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z | Nature structural & molecular biology | 20364130 | Nat Struct Mol Biol | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20364130 |
| Learning "graph-mer" motifs that predict gene expression trajectories in development. | Li X, Panea C, Wiggins CH, Reinke V, Leslie C | PLoS computational biology | 20454681 | PLoS Comput Biol | 2010 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/20454681 |
| Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. | Fei J, Bronson JE, Hofman JM, Srinivas RL, Wiggins CH, Gonzalez RL Jr | Proceedings of the National Academy of Sciences of the United States of America | 19717422 | Proc Natl Acad Sci U S A | 2009 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/19717422 |
| Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. | Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R | Blood | 19965633 | Blood | 2010 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/19965633 |
| NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. | Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP, Aster JC, Sigaux F, Soulier J, Look AT, Young RA, Califano A, Ferrando AA | Proceedings of the National Academy of Sciences of the United States of America | 17114293 | Proc Natl Acad Sci U S A | 2006 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/17114293 |
| Computer science. Automating science. | Waltz D, Buchanan BG | Science (New York, N.Y.) | 19342574 | Science | 2009 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/19342574 |
| ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. | Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G | Proceedings of the National Academy of Sciences of the United States of America | 19118200 | Proc Natl Acad Sci U S A | 2009 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/19118200 |
| A predictive model of the oxygen and heme regulatory network in yeast. | Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C | PLoS computational biology | 19008939 | PLoS Comput Biol | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19008939 |
| Is protein classification necessary? Toward alternative approaches to function annotation. | Petrey D, Honig B | Current opinion in structural biology | 19269161 | Curr Opin Struct Biol | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19269161 |
| Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. | Miloushev VZ, Bahna F, Ciatto C, Ahlsen G, Honig B, Shapiro L, Palmer AG 3rd | Structure (London, England : 1993) | 18682221 | Structure | 2008 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/18682221 |
| Natively unstructured regions in proteins identified from contact predictions. | Schlessinger A, Punta M, Rost B | Bioinformatics (Oxford, England) | 17709338 | Bioinformatics | 2007 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/17709338 |
| Probing genetic overlap among complex human phenotypes. | Rzhetsky A, Wajngurt D, Park N, Zheng T | Proceedings of the National Academy of Sciences of the United States of America | 17609372 | Proc Natl Acad Sci U S A | 2007 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/17609372 |
| Bayesian approach to network modularity. | Hofman JM, Wiggins CH | Physical review letters | 18643711 | Phys Rev Lett | 2008 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/18643711 |
| Dissecting complex transcriptional responses using pathway-level scores based on prior information. | Bussemaker HJ, Ward LD, Boorsma A | BMC bioinformatics | 17903287 | BMC Bioinformatics | 2007 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/17903287 |
| Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. | David LA, Wiggins CH | Annals of the New York Academy of Sciences | 17925346 | Ann N Y Acad Sci | 2007 Dec | https://www.ncbi.nlm.nih.gov/pubmed/17925346 |
| Exprtarget: an integrative approach to predicting human microRNA targets. | Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, Dolan ME, Zhang W | PloS one | 20975837 | PLoS One | 2010 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/20975837 |
| Hierarchical evolution of the bacterial sporulation network. | de Hoon MJ, Eichenberger P, Vitkup D | Current biology : CB | 20833318 | Curr Biol | 2010 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/20833318 |
| Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation. | Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J, Grunn A, Fangazio M, Capello D, Monti S, Cresta S, Gargiulo E, Forconi F, Guarini A, Arcaini L, Paulli M, Laurenti L, Larocca LM, Marasca R, Gattei V, Oscier D, Bertoni F, Mullighan CG, Foá R, Pasqualucci L, Rabadan R, Dalla-Favera R, Gaidano G | The Journal of experimental medicine | 21670202 | J Exp Med | 2011 Jul 4 | https://www.ncbi.nlm.nih.gov/pubmed/21670202 |
| Testing and Validating Machine Learning Classifiers by Metamorphic Testing. | Xie X, Ho JW, Murphy C, Kaiser G, Xu B, Chen TY | The Journal of systems and software | 21532969 | J Syst Softw | 2011 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/21532969 |
| PredUs: a web server for predicting protein interfaces using structural neighbors. | Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D | Nucleic acids research | 21609948 | Nucleic Acids Res | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21609948 |
| Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology. | Lee Y, Li J, Gamazon E, Chen JL, Tikhomirov A, Cox NJ, Lussier YA | Summit on translational bioinformatics | 21347143 | Summit Transl Bioinform | 2010 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347143 |
| Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers. | Yang X, Lee Y, Fan H, Sun X, Lussier YA | Chinese science bulletin = Kexue tongbao | 21340045 | Chin Sci Bull | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21340045 |
| Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs. | Mathew B, Jacobson JR, Berdyshev E, Huang Y, Sun X, Zhao Y, Gerhold LM, Siegler J, Evenoski C, Wang T, Zhou T, Zaidi R, Moreno-Vinasco L, Bittman R, Chen CT, LaRiviere PJ, Sammani S, Lussier YA, Dudek SM, Natarajan V, Weichselbaum RR, Garcia JG | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 21712494 | FASEB J | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21712494 |
| MetaSeq: privacy preserving meta-analysis of sequencing-based association studies. | Singh AP, Zafer S, Pe'er I | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 23424140 | Pac Symp Biocomput | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23424140 |
| A molecular signature predictive of indolent prostate cancer. | Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Le Magnen C, Guarnieri P, Sumazin P, Benson MC, Shen MM, Califano A, Abate-Shen C | Science translational medicine | 24027026 | Sci Transl Med | 2013 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/24027026 |
| Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. | Pefanis E, Wang J, Rothschild G, Lim J, Chao J, Rabadan R, Economides AN, Basu U | Nature | 25119026 | Nature | 2014 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/25119026 |
| Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma. | Sonabend AM, Carminucci AS, Amendolara B, Bansal M, Leung R, Lei L, Realubit R, Li H, Karan C, Yun J, Showers C, Rothcock R, O J, Califano A, Canoll P, Bruce JN | Neuro-oncology | 24637229 | Neuro Oncol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24637229 |
| ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2. | Ghosh HS, Ceribelli M, Matos I, Lazarovici A, Bussemaker HJ, Lasorella A, Hiebert SW, Liu K, Staudt LM, Reizis B | The Journal of experimental medicine | 24980046 | J Exp Med | 2014 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/24980046 |
| Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion. | Johnson S, van de Meent JW, Phillips R, Wiggins CH, Lindén M | Nucleic acids research | 25120267 | Nucleic Acids Res | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25120267 |
| Toward a "structural BLAST": using structural relationships to infer function. | Dey F, Cliff Zhang Q, Petrey D, Honig B | Protein science : a publication of the Protein Society | 23349097 | Protein Sci | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23349097 |
| Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease. | Prabhu S, Pe'er I | Genome research | 22767386 | Genome Res | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22767386 |
| Transforming fusions of FGFR and TACC genes in human glioblastoma. | Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A | Science (New York, N.Y.) | 22837387 | Science | 2012 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/22837387 |
| Wisdom of crowds for robust gene network inference. | Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G | Nature methods | 22796662 | Nat Methods | 2012 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/22796662 |
| STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma. | Bisikirska BC, Adam SJ, Alvarez MJ, Rajbhandari P, Cox R, Lefebvre C, Wang K, Rieckhof GE, Felsher DW, Califano A | Oncogene | 23178486 | Oncogene | 2013 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/23178486 |
| Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures. | Li C, Nguyen HT, Zhuang Y, Lin Z, Flemington EK, Zhuo Y, Kantrow SP, Morris GF, Sullivan DE, Shan B | Gene | 23036707 | Gene | 2012 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/23036707 |
| Quantifying pathogen surveillance using temporal genomic data. | Chan JM, Rabadan R | mBio | 23362319 | mBio | 2013 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/23362319 |
| How many neutrophils are enough (redux, redux)? | Silverstein SC, Rabadan R | The Journal of clinical investigation | 22820286 | J Clin Invest | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22820286 |
| Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia. | Rossi D, Khiabanian H, Spina V, Ciardullo C, Bruscaggin A, Famà R, Rasi S, Monti S, Deambrogi C, De Paoli L, Wang J, Gattei V, Guarini A, Foà R, Rabadan R, Gaidano G | Blood | 24501221 | Blood | 2014 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/24501221 |
| Genetic robustness and functional evolution of gene duplicates. | Plata G, Vitkup D | Nucleic acids research | 24288370 | Nucleic Acids Res | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24288370 |
| Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. | Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA | Cancer cell | 24291004 | Cancer Cell | 2013 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/24291004 |
| Genetic interactions between chromosomes 11 and 18 contribute to airway hyperresponsiveness in mice. | Ferreira CM, Chen JL, Li J, Shimomura K, Yang X, Lussier YA, Pinto LH, Solway J | PloS one | 22253740 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22253740 |
| An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. | Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A | Cell | 22000015 | Cell | 2011 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/22000015 |
| Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. | Martínez MR, Corradin A, Klein U, Álvarez MJ, Toffolo GM, di Camillo B, Califano A, Stolovitzky GA | Proceedings of the National Academy of Sciences of the United States of America | 22308355 | Proc Natl Acad Sci U S A | 2012 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/22308355 |
| A hidden Markov model for copy number variant prediction from whole genome resequencing data. | Shen Y, Gu Y, Pe'er I | BMC bioinformatics | 21989326 | BMC Bioinformatics | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21989326 |
| Convergent mutations and kinase fusions lead to oncogenic STAT3 activation in anaplastic large cell lymphoma. | Crescenzo R, Abate F, Lasorsa E, Tabbo' F, Gaudiano M, Chiesa N, Di Giacomo F, Spaccarotella E, Barbarossa L, Ercole E, Todaro M, Boi M, Acquaviva A, Ficarra E, Novero D, Rinaldi A, Tousseyn T, Rosenwald A, Kenner L, Cerroni L, Tzankov A, Ponzoni M, Paulli M, Weisenburger D, Chan WC, Iqbal J, Piris MA, Zamo' A, Ciardullo C, Rossi D, Gaidano G, Pileri S, Tiacci E, Falini B, Shultz LD, Mevellec L, Vialard JE, Piva R, Bertoni F, Rabadan R, Inghirami G, European T-Cell Lymphoma Study Group, T-Cell Project: Prospective Collection of Data in Patients with Peripheral T-Cell Lymphoma and the AIRC 5xMille Consortium “Genetics-Driven Targeted Management of Lymphoid Malignancies” | Cancer cell | 25873174 | Cancer Cell | 2015 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/25873174 |
| An information theoretic method to identify combinations of genomic alterations that promote glioblastoma. | Melamed RD, Wang J, Iavarone A, Rabadan R | Journal of molecular cell biology | 25941339 | J Mol Cell Biol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25941339 |
| Genotype to phenotype relationships in autism spectrum disorders. | Chang J, Gilman SR, Chiang AH, Sanders SJ, Vitkup D | Nature neuroscience | 25531569 | Nat Neurosci | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25531569 |
| A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation. | Abate F, Todaro M, van der Krogt JA, Boi M, Landra I, Machiorlatti R, Tabbò F, Messana K, Abele C, Barreca A, Novero D, Gaudiano M, Aliberti S, Di Giacomo F, Tousseyn T, Lasorsa E, Crescenzo R, Bessone L, Ficarra E, Acquaviva A, Rinaldi A, Ponzoni M, Longo DL, Aime S, Cheng M, Ruggeri B, Piccaluga PP, Pileri S, Tiacci E, Falini B, Pera-Gresely B, Cerchietti L, Iqbal J, Chan WC, Shultz LD, Kwee I, Piva R, Wlodarska I, Rabadan R, Bertoni F, Inghirami G, European T-cell Lymphoma Study Group | Leukemia | 25533804 | Leukemia | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25533804 |
| SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. | Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ | Methods in molecular biology (Clifton, N.J.) | 25151169 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25151169 |
| In search of the determinants of enhancer-promoter interaction specificity. | van Arensbergen J, van Steensel B, Bussemaker HJ | Trends in cell biology | 25160912 | Trends Cell Biol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25160912 |
| Co-regulated transcripts associated to cooperating eSNPs define Bi-fan motifs in human gene networks. | Kreimer A, Pe'er I | PLoS genetics | 25210734 | PLoS Genet | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25210734 |
| DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. | Alvarez MJ, Chen JC, Califano A | Bioinformatics (Oxford, England) | 26338767 | Bioinformatics | 2015 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/26338767 |
| Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. | Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C, Villagrasa-Gonzalez P, Viale A, Korkola JE, Houldsworth J, Feldman DR, Bosl GJ, Califano A, Chaganti RS | Stem cells (Dayton, Ohio) | 25336442 | Stem Cells | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25336442 |
| A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions. | Stockman VB, Ghamsari L, Lasso G, Honig B, Shapira SD, Wang HH | PloS one | 27936040 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27936040 |
| High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation. | Lencz T, Yu J, Palmer C, Carmi S, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Joseph V, Klein R, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Atzmon G, Pe'er I | Human genetics | 29705978 | Hum Genet | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29705978 |
| Context Sensitive Modeling of Cancer Drug Sensitivity. | Chen BJ, Litvin O, Ungar L, Pe'er D | PloS one | 26274927 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26274927 |
| Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain. | Sheng R, Jung DJ, Silkov A, Kim H, Singaram I, Wang ZG, Xin Y, Kim E, Park MJ, Thiagarajan-Rosenkranz P, Smrt S, Honig B, Baek K, Ryu S, Lorieau J, Kim YM, Cho W | The Journal of biological chemistry | 27334919 | J Biol Chem | 2016 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/27334919 |
| Imitating manual curation of text-mined facts in biomedicine. | Rodriguez-Esteban R, Iossifov I, Rzhetsky A | PLoS computational biology | 16965176 | PLoS Comput Biol | 2006 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/16965176 |
| SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. | Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C | BMC bioinformatics | 17570145 | BMC Bioinformatics | 2007 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/17570145 |
| Optimal signal processing in small stochastic biochemical networks. | Ziv E, Nemenman I, Wiggins CH | PloS one | 17957259 | PLoS One | 2007 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/17957259 |
| Functional specificity of a Hox protein mediated by the recognition of minor groove structure. | Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS | Cell | 17981120 | Cell | 2007 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/17981120 |
| Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. | Lim WK, Wang K, Lefebvre C, Califano A | Bioinformatics (Oxford, England) | 17646307 | Bioinformatics | 2007 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/17646307 |
| Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. | Pe'er I, Yelensky R, Altshuler D, Daly MJ | Genetic epidemiology | 18348202 | Genet Epidemiol | 2008 May | https://www.ncbi.nlm.nih.gov/pubmed/18348202 |
| Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. | Ward LD, Bussemaker HJ | Bioinformatics (Oxford, England) | 18586710 | Bioinformatics | 2008 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/18586710 |
| Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4. | Koehnke J, Jin X, Trbovic N, Katsamba PS, Brasch J, Ahlsen G, Scheiffele P, Honig B, Palmer AG 3rd, Shapiro L | Structure (London, England : 1993) | 18334216 | Structure | 2008 Mar | https://www.ncbi.nlm.nih.gov/pubmed/18334216 |
