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Program Publications

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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title Author Journal Name PubMedID Journal Abbreviation Publication Date PubMedLink
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
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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
CUDA optimization strategies for compute- and memory-bound neuroimaging algorithms. Lee D, Dinov I, Dong B, Gutman B, Yanovsky I, Toga AW Computer methods and programs in biomedicine 21159404 Comput Methods Programs Biomed 2012 Jun https://www.ncbi.nlm.nih.gov/pubmed/21159404
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
Neuroanatomical Correlates of Intelligence. Luders E, Narr KL, Thompson PM, Toga AW Intelligence 20160919 Intelligence 2009 Mar 1 https://www.ncbi.nlm.nih.gov/pubmed/20160919
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
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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
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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
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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
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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
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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
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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
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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
Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010. de Bruijn B, Cherry C, Kiritchenko S, Martin J, Zhu X Journal of the American Medical Informatics Association : JAMIA 21565856 J Am Med Inform Assoc 2011 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/21565856
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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Improving textual medication extraction using combined conditional random fields and rule-based systems. Tikk D, Solt I Journal of the American Medical Informatics Association : JAMIA 20819860 J Am Med Inform Assoc 2010 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/20819860
Automatic extraction of medication information from medical discharge summaries. Yang H Journal of the American Medical Informatics Association : JAMIA 20819861 J Am Med Inform Assoc 2010 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/20819861
Lancet: a high precision medication event extraction system for clinical text. Li Z, Liu F, Antieau L, Cao Y, Yu H Journal of the American Medical Informatics Association : JAMIA 20819865 J Am Med Inform Assoc 2010 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/20819865
Identification of rare germline copy number variations over-represented in five human cancer types. Park RW, Kim TM, Kasif S, Park PJ Molecular cancer 25644941 Mol Cancer 2015 Feb 3 https://www.ncbi.nlm.nih.gov/pubmed/25644941
A unified inference procedure for a class of measures to assess improvement in risk prediction systems with survival data. Uno H, Tian L, Cai T, Kohane IS, Wei LJ Statistics in medicine 23037800 Stat Med 2013 Jun 30 https://www.ncbi.nlm.nih.gov/pubmed/23037800
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Integration of Hive and cell software in the i2b2 architecture. Mendis M, Wattanasin N, Kuttan R, Pan W, Philips L, Hackett K, Gainer V, Chueh HC, Murphy S AMIA ... Annual Symposium proceedings. AMIA Symposium 18694146 AMIA Annu Symp Proc 2007 Oct 11 https://www.ncbi.nlm.nih.gov/pubmed/18694146
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Evaluating the state of the art in coreference resolution for electronic medical records. Uzuner O, Bodnari A, Shen S, Forbush T, Pestian J, South BR Journal of the American Medical Informatics Association : JAMIA 22366294 J Am Med Inform Assoc 2012 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/22366294
Influence of dietary sodium modulation on electrocardiographic voltage criteria for left ventricular hypertrophy in normotensive individuals. Larson C, Vaidya A, Sun B, Williams JS Journal of investigative medicine : the official publication of the American Federation for Clinical Research 22089249 J Investig Med 2012 Jan https://www.ncbi.nlm.nih.gov/pubmed/22089249
Integrating existing natural language processing tools for medication extraction from discharge summaries. Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H Journal of the American Medical Informatics Association : JAMIA 20819857 J Am Med Inform Assoc 2010 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/20819857
