Bioinformatics and Computational Biology
Bioinformatics and Computational Biology
Program Publications
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Search Results
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 |
|---|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Overcome support vector machine diagnosis overfitting. | Han H, Jiang X | Cancer informatics | 25574125 | Cancer Inform | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25574125 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Working together to put molecules on the map. | Field D | Nature | 18563126 | Nature | 2008 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/18563126 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Computational semantics in clinical text. | Wu S | Biomedical informatics insights | 23847422 | Biomed Inform Insights | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23847422 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Ontologies of cellular networks. | Arp R, Smith B | Science signaling | 19091693 | Sci Signal | 2008 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/19091693 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| Mining the ultimate phenome repository. | Shah NH | Nature biotechnology | 24316646 | Nat Biotechnol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24316646 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The 3D structure of real polymer foams. | Montminy MD, Tannenbaum AR, Macosko CW | Journal of colloid and interface science | 15476791 | J Colloid Interface Sci | 2004 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/15476791 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| Dysmorphogenic effects of first trimester-equivalent ethanol exposure in mice: a magnetic resonance microscopy-based study. | Parnell SE, Holloway HE, Baker LK, Styner MA, Sulik KK | Alcoholism, clinical and experimental research | 24931007 | Alcohol Clin Exp Res | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24931007 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cerebral white matter abnormalities and their associations with negative but not positive symptoms of schizophrenia. | Asami T, Hyuk Lee S, Bouix S, Rathi Y, Whitford TJ, Niznikiewicz M, Nestor P, McCarley RW, Shenton ME, Kubicki M | Psychiatry research | 24650453 | Psychiatry Res | 2014 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/24650453 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Neuropsychological variability, symptoms, and brain imaging in chronic schizophrenia. | Nestor PG, Kubicki M, Nakamura M, Niznikiewicz M, Levitt JJ, Shenton ME, McCarley RW | Brain imaging and behavior | 23011383 | Brain Imaging Behav | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23011383 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Geometric observers for dynamically evolving curves. | Niethammer M, Vela PA, Tannenbaum A | IEEE transactions on pattern analysis and machine intelligence | 18421113 | IEEE Trans Pattern Anal Mach Intell | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18421113 |
| A framework for image segmentation using shape models and kernel space shape priors. | Dambreville S, Rathi Y, Tannenbaum A | IEEE transactions on pattern analysis and machine intelligence | 18566493 | IEEE Trans Pattern Anal Mach Intell | 2008 Aug | https://www.ncbi.nlm.nih.gov/pubmed/18566493 |
| 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 |
| 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 |
| 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 |
| 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 |
| Spiny versus stubby: 3D reconstruction of human myenteric (type I) neurons. | Lindig TM, Kumar V, Kikinis R, Pieper S, Schrödl F, Neuhuber WL, Brehmer A | Histochemistry and cell biology | 18807064 | Histochem Cell Biol | 2009 Jan | https://www.ncbi.nlm.nih.gov/pubmed/18807064 |
| Reduced interhemispheric connectivity in schizophrenia-tractography based segmentation of the corpus callosum. | Kubicki M, Styner M, Bouix S, Gerig G, Markant D, Smith K, Kikinis R, McCarley RW, Shenton ME | Schizophrenia research | 18829262 | Schizophr Res | 2008 Dec | https://www.ncbi.nlm.nih.gov/pubmed/18829262 |
| A distributed spatio-temporal EEG/MEG inverse solver. | Ou W, Hämäläinen MS, Golland P | NeuroImage | 18603008 | Neuroimage | 2009 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/18603008 |
| 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 |
| Dynamic denoising of tracking sequences. | Michailovich O, Tannenbaum A | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 18482881 | IEEE Trans Image Process | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18482881 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Q-ball imaging of macaque white matter architecture. | Tuch DS, Wisco JJ, Khachaturian MH, Ekstrom LB, Kötter R, Vanduffel W | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 16087432 | Philos Trans R Soc Lond B Biol Sci | 2005 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/16087432 |
| 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 |
| 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 |
| 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 |
