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Bioinformatics and Computational Biology (1792)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Coping with confounds in multivoxel pattern analysis: what should we do about reaction time differences? A comment on Todd, Nystrom & Cohen 2013.Woolgar, Alexandra; Golland, Polina; Bode, StefanNeuroImage2014 Sep506-1224793832
Comparative analysis of metazoan chromatin organization.Ho, Joshua W K; Jung, Youngsook L; Liu, Tao; Alver, Burak H; Lee, Soohyun; Ikegami, Kohta; Sohn, Kyung-Ah; Minoda, Aki; Tolstorukov, Michael Y; Appert, Alex; Parker, Stephen C J; Gu, Tingting; Kundaje, Anshul; Riddle, Nicole C; Bishop, Eric; Egelhofer, ThNature2014 Aug 28449-5225164756
Text Mining for Adverse Drug Events: the Promise, Challenges, and State of the Art.Harpaz, Rave; Callahan, Alison; Tamang, Suzanne; Low, Yen; Odgers, David; Finlayson, Sam; Jung, Kenneth; LePendu, Paea; Shah, Nigam HDrug safety : an international journal of medical toxicology and drug experience2014 Aug 24NULL25151493
Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.Pefanis, Evangelos; Wang, Jiguang; Rothschild, Gerson; Lim, Junghyun; Chao, Jaime; Rabadan, Raul; Economides, Aris N; Basu, UttiyaNature2014 Aug 6NULL25119026
Efficient inverse isoparametric mapping algorithm for whole-body computed tomography registration using deformations predicted by nonlinear finite element modeling.Li, Mao; Wittek, Adam; Miller, KarolJournal of biomechanical engineering2014 AugNULL24828796
Colonoscopy Is Associated With a Reduced Risk for Colon Cancer and Mortality in Patients With Inflammatory Bowel Diseases.Ananthakrishnan, Ashwin N; Cagan, Andrew; Cai, Tianxi; Gainer, Vivian S; Shaw, Stanley Y; Churchill, Susanne; Karlson, Elizabeth W; Murphy, Shawn N; Kohane, Isaac; Liao, Katherine PClinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association2014 Jul 17NULL25041865
The automated function prediction SIG looks back at 2013 and prepares for 2014.Wass, Mark N; Mooney, Sean D; Linial, Michal; Radivojac, Predrag; Friedberg, IddoBioinformatics (Oxford, England)2014 Jul 152091-224590444
Characterization of living skin using multi-view stereo and isogeometric analysis.Tepole, Adrian Buganza; Gart, Michael; Gosain, Arun K; Kuhl, EllenActa biomaterialia2014 Jul 10NULL25016279
pSCANNER: patient-centered Scalable National Network for Effectiveness Research.Ohno-Machado, Lucila; Agha, Zia; Bell, Douglas S; Dahm, Lisa; Day, Michele E; Doctor, Jason N; Gabriel, Davera; Kahlon, Maninder K; Kim, Katherine K; Hogarth, Michael; Matheny, Michael E; Meeker, Daniella; Nebeker, Jonathan R; pSCANNER teamJournal of the American Medical Informatics Association : JAMIA2014 Jul-Aug621-624780722
Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture.Mandl, Kenneth D; Kohane, Isaac S; McFadden, Douglas; Weber, Griffin M; Natter, Marc; Mandel, Joshua; Schneeweiss, Sebastian; Weiler, Sarah; Klann, Jeffrey G; Bickel, Jonathan; Adams, William G; Ge, Yaorong; Zhou, Xiaobo; Perkins, James; Marsolo, Keith; BJournal of the American Medical Informatics Association : JAMIA2014 Jul615-2024821734
Dysmorphogenic effects of first trimester-equivalent ethanol exposure in mice: a magnetic resonance microscopy-based study.Parnell, Scott E; Holloway, Hunter E; Baker, Lorinda K; Styner, Martin A; Sulik, Kathleen KAlcoholism, clinical and experimental research2014 Jul2008-1424931007
Application of Finite Element Modeling to Optimize Flap Design with Tissue Expansion.Buganza-Tepole, Adrian; Steinberg, Jordan P; Kuhl, Ellen; Gosain, Arun KPlastic and reconstructive surgery2014 Jun 18NULL24945952
Inferring gene ontologies from pairwise similarity data.Kramer, Michael; Dutkowski, Janusz; Yu, Michael; Bafna, Vineet; Ideker, TreyBioinformatics (Oxford, England)2014 Jun 15i34-4224932003
More accurate neuronavigation data provided by biomechanical modeling instead of rigid registration.Garlapati, Revanth Reddy; Roy, Aditi; Joldes, Grand Roman; Wittek, Adam; Mostayed, Ahmed; Doyle, Barry; Warfield, Simon Keith; Kikinis, Ron; Knuckey, Neville; Bunt, Stuart; Miller, KarolJournal of neurosurgery2014 Jun1477-8324460486
Aldosterone dysregulation with aging predicts renal vascular function and cardiovascular risk.Brown, Jenifer M; Underwood, Patricia C; Ferri, Claudio; Hopkins, Paul N; Williams, Gordon H; Adler, Gail K; Vaidya, AnandHypertension2014 Jun1205-1124664291
Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells.Lewis, Caroline A; Parker, Seth J; Fiske, Brian P; McCloskey, Douglas; Gui, Dan Y; Green, Courtney R; Vokes, Natalie I; Feist, Adam M; Vander Heiden, Matthew G; Metallo, Christian MMolecular cell2014 May 28NULL24882210
Millisecond dynamics of RNA polymerase II translocation at atomic resolution.Silva, Daniel-Adriano; Weiss, Dahlia R; Pardo Avila, Fatima; Da, Lin-Tai; Levitt, Michael; Wang, Dong; Huang, XuhuiProceedings of the National Academy of Sciences of the United States of America2014 May 277665-7024753580
Response of Escherichia coli growth rate to osmotic shock.Rojas, Enrique; Theriot, Julie A; Huang, Kerwyn CaseyProceedings of the National Academy of Sciences of the United States of America2014 May 277807-1224821776
Structural and connectomic neuroimaging for the personalized study of longitudinal alterations in cortical shape, thickness and connectivity after traumatic brain injury.Irimia, A; Goh, S Y; Torgerson, C M; Vespa, P M; Van Horn, J DJournal of neurosurgical sciences2014 May 20NULL24844173
Multi-Channel neurodegenerative pattern analysis and its application in Alzheimer's disease characterization.Liu, Sidong; Cai, Weidong; Wen, Lingfeng; Feng, David Dagan; Pujol, Sonia; Kikinis, Ron; Fulham, Michael J; Eberl, Stefan; ADNIComputerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society2014 May 14NULL24933011
Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.Aytes, Alvaro; Mitrofanova, Antonina; Lefebvre, Celine; Alvarez, Mariano J; Castillo-Martin, Mireia; Zheng, Tian; Eastham, James A; Gopalan, Anuradha; Pienta, Kenneth J; Shen, Michael M; Califano, Andrea; Abate-Shen, CoryCancer cell2014 May 12638-5124823640
Stable Atlas-based Mapped Prior (STAMP) machine-learning segmentation for multicenter large-scale MRI data.Kim, Eun Young; Magnotta, Vincent A; Liu, Dawei; Johnson, Hans JMagnetic resonance imaging2014 May 9NULL24818817
Structural bioinformatics of the interactome.Petrey, Donald; Honig, BarryAnnual review of biophysics2014 May 6193-21024895853
Discovering body site and severity modifiers in clinical texts.Dligach, Dmitriy; Bethard, Steven; Becker, Lee; Miller, Timothy; Savova, Guergana KJournal of the American Medical Informatics Association : JAMIA2014 May-Jun448-5424091648
The EBI RDF platform: linked open data for the life sciences.Jupp, Simon; Malone, James; Bolleman, Jerven; Brandizi, Marco; Davies, Mark; Garcia, Leyla; Gaulton, Anna; Gehant, Sebastien; Laibe, Camille; Redaschi, Nicole; Wimalaratne, Sarala M; Martin, Maria; Le Novere, Nicolas; Parkinson, Helen; Birney, Ewan; JenkiBioinformatics (Oxford, England)2014 May 11338-924413672
Higher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases.Ananthakrishnan, A N; Cagan, A; Gainer, V S; Cheng, S-C; Cai, T; Szolovits, P; Shaw, S Y; Churchill, S; Karlson, E W; Murphy, S N; Kohane, I; Liao, K PAlimentary pharmacology & therapeutics2014 May1136-4224641590
Population-level evidence for an autoimmune etiology of epilepsy.Ong, Mei-Sing; Kohane, Isaac S; Cai, Tianxi; Gorman, Mark P; Mandl, Kenneth DJAMA neurology2014 May569-7424687183
Mutual information as a measure of image quality for 3D dynamic lung imaging with EIT.Crabb, M G; Davidson, J L; Little, R; Wright, P; Morgan, A R; Miller, C A; Naish, J H; Parker, G J M; Kikinis, R; McCann, H; Lionheart, W R BPhysiological measurement2014 May863-7924710978
Vision 20/20: perspectives on automated image segmentation for radiotherapy.Sharp, Gregory; Fritscher, Karl D; Pekar, Vladimir; Peroni, Marta; Shusharina, Nadya; Veeraraghavan, Harini; Yang, JinzhongMedical physics2014 May5090224784366
Automatic segmentation of head and neck CT images for radiotherapy treatment planning using multiple atlases, statistical appearance models, and geodesic active contours.Fritscher, Karl D; Peroni, Marta; Zaffino, Paolo; Spadea, Maria Francesca; Schubert, Rainer; Sharp, GregoryMedical physics2014 May5191024784389
Cerebral white matter abnormalities and their associations with negative but not positive symptoms of schizophrenia.Asami, Takeshi; Hyuk Lee, Sang; Bouix, Sylvain; Rathi, Yogesh; Whitford, Thomas J; Niznikiewicz, Margaret; Nestor, Paul; McCarley, Robert W; Shenton, Martha E; Kubicki, MarekPsychiatry research2014 Apr 3052-924650453
Evaluating marker-guided treatment selection strategies.Matsouaka, Roland A; Li, Junlong; Cai, TianxiBiometrics2014 Apr 29NULL24779731
Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.Bendall, Sean C; Davis, Kara L; Amir, El-Ad David; Tadmor, Michelle D; Simonds, Erin F; Chen, Tiffany J; Shenfeld, Daniel K; Nolan, Garry P; Pe'er, DanaCell2014 Apr 24714-2524766814
Application of Tolerance Limits to the Characterization of Image Registration Performance.Fedorov, Andriy; Wells, William; Kikinis, Ron; Tempany, Clare; Vangel, MarkIEEE transactions on medical imaging2014 Apr 16NULL24759985
Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.Lee, Eunjee; de Ridder, Jeroen; Kool, Jaap; Wessels, Lodewyk F A; Bussemaker, Harmen JProceedings of the National Academy of Sciences of the United States of America2014 Apr 155747-5224706889
Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness.Messina, Monica; Del Giudice, Ilaria; Khiabanian, Hossein; Rossi, Davide; Chiaretti, Sabina; Rasi, Silvia; Spina, Valeria; Holmes, Antony B; Marinelli, Marilisa; Fabbri, Giulia; Piciocchi, Alfonso; Mauro, Francesca R; Guarini, Anna; Gaidano, Gianluca; DalBlood2014 Apr 102378-8824550227
Toward Enhanced Pharmacovigilance Using Patient-Generated Data on the Internet.White, R W; Harpaz, R; Shah, N H; Dumouchel, W; Horvitz, EClinical pharmacology and therapeutics2014 Apr 8NULL24713590
Ensuring privacy in the study of pathogen genetics.Mehta, Sanjay R; Vinterbo, Staal A; Little, Susan JThe Lancet infectious diseases2014 Apr 7NULL24721230
Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia.Rossi, Davide; Khiabanian, Hossein; Spina, Valeria; Ciardullo, Carmela; Bruscaggin, Alessio; Fama, Rosella; Rasi, Silvia; Monti, Sara; Deambrogi, Clara; De Paoli, Lorenzo; Wang, Jiguang; Gattei, Valter; Guarini, Anna; Foa, Robin; Rabadan, Raul; Gaidano, GBlood2014 Apr 32139-4724501221
Reviewing the ketamine model for schizophrenia.Frohlich, Joel; Van Horn, John DJournal of psychopharmacology (Oxford, England)2014 Apr287-30224257811
SGPP: spatial Gaussian predictive process models for neuroimaging data.Hyun, Jung Won; Li, Yimei; Gilmore, John H; Lu, Zhaohua; Styner, Martin; Zhu, HongtuNeuroImage2014 Apr 170-8024269800
Predicting the restricted mean event time with the subject's baseline covariates in survival analysis.Tian, Lu; Zhao, Lihui; Wei, L JBiostatistics (Oxford, England)2014 Apr222-3324292992
Detecting Inappropriate Access to Electronic Health Records Using Collaborative Filtering.Menon, Aditya Krishna; Jiang, Xiaoqian; Kim, Jihoon; Vaidya, Jaideep; Ohno-Machado, LucilaMachine learning2014 Apr 187-10124683293
Response to letters regarding article, "unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine".Ghebremariam, Yohannes T; Lee, Jerry C; LePendu, Paea; Erlanson, Daniel A; Slaviero, Anna; Shah, Nigam H; Leiper, James M; Cooke, John PCirculation2014 Apr 1e42824687654
Knowledge-based fragment binding prediction.Tang, Grace W; Altman, Russ BPLoS computational biology2014 Apre100358924762971
Multi-atlas segmentation with particle-based group-wise image registration.Lee, Joohwi; Lyu, Ilwoo; Styner, MartinProceedings - Society of Photo-Optical Instrumentation Engineers2014 Mar 2190344725075158
Molecular testing of 163 patients with Morquio A (Mucopolysaccharidosis IVA) identifies 39 novel GALNS mutations.Morrone, A; Tylee, K L; Al-Sayed, M; Brusius-Facchin, A C; Caciotti, A; Church, H J; Coll, M J; Davidson, K; Fietz, M J; Gort, L; Hegde, M; Kubaski, F; Lacerda, L; Laranjeira, F; Leistner-Segal, S; Mooney, S; Pajares, S; Pollard, L; Ribeiro, I; Wang, R Y;Molecular genetics and metabolism2014 Mar 20NULL24726177
Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments.van de Meent, Jan-Willem; Bronson, Jonathan E; Wiggins, Chris H; Gonzalez Jr, Ruben LBiophysical journal2014 Mar 181327-3724655508
Bayesian energy landscape tilting: towards concordant models of molecular ensembles.Beauchamp, Kyle A; Pande, Vijay S; Das, RhijuBiophysical journal2014 Mar 181381-9024655513
Thromboprophylaxis Is Associated With Reduced Post-hospitalization Venous Thromboembolic Events in Patients With Inflammatory Bowel Diseases.Ananthakrishnan, Ashwin N; Cagan, Andrew; Gainer, Vivian S; Cheng, Su-Chun; Cai, Tianxi; Scoville, Elizabeth; Konijeti, Gauree G; Szolovits, Peter; Shaw, Stanley Y; Churchill, Susanne; Karlson, Elizabeth W; Murphy, Shawn N; Kohane, Isaac; Liao, Katherine Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association2014 Mar 12NULL24632349
EM-Navigated Catheter Placement for Gynecologic Brachytherapy: An Accuracy Study.Mehrtash, Alireza; Damato, Antonio; Pernelle, Guillaume; Barber, Lauren; Farhat, Nabgha; Viswanathan, Akila; Cormack, Robert; Kapur, TinaProceedings - Society of Photo-Optical Instrumentation Engineers2014 Mar 1290361F25076828
Pregnancy in women with a history of Kawasaki disease: management and outcomes.Gordon, Ct; Jimenez-Fernandez, S; Daniels, Lb; Kahn, Am; Tarsa, M; Matsubara, T; Shimizu, C; Burns, Jc; Gordon, JbBJOG : an international journal of obstetrics and gynaecology2014 Mar 6NULL24597833
Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB.Colavin, Alexandre; Hsin, Jen; Huang, Kerwyn CaseyProceedings of the National Academy of Sciences of the United States of America2014 Mar 43585-9024550504
Mining clinical text for signals of adverse drug-drug interactions.Iyer, Srinivasan V; Harpaz, Rave; LePendu, Paea; Bauer-Mehren, Anna; Shah, Nigam HJournal of the American Medical Informatics Association : JAMIA2014 Mar-Apr353-6224158091
HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads.Li, Pinghao; Jiang, Xiaoqian; Wang, Shuang; Kim, Jihoon; Xiong, Hongkai; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2014 Mar-Apr363-7324368726
Specificity of regulatory T cells that modulate vascular inflammation.Franco, Alessandra; Touma, Ranim; Song, Yali; Shimizu, Chisato; Tremoulet, Adriana H; Kanegaye, John T; Burns, Jane CAutoimmunity2014 Mar95-10424490882
A complete system for automatic extraction of left ventricular myocardium from CT images using shape segmentation and contour evolution.Liangjia Zhu; Yi Gao; Appia, Vikram; Yezzi, Anthony; Arepalli, Chesnal; Faber, Tracy; Stillman, Arthur; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2014 Mar1340-5124723531
Changes in tibiofemoral forces due to variations in muscle activity during walking.Demers, Matthew S; Pal, Saikat; Delp, Scott LJournal of orthopaedic research : official publication of the Orthopaedic Research Society2014 Feb 26769-7624615885
Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease.Ananthakrishnan, Ashwin N; Cagan, Andrew; Gainer, Vivian S; Cheng, Su-Chun; Cai, Tianxi; Szolovits, Peter; Shaw, Stanley Y; Churchill, Susanne; Karlson, Elizabeth W; Murphy, Shawn N; Kohane, Isaac; Liao, Katherine PJournal of Crohn's & colitis2014 Feb 18NULL24559536
Genetic robustness and functional evolution of gene duplicates.Plata, German; Vitkup, DennisNucleic acids research2014 Feb2405-1424288370
Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations.Patel, Anand; Schwab, Richard; Liu, Yu-Tsueng; Bafna, VineetGenome research2014 Feb318-2824307551
Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI.McGann, Christopher; Akoum, Nazem; Patel, Amit; Kholmovski, Eugene; Revelo, Patricia; Damal, Kavitha; Wilson, Brent; Cates, Josh; Harrison, Alexis; Ranjan, Ravi; Burgon, Nathan S; Greene, Tom; Kim, Dan; Dibella, Edward V R; Parker, Dennis; Macleod, Rob S;Circulation. Arrhythmia and electrophysiology2014 Feb23-3024363354
iPSC-derived neurons as a higher-throughput readout for autism: promises and pitfalls.Prilutsky, Daria; Palmer, Nathan P; Smedemark-Margulies, Niklas; Schlaeger, Thorsten M; Margulies, David M; Kohane, Isaac STrends in molecular medicine2014 Feb91-10424374161
On the mechanics of growing thin biological membranes.Rausch, Manuel K; Kuhl, EllenJournal of the mechanics and physics of solids2014 Feb 1128-14024563551
ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state.Chudnovsky, Yakov; Kim, Dohoon; Zheng, Siyuan; Whyte, Warren A; Bansal, Mukesh; Bray, Mark-Anthony; Gopal, Shuba; Theisen, Matthew A; Bilodeau, Steve; Thiru, Prathapan; Muffat, Julien; Yilmaz, Omer H; Mitalipova, Maya; Woolard, Kevin; Lee, Jeongwu; NishimCell reports2014 Jan 30313-2424440720
The long noncoding RNA THRIL regulates TNF* expression through its interaction with hnRNPL.Li, Zhonghan; Chao, Ti-Chun; Chang, Kung-Yen; Lin, Nianwei; Patil, Veena S; Shimizu, Chisato; Head, Steven R; Burns, Jane C; Rana, Tariq MProceedings of the National Academy of Sciences of the United States of America2014 Jan 211002-724371310
Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods.Chasin, Rachel; Rumshisky, Anna; Uzuner, Ozlem; Szolovits, PeterJournal of the American Medical Informatics Association : JAMIA2014 Jan 17NULL24441986
MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing.Mort, Matthew; Sterne-Weiler, Timothy; Li, Biao; Ball, Edward V; Cooper, David N; Radivojac, Predrag; Sanford, Jeremy R; Mooney, Sean DGenome biology2014 Jan 13R1924451234
Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes.Menon, Rajasree; Im, Hogune; Zhang, Emma Yue; Wu, Shiaw-Lin; Chen, Rui; Snyder, Michael; Hancock, William S; Omenn, Gilbert SJournal of proteome research2014 Jan 3212-2724111759
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.Farrah, Terry; Deutsch, Eric W; Omenn, Gilbert S; Sun, Zhi; Watts, Julian D; Yamamoto, Tadashi; Shteynberg, David; Harris, Micheleen M; Moritz, Robert LJournal of proteome research2014 Jan 360-7524261998
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.Doan, Son; Lin, Ko-Wei; Conway, Mike; Ohno-Machado, Lucila; Hsieh, Alex; Feupe, Stephanie Feudjio; Garland, Asher; Ross, Mindy K; Jiang, Xiaoqian; Farzaneh, Seena; Walker, Rebecca; Alipanah, Neda; Zhang, Jing; Xu, Hua; Kim, Hyeon-EuiJournal of the American Medical Informatics Association : JAMIA2014 Jan-Feb31-623989082
Prostate cancer detection and diagnosis: the role of MR and its comparison with other diagnostic modalities--a radiologist's perspective.Penzkofer, Tobias; Tempany-Afdhal, Clare MNMR in biomedicine2014 Jan15-Mar24000133
A novel strategy to identify the critical conditions for growth-induced instabilities.Javili, A; Steinmann, P; Kuhl, EJournal of the mechanical behavior of biomedical materials2014 Jan20-3224041754