| A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. | Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A | Molecular systems biology | 18277385 | Mol Syst Biol | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18277385 |
| Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. | Koehnke J, Jin X, Budreck EC, Posy S, Scheiffele P, Honig B, Shapiro L | Proceedings of the National Academy of Sciences of the United States of America | 18250328 | Proc Natl Acad Sci U S A | 2008 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/18250328 |
| Whole population, genome-wide mapping of hidden relatedness. | Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I | Genome research | 18971310 | Genome Res | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/18971310 |
| Novel opportunities for computational biology and sociology in drug discovery. | Yao L, Evans JA, Rzhetsky A | Trends in biotechnology | 20349528 | Trends Biotechnol | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20349528 |
| Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. | Yang X, Huang Y, Crowson M, Li J, Maitland ML, Lussier YA | Journal of biomedical informatics | 20434586 | J Biomed Inform | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20434586 |
| Current methodologies for translational bioinformatics. | Lussier YA, Butte AJ, Hunter L | Journal of biomedical informatics | 20470899 | J Biomed Inform | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20470899 |
| geWorkbench: an open source platform for integrative genomics. | Floratos A, Smith K, Ji Z, Watkinson J, Califano A | Bioinformatics (Oxford, England) | 20511363 | Bioinformatics | 2010 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/20511363 |
| Two-step adhesive binding by classical cadherins. | Harrison OJ, Bahna F, Katsamba PS, Jin X, Brasch J, Vendome J, Ahlsen G, Carroll KJ, Price SR, Honig B, Shapiro L | Nature structural & molecular biology | 20190754 | Nat Struct Mol Biol | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20190754 |
| High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. | Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D | Journal of structural and functional genomics | 20383749 | J Struct Funct Genomics | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20383749 |
| Harnessing gene expression to identify the genetic basis of drug resistance. | Chen BJ, Causton HC, Mancenido D, Goddard NL, Perlstein EO, Pe'er D | Molecular systems biology | 19888205 | Mol Syst Biol | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19888205 |
| Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene. | van Batenburg MF, Li H, Polman JA, Lachize S, Datson NA, Bussemaker HJ, Meijer OC | PloS one | 20098621 | PLoS One | 2010 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/20098621 |
| PUDGE: a flexible, interactive server for protein structure prediction. | Norel R, Petrey D, Honig B | Nucleic acids research | 20525783 | Nucleic Acids Res | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20525783 |
| MarkUs: a server to navigate sequence-structure-function space. | Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D | Nucleic acids research | 21672961 | Nucleic Acids Res | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21672961 |
| Statistical method for revealing form-function relations in biological networks. | Mugler A, Grinshpun B, Franks R, Wiggins CH | Proceedings of the National Academy of Sciences of the United States of America | 21183719 | Proc Natl Acad Sci U S A | 2011 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/21183719 |
| Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine. | Borlawsky TB, Li J, Shagina L, Crowson MG, Liu Y, Friedman C, Lussier YA | Summit on translational bioinformatics | 21347135 | Summit Transl Bioinform | 2010 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347135 |
| Benchmarking ontologies: bigger or better? | Yao L, Divoli A, Mayzus I, Evans JA, Rzhetsky A | PLoS computational biology | 21249231 | PLoS Comput Biol | 2011 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/21249231 |
| Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence. | Chen JL, Li J, Stadler WM, Lussier YA | Journal of the American Medical Informatics Association : JAMIA | 21672909 | J Am Med Inform Assoc | 2011 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/21672909 |
| Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. | Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D | Neuron | 21658583 | Neuron | 2011 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/21658583 |
| A cloud-based approach to medical NLP. | Chard K, Russell M, Lussier YA, Mendonça EA, Silverstein JC | AMIA ... Annual Symposium proceedings. AMIA Symposium | 22195072 | AMIA Annu Symp Proc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22195072 |
| Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. | Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS | Cell | 22153072 | Cell | 2011 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/22153072 |
| A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. | Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD | ACS chemical biology | 21967305 | ACS Chem Biol | 2011 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/21967305 |
| Analysis of the coding genome of diffuse large B-cell lymphoma. | Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R | Nature genetics | 21804550 | Nat Genet | 2011 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/21804550 |
| Novel opportunities for computational biology and sociology in drug discovery. | Yao L, Evans JA, Rzhetsky A | Trends in biotechnology | 19674801 | Trends Biotechnol | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19674801 |
| Viral reassortment as an information exchange between viral segments. | Greenbaum BD, Li OT, Poon LL, Levine AJ, Rabadan R | Proceedings of the National Academy of Sciences of the United States of America | 22331898 | Proc Natl Acad Sci U S A | 2012 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/22331898 |
| Leveraging models of cell regulation and GWAS data in integrative network-based association studies. | Califano A, Butte AJ, Friend S, Ideker T, Schadt E | Nature genetics | 22836096 | Nat Genet | 2012 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/22836096 |
| Systems biology. Conditional density-based analysis of T cell signaling in single-cell data. | Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP | Science (New York, N.Y.) | 25342659 | Science | 2014 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/25342659 |
| Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. | Abate F, Zairis S, Ficarra E, Acquaviva A, Wiggins CH, Frattini V, Lasorella A, Iavarone A, Inghirami G, Rabadan R | BMC systems biology | 25183062 | BMC Syst Biol | 2014 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/25183062 |
| Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. | Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A, Kim HR, Seviour EG, Luo Z, Sehgal V, Moss T, Lu Y, Ram P, Silva J, Mills GB, Califano A, Sumazin P | Genome research | 25378249 | Genome Res | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25378249 |
| Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast. | Fazlollahi M, Lee E, Muroff I, Lu XJ, Gomez-Alcala P, Causton HC, Bussemaker HJ | G3 (Bethesda, Md.) | 24938291 | G3 (Bethesda) | 2014 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/24938291 |
| Template-based prediction of protein function. | Petrey D, Chen TS, Deng L, Garzon JI, Hwang H, Lasso G, Lee H, Silkov A, Honig B | Current opinion in structural biology | 25678152 | Curr Opin Struct Biol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25678152 |
| Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins. | Carmi S, Hui KY, Kochav E, Liu X, Xue J, Grady F, Guha S, Upadhyay K, Ben-Avraham D, Mukherjee S, Bowen BM, Thomas T, Vijai J, Cruts M, Froyen G, Lambrechts D, Plaisance S, Van Broeckhoven C, Van Damme P, Van Marck H, Barzilai N, Darvasi A, Offit K, Bressman S, Ozelius LJ, Peter I, Cho JH, Ostrer H, Atzmon G, Clark LN, Lencz T, Pe'er I | Nature communications | 25203624 | Nat Commun | 2014 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/25203624 |
| Evolving insights on how cytosine methylation affects protein-DNA binding. | Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R | Briefings in functional genomics | 25319759 | Brief Funct Genomics | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25319759 |
| Variants in exons and in transcription factors affect gene expression in trans. | Kreimer A, Pe'er I | Genome biology | 23844908 | Genome Biol | 2013 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/23844908 |
| Structure-based prediction of protein-protein interactions on a genome-wide scale. | Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B | Nature | 23023127 | Nature | 2012 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/23023127 |