Extracting medical information from narrative patient records: the case of medication-related information. Deléger L, Grouin C, Zweigenbaum P Journal of the American Medical Informatics Association : JAMIA 20819863 J Am Med Inform Assoc 2010 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/20819863
Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents. Meystre SM, Thibault J, Shen S, Hurdle JF, South BR Journal of the American Medical Informatics Association : JAMIA 20819864 J Am Med Inform Assoc 2010 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/20819864
A knowledge discovery and reuse pipeline for information extraction in clinical notes. Patrick JD, Nguyen DH, Wang Y, Li M Journal of the American Medical Informatics Association : JAMIA 21737844 J Am Med Inform Assoc 2011 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/21737844
A multivariate approach for integrating genome-wide expression data and biological knowledge. Kong SW, Pu WT, Park PJ Bioinformatics (Oxford, England) 16877751 Bioinformatics 2006 Oct 1 https://www.ncbi.nlm.nih.gov/pubmed/16877751
Electronic health records: high-quality electronic data for higher-quality clinical research. Weiner MG, Lyman JA, Murphy S, Weiner M Informatics in primary care 17877874 Inform Prim Care 2007 https://www.ncbi.nlm.nih.gov/pubmed/17877874
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Kryukov GV, Pennacchio LA, Sunyaev SR American journal of human genetics 17357078 Am J Hum Genet 2007 Apr https://www.ncbi.nlm.nih.gov/pubmed/17357078
Evaluating the state-of-the-art in automatic de-identification. Uzuner O, Luo Y, Szolovits P Journal of the American Medical Informatics Association : JAMIA 17600094 J Am Med Inform Assoc 2007 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/17600094
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
Evaluating marker-guided treatment selection strategies. Matsouaka RA, Li J, Cai T Biometrics 24779731 Biometrics 2014 Sep https://www.ncbi.nlm.nih.gov/pubmed/24779731
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
Extracting medication information from clinical text. Uzuner O, Solti I, Cadag E Journal of the American Medical Informatics Association : JAMIA 20819854 J Am Med Inform Assoc 2010 Sep-Oct https://www.ncbi.nlm.nih.gov/pubmed/20819854
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
Towards automatic diabetes case detection and ABCS protocol compliance assessment. Mishra NK, Son RY, Arnzen JJ Clinical medicine & research 22634542 Clin Med Res 2012 Aug https://www.ncbi.nlm.nih.gov/pubmed/22634542
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
Subgroup specific incremental value of new markers for risk prediction. Zhou QM, Zheng Y, Cai T Lifetime data analysis 23263882 Lifetime Data Anal 2013 Apr https://www.ncbi.nlm.nih.gov/pubmed/23263882
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
Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, Kohane I Journal of the American Medical Informatics Association : JAMIA 20190053 J Am Med Inform Assoc 2010 Mar-Apr https://www.ncbi.nlm.nih.gov/pubmed/20190053
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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
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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
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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
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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
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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
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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
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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
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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
Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. Gooch P, Roudsari A Journal of biomedical informatics 22449720 J Biomed Inform 2012 Oct https://www.ncbi.nlm.nih.gov/pubmed/22449720
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
Implementing electronic medical record systems in developing countries. Fraser HS, Biondich P, Moodley D, Choi S, Mamlin BW, Szolovits P Informatics in primary care 15992493 Inform Prim Care 2005 https://www.ncbi.nlm.nih.gov/pubmed/15992493
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
Landmark Estimation of Survival and Treatment Effect in a Randomized Clinical Trial. Parast L, Tian L, Cai T Journal of the American Statistical Association 24659838 J Am Stat Assoc 2014 Jan 1 https://www.ncbi.nlm.nih.gov/pubmed/24659838
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
Potential for electronic health records and online social networking to redefine medical research. Pearson JF, Brownstein CA, Brownstein JS Clinical chemistry 21159898 Clin Chem 2011 Feb https://www.ncbi.nlm.nih.gov/pubmed/21159898