FMEM: functional mixed effects modeling for the analysis of longitudinal white matter Tract data.Yuan, Ying; Gilmore, John H; Geng, Xiujuan; Martin, Styner; Chen, Kehui; Wang, Jane-ling; Zhu, HongtuNeuroImage2014 Jan 1753-6424076225
Improved segmentation of white matter tracts with adaptive Riemannian metrics.Hao, Xiang; Zygmunt, Kristen; Whitaker, Ross T; Fletcher, P ThomasMedical image analysis2014 Jan161-7524211814
Growing matter: a review of growth in living systems.Kuhl, EllenJournal of the mechanical behavior of biomedical materials2014 Jan529-4324239171
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites.Shazman, Shula; Lee, Hunjoong; Socol, Yakov; Mann, Richard S; Honig, BarryNucleic acids research2014 Jan 1D167-7124271386
Associations of smoking and alcohol consumption with disease activity and functional status in rheumatoid arthritis.Lu, Bing; Rho, Young Hee; Cui, Jing; Iannaccone, Christine K; Frits, Michelle L; Karlson, Elizabeth W; Shadick, Nancy AThe Journal of rheumatology2014 Jan24-3024293566
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.Kohlhoff, Kai J; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R; Konerding, David E; Belov, Dan; Altman, Russ B; Pande, Vijay SNature chemistry2014 Jan15-2124345941
Regional neuroplastic brain changes in patients with chronic inflammatory and non-inflammatory visceral pain.Hong, Jui-Yang; Labus, Jennifer S; Jiang, Zhiguo; Ashe-Mcnalley, Cody; Dinov, Ivo; Gupta, Arpana; Shi, Yonggang; Stains, Jean; Heendeniya, Nuwanthi; Smith, Suzanne R; Tillisch, Kirsten; Mayer, Emeran APloS one2014e8456424416245
Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline.Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clementine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, MartinFrontiers in neuroinformatics2014724567717
Automated detection of off-label drug use.Jung, Kenneth; LePendu, Paea; Chen, William S; Iyer, Srinivasan V; Readhead, Ben; Dudley, Joel T; Shah, Nigam HPloS one2014e8932424586689
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, AndPloS one2014e8960624595056
MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data.Gan, Zhuohui; Wang, Jianwu; Salomonis, Nathan; Stowe, Jennifer C; Haddad, Gabriel G; McCulloch, Andrew D; Altintas, Ilkay; Zambon, Alexander CBMC bioinformatics20146924621103
High precision prediction of functional sites in protein structures.Buturovic, Ljubomir; Wong, Mike; Tang, Grace W; Altman, Russ B; Petkovic, DragutinPloS one2014e9124024632601
Developing image processing meta-algorithms with data mining of multiple metrics.Leung, Kelvin; Cunha, Alexandre; Toga, A W; Parker, D StottComputational and mathematical methods in medicine201438346524653748
Landmark Estimation of Survival and Treatment Effect in a Randomized Clinical Trial.Parast, Layla; Tian, Lu; Cai, TianxiJournal of the American Statistical Association2014 Jan 1384-39424659838
HD CAGnome: a search tool for huntingtin CAG repeat length-correlated genes.Galkina, Ekaterina I; Shin, Aram; Coser, Kathryn R; Shioda, Toshi; Kohane, Isaac S; Seong, Ihn Sik; Wheeler, Vanessa C; Gusella, James F; Macdonald, Marcy E; Lee, Jong-MinPloS one2014e9555624751919
Natural language processing in biomedicine: a unified system architecture overview.Doan, Son; Conway, Mike; Phuong, Tu Minh; Ohno-Machado, LucilaMethods in molecular biology (Clifton, N.J.)2014275-9424870142
Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats.Repunte-Canonigo, Vez; Lefebvre, Celine; George, Olivier; Kawamura, Tomoya; Morales, Marisela; Koob, George F; Califano, Andrea; Masliah, Eliezer; Sanna, Pietro PaoloMolecular neurodegeneration20142624980976
A mechanical model predicts morphological abnormalities in the developing human brain.Budday, Silvia; Raybaud, Charles; Kuhl, EllenScientific reports2014564425008163
Privacy preserving RBF kernel support vector machine.Li, Haoran; Xiong, Li; Ohno-Machado, Lucila; Jiang, XiaoqianBioMed research international201482737125013805
Robust Radiomics feature quantification using semiautomatic volumetric segmentation.Parmar, Chintan; Rios Velazquez, Emmanuel; Leijenaar, Ralph; Jermoumi, Mohammed; Carvalho, Sara; Mak, Raymond H; Mitra, Sushmita; Shankar, B Uma; Kikinis, Ron; Haibe-Kains, Benjamin; Lambin, Philippe; Aerts, Hugo J W LPloS one2014e10210725025374
LONGITUDINAL GROWTH MODELING OF DISCRETE-TIME FUNCTIONS WITH APPLICATION TO DTI TRACT EVOLUTION IN EARLY NEURODEVELOPMENT.Sharma, Anuja; Durrleman, Stanley; Gilmore, John H; Gerig, GuidoProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2013 Dec 311945-140024443681
SPATIOTEMPORAL MODELING OF DISCRETE-TIME DISTRIBUTION-VALUED DATA APPLIED TO DTI TRACT EVOLUTION IN INFANT NEURODEVELOPMENT.Sharma, Anuja; Fletcher, P Thomas; Gilmore, John H; Escolar, Maria L; Gupta, Aditya; Styner, Martin; Gerig, GuidoProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2013 Dec 31684-68724443688
ANALYZING IMAGING BIOMARKERS FOR TRAUMATIC BRAIN INJURY USING 4D MODELING OF LONGITUDINAL MRI.Wang, Bo; Prastawa, Marcel; Irimia, Andrei; Chambers, Micah C; Sadeghi, Neda; Vespa, Paul M; van Horn, John D; Gerig, GuidoProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2013 Dec 311392-139524443697
MODELING LONGITUDINAL MRI CHANGES IN POPULATIONS USING A LOCALIZED, INFORMATION-THEORETIC MEASURE OF CONTRAST.Vardhan, Avantika; Prastawa, Marcel; Sharma, Anuja; Piven, Joseph; Gerig, GuidoProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2013 Dec 311396-139924443698
Calculations of the electric fields in liquid solutions.Fried, Stephen D; Wang, Lee-Ping; Boxer, Steven G; Ren, Pengyu; Pande, Vijay SThe journal of physical chemistry. B2013 Dec 1916236-4824304155
SCISSORS: Practical Considerations.Kearnes, Steven M; Haque, Imran S; Pande, Vijay SJournal of chemical information and modeling2013 Dec 16NULL24289274
Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia.Piovan, Erich; Yu, Jiyang; Tosello, Valeria; Herranz, Daniel; Ambesi-Impiombato, Alberto; Da Silva, Ana Carolina; Sanchez-Martin, Marta; Perez-Garcia, Arianne; Rigo, Isaura; Castillo, Mireia; Indraccolo, Stefano; Cross, Justin R; de Stanchina, Elisa; PaieCancer cell2013 Dec 9766-7624291004
Immune-monitoring in Kawasaki disease patients treated with infliximab and intravenous immunoglobulin.Burns, J C; Song, Y; Bujold, M; Shimizu, C; Kanegaye, J T; Tremoulet, A H; Franco, AClinical and experimental immunology2013 Dec337-4423901839
MedTime: a temporal information extraction system for clinical narratives.Lin, Yu-Kai; Chen, Hsinchun; Brown, Randall AJournal of biomedical informatics2013 DecS20-823911344
Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population.Liao, Katherine P; Cai, Tianxi; Gainer, Vivian S; Cagan, Andrew; Murphy, Shawn N; Liu, Chihchin; Churchill, Susanne; Shaw, Stanley Y; Kohane, Isaac; Solomon, Daniel H; Plenge, Robert M; Karlson, Elizabeth WArthritis care & research2013 Dec2046-5023925980
Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical records.Lyalina, Svetlana; Percha, Bethany; LePendu, Paea; Iyer, Srinivasan V; Altman, Russ B; Shah, Nigam HJournal of the American Medical Informatics Association : JAMIA2013 Dece297-30523956017
A new tool for sharing and querying of clinical documents modeled using HL7 Version 3 standard.Slavov, Vasil; Rao, Praveen; Paturi, Srivenu; Swami, Tivakar Komara; Barnes, Michael; Rao, Deepthi; Palvai, RaghuvarunComputer methods and programs in biomedicine2013 Dec529-5224001923
Extraction of events and temporal expressions from clinical narratives.Jindal, Prateek; Roth, DanJournal of biomedical informatics2013 DecS13-924022023
Automatic segmentation of the left atrium from MR images via variational region growing with a moments-based shape prior.Zhu, Liangjia; Gao, Yi; Yezzi, Anthony; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2013 Dec5111-2224058026
TEMPTING system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries.Chang, Yung-Chun; Dai, Hong-Jie; Wu, Johnny Chi-Yang; Chen, Jian-Ming; Tsai, Richard Tzong-Han; Hsu, Wen-LianJournal of biomedical informatics2013 DecS54-6224060600
Temporal relation discovery between events and temporal expressions identified in clinical narrative.Cheng, Yao; Anick, Peter; Hong, Pengyu; Xue, NianwenJournal of biomedical informatics2013 DecS48-5324076508
Leveraging electronic health records to notify pediatric patients of a drug recall.Mendelson, Michael M; Zachariah, Justin P; de Ferranti, Sarah D; Bickel, Jonathan PJAMA pediatrics2013 Dec1170-124165895
In silico approaches and the role of ontologies in aging research.Fuellen, Georg; Boerries, Melanie; Busch, Hauke; de Grey, Aubrey; Hahn, Udo; Hiller, Thomas; Hoeflich, Andreas; Jansen, Ludger; Janssens, Georges E; Kaleta, Christoph; Meinema, Anne C; Schauble, Sascha; Simm, Andreas; Schofield, Paul N; Smith, Barry; SuhnRejuvenation research2013 Dec540-624188080
Towards generating a patient's timeline: extracting temporal relationships from clinical notes.Nikfarjam, Azadeh; Emadzadeh, Ehsan; Gonzalez, GracielaJournal of biomedical informatics2013 DecS40-724212118
Recent trends in biomedical informatics: a study based on JAMIA articles.Jiang, Xiaoqian; Tse, Krystal; Wang, Shuang; Doan, Son; Kim, Hyeoneui; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2013 Dece198-20524214018
Chronology of your health events: approaches to extracting temporal relations from medical narratives.Uzuner, Ozlem; Stubbs, Amber; Sun, WeiyiJournal of biomedical informatics2013 DecS1-424286753
Omnibus risk assessment via accelerated failure time kernel machine modeling.Sinnott, Jennifer A; Cai, TianxiBiometrics2013 Dec861-7324328713
Diffusion imaging quality control via entropy of principal direction distribution.Farzinfar, Mahshid; Oguz, Ipek; Smith, Rachel G; Verde, Audrey R; Dietrich, Cheryl; Gupta, Aditya; Escolar, Maria L; Piven, Joseph; Pujol, Sonia; Vachet, Clement; Gouttard, Sylvain; Gerig, Guido; Dager, Stephen; McKinstry, Robert C; Paterson, Sarah; EvansNeuroImage2013 Nov 1512-Jan23684874
Spatial-temporal atlas of human fetal brain development during the early second trimester.Zhan, Jinfeng; Dinov, Ivo D; Li, Junning; Zhang, Zhonghe; Hobel, Sam; Shi, Yonggang; Lin, Xiangtao; Zamanyan, Alen; Feng, Lei; Teng, Gaojun; Fang, Fang; Tang, Yuchun; Zang, Fengchao; Toga, Arthur W; Liu, ShuweiNeuroImage2013 Nov 15115-2623727529
Topology of viral evolution.Chan, Joseph Minhow; Carlsson, Gunnar; Rabadan, RaulProceedings of the National Academy of Sciences of the United States of America2013 Nov 1218566-7124170857
Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome.Davoli, Teresa; Xu, Andrew Wei; Mengwasser, Kristen E; Sack, Laura M; Yoon, John C; Park, Peter J; Elledge, Stephen JCell2013 Nov 7948-6224183448
Genome-wide DNA methylation changes with age in disease free human skeletal muscle.Zykovich, Artem; Hubbard, Alan; Flynn, James M; Tarnopolsky, Mark; Fraga, Mario F; Kerksick, Chad; Ogborn, Dan; Macneil, Lauren; Mooney, Sean D; Melov, SimonAging cell2013 Nov 7NULL24304487
Towards improved ultrasound-based analysis and 3D visualization of the fetal brain using the 3D Slicer.Oyama, R; Jakab, M; Kikuchi, A; Sugiyama, T; Kikinis, R; Pujol, SUltrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology2013 Nov609-1023576282
From connectivity models to region labels: identifying foci of a neurological disorder.Venkataraman, Archana; Kubicki, Marek; Golland, PolinaIEEE transactions on medical imaging2013 Nov2078-9823864168
Interactive medical image segmentation using PDE control of active contours.Karasev, Peter; Kolesov, Ivan; Fritscher, Karl; Vela, Patricio; Mitchell, Phillip; Tannenbaum, AllenIEEE transactions on medical imaging2013 Nov2127-3923893712
A locally adaptive regularization based on anisotropic diffusion for deformable image registration of sliding organs.Pace, Danielle F; Aylward, Stephen R; Niethammer, MarcIEEE transactions on medical imaging2013 Nov2114-2623899632
Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.Fan, Jung-wei; Yang, Elly W; Jiang, Min; Prasad, Rashmi; Loomis, Richard M; Zisook, Daniel S; Denny, Josh C; Xu, Hua; Huang, YangJournal of the American Medical Informatics Association : JAMIA2013 Nov-Dec1168-7723907286
Automated chart review for asthma cohort identification using natural language processing: an exploratory study.Wu, Stephen T; Sohn, Sunghwan; Ravikumar, K E; Wagholikar, Kavishwar; Jonnalagadda, Siddhartha R; Liu, Hongfang; Juhn, Young JAnnals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology2013 Nov364-924125142
Association Between Reduced Plasma 25-Hydroxy Vitamin D and Increased Risk of Cancer in Patients With Inflammatory Bowel Diseases.Ananthakrishnan, Ashwin N; Cheng, Su-Chun; Cai, Tianxi; Cagan, Andrew; Gainer, Vivian S; Szolovits, Peter; Shaw, Stanley Y; Churchill, Susanne; Karlson, Elizabeth W; Murphy, Shawn N; Kohane, Isaac; Liao, Katherine PClinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association2013 Oct 23NULL24161349
Human neuroimaging as a "Big Data" science.Van Horn, John Darrell; Toga, Arthur WBrain imaging and behavior2013 Oct 10NULL24113873
The structure of the corpus callosum in obsessive compulsive disorder.Di Paola, M; Luders, E; Rubino, I A; Siracusano, A; Manfredi, G; Girardi, P; Martinotti, G; Thompson, P M; Chou, Y-Y; Toga, A W; Caltagirone, C; Spalletta, GEuropean psychiatry : the journal of the Association of European Psychiatrists2013 Oct499-50623078960
Automatic delineation of the myocardial wall from CT images via shape segmentation and variational region growing.Zhu, Liangjia; Gao, Yi; Appia, Vikram; Yezzi, Anthony; Arepalli, Chesnal; Faber, Tracy; Stillman, Arthur; Tannenbaum, AllenIEEE transactions on bio-medical engineering2013 Oct2887-9523744658
Computational modeling of chemo-electro-mechanical coupling: a novel implicit monolithic finite element approach.Wong, J; Goktepe, S; Kuhl, EInternational journal for numerical methods in biomedical engineering2013 Oct1104-3323798328
Sparse texture active contour.Gao, Yi; Bouix, Sylvain; Shenton, Martha; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2013 Oct3866-7823799695
Adopting nested case-control quota sampling designs for the evaluation of risk markers.Zheng, Yingye; Cai, Tianxi; Pepe, Margaret SLifetime data analysis2013 Oct568-8823807695
Statistical shape modeling of cam femoroacetabular impingement.Harris, Michael D; Datar, Manasi; Whitaker, Ross T; Jurrus, Elizabeth R; Peters, Christopher L; Anderson, Andrew EJournal of orthopaedic research : official publication of the Orthopaedic Research Society2013 Oct1620-623832798
Longitudinal image registration with temporally-dependent image similarity measure.Csapo, Istvan; Davis, Brad; Shi, Yundi; Sanchez, Mar; Styner, Martin; Niethammer, MarcIEEE transactions on medical imaging2013 Oct1939-5123846465
Semantator: Semantic annotator for converting biomedical text to linked data.Tao, Cui; Song, Dezhao; Sharma, Deepak; Chute, Christopher GJournal of biomedical informatics2013 Oct882-9323867104
Electroencephalographic inverse localization of brain activity in acute traumatic brain injury as a guide to surgery, monitoring and treatment.Irimia, Andrei; Goh, S-Y Matthew; Torgerson, Carinna M; Stein, Nathan R; Chambers, Micah C; Vespa, Paul M; Van Horn, John DClinical neurology and neurosurgery2013 Oct2159-6524011495
Assessment of biomarkers for risk prediction with nested case-control studies.Zhou, Qian M; Zheng, Yingye; Cai, TianxiClinical trials (London, England)2013 Oct677-924013405
Opportunities for genomic clinical decision support interventions.Overby, Casey Lynnette; Kohane, Isaac; Kannry, Joseph L; Williams, Marc S; Starren, Justin; Bottinger, Erwin; Gottesman, Omri; Denny, Joshua C; Weng, Chunhua; Tarczy-Hornoch, Peter; Hripcsak, GeorgeGenetics in medicine : official journal of the American College of Medical Genetics2013 Oct817-2324051479
Cross-domain targeted ontology subsets for annotation: The case of SNOMED CORE and RxNorm.Lopez-Garcia, Pablo; Lependu, Paea; Musen, Mark; Illarramendi, ArantzaJournal of biomedical informatics2013 Oct 1NULL24095962
Differential privacy based on importance weighting.Ji, Zhanglong; Elkan, CharlesMachine learning2013 Oct163-18324482559
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.Blair, David R; Lyttle, Christopher S; Mortensen, Jonathan M; Bearden, Charles F; Jensen, Anders Boeck; Khiabanian, Hossein; Melamed, Rachel; Rabadan, Raul; Bernstam, Elmer V; Brunak, Soren; Jensen, Lars Juhl; Nicolae, Dan; Shah, Nigam H; Grossman, RobertCell2013 Sep 2670-8024074861
A molecular signature predictive of indolent prostate cancer.Irshad, Shazia; Bansal, Mukesh; Castillo-Martin, Mireia; Zheng, Tian; Aytes, Alvaro; Wenske, Sven; Le Magnen, Clementine; Guarnieri, Paolo; Sumazin, Pavel; Benson, Mitchell C; Shen, Michael M; Califano, Andrea; Abate-Shen, CoryScience translational medicine2013 Sep 11202ra12224027026
ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer.Aytes, Alvaro; Mitrofanova, Antonina; Kinkade, Carolyn Waugh; Lefebvre, Celine; Lei, Ming; Phelan, Vanessa; LeKaye, H Carl; Koutcher, Jason A; Cardiff, Robert D; Califano, Andrea; Shen, Michael M; Abate-Shen, CoryProceedings of the National Academy of Sciences of the United States of America2013 Sep 10E3506-1523918374
Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders.Zhou, Dan; Udpa, Nitin; Ronen, Roy; Stobdan, Tsering; Liang, Junbin; Appenzeller, Otto; Zhao, Huiwen W; Yin, Yi; Du, Yuanping; Guo, Lixia; Cao, Rui; Wang, Yu; Jin, Xin; Huang, Chen; Jia, Wenlong; Cao, Dandan; Guo, Guangwu; Gamboa, Jorge L; Villafuerte, FrAmerican journal of human genetics2013 Sep 5452-6223954164
Faceted Visualization of Three Dimensional Neuroanatomy By Combining Ontology with Faceted Search.Veeraraghavan, Harini; Miller, James VNeuroinformatics2013 Sep 5NULL24006207
Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology.Omenn, Gilbert S; Menon, Rajasree; Zhang, YangJournal of proteomics2013 Sep 228-3723603631
The right inhibition? Callosal correlates of hand performance in healthy children and adolescents callosal correlates of hand performance.Kurth, Florian; Mayer, Emeran A; Toga, Arthur W; Thompson, Paul M; Luders, EileenHuman brain mapping2013 Sep2259-6522438280
Longitudinal analysis of pain in patients with metastatic prostate cancer using natural language processing of medical record text.Heintzelman, Norris H; Taylor, Robert J; Simonsen, Lone; Lustig, Roger; Anderko, Doug; Haythornthwaite, Jennifer A; Childs, Lois C; Bova, George StevenJournal of the American Medical Informatics Association : JAMIA2013 Sep-Oct898-90523144336
HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses.Contreras-Galindo, Rafael; Kaplan, Mark H; He, Shirley; Contreras-Galindo, Angie C; Gonzalez-Hernandez, Marta J; Kappes, Ferdinand; Dube, Derek; Chan, Susana M; Robinson, Dan; Meng, Fan; Dai, Manhong; Gitlin, Scott D; Chinnaiyan, Arul M; Omenn, Gilbert S;Genome research2013 Sep1505-1323657884