| The integrated landscape of driver genomic alterations in glioblastoma. | Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Privé GG, Bigner DD, Lasorella A, Rabadan R, Iavarone A | Nature genetics | 23917401 | Nat Genet | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23917401 |
| Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor. | Chen J, Repunte-Canonigo V, Kawamura T, Lefebvre C, Shin W, Howell LL, Hemby SE, Harvey BK, Califano A, Morales M, Koob GF, Sanna PP | Nature communications | 23736082 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23736082 |
| Heterogeneity of tumor-induced gene expression changes in the human metabolic network. | Hu J, Locasale JW, Bielas JH, O'Sullivan J, Sheahan K, Cantley LC, Vander Heiden MG, Vitkup D | Nature biotechnology | 23604282 | Nat Biotechnol | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23604282 |
| MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples. | Trifonov V, Pasqualucci L, Dalla Favera R, Rabadan R | BMC systems biology | 23531283 | BMC Syst Biol | 2013 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/23531283 |
| Improving breast cancer survival analysis through competition-based multidimensional modeling. | Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA | PLoS computational biology | 23671412 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23671412 |
| OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. | Shazman S, Lee H, Socol Y, Mann RS, Honig B | Nucleic acids research | 24271386 | Nucleic Acids Res | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24271386 |
| Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments. | van de Meent JW, Bronson JE, Wiggins CH, Gonzalez RL Jr | Biophysical journal | 24655508 | Biophys J | 2014 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/24655508 |
| Evaluation of methods for modeling transcription factor sequence specificity. | Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR | Nature biotechnology | 23354101 | Nat Biotechnol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23354101 |
| Elucidating Compound Mechanism of Action by Network Perturbation Analysis. | Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A | Cell | 26186195 | Cell | 2015 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/26186195 |
| Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma. | Abate F, Ambrosio MR, Mundo L, Laginestra MA, Fuligni F, Rossi M, Zairis S, Gazaneo S, De Falco G, Lazzi S, Bellan C, Rocca BJ, Amato T, Marasco E, Etebari M, Ogwang M, Calbi V, Ndede I, Patel K, Chumba D, Piccaluga PP, Pileri S, Leoncini L, Rabadan R | PLoS pathogens | 26468873 | PLoS Pathog | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26468873 |
| Negative Regulation of Cytosolic Sensing of DNA. | Abe T, Shapira SD | International review of cell and molecular biology | 30798991 | Int Rev Cell Mol Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30798991 |
| Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidences from circulating and lymph nodal compartments. | Del Giudice I, Marinelli M, Wang J, Bonina S, Messina M, Chiaretti S, Ilari C, Cafforio L, Raponi S, Mauro FR, Di Maio V, De Propris MS, Nanni M, Ciardullo C, Rossi D, Gaidano G, Guarini A, Rabadan R, Foà R | British journal of haematology | 26597680 | Br J Haematol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26597680 |
| Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode. | Wang D, Kon N, Lasso G, Jiang L, Leng W, Zhu WG, Qin J, Honig B, Gu W | Nature | 27626385 | Nature | 2016 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/27626385 |
| Functional characterization of somatic mutations in cancer using network-based inference of protein activity. | Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A | Nature genetics | 27322546 | Nat Genet | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27322546 |
| ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. | Lachmann A, Giorgi FM, Lopez G, Califano A | Bioinformatics (Oxford, England) | 27153652 | Bioinformatics | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/27153652 |
| Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations. | Azad RN, Zafiropoulos D, Ober D, Jiang Y, Chiu TP, Sagendorf JM, Rohs R, Tullius TD | Nucleic acids research | 29390080 | Nucleic Acids Res | 2018 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/29390080 |
| Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. | Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I | Science translational medicine | 29321258 | Sci Transl Med | 2018 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/29321258 |
| SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins. | Park MJ, Sheng R, Silkov A, Jung DJ, Wang ZG, Xin Y, Kim H, Thiagarajan-Rosenkranz P, Song S, Yoon Y, Nam W, Kim I, Kim E, Lee DG, Chen Y, Singaram I, Wang L, Jang MH, Hwang CS, Honig B, Ryu S, Lorieau J, Kim YM, Cho W | Molecular cell | 27052731 | Mol Cell | 2016 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/27052731 |
| Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited. | Li Z, Ji BW, Dixit PD, Tchourine K, Lien EC, Hosios AM, Abbott KL, Rutter JC, Westermark AM, Gorodetsky EF, Sullivan LB, Vander Heiden MG, Vitkup D | Nature metabolism | 35739397 | Nat Metab | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35739397 |
| DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation. | Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe'er I | American journal of human genetics | 21620352 | Am J Hum Genet | 2011 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/21620352 |
| The architecture of long-range haplotypes shared within and across populations. | Gusev A, Palamara PF, Aponte G, Zhuang Z, Darvasi A, Gregersen P, Pe'er I | Molecular biology and evolution | 21984068 | Mol Biol Evol | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21984068 |
| Splice form dependence of beta-neurexin/neuroligin binding interactions. | Koehnke J, Katsamba PS, Ahlsen G, Bahna F, Vendome J, Honig B, Shapiro L, Jin X | Neuron | 20624592 | Neuron | 2010 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/20624592 |
| Identifying hosts of families of viruses: a machine learning approach. | Raj A, Dewar M, Palacios G, Rabadan R, Wiggins CH | PloS one | 22174744 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22174744 |
| MicroRNA expression characterizes oligometastasis(es). | Lussier YA, Xing HR, Salama JK, Khodarev NN, Huang Y, Zhang Q, Khan SA, Yang X, Hasselle MD, Darga TE, Malik R, Fan H, Perakis S, Filippo M, Corbin K, Lee Y, Posner MC, Chmura SJ, Hellman S, Weichselbaum RR | PloS one | 22174856 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22174856 |
| BRAF mutations in hairy-cell leukemia. | Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foà R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R, Falini B | The New England journal of medicine | 21663470 | N Engl J Med | 2011 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/21663470 |
| Beyond NPM-anaplastic lymphoma kinase driven lymphomagenesis: alternative drivers in anaplastic large cell lymphoma. | Tabbò F, Ponzoni M, Rabadan R, Bertoni F, Inghirami G, European T-cell Lymphoma Study Group | Current opinion in hematology | 23673339 | Curr Opin Hematol | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23673339 |
| viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. | Amir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D | Nature biotechnology | 23685480 | Nat Biotechnol | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23685480 |
| RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation. | Danussi C, Akavia UD, Niola F, Jovic A, Lasorella A, Pe'er D, Iavarone A | Cancer research | 23774217 | Cancer Res | 2013 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/23774217 |
| Diverse types of genetic variation converge on functional gene networks involved in schizophrenia. | Gilman SR, Chang J, Xu B, Bawa TS, Gogos JA, Karayiorgou M, Vitkup D | Nature neuroscience | 23143521 | Nat Neurosci | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23143521 |
| Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients. | Yang X, Li H, Regan K, Li J, Huang Y, Lussier YA | AMIA ... Annual Symposium proceedings. AMIA Symposium | 23304380 | AMIA Annu Symp Proc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23304380 |
| ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer. | Aytes A, Mitrofanova A, Kinkade CW, Lefebvre C, Lei M, Phelan V, LeKaye HC, Koutcher JA, Cardiff RD, Califano A, Shen MM, Abate-Shen C | Proceedings of the National Academy of Sciences of the United States of America | 23918374 | Proc Natl Acad Sci U S A | 2013 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/23918374 |