| 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 |
| Older adults with cognitive complaints show brain atrophy similar to that of amnestic MCI. | Saykin AJ, Wishart HA, Rabin LA, Santulli RB, Flashman LA, West JD, McHugh TL, Mamourian AC | Neurology | 16966547 | Neurology | 2006 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/16966547 |
| 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 |
| 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 |
| Detection of cortical thickness correlates of cognitive performance: Reliability across MRI scan sessions, scanners, and field strengths. | Dickerson BC, Fenstermacher E, Salat DH, Wolk DA, Maguire RP, Desikan R, Pacheco J, Quinn BT, Van der Kouwe A, Greve DN, Blacker D, Albert MS, Killiany RJ, Fischl B | NeuroImage | 17942325 | Neuroimage | 2008 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/17942325 |
| Characterizing the shape of anatomical structures with Poisson's equation. | Haidar H, Bouix S, Levitt JJ, McCarley RW, Shenton ME, Soul JS | IEEE transactions on medical imaging | 17024829 | IEEE Trans Med Imaging | 2006 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17024829 |
| 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 |
| 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 |
| Atlas stratification. | Blezek DJ, Miller JV | Medical image analysis | 17765003 | Med Image Anal | 2007 Oct | https://www.ncbi.nlm.nih.gov/pubmed/17765003 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study. | Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin CF, Kikinis R, Shenton ME | Biological psychiatry | 15978550 | Biol Psychiatry | 2005 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/15978550 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Morphometry of anatomical shape complexes with dense deformations and sparse parameters. | Durrleman S, Prastawa M, Charon N, Korenberg JR, Joshi S, Gerig G, Trouvé A | NeuroImage | 24973601 | Neuroimage | 2014 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/24973601 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Mapping connectivity damage in the case of Phineas Gage. | Van Horn JD, Irimia A, Torgerson CM, Chambers MC, Kikinis R, Toga AW | PloS one | 22616011 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22616011 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Empirical Likelihood for Estimating Equations with Nonignorably Missing Data. | Tang N, Zhao P, Zhu H | Statistica Sinica | 24976738 | Stat Sin | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24976738 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Multicenter reliability of diffusion tensor imaging. | Magnotta VA, Matsui JT, Liu D, Johnson HJ, Long JD, Bolster BD Jr, Mueller BA, Lim K, Mori S, Helmer KG, Turner JA, Reading S, Lowe MJ, Aylward E, Flashman LA, Bonett G, Paulsen JS | Brain connectivity | 23075313 | Brain Connect | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23075313 |
| 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 |
| Restoration of DWI data using a Rician LMMSE estimator. | Aja-Fernandez S, Niethammer M, Kubicki M, Shenton ME, Westin CF | IEEE transactions on medical imaging | 18815091 | IEEE Trans Med Imaging | 2008 Oct | https://www.ncbi.nlm.nih.gov/pubmed/18815091 |
| 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 |
| Fieldmap-free retrospective registration and distortion correction for EPI-based functional imaging. | Poynton C, Jenkinson M, Whalen S, Golby AJ, Wells W 3rd | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 18982615 | Med Image Comput Comput Assist Interv | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18982615 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Reduced microstructural integrity of the white matter underlying anterior cingulate cortex is associated with increased saccadic latency in schizophrenia. | Manoach DS, Ketwaroo GA, Polli FE, Thakkar KN, Barton JJ, Goff DC, Fischl B, Vangel M, Tuch DS | NeuroImage | 17590354 | Neuroimage | 2007 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/17590354 |
| 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 |
| 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 |
| Age-related deficits in fronto-temporal connections in schizophrenia: a diffusion tensor imaging study. | Rosenberger G, Kubicki M, Nestor PG, Connor E, Bushell GB, Markant D, Niznikiewicz M, Westin CF, Kikinis R, J Saykin A, McCarley RW, Shenton ME | Schizophrenia research | 18504117 | Schizophr Res | 2008 Jul | https://www.ncbi.nlm.nih.gov/pubmed/18504117 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Image registration for targeted MRI-guided transperineal prostate biopsy. | Fedorov A, Tuncali K, Fennessy FM, Tokuda J, Hata N, Wells WM, Kikinis R, Tempany CM | Journal of magnetic resonance imaging : JMRI | 22645031 | J Magn Reson Imaging | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22645031 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Strategies for plasma proteomic profiling of cancers. | Omenn GS | Proteomics | 16991194 | Proteomics | 2006 Oct | https://www.ncbi.nlm.nih.gov/pubmed/16991194 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