Human middle longitudinal fascicle: segregation and behavioral-clinical implications of two distinct fiber connections linking temporal pole and superior temporal gyrus with the angular gyrus or superior parietal lobule using multi-tensor tractography.Makris, N; Preti, M G; Wassermann, D; Rathi, Y; Papadimitriou, G M; Yergatian, C; Dickerson, B C; Shenton, M E; Kubicki, MBrain imaging and behavior2013 Sep335-5223686576
Magnetic resonance microscopy-based analyses of the neuroanatomical effects of gestational day 9 ethanol exposure in mice.Parnell, Scott E; Holloway, Hunter T; O'Leary-Moore, Shonagh K; Dehart, Deborah B; Paniaqua, Beatriz; Oguz, Ipek; Budin, Francois; Styner, Martin A; Johnson, G Allan; Sulik, Kathleen KNeurotoxicology and teratology2013 Sep-Oct77-8323911654
Multimodal deformable registration of traumatic brain injury MR volumes via the Bhattacharyya distance.Lou, Yifei; Irimia, Andrei; Vela, Patricio A; Chambers, Micah C; Van Horn, John D; Vespa, Paul M; Tannenbaum, Allen RIEEE transactions on bio-medical engineering2013 Sep2511-2023962986
On the effect of prestrain and residual stress in thin biological membranes.Rausch, Manuel K; Kuhl, EllenJournal of the mechanics and physics of solids2013 Sep 11955-196923976792
Tissue-specific profiling reveals transcriptome alterations in Arabidopsis mutants lacking morphological phenotypes.Simon, Marissa; Bruex, Angela; Kainkaryam, Raghunandan M; Zheng, Xiaohua; Huang, Ling; Woolf, Peter J; Schiefelbein, JohnThe Plant cell2013 Sep3175-8524014549
Nocturnal continuous glucose and sleep stage data in adults with type 1 diabetes in real-world conditions.Feupe, Stephanie Feudjio; Frias, Patrick F; Mednick, Sara C; McDevitt, Elizabeth A; Heintzman, Nathaniel DJournal of diabetes science and technology2013 Sep1337-4524124962
A Linked Science Investigation: Enhancing Climate Change Data Discovery with Semantic Technologies.Pouchard, Line C; Branstetter, Marcia L; Cook, Robert B; Devarakonda, Ranjeet; Green, Jim; Palanisamy, Giri; Alexander, Paul; Noy, Natalya FEarth science informatics2013 SepNULL24416086
Signal Processing and Machine Learning with Differential Privacy: Algorithms and challenges for continuous data.Sarwate, Anand D; Chaudhuri, KamalikaIEEE signal processing magazine2013 Sep 186-9424737929
Systematic improvement of a classical molecular model of water.Wang, Lee-Ping; Head-Gordon, Teresa; Ponder, Jay W; Ren, Pengyu; Chodera, John D; Eastman, Peter K; Martinez, Todd J; Pande, Vijay SThe journal of physical chemistry. B2013 Aug 299956-7223750713
Unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine.Ghebremariam, Yohannes T; LePendu, Paea; Lee, Jerry C; Erlanson, Daniel A; Slaviero, Anna; Shah, Nigam H; Leiper, James; Cooke, John PCirculation2013 Aug 20845-5323825361
Dominant effects of the Huntington's disease HTT CAG repeat length are captured in gene-expression data sets by a continuous analysis mathematical modeling strategy.Lee, Jong-Min; Galkina, Ekaterina I; Levantovsky, Rachel M; Fossale, Elisa; Anne Anderson, Mary; Gillis, Tammy; Srinidhi Mysore, Jayalakshmi; Coser, Kathryn R; Shioda, Toshi; Zhang, Bin; Furia, Matthew D; Derry, Jonathan; Kohane, Isaac S; Seong, Ihn Sik; Human molecular genetics2013 Aug 153227-3823595883
RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation.Danussi, Carla; Akavia, Uri David; Niola, Francesco; Jovic, Andreja; Lasorella, Anna; Pe'er, Dana; Iavarone, AntonioCancer research2013 Aug 155140-5023774217
Classifying temporal relations in clinical data: A hybrid, knowledge-rich approach.D'Souza, Jennifer; Ng, VincentJournal of biomedical informatics2013 Aug 14NULL23954311
The integrated landscape of driver genomic alterations in glioblastoma.Frattini, Veronique; Trifonov, Vladimir; Chan, Joseph Minhow; Castano, Angelica; Lia, Marie; Abate, Francesco; Keir, Stephen T; Ji, Alan X; Zoppoli, Pietro; Niola, Francesco; Danussi, Carla; Dolgalev, Igor; Porrati, Paola; Pellegatta, Serena; Heguy, AdriaNature genetics2013 Aug 5NULL23917401
GAB2 induces tumor angiogenesis in NRAS-driven melanoma.Yang, Y; Wu, J; Demir, A; Castillo-Martin, M; Melamed, R D; Zhang, G; Fukunaga-Kanabis, M; Perez-Lorenzo, R; Zheng, B; Silvers, D N; Brunner, G; Wang, S; Rabadan, R; Cordon-Cardo, C; Celebi, J TOncogene2013 Aug 13627-3722926523
Natural Language Processing to identify pneumonia from radiology reports.Dublin, Sascha; Baldwin, Eric; Walker, Rod L; Christensen, Lee M; Haug, Peter J; Jackson, Michael L; Nelson, Jennifer C; Ferraro, Jeffrey; Carrell, David; Chapman, Wendy WPharmacoepidemiology and drug safety2013 Aug834-4123554109
Privacy technology to support data sharing for comparative effectiveness research: a systematic review.Jiang, Xiaoqian; Sarwate, Anand D; Ohno-Machado, LucilaMedical care2013 AugS58-6523774511
Decreased axial diffusivity within language connections: A possible biomarker of schizophrenia risk.Kubicki, M; Shenton, M E; Maciejewski, P K; Pelavin, P E; Hawley, K J; Ballinger, T; Swisher, T; Jabbar, G A; Thermenos, H W; Keshavan, M S; Seidman, L J; Delisi, L ESchizophrenia research2013 Aug67-7323800617
Sarcomere lengths in human extensor carpi radialis brevis measured by microendoscopy.Cromie, Melinda J; Sanchez, Gabriel N; Schnitzer, Mark J; Delp, Scott LMuscle & nerve2013 Aug286-9223813625
PQM-1 Complements DAF-16 as a Key Transcriptional Regulator of DAF-2-Mediated Development and Longevity.Tepper, Ronald G; Ashraf, Jasmine; Kaletsky, Rachel; Kleemann, Gunnar; Murphy, Coleen T; Bussemaker, Harmen JCell2013 Aug 1676-9023911329
Particle Filters and Occlusion Handling for Rigid 2D-3D Pose Tracking.Lee, Jehoon; Sandhu, Romeil; Tannenbaum, AllenComputer vision and image understanding : CVIU2013 Aug 1922-93324058277
Localizing the human primary auditory cortex in vivo using structural MRI.Wasserthal, Christian; Brechmann, Andre; Stadler, Jorg; Fischl, Bruce; Engel, KarinNeuroImage2013 Jul 25NULL23891882
Annotating temporal information in clinical narratives.Sun, Weiyi; Rumshisky, Anna; Uzuner, OzlemJournal of biomedical informatics2013 Jul 19NULL23872518
Right, left, and center: how does cerebral asymmetry mix with callosal connectivity?Cherbuin, Nicolas; Luders, Eileen; Chou, Yi-Yu; Thompson, Paul M; Toga, Arthur W; Anstey, Kaarin JHuman brain mapping2013 Jul1728-3622419524
Extended Broca's area in the functional connectome of language in adults: combined cortical and subcortical single-subject analysis using fMRI and DTI tractography.Lemaire, Jean-Jacques; Golby, Alexandra; Wells 3rd, William M; Pujol, Sonia; Tie, Yanmei; Rigolo, Laura; Yarmarkovich, Alexander; Pieper, Steve; Westin, Carl-Fredrik; Jolesz, Ferenc; Kikinis, RonBrain topography2013 Jul428-4123001727
From single nucleotide polymorphism to transcriptional mechanism: a model for FRMD3 in diabetic nephropathy.Martini, Sebastian; Nair, Viji; Patel, Sanjeevkumar R; Eichinger, Felix; Nelson, Robert G; Weil, E Jennifer; Pezzolesi, Marcus G; Krolewski, Andrzej S; Randolph, Ann; Keller, Benjamin J; Werner, Thomas; Kretzler, MatthiasDiabetes2013 Jul2605-1223434934
Six-week gait retraining program reduces knee adduction moment, reduces pain, and improves function for individuals with medial compartment knee osteoarthritis.Shull, Pete B; Silder, Amy; Shultz, Rebecca; Dragoo, Jason L; Besier, Thor F; Delp, Scott L; Cutkosky, Mark RJournal of orthopaedic research : official publication of the Orthopaedic Research Society2013 Jul1020-523494804
Optical flow estimation for flame detection in videos.Mueller, Martin; Karasev, Peter; Kolesov, Ivan; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2013 Jul2786-9723613042
Reprever: resolving low-copy duplicated sequences using template driven assembly.Kim, Sangwoo; Medvedev, Paul; Paton, Tara A; Bafna, VineetNucleic acids research2013 Jul 1e12823658221
Beyond NPM-anaplastic lymphoma kinase driven lymphomagenesis: alternative drivers in anaplastic large cell lymphoma.Tabbo, Fabrizio; Ponzoni, Maurilio; Rabadan, Raul; Bertoni, Francesco; Inghirami, Giorgio; the European T-cell Lymphoma Study GroupCurrent opinion in hematology2013 Jul374-38123673339
Inference of historical migration rates via haplotype sharing.Palamara, Pier Francesco; Pe'er, ItsikBioinformatics (Oxford, England)2013 Jul 1i180-823812983
Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes.Andrews, Logan D; Fenn, Tim D; Herschlag, DanielPLoS biology2013 Jule100159923843744
A rolling constraint reproduces ground reaction forces and moments in dynamic simulations of walking, running, and crouch gait.Hamner, Samuel R; Seth, Ajay; Steele, Katherine M; Delp, Scott LJournal of biomechanics2013 Jun 211772-623702045
Biomechanical Model as a Registration Tool for Image-Guided Neurosurgery: Evaluation Against BSpline Registration.Mostayed, Ahmed; Garlapati, Revanth Reddy; Joldes, Grand Roman; Wittek, Adam; Roy, Aditi; Kikinis, Ron; Warfield, Simon K; Miller, KarolAnnals of biomedical engineering2013 Jun 15NULL23771299
Using Genome Query Language to uncover genetic variation.Kozanitis, Christos; Heiberg, Andrew; Varghese, George; Bafna, VineetBioinformatics (Oxford, England)2013 Jun 10NULL23751181
Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer.Zhang, Emma Yue; Cristofanilli, Massimo; Robertson, Fredika; Reuben, James M; Mu, Zhaomei; Beavis, Ronald C; Im, Hogune; Snyder, Michael; Hofree, Matan; Ideker, Trey; Omenn, Gilbert S; Fanayan, Susan; Jeong, Seul-Ki; Paik, Young-Ki; Zhang, Anna Fan; Wu, SJournal of proteome research2013 Jun 72805-1723647160
Normalization of Plasma 25-Hydroxy Vitamin D Is Associated with Reduced Risk of Surgery in Crohn's Disease.Ananthakrishnan, Ashwin N; Cagan, Andrew; Gainer, Vivian S; Cai, Tianxi; Cheng, Su-Chun; Savova, Guergana; Chen, Pei; Szolovits, Peter; Xia, Zongqi; De Jager, Philip L; Shaw, Stanley Y; Churchill, Susanne; Karlson, Elizabeth W; Kohane, Isaac; Plenge, RobeInflammatory bowel diseases2013 Jun 723751398
Forward and inverse electroencephalographic modeling in health and in acute traumatic brain injury.Irimia, Andrei; Matthew Goh, S Y; Torgerson, Carinna M; Chambers, Micah C; Kikinis, Ron; Van Horn, John DClinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology2013 Jun 5NULL23746499
Mechanical consequences of cell-wall turnover in the elongation of a Gram-positive bacterium.Misra, Gaurav; Rojas, Enrique R; Gopinathan, Ajay; Huang, Kerwyn CaseyBiophysical journal2013 Jun 42342-5223746506
Federated queries of clinical data repositories: the sum of the parts does not equal the whole.Weber, Griffin MJournal of the American Medical Informatics Association : JAMIA2013 June155-6123349080
How muscle fiber lengths and velocities affect muscle force generation as humans walk and run at different speeds.Arnold, Edith M; Hamner, Samuel R; Seth, Ajay; Millard, Matthew; Delp, Scott LThe Journal of experimental biology2013 Jun 12150-6023470656
A controlled greedy supervised approach for co-reference resolution on clinical text.Chowdhury, Md Faisal Mahbub; Zweigenbaum, PierreJournal of biomedical informatics2013 Jun506-1523562650
EXpectation Propagation LOgistic REgRession (EXPLORER): Distributed privacy-preserving online model learning.Wang, Shuang; Jiang, Xiaoqian; Wu, Yuan; Cui, Lijuan; Cheng, Samuel; Ohno-Machado, LucilaJournal of biomedical informatics2013 Jun480-9623562651
Improving Case Definition of Crohn's Disease and Ulcerative Colitis in Electronic Medical Records Using Natural Language Processing: A Novel Informatics Approach.Ananthakrishnan, Ashwin N; Cai, Tianxi; Savova, Guergana; Cheng, Su-Chun; Chen, Pei; Perez, Raul Guzman; Gainer, Vivian S; Murphy, Shawn N; Szolovits, Peter; Xia, Zongqi; Shaw, Stanley; Churchill, Susanne; Karlson, Elizabeth W; Kohane, Isaac; Plenge, RobeInflammatory bowel diseases2013 Jun1411-142023567779
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, N HClinical pharmacology and therapeutics2013 Jun539-4623571771
Pharmacovigilance using clinical notes.LePendu, P; Iyer, S V; Bauer-Mehren, A; Harpaz, R; Mortensen, J M; Podchiyska, T; Ferris, T A; Shah, N HClinical pharmacology and therapeutics2013 Jun547-5523571773
Heterogeneity of tumor-induced gene expression changes in the human metabolic network.Hu, Jie; Locasale, Jason W; Bielas, Jason H; O'Sullivan, Jacintha; Sheahan, Kieran; Cantley, Lewis C; Heiden, Matthew G Vander; Vitkup, DennisNature biotechnology2013 Jun522-923604282
On the mechanics of continua with boundary energies and growing surfaces.Papastavrou, Areti; Steinmann, Paul; Kuhl, EllenJournal of the mechanics and physics of solids2013 Jun 11446-146323606760
viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.Amir, El-ad David; Davis, Kara L; Tadmor, Michelle D; Simonds, Erin F; Levine, Jacob H; Bendall, Sean C; Shenfeld, Daniel K; Krishnaswamy, Smita; Nolan, Garry P; Pe'er, DanaNature biotechnology2013 Jun545-5223685480
Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls.Liao, Katherine P; Diogo, Dorothee; Cui, Jing; Cai, Tianxi; Okada, Yukinori; Gainer, Vivian S; Murphy, Shawn N; Gupta, Namrata; Mirel, Daniel; Ananthakrishnan, Ashwin N; Szolovits, Peter; Shaw, Stanley Y; Raychaudhuri, Soumya; Churchill, Susanne; Kohane, Annals of the rheumatic diseases2013 May 2823716066
A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text.Roberts, Kirk; Rink, Bryan; Harabagiu, Sanda MJournal of the American Medical Informatics Association : JAMIA2013 May 1823686936
Conformation guides molecular efficacy in docking screens of activated ýý-2 adrenergic G protein coupled receptor.Weiss, Dahlia R; Ahn, SeungKirl; Sassano, Maria F; Kleist, Andrew; Zhu, Xiao; Strachan, Ryan; Roth, Bryan L; Lefkowitz, Robert J; Shoichet, Brian KACS chemical biology2013 May 171018-2623485065
Classic "broken cell" techniques and newer live cell methods for cell cycle assessment.Henderson, Lindsay; Bortone, Dante S; Lim, Curtis; Zambon, Alexander CAmerican journal of physiology. Cell physiology2013 May 15C927-3823392113
Temporal reasoning over clinical text: the state of the art.Sun, Weiyi; Rumshisky, Anna; Uzuner, OzlemJournal of the American Medical Informatics Association : JAMIA2013 May 15NULL23676245
HIV Infection Reveals Wide-Spread Expansion of Novel Centromeric Human Endogenous Retroviruses.Contreras-Galindo, Rafael; Kaplan, Mark H; He, Shirley; Contreras-Galindo, Angie C; Gonzalez-Hernandez, Marta J; Kappes, Ferdinand; Dube, Derek; Chan, Susana M; Robinson, Dan; Meng, Fan; Dai, Manhong; Gitlin, Scott D; Chinnaiyan, Arul M; Omenn, Gilbert S;Genome research2013 May 823657884
Muscle contributions to vertical and fore-aft accelerations are altered in subjects with crouch gait.Steele, Katherine M; Seth, Ajay; Hicks, Jennifer L; Schwartz, Michael H; Delp, Scott LGait & posture2013 May86-9123200083
Privacy-preserving heterogeneous health data sharing.Mohammed, Noman; Jiang, Xiaoqian; Chen, Rui; Fung, Benjamin C M; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2013 May 1462-923242630
Web-scale pharmacovigilance: listening to signals from the crowd.White, Ryen W; Tatonetti, Nicholas P; Shah, Nigam H; Altman, Russ B; Horvitz, EricJournal of the American Medical Informatics Association : JAMIA2013 May 1404-823467469
Improving breast cancer survival analysis through competition-based multidimensional modeling.Bilal, Erhan; Dutkowski, Janusz; Guinney, Justin; Jang, In Sock; Logsdon, Benjamin A; Pandey, Gaurav; Sauerwine, Benjamin A; Shimoni, Yishai; Moen Vollan, Hans Kristian; Mecham, Brigham H; Rueda, Oscar M; Tost, Jorg; Curtis, Christina; Alvarez, Mariano J;PLoS computational biology2013 Maye100304723671412
Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway.Li, Gang; Diogo, Dorothee; Wu, Di; Spoonamore, Jim; Dancik, Vlado; Franke, Lude; Kurreeman, Fina; Rossin, Elizabeth J; Duclos, Grant; Hartland, Cathy; Zhou, Xuezhong; Li, Kejie; Liu, Jun; De Jager, Philip L; Siminovitch, Katherine A; Zhernakova, AlexandraPLoS genetics2013 Maye100348723696745
Studying PubMed usages in the field for complex problem solving: Implications for tool design.Mirel, Barbara; Song, Jean; Tonks, Jennifer Steiner; Meng, Fan; Xuan, Weijian; Ameziane, RafiqaJournal of the American Society for Information Science and Technology : JASIST2013 May 1NULL24376375
Genetic contributions to changes of fiber tracts of ventral visual stream in 22q11.2 deletion syndrome.Kikinis, Zora; Makris, Nikos; Finn, Christine T; Bouix, Sylvain; Lucia, Diandra; Coleman, Michael J; Tworog-Dube, Erica; Kikinis, Ron; Kucherlapati, Raju; Shenton, Martha E; Kubicki, MarekBrain imaging and behavior2013 Apr 2423612843
Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives.Kovacevic, Aleksandar; Dehghan, Azad; Filannino, Michele; Keane, John A; Nenadic, GoranJournal of the American Medical Informatics Association : JAMIA2013 Apr 2023605114
Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.Margolin, Adam A; Bilal, Erhan; Huang, Erich; Norman, Thea C; Ottestad, Lars; Mecham, Brigham H; Sauerwine, Ben; Kellen, Michael R; Mangravite, Lara M; Furia, Matthew D; Vollan, Hans Kristian Moen; Rueda, Oscar M; Guinney, Justin; Deflaux, Nicole A; Hoff,Science translational medicine2013 Apr 17181re123596205
Probing DNA shape and methylation state on a genomic scale with DNase I.Lazarovici, Allan; Zhou, Tianyin; Shafer, Anthony; Dantas Machado, Ana Carolina; Riley, Todd R; Sandstrom, Richard; Sabo, Peter J; Lu, Yan; Rohs, Remo; Stamatoyannopoulos, John A; Bussemaker, Harmen JProceedings of the National Academy of Sciences of the United States of America2013 Apr 166376-8123576721
Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways.Rardin, Matthew J; Newman, John C; Held, Jason M; Cusack, Michael P; Sorensen, Dylan J; Li, Biao; Schilling, Birgit; Mooney, Sean D; Kahn, C Ronald; Verdin, Eric; Gibson, Bradford WProceedings of the National Academy of Sciences of the United States of America2013 Apr 166601-623576753
Wessim: a whole-exome sequencing simulator based on in silico exome capture.Kim, Sangwoo; Jeong, Kyowon; Bafna, VineetBioinformatics (Oxford, England)2013 Apr 151076-723413434
NCBO Technology: Powering semantically aware applications.Whetzel, Patricia L; NCBO TeamJournal of biomedical semantics2013 Apr 15S823734708
Imaging patients with psychosis and a mouse model establishes a spreading pattern of hippocampal dysfunction and implicates glutamate as a driver.Schobel, Scott A; Chaudhury, Nashid H; Khan, Usman A; Paniagua, Beatriz; Styner, Martin A; Asllani, Iris; Inbar, Benjamin P; Corcoran, Cheryl M; Lieberman, Jeffrey A; Moore, Holly; Small, Scott ANeuron2013 Apr 1081-9323583108
Diffusion weighted imaging of prefrontal cortex in prodromal huntington's disease.Matsui, Joy T; Vaidya, Jatin G; Johnson, Hans J; Magnotta, Vincent A; Long, Jeffrey D; Mills, James A; Lowe, Mark J; Sakaie, Ken E; Rao, Stephen M; Smith, Megan M; Paulsen, Jane SHuman brain mapping2013 Apr 923568433
A hybrid system for temporal information extraction from clinical text.Tang, Buzhou; Wu, Yonghui; Jiang, Min; Chen, Yukun; Denny, Joshua C; Xu, HuaJournal of the American Medical Informatics Association : JAMIA2013 Apr 9NULL23571849