| PrePPI: a structure-informed database of protein-protein interactions. | Zhang QC, Petrey D, Garzón JI, Deng L, Honig B | Nucleic acids research | 23193263 | Nucleic Acids Res | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23193263 |
| GAB2 induces tumor angiogenesis in NRAS-driven melanoma. | Yang Y, Wu J, Demir A, Castillo-Martin M, Melamed RD, Zhang G, Fukunaga-Kanabis M, Perez-Lorenzo R, Zheng B, Silvers DN, Brunner G, Wang S, Rabadan R, Cordon-Cardo C, Celebi JT | Oncogene | 22926523 | Oncogene | 2013 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/22926523 |
| Correlating measurements across samples improves accuracy of large-scale expression profile experiments. | Alvarez MJ, Sumazin P, Rajbhandari P, Califano A | Genome biology | 20042104 | Genome Biol | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/20042104 |
| The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. | Zhao X, D' Arca D, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A | Developmental cell | 19686682 | Dev Cell | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19686682 |
| Structural relationships among proteins with different global topologies and their implications for function annotation strategies. | Petrey D, Fischer M, Honig B | Proceedings of the National Academy of Sciences of the United States of America | 19805138 | Proc Natl Acad Sci U S A | 2009 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/19805138 |
| A systems biology approach to transcription factor binding site prediction. | Zhou X, Sumazin P, Rajbhandari P, Califano A | PloS one | 20360861 | PLoS One | 2010 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/20360861 |
| Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. | Chastanet A, Vitkup D, Yuan GC, Norman TM, Liu JS, Losick RM | Proceedings of the National Academy of Sciences of the United States of America | 20404177 | Proc Natl Acad Sci U S A | 2010 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/20404177 |
| The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. | Lu XJ, Olson WK, Bussemaker HJ | Nucleic acids research | 20223772 | Nucleic Acids Res | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20223772 |
| The transcriptional network for mesenchymal transformation of brain tumours. | Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A | Nature | 20032975 | Nature | 2010 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/20032975 |
| Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. | Yang X, Huang Y, Chen JL, Xie J, Sun X, Lussier YA | BMC bioinformatics | 19761576 | BMC Bioinformatics | 2009 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/19761576 |
| The microRNA expression associated with morphogenesis of breast cancer cells in three-dimensional organotypic culture. | Nguyen HT, Li C, Lin Z, Zhuang Y, Flemington EK, Burow ME, Lin YI, Shan B | Oncology reports | 22576799 | Oncol Rep | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22576799 |
| Global probabilistic annotation of metabolic networks enables enzyme discovery. | Plata G, Fuhrer T, Hsiao TL, Sauer U, Vitkup D | Nature chemical biology | 22960854 | Nat Chem Biol | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22960854 |
| Inference of modules associated to eQTLs. | Kreimer A, Litvin O, Hao K, Molony C, Pe'er D, Pe'er I | Nucleic acids research | 22447449 | Nucleic Acids Res | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22447449 |
| TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements. | Tan AY, Riley TR, Coady T, Bussemaker HJ, Manley JL | Proceedings of the National Academy of Sciences of the United States of America | 22460799 | Proc Natl Acad Sci U S A | 2012 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/22460799 |
| Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions. | Chen Y, Sheng R, Källberg M, Silkov A, Tun MP, Bhardwaj N, Kurilova S, Hall RA, Honig B, Lu H, Cho W | Molecular cell | 22445486 | Mol Cell | 2012 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/22445486 |
| Single sample expression-anchored mechanisms predict survival in head and neck cancer. | Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EE, Xing HR, Lussier YA | PLoS computational biology | 22291585 | PLoS Comput Biol | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22291585 |
| Detecting identity by descent and homozygosity mapping in whole-exome sequencing data. | Zhuang Z, Gusev A, Cho J, Pe'er I | PloS one | 23071825 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23071825 |
| North African Jewish and non-Jewish populations form distinctive, orthogonal clusters. | Campbell CL, Palamara PF, Dubrovsky M, Botigué LR, Fellous M, Atzmon G, Oddoux C, Pearlman A, Hao L, Henn BM, Burns E, Bustamante CD, Comas D, Friedman E, Pe'er I, Ostrer H | Proceedings of the National Academy of Sciences of the United States of America | 22869716 | Proc Natl Acad Sci U S A | 2012 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/22869716 |
| Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes. | Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, Bussemaker HJ, Singer RH, Schirmacher P, Prives C | Molecular cell | 23102701 | Mol Cell | 2012 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/23102701 |
| Length distributions of identity by descent reveal fine-scale demographic history. | Palamara PF, Lencz T, Darvasi A, Pe'er I | American journal of human genetics | 23103233 | Am J Hum Genet | 2012 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/23103233 |
| Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness. | Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foà R | Blood | 24550227 | Blood | 2014 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/24550227 |
| Topology of viral evolution. | Chan JM, Carlsson G, Rabadan R | Proceedings of the National Academy of Sciences of the United States of America | 24170857 | Proc Natl Acad Sci U S A | 2013 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/24170857 |
| Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy. | Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, Eastham JA, Gopalan A, Pienta KJ, Shen MM, Califano A, Abate-Shen C | Cancer cell | 24823640 | Cancer Cell | 2014 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/24823640 |
| Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. | Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ | PloS one | 18769540 | PLoS One | 2008 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/18769540 |
| Caenorhabditis elegans mutant allele identification by whole-genome sequencing. | Sarin S, Prabhu S, O'Meara MM, Pe'er I, Hobert O | Nature methods | 18677319 | Nat Methods | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18677319 |
| Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. | Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I | PloS one | 19107202 | PLoS One | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/19107202 |
| Overlapping pools for high-throughput targeted resequencing. | Prabhu S, Pe'er I | Genome research | 19447964 | Genome Res | 2009 Jul | https://www.ncbi.nlm.nih.gov/pubmed/19447964 |
| Modularity and interactions in the genetics of gene expression. | Litvin O, Causton HC, Chen BJ, Pe'er D | Proceedings of the National Academy of Sciences of the United States of America | 19223586 | Proc Natl Acad Sci U S A | 2009 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/19223586 |
| Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. | Lowe JK, Maller JB, Pe'er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, Smith JG, Ji W, Noel M, Foo JN, Blundell ML, Skilling V, Garcia L, Sullivan ML, Lee HE, Labek A, Ferdowsian H, Auerbach SB, Lifton RP, Newton-Cheh C, Breslow JL, Stoffel M, Daly MJ, Altshuler DM, Friedman JM | PLoS genetics | 19197348 | PLoS Genet | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19197348 |
| Master regulators used as breast cancer metastasis classifier. | Lim WK, Lyashenko E, Califano A | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 19209726 | Pac Symp Biocomput | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19209726 |
| MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. | Stoyanovich J, Pe'er I | Bioinformatics (Oxford, England) | 18048395 | Bioinformatics | 2008 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/18048395 |
| Genomic assessment of a multikinase inhibitor, sorafenib, in a rodent model of pulmonary hypertension. | Moreno-Vinasco L, Gomberg-Maitland M, Maitland ML, Desai AA, Singleton PA, Sammani S, Sam L, Liu Y, Husain AN, Lang RM, Ratain MJ, Lussier YA, Garcia JG | Physiological genomics | 18303084 | Physiol Genomics | 2008 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/18303084 |
| TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. | Foat BC, Tepper RG, Bussemaker HJ | Nucleic acids research | 17947326 | Nucleic Acids Res | 2008 Jan | https://www.ncbi.nlm.nih.gov/pubmed/17947326 |