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
Graphical procedures for evaluating overall and subject-specific incremental values from new predictors with censored event time data. Uno H, Cai T, Tian L, Wei LJ Biometrics 21504421 Biometrics 2011 Dec https://www.ncbi.nlm.nih.gov/pubmed/21504421
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
A cascade of classifiers for extracting medication information from discharge summaries. Halgrim SR, Xia F, Solti I, Cadag E, Uzuner O Journal of biomedical semantics 21992591 J Biomed Semantics 2011 https://www.ncbi.nlm.nih.gov/pubmed/21992591
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
Identification and extraction of family history information from clinical reports. Goryachev S, Kim H, Zeng-Treitler Q AMIA ... Annual Symposium proceedings. AMIA Symposium 18999129 AMIA Annu Symp Proc 2008 Nov 6 https://www.ncbi.nlm.nih.gov/pubmed/18999129
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
Optimal screening for promising genes in 2-stage designs. Moerkerke B, Goetghebeur E Biostatistics (Oxford, England) 18349035 Biostatistics 2008 Oct https://www.ncbi.nlm.nih.gov/pubmed/18349035
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
Evaluating the informatics for integrating biology and the bedside system for clinical research. Deshmukh VG, Meystre SM, Mitchell JA BMC medical research methodology 19863809 BMC Med Res Methodol 2009 Oct 28 https://www.ncbi.nlm.nih.gov/pubmed/19863809
Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Dreyfuss JM, Johnson MD, Park PJ Molecular cancer 19732454 Mol Cancer 2009 Sep 4 https://www.ncbi.nlm.nih.gov/pubmed/19732454
Phenotyping patient-derived cells for translational studies in cardiovascular disease. Shaw SY, Brettman AD Circulation 22125190 Circulation 2011 Nov 29 https://www.ncbi.nlm.nih.gov/pubmed/22125190
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML Molecular systems biology 22146299 Mol Syst Biol 2011 Dec 6 https://www.ncbi.nlm.nih.gov/pubmed/22146299
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
The relationship between structural characteristics of 2010 challenge documents and ratings of document quality. Shen S, South BR, Butler J, Barrus R, Weir C AMIA ... Annual Symposium proceedings. AMIA Symposium 23304359 AMIA Annu Symp Proc 2012 https://www.ncbi.nlm.nih.gov/pubmed/23304359
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Regional 3D superimposition to assess temporomandibular joint condylar morphology. Schilling J, Gomes LC, Benavides E, Nguyen T, Paniagua B, Styner M, Boen V, Gonçalves JR, Cevidanes LH Dento maxillo facial radiology 24170802 Dentomaxillofac Radiol 2014 https://www.ncbi.nlm.nih.gov/pubmed/24170802
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Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality. Bronson JR, Levine JA, Whitaker RT Proceedings. International Meshing Roundtable 25309969 Proc Int Meshing Roundtable 2013 https://www.ncbi.nlm.nih.gov/pubmed/25309969
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The DTI connectivity of the human claustrum. Torgerson CM, Irimia A, Goh SY, Van Horn JD Human brain mapping 25339630 Hum Brain Mapp 2015 Mar https://www.ncbi.nlm.nih.gov/pubmed/25339630
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Quantification and Analysis of Large Multimodal Clinical Image Studies: Application to Stroke. Sridharan R, Dalca AV, Fitzpatrick KM, Cloonan L, Kanakis A, Wu O, Furie KL, Rosand J, Rost NS, Golland P Multimodal brain image analysis : third International Workshop, MBIA 2013, held in conjunction with MICCAI 2013, Nagoya, Japan, September 22, 2013 : proceedings. MBIA (Workshop) (3rd : 2013 : Nagoya-shi, Japan) 25632408 Multimodal Brain Image Anal (2013) 2013 https://www.ncbi.nlm.nih.gov/pubmed/25632408
Multifold Bayesian kernelization in Alzheimer's diagnosis. Liu S, Song Y, Cai W, Pujol S, Kikinis R, Wang X, Feng D Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 24579154 Med Image Comput Comput Assist Interv 2013 https://www.ncbi.nlm.nih.gov/pubmed/24579154
A complete system for automatic extraction of left ventricular myocardium from CT images using shape segmentation and contour evolution. Liangjia Zhu, Yi Gao, Appia V, Yezzi A, Arepalli C, Faber T, Stillman A, Tannenbaum A IEEE transactions on image processing : a publication of the IEEE Signal Processing Society 24723531 IEEE Trans Image Process 2014 Mar https://www.ncbi.nlm.nih.gov/pubmed/24723531
BrainPrint: a discriminative characterization of brain morphology. Wachinger C, Golland P, Kremen W, Fischl B, Reuter M, Alzheimer's Disease Neuroimaging Initiative NeuroImage 25613439 Neuroimage 2015 Apr 1 https://www.ncbi.nlm.nih.gov/pubmed/25613439
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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