Eventual situations for timeline extraction from clinical reports.Grouin, Cyril; Grabar, Natalia; Hamon, Thierry; Rosset, Sophie; Tannier, Xavier; Zweigenbaum, PierreJournal of the American Medical Informatics Association : JAMIA2013 Apr 9NULL23571851
Evaluating temporal relations in clinical text: 2012 i2b2 Challenge.Sun, Weiyi; Rumshisky, Anna; Uzuner, OzlemJournal of the American Medical Informatics Association : JAMIA2013 Apr 5NULL23564629
Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification.Sohn, Sunghwan; Wagholikar, Kavishwar B; Li, Dingcheng; Jonnalagadda, Siddhartha R; Tao, Cui; Elayavilli, Ravikumar Komandur; Liu, HongfangJournal of the American Medical Informatics Association : JAMIA2013 Apr 4NULL23558168
Ventricular enlargement and its clinical correlates in the imaging cohort from the ADCS MCI donepezil/vitamin E study.Apostolova, Liana G; Babakchanian, Sona; Hwang, Kristy S; Green, Amity E; Zlatev, Dimitar; Chou, Yi-Yu; DeCarli, Charlie; Jack Jr, Clifford R; Petersen, Ronald C; Aisen, Paul S; Cummings, Jeffrey L; Toga, Arthur W; Thompson, Paul MAlzheimer disease and associated disorders2013 Apr-Jun174-8123694947
Growth on demand: Reviewing the mechanobiology of stretched skin.Zollner, Alexander M; Holland, Maria A; Honda, Kord S; Gosain, Arun K; Kuhl, EllenJournal of the mechanical behavior of biomedical materials2013 Apr 323623569
Automating the study of population variation of electrocardiographic features.Kohane, Isaac SCirculation2013 Apr 21357-823463856
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes.Zakov, Shay; Kinsella, Marcus; Bafna, VineetProceedings of the National Academy of Sciences of the United States of America2013 Apr 25546-5123503850
Stabilisation of walking by intrinsic muscle properties revealed in a three-dimensional muscle-driven simulation.John, Chand T; Anderson, Frank C; Higginson, Jill S; Delp, Scott LComputer methods in biomechanics and biomedical engineering2013 Apr451-6222224406
In search of the functional neuroanatomy of sociality: MRI subdivisions of orbital frontal cortex and social cognition.Nestor, Paul G; Nakamura, Motoaki; Niznikiewicz, Margaret; Thompson, Elizabeth; Levitt, James J; Choate, Victoria; Shenton, Martha E; McCarley, Robert WSocial cognitive and affective neuroscience2013 Apr460-722345366
A mega-analysis of genome-wide association studies for major depressive disorder.Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium; Ripke, Stephan; Wray, Naomi R; Lewis, Cathryn M; Hamilton, Steven P; Weissman, Myrna M; Breen, Gerome; Byrne, Enda M; Blackwood, Douglas H R; Boomsma, Dorret I; Cichon, Sven; HeatMolecular psychiatry2013 Apr497-51122472876
The influence of sodium- and calcium-regulatory hormone interventions on adipocytokines in obesity and diabetes.Vaidya, Anand; Underwood, Patricia C; Annes, Justin P; Sun, Bei; Williams, Gordon H; Forman, John P; Williams, Jonathan SMetabolism: clinical and experimental2013 Apr539-4723142162
Toward an understanding of the short bone phenotype associated with multiple osteochondromas.Jones, Kevin B; Datar, Manasi; Ravichandran, Sandhya; Jin, Huifeng; Jurrus, Elizabeth; Whitaker, Ross; Capecchi, Mario RJournal of orthopaedic research : official publication of the Orthopaedic Research Society2013 Apr651-723192691
Tissue plasminogen activator prevents mortality from sulfur mustard analog-induced airway obstruction.Veress, Livia A; Hendry-Hofer, Tara B; Loader, Joan E; Rioux, Jacqueline S; Garlick, Rhonda B; White, Carl WAmerican journal of respiratory cell and molecular biology2013 Apr439-4723258228
Subgroup specific incremental value of new markers for risk prediction.Zhou, Qian M; Zheng, Yingye; Cai, TianxiLifetime data analysis2013 Apr142-6923263882
Systems-based approaches toward wound healing.Buganza Tepole, Adrian; Kuhl, EllenPediatric research2013 Apr553-6323314298
Similar risk of depression and anxiety following surgery or hospitalization for Crohn's disease and ulcerative colitis.Ananthakrishnan, Ashwin N; Gainer, Vivian S; Cai, Tianxi; Perez, Raul Guzman; Cheng, Su-Chun; Savova, Guergana; Chen, Pei; Szolovits, Peter; Xia, Zongqi; De Jager, Philip L; Shaw, Stanley; Churchill, Susanne; Karlson, Elizabeth W; Kohane, Isaac; Perlis, RThe American journal of gastroenterology2013 Apr594-60123337479
Toward a "structural BLAST": using structural relationships to infer function.Dey, Fabian; Cliff Zhang, Qiangfeng; Petrey, Donald; Honig, BarryProtein science : a publication of the Protein Society2013 Apr359-6623349097
Detecting concept relations in clinical text: insights from a state-of-the-art model.Zhu, Xiaodan; Cherry, Colin; Kiritchenko, Svetlana; Martin, Joel; de Bruijn, BerryJournal of biomedical informatics2013 Apr275-8523380683
Abnormal aldosterone physiology and cardiometabolic risk factors.Vaidya, Anand; Underwood, Patricia C; Hopkins, Paul N; Jeunemaitre, Xavier; Ferri, Claudio; Williams, Gordon H; Adler, Gail KHypertension2013 Apr886-9323399714
Joint CT/CBCT deformable registration and CBCT enhancement for cancer radiotherapy.Lou, Yifei; Niu, Tianye; Jia, Xun; Vela, Patricio A; Zhu, Lei; Tannenbaum, Allen RMedical image analysis2013 Apr387-40023433756
Differential-Private Data Publishing Through Component Analysis.Jiang, Xiaoqian; Ji, Zhanglong; Wang, Shuang; Mohammed, Noman; Cheng, Samuel; Ohno-Machado, LucilaTransactions on data privacy2013 Apr19-3424409205
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, Wouter S; Perlis, Roy H; Smoller, Jordan W; Zeng-Treitler, Qing; Gainer, Vivian S; Murphy, Shawn N; Churchill, Susanne E; Kohane, Isaac S; Shenton, Martha E; Iosifescu, Dan VPsychiatry research2013 Mar 30202-1323149041
Lateral ventricle morphology analysis via mean latitude axis.Paniagua, Beatriz; Lyall, Amanda; Berger, Jean-Baptiste; Vachet, Clement; Hamer, Robert M; Woolson, Sandra; Lin, Weili; Gilmore, John; Styner, MartinProceedings - Society of Photo-Optical Instrumentation Engineers2013 Mar 2923606800
3D of Brain Shape and Volume After Cranial Vault Remodeling Surgery for Craniosynostosis Correction in Infants.Paniagua, Beatriz; Emodi, Omri; Hill, Jonathan; Fishbaugh, James; Pimenta, Luiz A; Aylward, Stephen R; Andinet, Enquobahrie; Gerig, Guido; Gilmore, John; van Aalst, John A; Styner, MartinProceedings - Society of Photo-Optical Instrumentation Engineers2013 Mar 2986720V24465118
A la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge.Cherry, Colin; Zhu, Xiaodan; Martin, Joel; de Bruijn, BerryJournal of the American Medical Informatics Association : JAMIA2013 Mar 2323523875
White Matter Microstructure and Atypical Visual Orienting in 7-Month-Olds at Risk for Autism.Elison, Jed T; Paterson, Sarah J; Wolff, Jason J; Reznick, J Steven; Sasson, Noah J; Gu, Hongbin; Botteron, Kelly N; Dager, Stephen R; Estes, Annette M; Evans, Alan C; Gerig, Guido; Hazlett, Heather C; Schultz, Robert T; Styner, Martin; Zwaigenbaum, LonniThe American journal of psychiatry2013 Mar 2023511344
Landmark risk prediction of residual life for breast cancer survival.Parast, Layla; Cai, TianxiStatistics in medicine2013 Mar 14NULL23494768
DTI Quality Control Assessment via Error Estimation From Monte Carlo Simulations.Farzinfar, Mahshid; Li, Yin; Verde, Audrey R; Oguz, Ipek; Gerig, Guido; Styner, Martin AProceedings - Society of Photo-Optical Instrumentation Engineers2013 Mar 13166754923833547
Fiber feature map based landmark initialization for highly deformable DTI registration.Gupta, Aditya; Toews, Matthew; Janardhana, Ravikiran; Rathi, Yogesh; Gilmore, John; Escolar, Maria; Styner, MartinProceedings - Society of Photo-Optical Instrumentation Engineers2013 Mar 13NULL24353392
Software-based Diffusion MR Human Brain Phantom for Evaluating Fiber-tracking Algorithms.Shi, Yundi; Roger, Gwendoline; Vachet, Clement; Budin, Francois; Maltbie, Eric; Verde, Audrey; Hoogstoel, Marion; Berger, Jean-Baptiste; Styner, MartinProceedings - Society of Photo-Optical Instrumentation Engineers2013 Mar 13NULL24357914
Stochastic Image Registration with User Constraints.Kolesov, Ivan; Lee, Jehoon; Vela, Patricio; Tannenbaum, AllenProceedings - Society of Photo-Optical Instrumentation Engineers2013 Mar 13NULL24357915
Cortical Correspondence via Sulcal Curve-Constrained Spherical Registration with Application to Macaque Studies.Lyu, Ilwoo; Kim, Sun Hyung; Seong, Joon-Kyung; Yoo, Sang Wook; Evans, Alan C; Shi, Yundi; Sanchez, Mar; Niethammer, Marc; Styner, MartinProceedings - Society of Photo-Optical Instrumentation Engineers2013 Mar 13NULL24357916
UNC-Utah NA-MIC DTI framework: Atlas Based Fiber Tract Analysis with Application to a Study of Nicotine Smoking Addiction.Verde, Audrey R; Berger, Jean-Baptiste; Gupta, Aditya; Farzinfar, Mahshid; Kaiser, Adrien; Chanon, Vicki W; Boettiger, Charlotte; Goodlett, Casey; Shi, Yundi; Zhu, Hongtu; Gerig, Guido; Gouttard, Sylvain; Vachet, Clement; Styner, MartinProceedings of SPIE2013 Mar 13NULL24386543
An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge.Xu, Yan; Wang, Yining; Liu, Tianren; Tsujii, Junichi; Chang, Eric I-ChaoJournal of the American Medical Informatics Association : JAMIA2013 Mar 623467472
Polymorphisms in the serum- and glucocorticoid-inducible kinase 1 gene are associated with blood pressure and renin response to dietary salt intake.Rao, A D; Sun, B; Saxena, A; Hopkins, P N; Jeunemaitre, X; Brown, N J; Adler, G K; Williams, J SJournal of human hypertension2013 Mar176-8022648267
Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives.Jindal, Prateek; Roth, DanJournal of the American Medical Informatics Association : JAMIA2013 Mar-Apr356-6222781192
Neuropsychological variability, symptoms, and brain imaging in chronic schizophrenia.Nestor, Paul G; Kubicki, Marek; Nakamura, Motoaki; Niznikiewicz, Margaret; Levitt, James J; Shenton, Martha E; McCarley, Robert WBrain imaging and behavior2013 Mar68-7623011383
Changes in in vivo knee contact forces through gait modification.Kinney, Allison L; Besier, Thor F; Silder, Amy; Delp, Scott L; D'Lima, Darryl D; Fregly, Benjamin JJournal of orthopaedic research : official publication of the Orthopaedic Research Society2013 Mar434-4023027590
Patellar maltracking is prevalent among patellofemoral pain subjects with patella alta: an upright, weightbearing MRI study.Pal, Saikat; Besier, Thor F; Beaupre, Gary S; Fredericson, Michael; Delp, Scott L; Gold, Garry EJournal of orthopaedic research : official publication of the Orthopaedic Research Society2013 Mar448-5723165335
Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls.Liao, Katherine P; Kurreeman, Fina; Li, Gang; Duclos, Grant; Murphy, Shawn; Guzman, Raul; Cai, Tianxi; Gupta, Namrata; Gainer, Vivian; Schur, Peter; Cui, Jing; Denny, Joshua C; Szolovits, Peter; Churchill, Susanne; Kohane, Isaac; Karlson, Elizabeth W; PleArthritis and rheumatism2013 Mar571-8123233247
Regional characterization of longitudinal DT-MRI to study white matter maturation of the early developing brain.Sadeghi, Neda; Prastawa, Marcel; Fletcher, P Thomas; Wolff, Jason; Gilmore, John H; Gerig, GuidoNeuroImage2013 Mar236-4723235270
The variance of identity-by-descent sharing in the Wright-Fisher model.Carmi, Shai; Palamara, Pier Francesco; Vacic, Vladimir; Lencz, Todd; Darvasi, Ariel; Pe'er, ItsikGenetics2013 Mar911-2823267057
A large-scale evaluation of computational protein function prediction.Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, MichaeNature methods2013 Mar221-723353650
Gene expression alterations in bipolar disorder postmortem brains.Chen, Haiming; Wang, Nulang; Zhao, Xin; Ross, Christopher A; O'Shea, K Sue; McInnis, Melvin GBipolar disorders2013 Mar177-8723360497
Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis.Thawait, Shrey K; Kim, Jihoon; Klufas, Roman A; Morrison, William B; Flanders, Adam E; Carrino, John A; Ohno-Machado, LucilaAJR. American journal of roentgenology2013 Mar493-50223436836
The stationary configuration of the knee.Kim, Wangdo; Veloso, Antonio P; Vleck, Veronica E; Andrade, Carlos; Kohles, Sean SJournal of the American Podiatric Medical Association2013 Mar-Apr126-3523536503
VARYING COEFFICIENT MODEL FOR MODELING DIFFUSION TENSORS ALONG WHITE MATTER TRACTS.Yuan, Ying; Zhu, Hongtu; Styner, Martin; Gilmore, John H; Marron, J SThe annals of applied statistics2013 Mar102-12524533040
Muscle contributions to fore-aft and vertical body mass center accelerations over a range of running speeds.Hamner, Samuel R; Delp, Scott LJournal of biomechanics2013 Feb 22780-723246045
OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.Maguire, Eamonn; Gonzalez-Beltran, Alejandra; Whetzel, Patricia L; Sansone, Susanna-Assunta; Rocca-Serra, PhilippeBioinformatics (Oxford, England)2013 Feb 15525-723267176
Brain growth rate abnormalities visualized in adolescents with autism.Hua, Xue; Thompson, Paul M; Leow, Alex D; Madsen, Sarah K; Caplan, Rochelle; Alger, Jeffry R; O'Neill, Joseph; Joshi, Kishori; Smalley, Susan L; Toga, Arthur W; Levitt, Jennifer GHuman brain mapping2013 Feb425-3622021093
The role of TGF-ýý and myofibroblasts in the arteritis of Kawasaki disease.Shimizu, Chisato; Oharaseki, Toshiaki; Takahashi, Kei; Kottek, Aubri; Franco, Alessandra; Burns, Jane CHuman pathology2013 Feb189-9822955109
Terminology representation guidelines for biomedical ontologies in the semantic web notations.Tao, Cui; Pathak, Jyotishman; Solbrig, Harold R; Wei, Wei-Qi; Chute, Christopher GJournal of biomedical informatics2013 Feb128-3823026232
The plant ontology as a tool for comparative plant anatomy and genomic analyses.Cooper, Laurel; Walls, Ramona L; Elser, Justin; Gandolfo, Maria A; Stevenson, Dennis W; Smith, Barry; Preece, Justin; Athreya, Balaji; Mungall, Christopher J; Rensing, Stefan; Hiss, Manuel; Lang, Daniel; Reski, Ralf; Berardini, Tanya Z; Li, Donghui; HualaPlant & cell physiology2013 Febe123220694
To milliseconds and beyond: challenges in the simulation of protein folding.Lane, Thomas J; Shukla, Diwakar; Beauchamp, Kyle A; Pande, Vijay SCurrent opinion in structural biology2013 Feb58-6523237705
Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease.Ananthakrishnan, A N; Gainer, V S; Perez, R G; Cai, T; Cheng, S-C; Savova, G; Chen, P; Szolovits, P; Xia, Z; De Jager, P L; Shaw, S Y; Churchill, S; Karlson, E W; Kohane, I; Perlis, R H; Plenge, R M; Murphy, S N; Liao, K PAlimentary pharmacology & therapeutics2013 Feb445-5423289600
Abnormalities of middle longitudinal fascicle and disorganization in patients with schizophrenia.Asami, Takeshi; Saito, Yukiko; Whitford, Thomas J; Makris, Nikos; Niznikiewicz, Margaret; McCarley, Robert W; Shenton, Martha E; Kubicki, MarekSchizophrenia research2013 Feb253-923290607
Evaluation of methods for modeling transcription factor sequence specificity.Weirauch, Matthew T; Cote, Atina; Norel, Raquel; Annala, Matti; Zhao, Yue; Riley, Todd R; Saez-Rodriguez, Julio; Cokelaer, Thomas; Vedenko, Anastasia; Talukder, Shaheynoor; DREAM5 Consortium; Bussemaker, Harmen J; Morris, Quaid D; Bulyk, Martha L; StoloviNature biotechnology2013 Feb126-3423354101
Flexing computational muscle: modeling and simulation of musculotendon dynamics.Millard, Matthew; Uchida, Thomas; Seth, Ajay; Delp, Scott LJournal of biomechanical engineering2013 Feb02100523445050
A New Distance Measure Based on Generalized Image Normalized Cross-Correlation for Robust Video Tracking and Image Recognition.Nakhmani, Arie; Tannenbaum, AllenPattern recognition letters2013 Feb 1315-32123503649
Localized differences in caudate and hippocampal shape are associated with schizophrenia but not antipsychotic type.McClure, Robert K; Styner, Martin; Maltbie, Eric; Lieberman, Jeffrey A; Gouttard, Sylvain; Gerig, Guido; Shi, Xiaoyan; Zhu, HongtuPsychiatry research2013 Jan 301-1023142194
White matter fractional anisotropy is inversely related to anxious symptoms in older adults with atherosclerosis.Bijanki, Kelly R; Stillman, Ashley N; Arndt, Stephan; Magnotta, Vincent A; Fiedorowicz, Jess G; Haynes, William G; Matsui, Joy T; Johnson, Hans J; Moser, David JInternational journal of geriatric psychiatry2013 Jan 2423348834
Adaptive prior probability and spatial temporal intensity change estimation for segmentation of the one-year-old human brain.Kim, Sun Hyung; Fonov, Vladimir S; Dietrich, Cheryl; Vachet, Clement; Hazlett, Heather C; Smith, Rachel G; Graves, Michael M; Piven, Joseph; Gilmore, John H; Dager, Stephen R; McKinstry, Robert C; Paterson, Sarah; Evans, Alan C; Collins, D Louis; Gerig, GJournal of neuroscience methods2013 Jan 1543-5523032117
Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis.Diogo, Dorothee; Kurreeman, Fina; Stahl, Eli A; Liao, Katherine P; Gupta, Namrata; Greenberg, Jeffrey D; Rivas, Manuel A; Hickey, Brendan; Flannick, Jason; Thomson, Brian; Guiducci, Candace; Ripke, Stephan; Adzhubey, Ivan; Barton, Anne; Kremer, Joel M; AlAmerican journal of human genetics2013 Jan 1015-2723261300
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.Eastman, Peter; Friedrichs, Mark S; Chodera, John D; Radmer, Randall J; Bruns, Christopher M; Ku, Joy P; Beauchamp, Kyle A; Lane, Thomas J; Wang, Lee-Ping; Shukla, Diwakar; Tye, Tony; Houston, Mike; Stich, Timo; Klein, Christoph; Shirts, Michael R; Pande,Journal of chemical theory and computation2013 Jan 8461-46923316124
Toe-in gait reduces the first peak knee adduction moment in patients with medial compartment knee osteoarthritis.Shull, Pete B; Shultz, Rebecca; Silder, Amy; Dragoo, Jason L; Besier, Thor F; Cutkosky, Mark R; Delp, Scott LJournal of biomechanics2013 Jan 4122-823146322
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.Liu, Suli; Im, Hogune; Bairoch, Amos; Cristofanilli, Massimo; Chen, Rui; Deutsch, Eric W; Dalton, Stephen; Fenyo, David; Fanayan, Susan; Gates, Chris; Gaudet, Pascale; Hincapie, Marina; Hanash, Samir; Kim, Hoguen; Jeong, Seul-Ki; Lundberg, Emma; Mias, GeoJournal of proteome research2013 Jan 445-5723259914
Diffusion tensor imaging-based characterization of brain neurodevelopment in primates.Shi, Yundi; Short, Sarah J; Knickmeyer, Rebecca C; Wang, Jiaping; Coe, Christopher L; Niethammer, Marc; Gilmore, John H; Zhu, Hongtu; Styner, Martin ACerebral cortex (New York, N.Y. : 1991)2013 Jan36-4822275483
Associations between white matter microstructure and infants' working memory.Short, Sarah J; Elison, Jed T; Goldman, Barbara Davis; Styner, Martin; Gu, Hongbin; Connelly, Mark; Maltbie, Eric; Woolson, Sandra; Lin, Weili; Gerig, Guido; Reznick, J Steven; Gilmore, John HNeuroImage2013 Jan 1156-6622989623
Setting up an intronic miRNA database.Hinske, Ludwig Christian; Heyn, Jens; Galante, Pedro A F; Ohno-Machado, Lucila; Kreth, SimoneMethods in molecular biology (Clifton, N.J.)201369-7623007499
SHARE: system design and case studies for statistical health information release.Gardner, James; Xiong, Li; Xiao, Yonghui; Gao, Jingjing; Post, Andrew R; Jiang, Xiaoqian; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2013 Jan 1109-1623059729