| Topological analysis of large-scale biomedical terminology structures. | Bales ME, Lussier YA, Johnson SB | Journal of the American Medical Informatics Association : JAMIA | 17712094 | J Am Med Inform Assoc | 2007 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/17712094 |
| Information theory applied to the sparse gene ontology annotation network to predict novel gene function. | Tao Y, Sam L, Li J, Friedman C, Lussier YA | Bioinformatics (Oxford, England) | 17646340 | Bioinformatics | 2007 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/17646340 |
| Evaluation of high-throughput functional categorization of human disease genes. | Chen JL, Liu Y, Sam LT, Li J, Lussier YA | BMC bioinformatics | 17493290 | BMC Bioinformatics | 2007 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/17493290 |
| Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. | Sosinsky A, Honig B, Mann RS, Califano A | Proceedings of the National Academy of Sciences of the United States of America | 17395715 | Proc Natl Acad Sci U S A | 2007 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/17395715 |
| Detecting transcriptionally active regions using genomic tiling arrays. | Halasz G, van Batenburg MF, Perusse J, Hua S, Lu XJ, White KP, Bussemaker HJ | Genome biology | 16859498 | Genome Biol | 2006 | https://www.ncbi.nlm.nih.gov/pubmed/16859498 |
| Bio-Ontology and text: bridging the modeling gap. | Friedman C, Borlawsky T, Shagina L, Xing HR, Lussier YA | Bioinformatics (Oxford, England) | 16870928 | Bioinformatics | 2006 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/16870928 |
| Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. | Foat BC, Morozov AV, Bussemaker HJ | Bioinformatics (Oxford, England) | 16873464 | Bioinformatics | 2006 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/16873464 |
| CONFU: Configuration Fuzzing Testing Framework for Software Vulnerability Detection. | Dai H, Murphy C, Kaiser G | International journal of secure software engineering | 21037923 | Int J Secur Softw Eng | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21037923 |
| Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis. | LaFramboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML | PLoS genetics | 20824129 | PLoS Genet | 2010 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/20824129 |
| Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. | Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B | Cell | 20888037 | Cell | 2010 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/20888037 |
| The rate of the molecular clock and the cost of gratuitous protein synthesis. | Plata G, Gottesman ME, Vitkup D | Genome biology | 20920270 | Genome Biol | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20920270 |
| Automatic Detection of Previously-Unseen Application States for Deployment Environment Testing and Analysis. | Murphy C, Vaughan M, Ilahi W, Kaiser G | Proceedings of the ... International Workshop on Automation of Software Test. International Workshop on Automation of Software Test | 21197140 | Proc Int Workshop Autom Softw Test | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21197140 |
| Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes. | Ross KA | BMC medicine | 21291537 | BMC Med | 2011 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/21291537 |
| Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. | Yang X, Lee Y, Huang Y, Chen JL, Xing RH, Lussier YA | BMC bioinformatics | 21044358 | BMC Bioinformatics | 2010 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/21044358 |
| A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. | Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A | Molecular systems biology | 20531406 | Mol Syst Biol | 2010 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/20531406 |
| Protein interface conservation across structure space. | Zhang QC, Petrey D, Norel R, Honig BH | Proceedings of the National Academy of Sciences of the United States of America | 20534496 | Proc Natl Acad Sci U S A | 2010 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/20534496 |
| Amino Acids Rather than Glucose Account for the Majority of Cell Mass in Proliferating Mammalian Cells. | Hosios AM, Hecht VC, Danai LV, Johnson MO, Rathmell JC, Steinhauser ML, Manalis SR, Vander Heiden MG | Developmental cell | 26954548 | Dev Cell | 2016 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/26954548 |
| Comparative analysis of metazoan chromatin organization. | Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ | Nature | 25164756 | Nature | 2014 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/25164756 |
| Direct ChIP-Seq significance analysis improves target prediction. | Bansal M, Mendiratta G, Anand S, Kushwaha R, Kim R, Kustagi M, Iyer A, Chaganti RS, Califano A, Sumazin P | BMC genomics | 26040656 | BMC Genomics | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26040656 |
| Integration of genomic data enables selective discovery of breast cancer drivers. | Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia UD, Chen BJ, Saucedo-Cuevas L, Rodriguez Barrueco R, Llobet-Navas D, Silva JM, Pe'er D | Cell | 25433701 | Cell | 2014 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/25433701 |
| Statistical inference for nanopore sequencing with a biased random walk model. | Emmett KJ, Rosenstein JK, van de Meent JW, Shepard KL, Wiggins CH | Biophysical journal | 25902425 | Biophys J | 2015 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/25902425 |
| RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. | Pefanis E, Wang J, Rothschild G, Lim J, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu ZP, Economides AN, Bradner JE, Rabadan R, Basu U | Cell | 25957685 | Cell | 2015 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/25957685 |
| Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats. | Repunte-Canonigo V, Lefebvre C, George O, Kawamura T, Morales M, Koob GF, Califano A, Masliah E, Sanna PP | Molecular neurodegeneration | 24980976 | Mol Neurodegener | 2014 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/24980976 |
| Data-driven discovery of seasonally linked diseases from an Electronic Health Records system. | Melamed RD, Khiabanian H, Rabadan R | BMC bioinformatics | 25078762 | BMC Bioinformatics | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25078762 |
| Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks. | Chen JC, Alvarez MJ, Talos F, Dhruv H, Rieckhof GE, Iyer A, Diefes KL, Aldape K, Berens M, Shen MM, Califano A | Cell | 25303533 | Cell | 2014 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/25303533 |
| Inferring protein modulation from gene expression data using conditional mutual information. | Giorgi FM, Lopez G, Woo JH, Bisikirska B, Califano A, Bansal M | PloS one | 25314274 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25314274 |
| Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. | Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D | Cell | 24766814 | Cell | 2014 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/24766814 |
| Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. | Ward LD, Wang J, Bussemaker HJ | BMC genomics | 24947676 | BMC Genomics | 2014 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/24947676 |
| Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. | Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Vander Heiden MG, Metallo CM | Molecular cell | 24882210 | Mol Cell | 2014 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/24882210 |
| Structural bioinformatics of the interactome. | Petrey D, Honig B | Annual review of biophysics | 24895853 | Annu Rev Biophys | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24895853 |
| Transient pairing of homologous Oct4 alleles accompanies the onset of embryonic stem cell differentiation. | Hogan MS, Parfitt DE, Zepeda-Mendoza CJ, Shen MM, Spector DL | Cell stem cell | 25748933 | Cell Stem Cell | 2015 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/25748933 |
| Quantitative modeling of transcription factor binding specificities using DNA shape. | Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R | Proceedings of the National Academy of Sciences of the United States of America | 25775564 | Proc Natl Acad Sci U S A | 2015 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/25775564 |
| Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes. | Melamed RD, Emmett KJ, Madubata C, Rzhetsky A, Rabadan R | Nature communications | 25926297 | Nat Commun | 2015 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/25926297 |
| Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia. | Wang J, Khiabanian H, Rossi D, Fabbri G, Gattei V, Forconi F, Laurenti L, Marasca R, Del Poeta G, Foà R, Pasqualucci L, Gaidano G, Rabadan R | eLife | 25496728 | Elife | 2014 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/25496728 |
| FYN-TRAF3IP2 induces NF-κB signaling-driven peripheral T cell lymphoma. | Moon CS, Reglero C, Cortes JR, Quinn SA, Alvarez S, Zhao J, Lin WW, Cooke AJ, Abate F, Soderquist CR, Fiñana C, Inghirami G, Campo E, Bhagat G, Rabadan R, Palomero T, Ferrando AA | Nature cancer | 33928261 | Nat Cancer | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33928261 |