A fully implicit finite element method for bidomain models of cardiac electromechanics.Dal, Husnu; Goktepe, Serdar; Kaliske, Michael; Kuhl, EllenComputer methods in applied mechanics and engineering2013 Jan 1323-33623175588
PrePPI: a structure-informed database of protein-protein interactions.Zhang, Qiangfeng Cliff; Petrey, Donald; Garzon, Jose Ignacio; Deng, Lei; Honig, BarryNucleic acids research2013 JanD828-3323193263
ArrayExpress update--trends in database growth and links to data analysis tools.Rustici, Gabriella; Kolesnikov, Nikolay; Brandizi, Marco; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Farne, Anna; Hastings, Emma; Ison, Jon; Keays, Maria; Kurbatova, Natalja; Malone, James; Mani, Roby; Mupo, Annalisa; Pedro Pereira, Rui; Pilicheva, EkNucleic acids research2013 JanD987-9023193272
Sharing data for the public good and protecting individual privacy: informatics solutions to combine different goals.Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2013 Jan 1123243087
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GBM volumetry using the 3D Slicer medical image computing platform.Egger, Jan; Kapur, Tina; Fedorov, Andriy; Pieper, Steve; Miller, James V; Veeraraghavan, Harini; Freisleben, Bernd; Golby, Alexandra J; Nimsky, Christopher; Kikinis, RonScientific reports2013136423455483
Differential expression of miR-145 in children with Kawasaki disease.Shimizu, Chisato; Kim, Jihoon; Stepanowsky, Petra; Trinh, Christine; Lau, Hubert D; Akers, Johnny C; Chen, Clark; Kanegaye, John T; Tremoulet, Adriana; Ohno-Machado, Lucila; Burns, Jane CPloS one2013e5815923483985
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Practice-based evidence: profiling the safety of cilostazol by text-mining of clinical notes.Leeper, Nicholas J; Bauer-Mehren, Anna; Iyer, Srinivasan V; Lependu, Paea; Olson, Cliff; Shah, Nigam HPloS one2013e6349923717437
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Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records.Lin, Chen; Karlson, Elizabeth W; Canhao, Helena; Miller, Timothy A; Dligach, Dmitriy; Chen, Pei Jun; Perez, Raul Natanael Guzman; Shen, Yuanyan; Weinblatt, Michael E; Shadick, Nancy A; Plenge, Robert M; Savova, Guergana KPloS one2013e6993223976944
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Building and evaluating an ontology-based tool for reasoning about consent permission.Grando, Adela; Schwab, RichardAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2013514-2324551354
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Regionally selective atrophy of subcortical structures in prodromal HD as revealed by statistical shape analysis.Younes, Laurent; Ratnanather, J Tilak; Brown, Timothy; Aylward, Elizabeth; Nopoulos, Peg; Johnson, Hans; Magnotta, Vincent A; Paulsen, Jane S; Margolis, Russell L; Albin, Roger L; Miller, Michael I; Ross, Christopher A; and the PREDICT-HD Investigators anHuman brain mapping2012 Dec 2023281100
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Image registration for targeted MRI-guided transperineal prostate biopsy.Fedorov, Andriy; Tuncali, Kemal; Fennessy, Fiona M; Tokuda, Junichi; Hata, Nobuhiko; Wells, William M; Kikinis, Ron; Tempany, Clare MJournal of magnetic resonance imaging : JMRI2012 Oct987-9222645031
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Disease and genetic contributions toward local tissue volume disturbances in schizophrenia: a tensor-based morphometry study.Yang, Yaling; Nuechterlein, Keith H; Phillips, Owen R; Gutman, Boris; Kurth, Florian; Dinov, Ivo; Thompson, Paul M; Asarnow, Robert F; Toga, Arthur W; Narr, Katherine LHuman brain mapping2012 Sep2081-9122241649
Evaluating the state of the art in coreference resolution for electronic medical records.Uzuner, Ozlem; Bodnari, Andreea; Shen, Shuying; Forbush, Tyler; Pestian, John; South, Brett RJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct786-9122366294
Integration of the OpenIGTLink network protocol for image-guided therapy with the medical platform MeVisLab.Egger, Jan; Tokuda, Junichi; Chauvin, Laurent; Freisleben, Bernd; Nimsky, Christopher; Kapur, Tina; Wells, WilliamThe international journal of medical robotics + computer assisted surgery : MRCAS2012 Sep282-9022374845
Anterior limb of the internal capsule in schizophrenia: a diffusion tensor tractography study.Rosenberger, Gudrun; Nestor, Paul G; Oh, Jungsu S; Levitt, James J; Kindleman, Gordon; Bouix, Sylvain; Fitzsimmons, Jennifer; Niznikiewicz, Margaret; Westin, Carl-Fredrik; Kikinis, Ron; McCarley, Robert W; Shenton, Martha E; Kubicki, MarekBrain imaging and behavior2012 Sep417-2522415192
MCORES: a system for noun phrase coreference resolution for clinical records.Bodnari, Andreea; Szolovits, Peter; Uzuner, OzlemJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct906-1222419739
A classification approach to coreference in discharge summaries: 2011 i2b2 challenge.Xu, Yan; Liu, Jiahua; Wu, Jiajun; Wang, Yue; Tu, Zhuowen; Sun, Jian-Tao; Tsujii, Junichi; Chang, Eric I-ChaoJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct897-90522505762
Grid Binary LOgistic REgression (GLORE): building shared models without sharing data.Wu, Yuan; Jiang, Xiaoqian; Kim, Jihoon; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct758-6422511014
Protecting count queries in study design.Vinterbo, Staal A; Sarwate, Anand D; Boxwala, Aziz AJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct750-722511018
Coreference resolution of medical concepts in discharge summaries by exploiting contextual information.Dai, Hong-Jie; Chen, Chun-Yu; Wu, Chi-Yang; Lai, Po-Ting; Tsai, Richard Tzong-Han; Hsu, Wen-LianJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct888-9622556185
Machine learning-based coreference resolution of concepts in clinical documents.Ware, Henry; Mullett, Charles J; Jagannathan, Vasudevan; El-Rawas, OussamaJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct883-722582205
A supervised framework for resolving coreference in clinical records.Rink, Bryan; Roberts, Kirk; Harabagiu, Sanda MJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct875-8222610493
Active learning for clinical text classification: is it better than random sampling?Figueroa, Rosa L; Zeng-Treitler, Qing; Ngo, Long H; Goryachev, Sergey; Wiechmann, Eduardo PJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct809-1622707743
Reviewing social media use by clinicians.von Muhlen, Marcio; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2012 Sep-Oct777-8122759618
Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model.Floc'h, Nicolas; Kinkade, Carolyn Waugh; Kobayashi, Takashi; Aytes, Alvaro; Lefebvre, Celine; Mitrofanova, Antonina; Cardiff, Robert D; Califano, Andrea; Shen, Michael M; Abate-Shen, CoryCancer research2012 Sep 14483-9322815528
The Measurement of Local Variation in Shape.Marquez, Eladio J; Cabeen, Ryan; Woods, Roger P; Houle, DavidEvolutionary biology2012 Sep 1419-43923180896
A Randomized Response Model For Privacy Preserving Smart Metering.Wang, Shuang; Cui, Lijuan; Que, Jialan; Choi, Dae-Hyun; Jiang, Xiaoqian; Cheng, Samuel; Xie, LeIEEE transactions on smart grid2012 Sep1317-132423243488
Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows.Torri, Federica; Dinov, Ivo D; Zamanyan, Alen; Hobel, Sam; Genco, Alex; Petrosyan, Petros; Clark, Andrew P; Liu, Zhizhong; Eggert, Paul; Pierce, Jonathan; Knowles, James A; Ames, Joseph; Kesselman, Carl; Toga, Arthur W; Potkin, Steven G; Vawter, Marquis PGenes2012 Aug 30545-57523139896
Designing a public square for research computing.Masys, Daniel R; Harris, Paul A; Fearn, Paul A; Kohane, Isaac SScience translational medicine2012 Aug 29149fs3222932220
North African Jewish and non-Jewish populations form distinctive, orthogonal clusters.Campbell, Christopher L; Palamara, Pier F; Dubrovsky, Maya; Botigue, Laura R; Fellous, Marc; Atzmon, Gil; Oddoux, Carole; Pearlman, Alexander; Hao, Li; Henn, Brenna M; Burns, Edward; Bustamante, Carlos D; Comas, David; Friedman, Eitan; Pe'er, Itsik; OstreProceedings of the National Academy of Sciences of the United States of America2012 Aug 2113865-7022869716
A role for ephrin-A5 in axonal sprouting, recovery, and activity-dependent plasticity after stroke.Overman, Justine J; Clarkson, Andrew N; Wanner, Ina B; Overman, William T; Eckstein, Ilya; Maguire, Jaime L; Dinov, Ivo D; Toga, Arthur W; Carmichael, S ThomasProceedings of the National Academy of Sciences of the United States of America2012 Aug 14E2230-922837401
An approach to improve LOINC mapping through augmentation of local test names.Kim, Hyeoneui; El-Kareh, Robert; Goel, Anupam; Vineet, F N U; Chapman, Wendy WJournal of biomedical informatics2012 Aug651-722210167
Prenatal isolated mild ventriculomegaly is associated with persistent ventricle enlargement at ages 1 and 2.Lyall, Amanda E; Woolson, Sandra; Wolfe, Honor M; Goldman, Barbara Davis; Reznick, J Steven; Hamer, Robert M; Lin, Weili; Styner, Martin; Gerig, Guido; Gilmore, John HEarly human development2012 Aug691-822445211
Central nervous system endoplasmic reticulum stress in a murine model of type 2 diabetes.Sims-Robinson, C; Zhao, S; Hur, J; Feldman, E LDiabetologia2012 Aug2276-8422581041
Whole brain resting state functional connectivity abnormalities in schizophrenia.Venkataraman, Archana; Whitford, Thomas J; Westin, Carl-Fredrik; Golland, Polina; Kubicki, MarekSchizophrenia research2012 Aug7-1222633528
Towards automatic diabetes case detection and ABCS protocol compliance assessment.Mishra, Ninad K; Son, Roderick Y; Arnzen, James JClinical medicine & research2012 Aug106-2122634542
Wisdom of crowds for robust gene network inference.Marbach, Daniel; Costello, James C; Kuffner, Robert; Vega, Nicole M; Prill, Robert J; Camacho, Diogo M; Allison, Kyle R; DREAM5 Consortium; Kellis, Manolis; Collins, James J; Stolovitzky, GustavoNature methods2012 Aug796-80422796662
How many neutrophils are enough (redux, redux)?Silverstein, Samuel C; Rabadan, RaulThe Journal of clinical investigation2012 Aug 12776-922820286
A 3D interactive multi-object segmentation tool using local robust statistics driven active contours.Gao, Yi; Kikinis, Ron; Bouix, Sylvain; Shenton, Martha; Tannenbaum, AllenMedical image analysis2012 Aug1216-2722831773
Leveraging models of cell regulation and GWAS data in integrative network-based association studies.Califano, Andrea; Butte, Atul J; Friend, Stephen; Ideker, Trey; Schadt, EricNature genetics2012 Aug841-722836096
Ontologies as integrative tools for plant science.Walls, Ramona L; Athreya, Balaji; Cooper, Laurel; Elser, Justin; Gandolfo, Maria A; Jaiswal, Pankaj; Mungall, Christopher J; Preece, Justin; Rensing, Stefan; Smith, Barry; Stevenson, Dennis WAmerican journal of botany2012 Aug1263-7522847540
Human middle longitudinal fascicle: variations in patterns of anatomical connections.Makris, N; Preti, M G; Asami, T; Pelavin, P; Campbell, B; Papadimitriou, G M; Kaiser, J; Baselli, G; Westin, C F; Shenton, M E; Kubicki, MBrain structure & function2012 Jul 1122782432
Quantitative tract-based white matter development from birth to age 2years.Geng, Xiujuan; Gouttard, Sylvain; Sharma, Anuja; Gu, Hongbin; Styner, Martin; Lin, Weili; Gerig, Guido; Gilmore, John HNeuroImage2012 Jul 2542-5722510254
Growing skin: tissue expansion in pediatric forehead reconstruction.Zollner, Alexander M; Buganza Tepole, Adrian; Gosain, Arun K; Kuhl, EllenBiomechanics and modeling in mechanobiology2012 Jul855-6722052000
Reverse-engineering human regulatory networks.Lefebvre, Celine; Rieckhof, Gabrielle; Califano, AndreaWiley interdisciplinary reviews. Systems biology and medicine2012 Jul-Aug311-2522246697
A system for coreference resolution for the clinical narrative.Zheng, Jiaping; Chapman, Wendy W; Miller, Timothy A; Lin, Chen; Crowley, Rebecca S; Savova, Guergana KJournal of the American Medical Informatics Association : JAMIA2012 Jul-Aug660-722298565
Self-crossing detection and location for parametric active contours.Nakhmani, Arie; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2012 Jul3150-622374361
White matter integrity, language, and childhood onset schizophrenia.Clark, Kristi; Narr, Katherine L; O'Neill, Joseph; Levitt, Jennifer; Siddarth, Prabha; Phillips, Owen; Toga, Arthur; Caplan, RochelleSchizophrenia research2012 Jul150-622405729
Inference of modules associated to eQTLs.Kreimer, Anat; Litvin, Oren; Hao, Ke; Molony, Cliona; Pe'er, Dana; Pe'er, ItsikNucleic acids research2012 Jule9822447449
An image analysis toolbox for high-throughput C. elegans assays.Wahlby, Carolina; Kamentsky, Lee; Liu, Zihan H; Riklin-Raviv, Tammy; Conery, Annie L; O'Rourke, Eyleen J; Sokolnicki, Katherine L; Visvikis, Orane; Ljosa, Vebjorn; Irazoqui, Javier E; Golland, Polina; Ruvkun, Gary; Ausubel, Frederick M; Carpenter, Anne ENature methods2012 Jul714-622522656
Lysine-specific demethylase 1: an epigenetic regulator of salt-sensitive hypertension.Williams, Jonathan S; Chamarthi, Bindu; Goodarzi, Mark O; Pojoga, Luminita H; Sun, Bei; Garza, Amanda E; Raby, Benjamin A; Adler, Gail K; Hopkins, Paul N; Brown, Nancy J; Jeunemaitre, Xavier; Ferri, Claudio; Fang, Rui; Leonor, Thiago; Cui, Jinrui; Guo, XiAmerican journal of hypertension2012 Jul812-722534796
Vitamin D3 therapy corrects the tissue sensitivity to angiotensin ii akin to the action of a converting enzyme inhibitor in obese hypertensives: an interventional study.Vaidya, Anand; Sun, Bei; Larson, Carol; Forman, John P; Williams, Jonathan SThe Journal of clinical endocrinology and metabolism2012 Jul2456-6522539586
Crouched posture maximizes ground reaction forces generated by muscles.Hoang, Hoa X; Reinbolt, Jeffrey AGait & posture2012 Jul405-822542242
The microRNA expression associated with morphogenesis of breast cancer cells in three-dimensional organotypic culture.Nguyen, Hong T; Li, Cui; Lin, Zhen; Zhuang, Yan; Flemington, Erik K; Burow, Matthew E; Lin, Yi; Shan, BinOncology reports2012 Jul117-2622576799
A survey of informatics platforms that enable distributed comparative effectiveness research using multi-institutional heterogenous clinical data.Sittig, Dean F; Hazlehurst, Brian L; Brown, Jeffrey; Murphy, Shawn; Rosenman, Marc; Tarczy-Hornoch, Peter; Wilcox, Adam BMedical care2012 JulS49-5922692259
DEFOG: discrete enrichment of functionally organized genes.Wittkop, Tobias; Berman, Ari E; Fleisch, K Mathew; Mooney, Sean DIntegrative biology : quantitative biosciences from nano to macro2012 Jul795-80422706384
Mining the pharmacogenomics literature--a survey of the state of the art.Hahn, Udo; Cohen, K Bretonnel; Garten, Yael; Shah, Nigam HBriefings in bioinformatics2012 Jul460-9422833496
Predicting the metabolic cost of incline walking from muscle activity and walking mechanics.Silder, Amy; Besier, Thor; Delp, Scott LJournal of biomechanics2012 Jun 261842-922578744
Genome-wide association identifies the T gene as a novel asthma pharmacogenetic locus.Tantisira, Kelan G; Damask, Amy; Szefler, Stanley J; Schuemann, Brooke; Markezich, Amy; Su, Jessica; Klanderman, Barbara; Sylvia, Jody; Wu, Rongling; Martinez, Fernando; Boushey, Homer A; Chinchilli, Vernon M; Mauger, Dave; Weiss, Scott T; Israel, Elliot;American journal of respiratory and critical care medicine2012 Jun 151286-9122538805
CUDA optimization strategies for compute- and memory-bound neuroimaging algorithms.Lee, Daren; Dinov, Ivo; Dong, Bin; Gutman, Boris; Yanovsky, Igor; Toga, Arthur WComputer methods and programs in biomedicine2012 Jun175-8721159404
Technical desiderata for the integration of genomic data into Electronic Health Records.Masys, Daniel R; Jarvik, Gail P; Abernethy, Neil F; Anderson, Nicholas R; Papanicolaou, George J; Paltoo, Dina N; Hoffman, Mark A; Kohane, Isaac S; Levy, Howard PJournal of biomedical informatics2012 Jun419-2222223081
Differences in white matter fiber tract development present from 6 to 24 months in infants with autism.Wolff, Jason J; Gu, Hongbin; Gerig, Guido; Elison, Jed T; Styner, Martin; Gouttard, Sylvain; Botteron, Kelly N; Dager, Stephen R; Dawson, Geraldine; Estes, Annette M; Evans, Alan C; Hazlett, Heather C; Kostopoulos, Penelope; McKinstry, Robert C; Paterson,The American journal of psychiatry2012 Jun589-60022362397
Portability of an algorithm to identify rheumatoid arthritis in electronic health records.Carroll, Robert J; Thompson, Will K; Eyler, Anne E; Mandelin, Arthur M; Cai, Tianxi; Zink, Raquel M; Pacheco, Jennifer A; Boomershine, Chad S; Lasko, Thomas A; Xu, Hua; Karlson, Elizabeth W; Perez, Raul G; Gainer, Vivian S; Murphy, Shawn N; Ruderman, EricJournal of the American Medical Informatics Association : JAMIA2012 June162-922374935
Bayesian lasso for semiparametric structural equation models.Guo, Ruixin; Zhu, Hongtu; Chow, Sy-Miin; Ibrahim, Joseph GBiometrics2012 Jun567-7722376150
A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support.Jiang, Xiaoqian; Boxwala, Aziz A; El-Kareh, Robert; Kim, Jihoon; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2012 Jun 1e137-e14422493049
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.Wu, Stephen T; Liu, Hongfang; Li, Dingcheng; Tao, Cui; Musen, Mark A; Chute, Christopher G; Shah, Nigam HJournal of the American Medical Informatics Association : JAMIA2012 June149-5622493050
Using ontology-based annotation to profile disease research.Liu, Yi; Coulet, Adrien; LePendu, Paea; Shah, Nigam HJournal of the American Medical Informatics Association : JAMIA2012 June177-8622494789
Novel data-mining methodologies for adverse drug event discovery and analysis.Harpaz, R; DuMouchel, W; Shah, N H; Madigan, D; Ryan, P; Friedman, CClinical pharmacology and therapeutics2012 Jun1010-2122549283
Brain volume findings in 6-month-old infants at high familial risk for autism.Hazlett, Heather Cody; Gu, Hongbin; McKinstry, Robert C; Shaw, Dennis W W; Botteron, Kelly N; Dager, Stephen R; Styner, Martin; Vachet, Clement; Gerig, Guido; Paterson, Sarah J; Schultz, Robert T; Estes, Annette M; Evans, Alan C; Piven, Joseph; IBIS NetwoThe American journal of psychiatry2012 Jun601-822684595
Genetics insights into the pathogenesis of Kawasaki disease.Burns, Jane C; Newburger, Jane WCirculation. Cardiovascular genetics2012 Jun277-822715279
The coming age of data-driven medicine: translational bioinformatics' next frontier.Shah, Nigam H; Tenenbaum, Jessica DJournal of the American Medical Informatics Association : JAMIA2012 June2-422718035
Computational Optogenetics: A Novel Continuum Framework for the Photoelectrochemistry of Living Systems.Wong, Jonathan; Abilez, Oscar J; Kuhl, EllenJournal of the mechanics and physics of solids2012 Jun 11158-117822773861
Frontiers in growth and remodeling.Menzel, Andreas; Kuhl, EllenMechanics research communications2012 Jun 11-1422919118
Nanoinformatics: developing new computing applications for nanomedicine.Maojo, V; Fritts, M; Martin-Sanchez, F; De la Iglesia, D; Cachau, R E; Garcia-Remesal, M; Crespo, J; Mitchell, J A; Anguita, A; Baker, N; Barreiro, J M; Benitez, S E; De la Calle, G; Facelli, J C; Ghazal, P; Geissbuhler, A; Gonzalez-Nilo, F; Graf, N; GranComputing in science & engineering2012 Jun 1521-53922942787