| An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. | Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA | PLoS computational biology | 17112314 | PLoS Comput Biol | 2006 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/17112314 |
| Predictive modeling of genome-wide mRNA expression: from modules to molecules. | Bussemaker HJ, Foat BC, Ward LD | Annual review of biophysics and biomolecular structure | 17311525 | Annu Rev Biophys Biomol Struct | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17311525 |
| Natively unstructured loops differ from other loops. | Schlessinger A, Liu J, Rost B | PLoS computational biology | 17658943 | PLoS Comput Biol | 2007 Jul | https://www.ncbi.nlm.nih.gov/pubmed/17658943 |
| Discovery of protein interaction networks shared by diseases. | Sam L, Liu Y, Li J, Friedman C, Lussier YA | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 17992746 | Pac Symp Biocomput | 2007 | https://www.ncbi.nlm.nih.gov/pubmed/17992746 |
| Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? | Posy S, Shapiro L, Honig B | Journal of molecular biology | 18395225 | J Mol Biol | 2008 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/18395225 |
| Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry. | Atzmon G, Hao L, Pe'er I, Velez C, Pearlman A, Palamara PF, Morrow B, Friedman E, Oddoux C, Burns E, Ostrer H | American journal of human genetics | 20560205 | Am J Hum Genet | 2010 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/20560205 |
| Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. | Floc'h N, Kinkade CW, Kobayashi T, Aytes A, Lefebvre C, Mitrofanova A, Cardiff RD, Califano A, Shen MM, Abate-Shen C | Cancer research | 22815528 | Cancer Res | 2012 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/22815528 |
| The variance of identity-by-descent sharing in the Wright-Fisher model. | Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe'er I | Genetics | 23267057 | Genetics | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23267057 |
| B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. | Wang J, Kobayashi T, Floc'h N, Kinkade CW, Aytes A, Dankort D, Lefebvre C, Mitrofanova A, Cardiff RD, McMahon M, Califano A, Shen MM, Abate-Shen C | Cancer research | 22836754 | Cancer Res | 2012 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/22836754 |
| Emergence of fatal avian influenza in New England harbor seals. | Anthony SJ, St Leger JA, Pugliares K, Ip HS, Chan JM, Carpenter ZW, Navarrete-Macias I, Sanchez-Leon M, Saliki JT, Pedersen J, Karesh W, Daszak P, Rabadan R, Rowles T, Lipkin WI | mBio | 22851656 | mBio | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22851656 |
| Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis. | Lee E, de Ridder J, Kool J, Wessels LF, Bussemaker HJ | Proceedings of the National Academy of Sciences of the United States of America | 24706889 | Proc Natl Acad Sci U S A | 2014 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/24706889 |
| A community effort to assess and improve drug sensitivity prediction algorithms. | Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G | Nature biotechnology | 24880487 | Nat Biotechnol | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24880487 |
| hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. | Jang IS, Margolin A, Califano A | Interface focus | 24511376 | Interface Focus | 2013 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/24511376 |
| ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. | Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RG, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG | Cell reports | 24440720 | Cell Rep | 2014 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/24440720 |
| SAVI: a statistical algorithm for variant frequency identification. | Trifonov V, Pasqualucci L, Tiacci E, Falini B, Rabadan R | BMC systems biology | 24564980 | BMC Syst Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24564980 |
| An integrated approach to uncover drivers of cancer. | Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D | Cell | 21129771 | Cell | 2010 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/21129771 |
| Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. | Plata G, Hsiao TL, Olszewski KL, Llinás M, Vitkup D | Molecular systems biology | 20823846 | Mol Syst Biol | 2010 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/20823846 |
| Identifying the genetic determinants of transcription factor activity. | Lee E, Bussemaker HJ | Molecular systems biology | 20865005 | Mol Syst Biol | 2010 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/20865005 |
| Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. | Dapito DH, Mencin A, Gwak GY, Pradere JP, Jang MK, Mederacke I, Caviglia JM, Khiabanian H, Adeyemi A, Bataller R, Lefkowitch JH, Bower M, Friedman R, Sartor RB, Rabadan R, Schwabe RF | Cancer cell | 22516259 | Cancer Cell | 2012 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/22516259 |
| Using systems and structure biology tools to dissect cellular phenotypes. | Floratos A, Honig B, Pe'er D, Califano A | Journal of the American Medical Informatics Association : JAMIA | 22081223 | J Am Med Inform Assoc | 2012 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/22081223 |
| Reverse-engineering human regulatory networks. | Lefebvre C, Rieckhof G, Califano A | Wiley interdisciplinary reviews. Systems biology and medicine | 22246697 | Wiley Interdiscip Rev Syst Biol Med | 2012 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/22246697 |
| Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. | Pantazatos SP, Li J, Pavlidis P, Lussier YA | Summit on translational bioinformatics | 21347176 | Summit Transl Bioinform | 2009 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/21347176 |
| GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. | Yang X, Li J, Lee Y, Lussier YA | Bioinformatics (Oxford, England) | 21421553 | Bioinformatics | 2011 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/21421553 |
| Configuration Fuzzing for Software Vulnerability Detection. | Dai H, Murphy C, Kaiser G | Proceedings. International Conference on Availability, Security, and Reliability | 21461049 | Proc Int Conf Availab Reliab Secur | 2010 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/21461049 |
| Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. | Shen Y, Song R, Pe'er I | Bioinformatics (Oxford, England) | 21636589 | Bioinformatics | 2011 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/21636589 |
| Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. | Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS | Nature biotechnology | 19465925 | Nat Biotechnol | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19465925 |
| A stochastic spectral analysis of transcriptional regulatory cascades. | Walczak AM, Mugler A, Wiggins CH | Proceedings of the National Academy of Sciences of the United States of America | 19351901 | Proc Natl Acad Sci U S A | 2009 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/19351901 |
| The role of DNA shape in protein-DNA recognition. | Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B | Nature | 19865164 | Nature | 2009 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/19865164 |
| Spectral solutions to stochastic models of gene expression with bursts and regulation. | Mugler A, Walczak AM, Wiggins CH | Physical review. E, Statistical, nonlinear, and soft matter physics | 19905356 | Phys Rev E Stat Nonlin Soft Matter Phys | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19905356 |
| Quantifying evolvability in small biological networks. | Mugler A, Ziv E, Nemenman I, Wiggins CH | IET systems biology | 21028928 | IET Syst Biol | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21028928 |
| Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli. | Patwa LG, Fan TJ, Tchaptchet S, Liu Y, Lussier YA, Sartor RB, Hansen JJ | Gastroenterology | 21726510 | Gastroenterology | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21726510 |
| Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response. | Shechtman CF, Henneberry AL, Seimon TA, Tinkelenberg AH, Wilcox LJ, Lee E, Fazlollahi M, Munkacsi AB, Bussemaker HJ, Tabas I, Sturley SL | The Journal of biological chemistry | 21266578 | J Biol Chem | 2011 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/21266578 |
| Application of Metamorphic Testing to Supervised Classifiers. | Xie X, Ho J, Murphy C, Kaiser G, Xu B, Chen TY | Proceedings. International Conference on Quality Software | 21243103 | Proc Int Conf Qual Softw | 2010 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/21243103 |
| PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. | Sam LT, Mendonça EA, Li J, Blake J, Friedman C, Lussier YA | BMC bioinformatics | 19208196 | BMC Bioinformatics | 2009 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/19208196 |