Nanoinformatics: developing new computing applications for nanomedicine.Maojo, V; Fritts, M; Martin-Sanchez, F; De la Iglesia, D; Cachau, R E; Garcia-Remesal, M; Crespo, J; Mitchell, J A; Anguita, A; Baker, N; Barreiro, J M; Benitez, S E; De la Calle, G; Facelli, J C; Ghazal, P; Geissbuhler, A; Gonzalez-Nilo, F; Graf, N; Grangeat, P; Hermosilla, I; Hussein, R; Kern, J; Koch, S; Legre, Y; Lopez-Alonso, V; Lopez-Campos, G; Milanesi, L; Moustakis, V; Munteanu, C; Otero, P; Pazos, A; Perez-Rey, D; Potamias, G; Sanz, F; Kulikowski, CComputing in science & engineering2012 Jun 1521-53922942787
Exact statistical tests for the intersection of independent lists of genes.Natarajan, Loki; Pu, Minya; Messer, KarenThe annals of applied statistics2012 Jun521-54123335952
Metab2MeSH: annotating compounds with medical subject headings.Sartor, Maureen A; Ade, Alex; Wright, Zach; States, David; Omenn, Gilbert S; Athey, Brian; Karnovsky, AllaBioinformatics (Oxford, England)2012 May 151408-1022492643
A platform for dynamic simulation and control of movement based on OpenSim and MATLAB.Mansouri, Misagh; Reinbolt, Jeffrey AJournal of biomechanics2012 May 111517-2122464351
Effects of ApoE4 and maternal history of dementia on hippocampal atrophy.Andrawis, John P; Hwang, Kristy S; Green, Amity E; Kotlerman, Jenny; Elashoff, David; Morra, Jonathan H; Cummings, Jeffrey L; Toga, Arthur W; Thompson, Paul M; Apostolova, Liana GNeurobiology of aging2012 May856-6620833446
Replication and meta-analysis of the gene-environment interaction between body mass index and the interleukin-6 promoter polymorphism with higher insulin resistance.Underwood, Patricia C; Chamarthi, Bindu; Williams, Jonathan S; Sun, Bei; Vaidya, Anand; Raby, Benjamin A; Lasky-Su, Jessica; Hopkins, Paul N; Adler, Gail K; Williams, Gordon HMetabolism: clinical and experimental2012 May667-7122075267
TwinMARM: two-stage multiscale adaptive regression methods for twin neuroimaging data.Li, Yimei; Gilmore, John H; Wang, Jiaping; Styner, Martin; Lin, Weili; Zhu, HongtuIEEE transactions on medical imaging2012 May1100-1222287236
How robust is human gait to muscle weakness?van der Krogt, Marjolein M; Delp, Scott L; Schwartz, Michael HGait & posture2012 May113-922386624
Evolutionary molecular medicine.Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert SJournal of molecular medicine (Berlin, Germany)2012 May509-2222544168
Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions.Chen, Yong; Sheng, Ren; Kallberg, Morten; Silkov, Antonina; Tun, Moe P; Bhardwaj, Nitin; Kurilova, Svetlana; Hall, Randy A; Honig, Barry; Lu, Hui; Cho, WonhwaMolecular cell2012 Apr 27226-3722445486
TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements.Tan, Adelene Y; Riley, Todd R; Coady, Tristan; Bussemaker, Harmen J; Manley, James LProceedings of the National Academy of Sciences of the United States of America2012 Apr 176030-522460799
Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4.Dapito, Dianne H; Mencin, Ali; Gwak, Geum-Youn; Pradere, Jean-Philippe; Jang, Myoung-Kuk; Mederacke, Ingmar; Caviglia, Jorge M; Khiabanian, Hossein; Adeyemi, Adebowale; Bataller, Ramon; Lefkowitch, Jay H; Bower, Maureen; Friedman, Richard; Sartor, R BalfoCancer cell2012 Apr 17504-1622516259
Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4.Mysinger, Michael M; Weiss, Dahlia R; Ziarek, Joshua J; Gravel, Stephanie; Doak, Allison K; Karpiak, Joel; Heveker, Nikolaus; Shoichet, Brian K; Volkman, Brian FProceedings of the National Academy of Sciences of the United States of America2012 Apr 35517-2222431600
Circular representation of human cortical networks for subject and population-level connectomic visualization.Irimia, Andrei; Chambers, Micah C; Torgerson, Carinna M; Horn, John D VanNeuroImage2012 Apr 21340-5122305988
Regional brain volume reductions relate to facial dysmorphology and neurocognitive function in fetal alcohol spectrum disorders.Roussotte, Florence F; Sulik, Kathleen K; Mattson, Sarah N; Riley, Edward P; Jones, Kenneth L; Adnams, Colleen M; May, Philip A; O'Connor, Mary J; Narr, Katherine L; Sowell, Elizabeth RHuman brain mapping2012 Apr920-3721416562
Grand challenge competition to predict in vivo knee loads.Fregly, Benjamin J; Besier, Thor F; Lloyd, David G; Delp, Scott L; Banks, Scott A; Pandy, Marcus G; D'Lima, Darryl DJournal of orthopaedic research : official publication of the Orthopaedic Research Society2012 Apr503-1322161745
Compressive tibiofemoral force during crouch gait.Steele, Katherine M; Demers, Matthew S; Schwartz, Michael H; Delp, Scott LGait & posture2012 Apr556-6022206783
On the covariate-adjusted estimation for an overall treatment difference with data from a randomized comparative clinical trial.Tian, Lu; Cai, Tianxi; Zhao, Lihui; Wei, Lee-JenBiostatistics (Oxford, England)2012 Apr256-7322294672
Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease.Ananthakrishnan, A N; Guzman-Perez, R; Gainer, V; Cai, T; Churchill, S; Kohane, I; Plenge, R M; Murphy, SAlimentary pharmacology & therapeutics2012 Apr789-9522360370
Size and shape of the caudate nucleus in individuals with bipolar affective disorder.Ong, Daniel; Walterfang, Mark; Malhi, Gin S; Styner, Martin; Velakoulis, Dennis; Pantelis, ChristosThe Australian and New Zealand journal of psychiatry2012 Apr340-5122368240
SRM targeted proteomics in search for biomarkers of HCV-induced progression of fibrosis to cirrhosis in HALT-C patients.Qin, Shizhen; Zhou, Yong; Lok, Anna S; Tsodikov, Alex; Yan, Xiaowei; Gray, Li; Yuan, Min; Moritz, Robert L; Galas, David; Omenn, Gilbert S; Hood, LeroyProteomics2012 Apr1244-5222577025
A Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury.Wang, Bo; Prastawa, Marcel; Irimia, Andrei; Chambers, Micah C; Vespa, Paul M; Van Horn, John D; Gerig, GuidoProceedings - Society of Photo-Optical Instrumentation Engineers2012 Mar 2383140224465115
On the biomechanics and mechanobiology of growing skin.Zollner, Alexander M; Buganza Tepole, Adrian; Kuhl, EllenJournal of theoretical biology2012 Mar 21166-7522227432
Analytic regularization for landmark-based image registration.Shusharina, Nadezhda; Sharp, GregoryPhysics in medicine and biology2012 Mar 211477-9822390947
Ratcheting up cancer potency estimates.Crouch, Edmund A C; Omenn, Gilbert SEnvironmental science & technology2012 Mar 62538-4422296526
Computational modeling of bone density profiles in response to gait: a subject-specific approach.Pang, Henry; Shiwalkar, Abhishek P; Madormo, Chris M; Taylor, Rebecca E; Andriacchi, Thomas P; Kuhl, EllenBiomechanics and modeling in mechanobiology2012 Mar379-9021604146
The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis.Kapur, Tina; Pieper, Steve; Whitaker, Ross; Aylward, Stephen; Jakab, Marianna; Schroeder, Will; Kikinis, RonJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr176-8022081219
The National Center for Biomedical Ontology.Musen, Mark A; Noy, Natalya F; Shah, Nigam H; Whetzel, Patricia L; Chute, Christopher G; Story, Margaret-Anne; Smith, Barry; NCBO teamJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr190-522081220
The Center for Computational Biology: resources, achievements, and challenges.Toga, Arthur W; Dinov, Ivo D; Thompson, Paul M; Woods, Roger P; Van Horn, John D; Shattuck, David W; Parker, D StottJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr202-622081221
Simbios: an NIH national center for physics-based simulation of biological structures.Delp, Scott L; Ku, Joy P; Pande, Vijay S; Sherman, Michael A; Altman, Russ BJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr186-922081222
Using systems and structure biology tools to dissect cellular phenotypes.Floratos, Aris; Honig, Barry; Pe'er, Dana; Califano, AndreaJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr171-522081223
iDASH: integrating data for analysis, anonymization, and sharing.Ohno-Machado, Lucila; Bafna, Vineet; Boxwala, Aziz A; Chapman, Brian E; Chapman, Wendy W; Chaudhuri, Kamalika; Day, Michele E; Farcas, Claudiu; Heintzman, Nathaniel D; Jiang, Xiaoqian; Kim, Hyeoneui; Kim, Jihoon; Matheny, Michael E; Resnic, Frederic S; ViJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr196-20122081224
A translational engine at the national scale: informatics for integrating biology and the bedside.Kohane, Isaac S; Churchill, Susanne E; Murphy, Shawn NJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr181-522081225
The NIH National Center for Integrative Biomedical Informatics (NCIBI).Athey, Brian D; Cavalcoli, James D; Jagadish, H V; Omenn, Gilbert S; Mirel, Barbara; Kretzler, Matthias; Burant, Charles; Isokpehi, Raphael D; DeLisi, Charles; NCIBI faculty, trainees, and staffJournal of the American Medical Informatics Association : JAMIA2012 Mar-Apr166-7022101971
Registration of images with varying topology using embedded maps.Li, Xiaoxing; Long, Xiaojing; Laurienti, Paul; Wyatt, Christopher; Alzheimerýýýs Disease Neuroimaging InitiativeIEEE transactions on medical imaging2012 Mar749-6522194239
Where to Publish and Find Ontologies? A Survey of Ontology Libraries.d'Aquin, Mathieu; Noy, Natalya FWeb semantics (Online)2012 Mar 196-11122408576
Clinical Decision Support and Closed-Loop Control for Cardiopulmonary Management and Intensive Care Unit Sedation Using Expert Systems.Gholami, Behnood; Bailey, James M; Haddad, Wassim M; Tannenbaum, Allen RIEEE transactions on control systems technology : a publication of the IEEE Control Systems Society2012 Mar1343-135023620646
Intrinsic Regression Models for Medial Representation of Subcortical Structures.Shi, Xiaoyan; Zhu, Hongtu; Ibrahim, Joseph G; Liang, Faming; Lieberman, Jeffrey; Styner, MartinJournal of the American Statistical Association2012 Mar 112-2323794769
Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints.Lin, Tungyou; Guyader, Carole Le; Dinov, Ivo; Thompson, Paul; Toga, Arthur; Vese, LuminitaJournal of scientific computing2012 MarNULL24273381
Viral reassortment as an information exchange between viral segments.Greenbaum, Benjamin D; Li, Olive T W; Poon, Leo L M; Levine, Arnold J; Rabadan, RaulProceedings of the National Academy of Sciences of the United States of America2012 Feb 283341-622331898
Measures for Validation of DTI Tractography.Gouttard, Sylvain; Goodlett, Casey B; Kubicki, Marek; Gerig, GuidoProceedings - Society of Photo-Optical Instrumentation Engineers2012 Feb 23NULL24353381
A framework for longitudinal data analysis via shape regression.Fishbaugh, James; Durrleman, Stanley; Piven, Joseph; Gerig, GuidoProceedings of SPIE2012 Feb 23NULL24392201
Along-tract statistics allow for enhanced tractography analysis.Colby, John B; Soderberg, Lindsay; Lebel, Catherine; Dinov, Ivo D; Thompson, Paul M; Sowell, Elizabeth RNeuroImage2012 Feb 153227-4222094644
Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis.Martinez, Maria Rodriguez; Corradin, Alberto; Klein, Ulf; Alvarez, Mariano Javier; Toffolo, Gianna M; di Camillo, Barbara; Califano, Andrea; Stolovitzky, Gustavo AProceedings of the National Academy of Sciences of the United States of America2012 Feb 142672-722308355
Patients with patellofemoral pain exhibit elevated bone metabolic activity at the patellofemoral joint.Draper, Christine E; Fredericson, Michael; Gold, Garry E; Besier, Thor F; Delp, Scott L; Beaupre, Gary S; Quon, AndrewJournal of orthopaedic research : official publication of the Orthopaedic Research Society2012 Feb209-1321812024
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Brain surface conformal parameterization with the Ricci flow.Wang, Yalin; Shi, Jie; Yin, Xiaotian; Gu, Xianfeng; Chan, Tony F; Yau, Shing-Tung; Toga, Arthur W; Thompson, Paul MIEEE transactions on medical imaging2012 Feb251-6421926017
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Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-ýýB family DNA binding.Siggers, Trevor; Chang, Abraham B; Teixeira, Ana; Wong, Daniel; Williams, Kevin J; Ahmed, Bilal; Ragoussis, Jiannis; Udalova, Irina A; Smale, Stephen T; Bulyk, Martha LNature immunology2012 Jan95-10222101729
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Characteristics associated with improved knee extension after strength training for individuals with cerebral palsy and crouch gait.Steele, K M; Damiano, D L; Eek, M N; Unger, M; Delp, S LJournal of pediatric rehabilitation medicine201299-10622699100
Emergence of fatal avian influenza in New England harbor seals.Anthony, S J; St Leger, J A; Pugliares, K; Ip, H S; Chan, J M; Carpenter, Z W; Navarrete-Macias, I; Sanchez-Leon, M; Saliki, J T; Pedersen, J; Karesh, W; Daszak, P; Rabadan, R; Rowles, T; Lipkin, W ImBio2012e00166-1222851656
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LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types.Kim, Jung H; Karnovsky, Alla; Mahavisno, Vasudeva; Weymouth, Terry; Pande, Manjusha; Dolinoy, Dana C; Rozek, Laura S; Sartor, Maureen ABMC genomics201252623033966
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A genome-scale RNA-interference screen identifies RRAS signaling as a pathologic feature of Huntington's disease.Miller, John P; Yates, Bridget E; Al-Ramahi, Ismael; Berman, Ari E; Sanhueza, Mario; Kim, Eugene; de Haro, Maria; DeGiacomo, Francesco; Torcassi, Cameron; Holcomb, Jennifer; Gafni, Juliette; Mooney, Sean D; Botas, Juan; Ellerby, Lisa M; Hughes, Robert EPLoS genetics2012e100304223209424
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Pituitary adenoma volumetry with 3D Slicer.Egger, Jan; Kapur, Tina; Nimsky, Christopher; Kikinis, RonPloS one2012e5178823240062
MicroRNA-centric measurement improves functional enrichment analysis of co-expressed and differentially expressed microRNA clusters.Lee, Su Yeon; Sohn, Kyung-Ah; Kim, Ju HanBMC genomics2012S1723281707
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Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes.Bray, Jenelle K; Weiss, Dahlia R; Levitt, MichaelBiophysical journal2011 Dec 212966-922208195
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Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers.Menon, Rajasree; Roy, Ambrish; Mukherjee, Srayanta; Belkin, Saveliy; Zhang, Yang; Omenn, Gilbert SJournal of proteome research2011 Dec 25503-1122003824
Computational modeling of growth: systemic and pulmonary hypertension in the heart.Rausch, M K; Dam, A; Goktepe, S; Abilez, O J; Kuhl, EBiomechanics and modeling in mechanobiology2011 Dec799-81121188611
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Graphical procedures for evaluating overall and subject-specific incremental values from new predictors with censored event time data.Uno, Hajime; Cai, Tianxi; Tian, Lu; Wei, L JBiometrics2011 Dec1389-9621504421
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Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding.Liu, Tianyun; Altman, Russ BPLoS computational biology2011 Dece100232622219723
Morphometric analysis of subcortical structures in progressive supranuclear palsy: In vivo evidence of neostriatal and mesencephalic atrophy.Looi, Jeffrey C L; Macfarlane, Matthew D; Walterfang, Mark; Styner, Martin; Velakoulis, Dennis; Latt, Jimmy; van Westen, Danielle; Nilsson, ChristerPsychiatry research2011 Nov 30163-7521899988
Phenotyping patient-derived cells for translational studies in cardiovascular disease.Shaw, Stanley Y; Brettman, Ari DCirculation2011 Nov 292444-5522125190
Phase II study of neoadjuvant bevacizumab and radiotherapy for resectable soft tissue sarcomas.Yoon, Sam S; Duda, Dan G; Karl, Daniel L; Kim, Tae-Min; Kambadakone, Avinash R; Chen, Yen-Lin; Rothrock, Courtney; Rosenberg, Andrew E; Nielsen, G Petur; Kirsch, David G; Choy, Edwin; Harmon, David C; Hornicek, Francis J; Dreyfuss, Jonathan; Ancukiewicz, International journal of radiation oncology, biology, physics2011 Nov 151081-9020932656
Topographical relationships between arcuate fasciculus connectivity and cortical thickness.Phillips, Owen R; Clark, Kristi A; Woods, Roger P; Subotnik, Kenneth L; Asarnow, Robert F; Nuechterlein, Keith H; Toga, Arthur W; Narr, Katherine LHuman brain mapping2011 Nov1788-80120886580
Nonparametric clustering for studying RNA conformations.Le Faucheur, Xavier; Hershkovits, Eli; Tannenbaum, Rina; Tannenbaum, AllenIEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM2011 Nov-Dec1604-1921173460
Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli.Patwa, Laura G; Fan, Ting-Jia; Tchaptchet, Sandrine; Liu, Yang; Lussier, Yves A; Sartor, R Balfour; Hansen, Jonathan JGastroenterology2011 Nov1842-51.e1-1021726510
Comparison of acute and chronic traumatic brain injury using semi-automatic multimodal segmentation of MR volumes.Irimia, Andrei; Chambers, Micah C; Alger, Jeffry R; Filippou, Maria; Prastawa, Marcel W; Wang, Bo; Hovda, David A; Gerig, Guido; Toga, Arthur W; Kikinis, Ron; Vespa, Paul M; Van Horn, John DJournal of neurotrauma2011 Nov2287-30621787171
Differential effects of the Huntington's disease CAG mutation in striatum and cerebellum are quantitative not qualitative.Fossale, Elisa; Seong, Ihn Sik; Coser, Kathryn R; Shioda, Toshi; Kohane, Isaac S; Wheeler, Vanessa C; Gusella, James F; MacDonald, Marcy E; Lee, Jong-MinHuman molecular genetics2011 Nov 14258-6721840924
The identification of gene expression profiles associated with progression of human diabetic neuropathy.Hur, Junguk; Sullivan, Kelli A; Pande, Manjusha; Hong, Yu; Sima, Anders A F; Jagadish, Hosagrahar V; Kretzler, Matthias; Feldman, Eva LBrain : a journal of neurology2011 Nov3222-3521926103
An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma.Sumazin, Pavel; Yang, Xuerui; Chiu, Hua-Sheng; Chung, Wei-Jen; Iyer, Archana; Llobet-Navas, David; Rajbhandari, Presha; Bansal, Mukesh; Guarnieri, Paolo; Silva, Jose; Califano, AndreaCell2011 Oct 14370-8122000015
Regional gray matter correlates of perceived emotional intelligence.Koven, Nancy S; Roth, Robert M; Garlinghouse, Matthew A; Flashman, Laura A; Saykin, Andrew JSocial cognitive and affective neuroscience2011 Oct582-9020934987
Object tracking and target reacquisition based on 3-D range data for moving vehicles.Lee, Jehoon; Lankton, Shawn; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2011 Oct2912-2421486717
Mapping corticocortical structural integrity in schizophrenia and effects of genetic liability.Phillips, Owen R; Nuechterlein, Keith H; Asarnow, Robert F; Clark, Kristi A; Cabeen, Ryan; Yang, Yaling; Woods, Roger P; Toga, Arthur W; Narr, Katherine LBiological psychiatry2011 Oct 1680-921571255
Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs.Mathew, Biji; Jacobson, Jeffrey R; Berdyshev, Evgeny; Huang, Yong; Sun, Xiaoguang; Zhao, Yutong; Gerhold, Lynnette M; Siegler, Jessica; Evenoski, Carrie; Wang, Ting; Zhou, Tong; Zaidi, Rafe; Moreno-Vinasco, Liliana; Bittman, Robert; Chen, Chin Tu; LaRivieFASEB journal : official publication of the Federation of American Societies for Experimental Biology2011 Oct3388-40021712494
Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing.Quinn, T A; Granite, S; Allessie, M A; Antzelevitch, C; Bollensdorff, C; Bub, G; Burton, R A B; Cerbai, E; Chen, P S; Delmar, M; Difrancesco, D; Earm, Y E; Efimov, I R; Egger, M; Entcheva, E; Fink, M; Fischmeister, R; Franz, M R; Garny, A; Giles, W R; HanProgress in biophysics and molecular biology2011 Oct4-1021745496
Fiber geometry in the corpus callosum in schizophrenia: evidence for transcallosal misconnection.Whitford, Thomas J; Savadjiev, Peter; Kubicki, Marek; O'Donnell, Lauren J; Terry, Douglas P; Bouix, Sylvain; Westin, Carl-Fredrik; Schneiderman, Jason S; Bobrow, Laurel; Rausch, Andrew C; Niznikiewicz, Margaret; Nestor, Paul G; Pantelis, Christos; Wood, SSchizophrenia research2011 Oct69-7421831601
CYP4A11 T8590C polymorphism, salt-sensitive hypertension, and renal blood flow.Williams, Jonathan S; Hopkins, Paul N; Jeunemaitre, Xavier; Brown, Nancy JJournal of hypertension2011 Oct1913-821873888
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Error bounds on the SCISSORS approximation method.Haque, Imran S; Pande, Vijay SJournal of chemical information and modeling2011 Sep 262248-5321851122
Anatomy of high-performance 2D similarity calculations.Haque, Imran S; Pande, Vijay S; Walters, W PatrickJournal of chemical information and modeling2011 Sep 262345-5121854053
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The effects of physical activity, education, and body mass index on the aging brain.Ho, April J; Raji, Cyrus A; Becker, James T; Lopez, Oscar L; Kuller, Lewis H; Hua, Xue; Dinov, Ivo D; Stein, Jason L; Rosano, Caterina; Toga, Arthur W; Thompson, Paul MHuman brain mapping2011 Sep1371-8220715081
Outcome quantification using SPHARM-PDM toolbox in orthognathic surgery.Paniagua, Beatriz; Cevidanes, Lucia; Zhu, Hongtu; Styner, MartinInternational journal of computer assisted radiology and surgery2011 Sep617-2621161693
Brain structure correlates of individual differences in the acquisition and inhibition of conditioned fear.Hartley, Catherine A; Fischl, Bruce; Phelps, Elizabeth ACerebral cortex (New York, N.Y. : 1991)2011 Sep1954-6221263037
Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010.de Bruijn, Berry; Cherry, Colin; Kiritchenko, Svetlana; Martin, Joel; Zhu, XiaodanJournal of the American Medical Informatics Association : JAMIA2011 Sep-Oct557-6221565856
Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification.Minard, Anne-Lyse; Ligozat, Anne-Laure; Ben Abacha, Asma; Bernhard, Delphine; Cartoni, Bruno; Deleger, Louise; Grau, Brigitte; Rosset, Sophie; Zweigenbaum, Pierre; Grouin, CyrilJournal of the American Medical Informatics Association : JAMIA2011 Sep-Oct588-9321597105
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas.Farrah, Terry; Deutsch, Eric W; Omenn, Gilbert S; Campbell, David S; Sun, Zhi; Bletz, Julie A; Mallick, Parag; Katz, Jonathan E; Malmstrom, Johan; Ossola, Reto; Watts, Julian D; Lin, Biaoyang; Zhang, Hui; Moritz, Robert L; Aebersold, RuediMolecular & cellular proteomics : MCP2011 SepM110.00635321632744
Populations with elevated mutation load do not benefit from the operation of sexual selection.Hollis, B; Houle, DJournal of evolutionary biology2011 Sep1918-2621658188
2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text.Uzuner, Ozlem; South, Brett R; Shen, Shuying; DuVall, Scott LJournal of the American Medical Informatics Association : JAMIA2011 Sep-Oct552-621685143
Using machine learning for concept extraction on clinical documents from multiple data sources.Torii, Manabu; Wagholikar, Kavishwar; Liu, HongfangJournal of the American Medical Informatics Association : JAMIA2011 Sep-Oct580-721709161
A knowledge discovery and reuse pipeline for information extraction in clinical notes.Patrick, Jon D; Nguyen, Dung H M; Wang, Yefeng; Li, MinJournal of the American Medical Informatics Association : JAMIA2011 Sep-Oct574-921737844
Fast flexible modeling of RNA structure using internal coordinates.Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ BiagioIEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM2011 Sep-Oct1247-5721778523
Analysis of the coding genome of diffuse large B-cell lymphoma.Pasqualucci, Laura; Trifonov, Vladimir; Fabbri, Giulia; Ma, Jing; Rossi, Davide; Chiarenza, Annalisa; Wells, Victoria A; Grunn, Adina; Messina, Monica; Elliot, Oliver; Chan, Joseph; Bhagat, Govind; Chadburn, Amy; Gaidano, Gianluca; Mullighan, Charles G; RNature genetics2011 Sep830-721804550
Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions.Chapman, Wendy W; Nadkarni, Prakash M; Hirschman, Lynette; D'Avolio, Leonard W; Savova, Guergana K; Uzuner, OzlemJournal of the American Medical Informatics Association : JAMIA2011 Sep-Oct540-321846785
Natural language processing: an introduction.Nadkarni, Prakash M; Ohno-Machado, Lucila; Chapman, Wendy WJournal of the American Medical Informatics Association : JAMIA2011 Sep-Oct544-5121846786
Robust brain extraction across datasets and comparison with publicly available methods.Iglesias, Juan Eugenio; Liu, Cheng-Yi; Thompson, Paul M; Tu, ZhuowenIEEE transactions on medical imaging2011 Sep1617-3421880566
NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources.Jonquet, Clement; Lependu, Paea; Falconer, Sean; Coulet, Adrien; Noy, Natalya F; Musen, Mark A; Shah, Nigam HWeb semantics (Online)2011 Sep 1316-32421918645
Voxel-based morphometry (VBM) studies in schizophrenia-can white matter changes be reliably detected with VBM?Melonakos, Eric D; Shenton, Martha E; Rathi, Yogesh; Terry, Douglas P; Bouix, Sylvain; Kubicki, MarekPsychiatry research2011 Aug 3065-7021684124
Enhanced brain connectivity in long-term meditation practitioners.Luders, Eileen; Clark, Kristi; Narr, Katherine L; Toga, Arthur WNeuroImage2011 Aug 151308-1621664467
CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.Kohlhoff, Kai J; Sosnick, Marc H; Hsu, William T; Pande, Vijay S; Altman, Russ BBioinformatics (Oxford, England)2011 Aug 152322-321712246
The Cardiac Atlas Project--an imaging database for computational modeling and statistical atlases of the heart.Fonseca, Carissa G; Backhaus, Michael; Bluemke, David A; Britten, Randall D; Chung, Jae Do; Cowan, Brett R; Dinov, Ivo D; Finn, J Paul; Hunter, Peter J; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Medrano-Gracia, Pau; Shivkumar, Kalyanam; SuinesiaputraBioinformatics (Oxford, England)2011 Aug 152288-9521737439
Mapping human cortical areas in vivo based on myelin content as revealed by T1- and T2-weighted MRI.Glasser, Matthew F; Van Essen, David CThe Journal of neuroscience : the official journal of the Society for Neuroscience2011 Aug 1011597-61621832190
Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.Beauchamp, Kyle A; Ensign, Daniel L; Das, Rhiju; Pande, Vijay SProceedings of the National Academy of Sciences of the United States of America2011 Aug 212734-921768345
The association of the angiotensinogen gene with insulin sensitivity in humans: a tagging single nucleotide polymorphism and haplotype approach.Underwood, Patricia C; Sun, Bei; Williams, Jonathan S; Pojoga, Luminita H; Raby, Benjamin; Lasky-Su, Jessica; Hunt, Steven; Hopkins, Paul N; Jeunemaitre, Xavier; Adler, Gail K; Williams, Gordon HMetabolism: clinical and experimental2011 Aug1150-721306748
Diffusion tensor imaging of anterior commissural fibers in patients with schizophrenia.Choi, Hongyoon; Kubicki, Marek; Whitford, Thomas J; Alvarado, Jorge L; Terry, Douglas P; Niznikiewicz, Margaret; McCarley, Robert W; Kwon, Jun Soo; Shenton, Martha ESchizophrenia research2011 Aug78-8521561738
Variants of the caveolin-1 gene: a translational investigation linking insulin resistance and hypertension.Pojoga, Luminita H; Underwood, Patricia C; Goodarzi, Mark O; Williams, Jonathan S; Adler, Gail K; Jeunemaitre, Xavier; Hopkins, Paul N; Raby, Benjamin A; Lasky-Su, Jessica; Sun, Bei; Cui, Jinrui; Guo, Xiuqing; Taylor, Kent D; Chen, Yii-Der Ida; Xiang, AnnThe Journal of clinical endocrinology and metabolism2011 AugE1288-9221613355
RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways.Mitra, Somdeb; Laederach, Alain; Golden, Barbara L; Altman, Russ B; Brenowitz, MichaelRNA (New York, N.Y.)2011 Aug1589-60321712400
Neurological imaging: statistics behind the pictures.Dinov, Ivo DImaging in medicine2011 Aug 1423-43222180753
Preliminary evidence of within-subject changes in gray matter density associated with remission of bipolar depression.Brooks 3rd, John O; Foland-Ross, Lara C; Thompson, Paul M; Altshuler, Lori LPsychiatry research2011 Jul 3053-521561743
HD CAG-correlated gene expression changes support a simple dominant gain of function.Jacobsen, Jessie C; Gregory, Gillian C; Woda, Juliana M; Thompson, Morgan N; Coser, Kathryn R; Murthy, Vidya; Kohane, Isaac S; Gusella, James F; Seong, Ihn Sik; MacDonald, Marcy E; Shioda, Toshi; Lee, Jong-MinHuman molecular genetics2011 Jul 152846-6021536587
Intelligence and cortical thickness in children with complex partial seizures.Tosun, Duygu; Caplan, Rochelle; Siddarth, Prabha; Seidenberg, Michael; Gurbani, Suresh; Toga, Arthur W; Hermann, BruceNeuroImage2011 Jul 15337-4521586333
Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.Shen, Yufeng; Song, Ruijie; Pe'er, ItsikBioinformatics (Oxford, England)2011 Jul 151995-721636589
Structure-based prediction reveals capping motifs that inhibit ýý-helix aggregation.Bryan Jr, Allen W; Starner-Kreinbrink, Jennifer L; Hosur, Raghavendra; Clark, Patricia L; Berger, BonnieProceedings of the National Academy of Sciences of the United States of America2011 Jul 511099-10421685332
Dark regions of no-reflow on late gadolinium enhancement magnetic resonance imaging result in scar formation after atrial fibrillation ablation.McGann, Christopher; Kholmovski, Eugene; Blauer, Joshua; Vijayakumar, Sathya; Haslam, Thomas; Cates, Joshua; DiBella, Edward; Burgon, Nathan; Wilson, Brent; Alexander, Alton; Prastawa, Marcel; Daccarett, Marcos; Vergara, Gaston; Akoum, Nazem; Parker, DennJournal of the American College of Cardiology2011 Jul 5177-8521718914
Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation.Fabbri, Giulia; Rasi, Silvia; Rossi, Davide; Trifonov, Vladimir; Khiabanian, Hossein; Ma, Jing; Grunn, Adina; Fangazio, Marco; Capello, Daniela; Monti, Sara; Cresta, Stefania; Gargiulo, Ernesto; Forconi, Francesco; Guarini, Anna; Arcaini, Luca; Paulli, MaThe Journal of experimental medicine2011 Jul 41389-40121670202
Clinical application of SPHARM-PDM to quantify temporomandibular joint osteoarthritis.Paniagua, Beatriz; Cevidanes, Lucia; Walker, David; Zhu, Hongtu; Guo, Ruixin; Styner, MartinComputerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society2011 Jul345-5221185694
Mean diffusivity and fractional anisotropy as indicators of disease and genetic liability to schizophrenia.Clark, Kristi A; Nuechterlein, Keith H; Asarnow, Robert F; Hamilton, Liberty S; Phillips, Owen R; Hageman, Nathan S; Woods, Roger P; Alger, Jeffry R; Toga, Arthur W; Narr, Katherine LJournal of psychiatric research2011 Jul980-821306734
In vitro validation of finite element analysis of blood flow in deformable models.Kung, Ethan O; Les, Andrea S; Figueroa, C Alberto; Medina, Francisco; Arcaute, Karina; Wicker, Ryan B; McConnell, Michael V; Taylor, Charles AAnnals of biomedical engineering2011 Jul1947-6021404126
In vivo evidence of disseminated subpial T2* signal changes in multiple sclerosis at 7 T: a surface-based analysis.Cohen-Adad, J; Benner, T; Greve, D; Kinkel, R P; Radding, A; Fischl, B; Rosen, B R; Mainero, CNeuroImage2011 Jul 155-6221511042
Translational bioinformatics: linking knowledge across biological and clinical realms.Sarkar, Indra Neil; Butte, Atul J; Lussier, Yves A; Tarczy-Hornoch, Peter; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2011 Jul-Aug354-721561873
PredUs: a web server for predicting protein interfaces using structural neighbors.Zhang, Qiangfeng Cliff; Deng, Lei; Fisher, Markus; Guan, Jihong; Honig, Barry; Petrey, DonaldNucleic acids research2011 JulW283-721609948
Transcriptional profiling of diabetic neuropathy in the BKS db/db mouse: a model of type 2 diabetes.Pande, Manjusha; Hur, Junguk; Hong, Yu; Backus, Carey; Hayes, John M; Oh, Sang Su; Kretzler, Matthias; Feldman, Eva LDiabetes2011 Jul1981-921617178
Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA.Butte, Atul J; Shah, Nigam HJournal of the American Medical Informatics Association : JAMIA2011 Jul-Aug352-321672904
2010 translational bioinformatics year in review.Altman, Russ B; Miller, Katharine SJournal of the American Medical Informatics Association : JAMIA2011 Jul-Aug358-6621672905
Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence.Chen, James L; Li, Jianrong; Stadler, Walter M; Lussier, Yves AJournal of the American Medical Informatics Association : JAMIA2011 Jul-Aug392-40221672909
Using statistical and machine learning to help institutions detect suspicious access to electronic health records.Boxwala, Aziz A; Kim, Jihoon; Grillo, Janice M; Ohno-Machado, LucilaJournal of the American Medical Informatics Association : JAMIA2011 Jul-Aug498-50521672912
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark ANucleic acids research2011 JulW541-521672956
MarkUs: a server to navigate sequence-structure-function space.Fischer, Markus; Zhang, Qiangfeng Cliff; Dey, Fabian; Chen, Brian Y; Honig, Barry; Petrey, DonaldNucleic acids research2011 JulW357-6121672961
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.Kim, Jung H; Dhanasekaran, Saravana M; Prensner, John R; Cao, Xuhong; Robinson, Daniel; Kalyana-Sundaram, Shanker; Huang, Christina; Shankar, Sunita; Jing, Xiaojun; Iyer, Matthew; Hu, Ming; Sam, Lee; Grasso, Catherine; Maher, Christopher A; Palanisamy, NaGenome research2011 Jul1028-4121724842
fMRI of syntactic processing in typically developing children: structural correlates in the inferior frontal gyrus.Nunez, S Christopher; Dapretto, Mirella; Katzir, Tami; Starr, Ariel; Bramen, Jennifer; Kan, Eric; Bookheimer, Susan; Sowell, Elizabeth RDevelopmental cognitive neuroscience : a journal for cognitive, affective and social developmental neuroscience2011 Jul 1313-32321743820
Modeling diffusion-weighted MRI as a spatially variant gaussian mixture: application to image denoising.Gonzalez, Juan Eugenio Iglesias; Thompson, Paul M; Zhao, Aishan; Tu, ZhuowenMedical physics2011 Jul4350-6421859036
Informatics and standards for nanomedicine technology.Thomas, Dennis G; Klaessig, Fred; Harper, Stacey L; Fritts, Martin; Hoover, Mark D; Gaheen, Sharon; Stokes, Todd H; Reznik-Zellen, Rebecca; Freund, Elaine T; Klemm, Juli D; Paik, David S; Baker, Nathan AWiley interdisciplinary reviews. Nanomedicine and nanobiotechnology2011 Jun 30NULL21721140
BRAF mutations in hairy-cell leukemia.Tiacci, Enrico; Trifonov, Vladimir; Schiavoni, Gianluca; Holmes, Antony; Kern, Wolfgang; Martelli, Maria Paola; Pucciarini, Alessandra; Bigerna, Barbara; Pacini, Roberta; Wells, Victoria A; Sportoletti, Paolo; Pettirossi, Valentina; Mannucci, Roberta; EllThe New England journal of medicine2011 Jun 162305-1521663470
Surface-based TBM boosts power to detect disease effects on the brain: an N=804 ADNI study.Wang, Yalin; Song, Yang; Rajagopalan, Priya; An, Tuo; Liu, Krystal; Chou, Yi-Yu; Gutman, Boris; Toga, Arthur W; Thompson, Paul M; Alzheimer's Disease Neuroimaging InitiativeNeuroImage2011 Jun 151993-201021440071
DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation.Gusev, Alexander; Kenny, Eimear E; Lowe, Jennifer K; Salit, Jaqueline; Saxena, Richa; Kathiresan, Sekar; Altshuler, David M; Friedman, Jeffrey M; Breslow, Jan L; Pe'er, ItsikAmerican journal of human genetics2011 Jun 10706-1721620352
Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.Gilman, Sarah R; Iossifov, Ivan; Levy, Dan; Ronemus, Michael; Wigler, Michael; Vitkup, DennisNeuron2011 Jun 9898-90721658583
A nonrigid kernel-based framework for 2D-3D pose estimation and 2D image segmentation.Sandhu, Romeil; Dambreville, Samuel; Yezzi, Anthony; Tannenbaum, AllenIEEE transactions on pattern analysis and machine intelligence2011 Jun1098-11520733218
FADTTS: functional analysis of diffusion tensor tract statistics.Zhu, Hongtu; Kong, Linglong; Li, Runze; Styner, Martin; Gerig, Guido; Lin, Weili; Gilmore, John HNeuroImage2011 Jun 11412-2521335092
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, Anand; Forman, John P; Underwood, Patricia C; Hopkins, Paul N; Williams, Gordon H; Pojoga, Luminita H; Williams, Jonathan SEuropean journal of endocrinology / European Federation of Endocrine Societies2011 Jun995-100221402748
Planum temporale grey matter asymmetries in chimpanzees (Pan troglodytes), vervet (Chlorocebus aethiops sabaeus), rhesus (Macaca mulatta) and bonnet (Macaca radiata) monkeys.Lyn, Heidi; Pierre, Peter; Bennett, Allyson J; Fears, Scott; Woods, Roger; Hopkins, William DNeuropsychologia2011 Jun2004-1221447349
The Fok1 vitamin D receptor gene polymorphism is associated with plasma renin activity in Caucasians.Vaidya, Anand; Sun, Bei; Forman, John P; Hopkins, Paul N; Brown, Nancy J; Kolatkar, Nikheel S; Williams, Gordon H; Williams, Jonathan SClinical endocrinology2011 Jun783-9021521263
Regulation of X-chromosome inactivation by the X-inactivation centre.Augui, Sandrine; Nora, Elphege P; Heard, EdithNature reviews. Genetics2011 Jun429-4221587299
Can biomechanical variables predict improvement in crouch gait?Hicks, Jennifer L; Delp, Scott L; Schwartz, Michael HGait & posture2011 Jun197-20121616666
Characterization of KRAS Rearrangements in Metastatic Prostate Cancer.Wang, Xiao-Song; Shankar, Sunita; Dhanasekaran, Saravana M; Ateeq, Bushra; Sasaki, Atsuo T; Jing, Xiaojun; Robinson, Daniel; Cao, Qi; Prensner, John R; Yocum, Anastasia K; Wang, Rui; Fries, Daniel F; Han, Bo; Asangani, Irfan A; Cao, Xuhong; Li, Yong; OmenCancer discovery2011 Jun 135-4322140652
Fibre operating lengths of human lower limb muscles during walking.Arnold, Edith M; Delp, Scott LPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2011 May 271530-921502124
Detecting stable distributed patterns of brain activation using Gini contrast.Langs, Georg; Menze, Bjoern H; Lashkari, Danial; Golland, PolinaNeuroImage2011 May 15497-50720709176
GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns.Yang, Xinan; Li, Jianrong; Lee, Younghee; Lussier, Yves ABioinformatics (Oxford, England)2011 May 151444-621421553
Automated hippocampal shape analysis predicts the onset of dementia in mild cognitive impairment.Costafreda, Sergi G; Dinov, Ivo D; Tu, Zhuowen; Shi, Yonggang; Liu, Cheng-Yi; Kloszewska, Iwona; Mecocci, Patrizia; Soininen, Hilkka; Tsolaki, Magda; Vellas, Bruno; Wahlund, Lars-Olof; Spenger, Christian; Toga, Arthur W; Lovestone, Simon; Simmons, AndrewNeuroImage2011 May 1212-921272654
Spatially regularized compressed sensing for high angular resolution diffusion imaging.Michailovich, Oleg; Rathi, Yogesh; Dolui, SudiptoIEEE transactions on medical imaging2011 May1100-1521536524