| Murine lung responses to ambient particulate matter: genomic analysis and influence on airway hyperresponsiveness. | Wang T, Moreno-Vinasco L, Huang Y, Lang GD, Linares JD, Goonewardena SN, Grabavoy A, Samet JM, Geyh AS, Breysse PN, Lussier YA, Natarajan V, Garcia JG | Environmental health perspectives | 19057703 | Environ Health Perspect | 2008 Nov | https://www.ncbi.nlm.nih.gov/pubmed/19057703 |
| Neural networks predict protein structure and function. | Punta M, Rost B | Methods in molecular biology (Clifton, N.J.) | 19065812 | Methods Mol Biol | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/19065812 |
| Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. | Compagno M, Lim WK, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A, Bhagat G, Chadburn A, Dalla-Favera R, Pasqualucci L | Nature | 19412164 | Nature | 2009 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/19412164 |
| Dissecting the interface between signaling and transcriptional regulation in human B cells. | Wang K, Alvarez MJ, Bisikirska BC, Linding R, Basso K, Dalla Favera R, Califano A | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 19209707 | Pac Symp Biocomput | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19209707 |
| Long-term phenotypic evolution of bacteria. | Plata G, Henry CS, Vitkup D | Nature | 25363780 | Nature | 2015 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/25363780 |
| A community computational challenge to predict the activity of pairs of compounds. | Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community | Nature biotechnology | 25419740 | Nat Biotechnol | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25419740 |
| Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice. | Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C | Proceedings of the National Academy of Sciences of the United States of America | 25362052 | Proc Natl Acad Sci U S A | 2014 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/25362052 |
| Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma. | Litvin O, Schwartz S, Wan Z, Schild T, Rocco M, Oh NL, Chen BJ, Goddard N, Pratilas C, Pe'er D | Molecular cell | 25684207 | Mol Cell | 2015 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/25684207 |
| Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. | Pantazatos SP, Li J, Pavlidis P, Lussier YA | Cancer informatics | 20495688 | Cancer Inform | 2009 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/20495688 |
| Origins of specificity in protein-DNA recognition. | Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS | Annual review of biochemistry | 20334529 | Annu Rev Biochem | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20334529 |
| Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. | Chen J, Sam L, Huang Y, Lee Y, Li J, Liu Y, Xing HR, Lussier YA | Journal of biomedical informatics | 20350617 | J Biomed Inform | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20350617 |
| Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. | Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW, Gerstein MB, Weichselbaum RR, Xing HR, Lussier YA | PLoS computational biology | 20369013 | PLoS Comput Biol | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20369013 |
| An information-theoretic derivation of min-cut-based clustering. | Raj A, Wiggins CH | IEEE transactions on pattern analysis and machine intelligence | 20431126 | IEEE Trans Pattern Anal Mach Intell | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20431126 |
| JISTIC: identification of significant targets in cancer. | Sanchez-Garcia F, Akavia UD, Mozes E, Pe'er D | BMC bioinformatics | 20398270 | BMC Bioinformatics | 2010 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/20398270 |
| Inference of historical migration rates via haplotype sharing. | Palamara PF, Pe'er I | Bioinformatics (Oxford, England) | 23812983 | Bioinformatics | 2013 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/23812983 |
| Probing DNA shape and methylation state on a genomic scale with DNase I. | Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ | Proceedings of the National Academy of Sciences of the United States of America | 23576721 | Proc Natl Acad Sci U S A | 2013 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/23576721 |
| PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity. | Tepper RG, Ashraf J, Kaletsky R, Kleemann G, Murphy CT, Bussemaker HJ | Cell | 23911329 | Cell | 2013 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/23911329 |
| Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization. | Abe T, Lee A, Sitharam R, Kesner J, Rabadan R, Shapira SD | Immunity | 28423339 | Immunity | 2017 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/28423339 |
| High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants. | Emmett KJ, Lee A, Khiabanian H, Rabadan R | PLoS currents | 25737802 | PLoS Curr | 2015 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/25737802 |
| ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs. | Nicoletti P, Bansal M, Lefebvre C, Guarnieri P, Shen Y, Pe'er I, Califano A, Floratos A | PloS one | 26110827 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26110827 |
| The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis. | Ikiz B, Alvarez MJ, Ré DB, Le Verche V, Politi K, Lotti F, Phani S, Pradhan R, Yu C, Croft GF, Jacquier A, Henderson CE, Califano A, Przedborski S | Cell reports | 26146077 | Cell Rep | 2015 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/26146077 |
| Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. | Levine JH, Simonds EF, Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, Nolan GP | Cell | 26095251 | Cell | 2015 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/26095251 |
| Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models. | Mitrofanova A, Aytes A, Zou M, Shen MM, Abate-Shen C, Califano A | Cell reports | 26387954 | Cell Rep | 2015 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/26387954 |
| weHelp: A Reference Architecture for Social Recommender Systems. | Sheth S, Arora N, Murphy C, Kaiser G | IEEE/ACM International Conference on Automated Software Engineering workshops. IEEE/ACM International Conference on Automated Software Engineering | 25285237 | IEEE/ACM Int Conf Autom Softw Eng Workshops | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/25285237 |
| Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. | Greenfeld M, van de Meent JW, Pavlichin DS, Mabuchi H, Wiggins CH, Gonzalez RL Jr, Herschlag D | BMC bioinformatics | 25591752 | BMC Bioinformatics | 2015 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/25591752 |
| Expanded genetic screening panel for the Ashkenazi Jewish population. | Baskovich B, Hiraki S, Upadhyay K, Meyer P, Carmi S, Barzilai N, Darvasi A, Ozelius L, Peter I, Cho JH, Atzmon G, Clark L, Yu J, Lencz T, Pe'er I, Ostrer H, Oddoux C | Genetics in medicine : official journal of the American College of Medical Genetics | 26334176 | Genet Med | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26334176 |
| Elucidation and Pharmacological Targeting of Novel Molecular Drivers of Follicular Lymphoma Progression. | Bisikirska B, Bansal M, Shen Y, Teruya-Feldstein J, Chaganti R, Califano A | Cancer research | 26589882 | Cancer Res | 2016 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26589882 |
| Assembly and interrogation of Alzheimer's disease genetic networks reveal novel regulators of progression. | Aubry S, Shin W, Crary JF, Lefort R, Qureshi YH, Lefebvre C, Califano A, Shelanski ML | PloS one | 25781952 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25781952 |
| Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. | Repunte-Canonigo V, Shin W, Vendruscolo LF, Lefebvre C, van der Stap L, Kawamura T, Schlosburg JE, Alvarez M, Koob GF, Califano A, Sanna PP | Genome biology | 25886852 | Genome Biol | 2015 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/25886852 |
| A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies. | Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, Nik-Zainal S | Nature cancer | 32118208 | Nat Cancer | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32118208 |
| Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. | Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I | Neuron | 33756103 | Neuron | 2021 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/33756103 |
| Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia. | Oshima K, Zhao J, Pérez-Durán P, Brown JA, Patiño-Galindo JA, Chu T, Quinn A, Gunning T, Belver L, Ambesi-Impiombato A, Tosello V, Wang Z, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Balbin M, Nicolas C, Gastier-Foster JM, Devidas M, Loh ML, Paietta E, Tallman MS, Rowe JM, Litzow M, Minden MD, Meijerink J, Rabadan R, Ferrando A | Nature cancer | 33796864 | Nat Cancer | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33796864 |