Early brain overgrowth in autism associated with an increase in cortical surface area before age 2 years.Hazlett, Heather Cody; Poe, Michele D; Gerig, Guido; Styner, Martin; Chappell, Chad; Smith, Rachel Gimpel; Vachet, Clement; Piven, JosephArchives of general psychiatry2011 May467-7621536976
Shape alterations in the striatum in chorea-acanthocytosis.Walterfang, Mark; Looi, Jeffrey Chee Leong; Styner, Martin; Walker, Ruth H; Danek, Adrian; Niethammer, Marc; Evans, Andrew; Kotschet, Katya; Rodrigues, Guilherme R; Hughes, Andrew; Velakoulis, DennisPsychiatry research2011 Apr 3029-3621377843
DTI registration in atlas based fiber analysis of infantile Krabbe disease.Wang, Yi; Gupta, Aditya; Liu, Zhexing; Zhang, Hui; Escolar, Maria L; Gilmore, John H; Gouttard, Sylvain; Fillard, Pierre; Maltbie, Eric; Gerig, Guido; Styner, MartinNeuroImage2011 Apr 151577-8621256236
Stochastic tractography study of Inferior Frontal Gyrus anatomical connectivity in schizophrenia.Kubicki, Marek; Alvarado, Jorge L; Westin, Carl-Fredrik; Tate, David F; Markant, Douglas; Terry, Douglas P; Whitford, Thomas J; De Siebenthal, Julien; Bouix, Sylvain; McCarley, Robert W; Kikinis, Ron; Shenton, Martha ENeuroImage2011 Apr 151657-6421256966
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.Kinsella, Marcus; Harismendy, Olivier; Nakano, Masakazu; Frazer, Kelly A; Bafna, VineetBioinformatics (Oxford, England)2011 Apr 151068-7521330288
Remote thioredoxin recognition using evolutionary conservation and structural dynamics.Tang, Grace W; Altman, Russ BStructure (London, England : 1993)2011 Apr 13461-7021481770
Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response.Shechtman, Caryn F; Henneberry, Annette L; Seimon, Tracie A; Tinkelenberg, Arthur H; Wilcox, Lisa J; Lee, Eunjee; Fazlollahi, Mina; Munkacsi, Andrew B; Bussemaker, Harmen J; Tabas, Ira; Sturley, Stephen LThe Journal of biological chemistry2011 Apr 811951-921266578
Analysis of randomized comparative clinical trial data for personalized treatment selections.Cai, Tianxi; Tian, Lu; Wong, Peggy H; Wei, L JBiostatistics (Oxford, England)2011 Apr270-8220876663
Effects of childhood absence epilepsy on associations between regional cortical morphometry and aging and cognitive abilities.Tosun, Duygu; Siddarth, Prabha; Toga, Arthur W; Hermann, Bruce; Caplan, RochelleHuman brain mapping2011 Apr580-9121391248
Deformation-based morphometry of prospective neurodevelopmental changes in new onset paediatric epilepsy.Tosun, Duygu; Dabbs, Kevin; Caplan, Rochelle; Siddarth, Prabha; Toga, Arthur; Seidenberg, Michael; Hermann, BruceBrain : a journal of neurology2011 Apr1003-1421398377
In vitro validation of finite-element model of AAA hemodynamics incorporating realistic outlet boundary conditions.Kung, Ethan O; Les, Andrea S; Medina, Francisco; Wicker, Ryan B; McConnell, Michael V; Taylor, Charles AJournal of biomechanical engineering2011 Apr04100321428677
Impact of nonrigid motion correction technique on pixel-wise pharmacokinetic analysis of free-breathing pulmonary dynamic contrast-enhanced MR imaging.Tokuda, Junichi; Mamata, Hatsuho; Gill, Ritu R; Hata, Nobuhiko; Kikinis, Ron; Padera Jr, Robert F; Lenkinski, Robert E; Sugarbaker, David J; Hatabu, HirotoJournal of magnetic resonance imaging : JMRI2011 Apr968-7321448965
Testing and Validating Machine Learning Classifiers by Metamorphic Testing.Xie, Xiaoyuan; Ho, Joshua W K; Murphy, Christian; Kaiser, Gail; Xu, Baowen; Chen, Tsong YuehThe Journal of systems and software2011 Apr 1544-55821532969
Deformable Image Registration of Sliding Organs Using Anisotropic Diffusive Regularization.Pace, Danielle F; Enquobahrie, Andinet; Yang, Hua; Aylward, Stephen R; Niethammer, MarcProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2011 Mar 30407-41321785755
BDNF gene effects on brain circuitry replicated in 455 twins.Chiang, Ming-Chang; Barysheva, Marina; Toga, Arthur W; Medland, Sarah E; Hansell, Narelle K; James, Michael R; McMahon, Katie L; de Zubicaray, Greig I; Martin, Nicholas G; Wright, Margaret J; Thompson, Paul MNeuroImage2011 Mar 15448-5421195196
Particle Filtering with Region-based Matching for Tracking of Partially Occluded and Scaled Targets.Nakhmani, Arie; Tannenbaum, AllenSIAM journal on imaging sciences2011 Mar 9220-24222506088
Puberty influences medial temporal lobe and cortical gray matter maturation differently in boys than girls matched for sexual maturity.Bramen, Jennifer E; Hranilovich, Jennifer A; Dahl, Ronald E; Forbes, Erika E; Chen, Jessica; Toga, Arthur W; Dinov, Ivo D; Worthman, Carol M; Sowell, Elizabeth RCerebral cortex (New York, N.Y. : 1991)2011 Mar636-4620713504
Differences in patellofemoral kinematics between weight-bearing and non-weight-bearing conditions in patients with patellofemoral pain.Draper, Christine E; Besier, Thor F; Fredericson, Michael; Santos, Juan M; Beaupre, Gary S; Delp, Scott L; Gold, Garry EJournal of orthopaedic research : official publication of the Orthopaedic Research Society2011 Mar312-720949442
The association of plasma resistin with dietary sodium manipulation, the renin-angiotensin-aldosterone system, and 25-hydroxyvitamin D3 in human hypertension.Vaidya, Anand; Pojoga, Luminita; Underwood, Patricia C; Forman, John P; Hopkins, Paul N; Williams, Gordon H; Williams, Jonathan SClinical endocrinology2011 Mar294-921050256
The generation of tetrahedral mesh models for neuroanatomical MRI.Lederman, Carl; Joshi, Anand; Dinov, Ivo; Vese, Luminita; Toga, Arthur; Van Horn, John DarrellNeuroImage2011 Mar 1153-6421073968
Resting-state fMRI can reliably map neural networks in children.Thomason, Moriah E; Dennis, Emily L; Joshi, Anand A; Joshi, Shantanu H; Dinov, Ivo D; Chang, Catie; Henry, Melissa L; Johnson, Rebecca F; Thompson, Paul M; Toga, Arthur W; Glover, Gary H; Van Horn, John D; Gotlib, Ian HNeuroImage2011 Mar 1165-7521134471
A new metric for detecting change in slowly evolving brain tumors: validation in meningioma patients.Pohl, Kilian M; Konukoglu, Ender; Novellas, Sebastian; Ayache, Nicholas; Fedorov, Andriy; Talos, Ion-Florin; Golby, Alexandra; Wells, William M; Kikinis, Ron; Black, Peter MNeurosurgery2011 Mar225-3321206318
The emerging role of electronic medical records in pharmacogenomics.Wilke, R A; Xu, H; Denny, J C; Roden, D M; Krauss, R M; McCarty, C A; Davis, R L; Skaar, T; Lamba, J; Savova, GClinical pharmacology and therapeutics2011 Mar379-8621248726
Double dissociation in the anatomy of socioemotional disinhibition and executive functioning in dementia.Krueger, Casey E; Laluz, Victor; Rosen, Howard J; Neuhaus, John M; Miller, Bruce L; Kramer, Joel HNeuropsychology2011 Mar249-5921381829
Compressing genomic sequence fragments using SlimGene.Kozanitis, Christos; Saunders, Chris; Kruglyak, Semyon; Bafna, Vineet; Varghese, GeorgeJournal of computational biology : a journal of computational molecular cell biology2011 Mar401-1321385043
Increased SRF transcriptional activity in human and mouse skeletal muscle is a signature of insulin resistance.Jin, Wanzhu; Goldfine, Allison B; Boes, Tanner; Henry, Robert R; Ciaraldi, Theodore P; Kim, Eun-Young; Emecan, Merve; Fitzpatrick, Connor; Sen, Anish; Shah, Ankit; Mun, Edward; Vokes, Vokes; Schroeder, Joshua; Tatro, Elizabeth; Jimenez-Chillaron, Jose; PaThe Journal of clinical investigation2011 Mar918-2921393865
Differentially Private Empirical Risk Minimization.Chaudhuri, Kamalika; Monteleoni, Claire; Sarwate, Anand DJournal of machine learning research : JMLR2011 Mar1069-110921892342
The contribution of genes to cortical thickness and volume.Joshi, Anand A; Lepore, Natasha; Joshi, Shantanu H; Lee, Agatha D; Barysheva, Marina; Stein, Jason L; McMahon, Katie L; Johnson, Kori; de Zubicaray, Greig I; Martin, Nicholas G; Wright, Margaret J; Toga, Arthur W; Thompson, Paul MNeuroreport2011 Feb 16101-521233781
Thickness of the human cerebral cortex is associated with metrics of cerebrovascular health in a normative sample of community dwelling older adults.Leritz, Elizabeth C; Salat, David H; Williams, Victoria J; Schnyer, David M; Rudolph, James L; Lipsitz, Lewis; Fischl, Bruce; McGlinchey, Regina E; Milberg, William PNeuroImage2011 Feb 142659-7121035552
Abnormal brain activation during working memory in children with prenatal exposure to drugs of abuse: the effects of methamphetamine, alcohol, and polydrug exposure.Roussotte, Florence F; Bramen, Jennifer E; Nunez, S Christopher; Quandt, Lorna C; Smith, Lynne; O'Connor, Mary J; Bookheimer, Susan Y; Sowell, Elizabeth RNeuroImage2011 Feb 143067-7521040792
Sex differences in orbitofrontal gray as a partial explanation for sex differences in antisocial personality.Raine, A; Yang, Y; Narr, K L; Toga, A WMolecular psychiatry2011 Feb227-3620029391
Towards an ontological representation of resistance: the case of MRSA.Goldfain, Albert; Smith, Barry; Cowell, Lindsay GJournal of biomedical informatics2011 Feb35-4120206294
NanoParticle Ontology for cancer nanotechnology research.Thomas, Dennis G; Pappu, Rohit V; Baker, Nathan AJournal of biomedical informatics2011 Feb59-7420211274
Efficient path-based stereo matching with subpixel accuracy.Donate, Arturo; Liu, Xiuwen; Collins, Emmanuel GIEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society2011 Feb183-9520570775
A web-based brain atlas of the vervet monkey, Chlorocebus aethiops.Woods, Roger P; Fears, Scott C; Jorgensen, Matthew J; Fairbanks, Lynn A; Toga, Arthur W; Freimer, Nelson BNeuroImage2011 Feb 11872-8020923706
The link between callosal thickness and intelligence in healthy children and adolescents.Luders, Eileen; Thompson, Paul M; Narr, Katherine L; Zamanyan, Alen; Chou, Yi-Yu; Gutman, Boris; Dinov, Ivo D; Toga, Arthur WNeuroImage2011 Feb 11823-3020932920
The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.Tenenbaum, Jessica D; Whetzel, Patricia L; Anderson, Kent; Borromeo, Charles D; Dinov, Ivo D; Gabriel, Davera; Kirschner, Beth; Mirel, Barbara; Morris, Tim; Noy, Natasha; Nyulas, Csongor; Rubenson, David; Saxman, Paul R; Singh, Harpreet; Whelan, Nancy; WrJournal of biomedical informatics2011 Feb137-4520955817
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Transforming growth factor-beta signaling pathway in patients with Kawasaki disease.Shimizu, Chisato; Jain, Sonia; Davila, Sonia; Hibberd, Martin L; Lin, Kevin O; Molkara, Delaram; Frazer, Jeffrey R; Sun, Shelly; Baker, Annette L; Newburger, Jane W; Rowley, Anne H; Shulman, Stanford T; Davila, Sonia; Burgner, David; Breunis, Willemijn B;Circulation. Cardiovascular genetics2011 Feb16-2521127203
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Potential for electronic health records and online social networking to redefine medical research.Pearson, John F; Brownstein, Catherine A; Brownstein, John SClinical chemistry2011 Feb196-20421159898
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A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations.Yan, Xiaowei; Ma, Li; Yi, Danielle; Yoon, Jae-geun; Diercks, Alan; Foltz, Gregory; Price, Nathan D; Hood, Leroy E; Tian, QiangProceedings of the National Academy of Sciences of the United States of America2011 Jan 251591-621220328
Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation.Stumpe, Martin C; Blinov, Nikolay; Wishart, David; Kovalenko, Andriy; Pande, Vijay SThe journal of physical chemistry. B2011 Jan 20319-2821174421
Statistical method for revealing form-function relations in biological networks.Mugler, Andrew; Grinshpun, Boris; Franks, Riley; Wiggins, Chris HProceedings of the National Academy of Sciences of the United States of America2011 Jan 11446-5121183719
Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records.Kurreeman, Fina; Liao, Katherine; Chibnik, Lori; Hickey, Brendan; Stahl, Eli; Gainer, Vivian; Li, Gang; Bry, Lynn; Mahan, Scott; Ardlie, Kristin; Thomson, Brian; Szolovits, Peter; Churchill, Susanne; Murphy, Shawn N; Cai, Tianxi; Raychaudhuri, Soumya; KohAmerican journal of human genetics2011 Jan 757-6921211616
Image registration of pre-procedural MRI and intra-procedural CT images to aid CT-guided percutaneous cryoablation of renal tumors.Oguro, Sota; Tuncali, Kemal; Elhawary, Haytham; Morrison, Paul R; Hata, Nobuhiko; Silverman, Stuart GInternational journal of computer assisted radiology and surgery2011 Jan111-720499194
Three-dimensional hemodynamics in the human pulmonary arteries under resting and exercise conditions.Tang, Beverly T; Fonte, Tim A; Chan, Frandics P; Tsao, Philip S; Feinstein, Jeffrey A; Taylor, Charles AAnnals of biomedical engineering2011 Jan347-5820640512
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Quantitative in vivo evidence for broad regional gradients in the timing of white matter maturation during adolescence.Colby, John B; Van Horn, John D; Sowell, Elizabeth RNeuroImage2011 Jan 125-3120708693
A role for coding functional variants in HNF4A in type 2 diabetes susceptibility.Jafar-Mohammadi, B; Groves, C J; Gjesing, A P; Herrera, B M; Winckler, W; Stringham, H M; Morris, A P; Lauritzen, T; Doney, A S F; Morris, A D; Weedon, M N; Swift, A J; Kuusisto, J; Laakso, M; Altshuler, D; Hattersley, A T; Collins, F S; Boehnke, M; HanseDiabetologia2011 Jan111-920878384
An evolutionary approach to realism-based adverse event representations.Ceusters, W; Capolupo, M; de Moor, G; Devlies, J; Smith, BMethods of information in medicine201162-7321057717
Apolipoprotein E genotype is associated with temporal and hippocampal atrophy rates in healthy elderly adults: a tensor-based morphometry study.Lu, Po H; Thompson, Paul M; Leow, Alex; Lee, Grace J; Lee, Agatha; Yanovsky, Igor; Parikshak, Neelroop; Khoo, Theresa; Wu, Stephanie; Geschwind, Daniel; Bartzokis, GeorgeJournal of Alzheimer's disease : JAD2011433-4221098974
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, Dale L; Radmer, Randall J; Holbert, Sean; Klein, Teri EPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2011193-20421121047
Structural insights into pre-translocation ribosome motions.Flores, Samuel Coulbourn; Altman, RussPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2011205-1121121048
Benchmarking ontologies: bigger or better?Yao, Lixia; Divoli, Anna; Mayzus, Ilya; Evans, James A; Rzhetsky, AndreyPLoS computational biology2011e100105521249231
Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes.Ross, Kenneth AndrewBMC medicine20111221291537
Comprehensive genetic assessment of a functional TLR9 promoter polymorphism: no replicable association with asthma or asthma-related phenotypes.Lange, Nancy E; Zhou, Xiaobo; Lasky-Su, Jessica; Himes, Blanca E; Lazarus, Ross; Soto-Quiros, Manuel; Avila, Lydiana; Celedon, Juan C; Hawrylowicz, Catherine M; Raby, Benjamin A; Litonjua, Augusto ABMC medical genetics20112621324137
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Appearance frequency modulated gene set enrichment testing.Ma, Jun; Sartor, Maureen A; Jagadish, H VBMC bioinformatics20118121418606
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Adaptive Riemannian metrics for improved geodesic tracking of white matter.Hao, Xiang; Whitaker, Ross T; Fletcher, P ThomasInformation processing in medical imaging : proceedings of the ... conference201113-2421761642
Optimal data-driven sparse parameterization of diffeomorphisms for population analysis.Durrleman, Sandy; Prastawa, Marcel; Gerig, Guido; Joshi, SarangInformation processing in medical imaging : proceedings of the ... conference2011123-3421761651
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White matter bundle registration and population analysis based on Gaussian processes.Wassermann, Demian; Rathi, Yogesh; Bouix, Sylvain; Kubicki, Marek; Kikinis, Ron; Shenton, Martha; Westin, Carl-FredrikInformation processing in medical imaging : proceedings of the ... conference2011320-3221761667
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Applications of the pipeline environment for visual informatics and genomics computations.Dinov, Ivo D; Torri, Federica; Macciardi, Fabio; Petrosyan, Petros; Liu, Zhizhong; Zamanyan, Alen; Eggert, Paul; Pierce, Jonathan; Genco, Alex; Knowles, James A; Clark, Andrew P; Van Horn, John D; Ames, Joseph; Kesselman, Carl; Toga, Arthur WBMC bioinformatics201130421791102
Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network.Hur, Junguk; Xiang, Zuoshuang; Feldman, Eva L; He, YongqunBMC immunology20114921871085
Efficient Probabilistic and Geometric Anatomical Mapping Using Particle Mesh Approximation on GPUs.Ha, Linh; Prastawa, Marcel; Gerig, Guido; Gilmore, John H; Silva, Claudio T; Joshi, SarangInternational journal of biomedical imaging201157218721941523
Cortical and hippocampal atrophy in patients with autosomal dominant familial Alzheimer's disease.Apostolova, Liana G; Hwang, Kristy S; Medina, Luis D; Green, Amity E; Braskie, Meredith N; Dutton, Rebecca A; Lai, Jeffrey; Geschwind, Daniel H; Cummings, Jeffrey L; Thompson, Paul M; Ringman, John MDementia and geriatric cognitive disorders2011118-2521952501
A hidden Markov model for copy number variant prediction from whole genome resequencing data.Shen, Yufeng; Gu, Yiwei; Pe'er, ItsikBMC bioinformatics2011S421989326
Geometric correspondence for ensembles of nonregular shapes.Datar, Manasi; Gur, Yaniv; Paniagua, Beatriz; Styner, Martin; Whitaker, RossMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2011368-7521995050
Estimation of smooth growth trajectories with controlled acceleration from time series shape data.Fishbaugh, James; Durrleman, Stanley; Gerig, GuidoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2011401-821995054
Iterative refinement of point correspondences for 3D statistical shape models.Seshamani, Sharmishtaa; Chintalapani, Gouthami; Taylor, RussellMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2011417-2521995056
Fast shape-based nearest-neighbor search for brain MRIs using hierarchical feature matching.Zhu, Peihong; Awate, Suyash P; Gerber, Samuel; Whitaker, RossMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2011484-9121995064
Geometric metamorphosis.Niethammer, Marc; Hart, Gabriel L; Pace, Danielle F; Vespa, Paul M; Irimia, Andrei; Van Horn, John D; Aylward, Stephen RMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2011639-4621995083
Segmentation of nerve bundles and ganglia in spine MRI using particle filters.Dalca, Adrian; Danagoulian, Giovanna; Kikinis, Ron; Schmidt, Ehud; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2011537-4522003741
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.Siggers, Trevor; Duyzend, Michael H; Reddy, Jessica; Khan, Sidra; Bulyk, Martha LMolecular systems biology201155522146299
Empirical comparison of cross-platform normalization methods for gene expression data.Rudy, Jason; Valafar, FaramarzBMC bioinformatics201146722151536
Identifying hosts of families of viruses: a machine learning approach.Raj, Anil; Dewar, Michael; Palacios, Gustavo; Rabadan, Raul; Wiggins, Christopher HPloS one2011e2763122174744
MicroRNA expression characterizes oligometastasis(es).Lussier, Yves A; Xing, H Rosie; Salama, Joseph K; Khodarev, Nikolai N; Huang, Yong; Zhang, Qingbei; Khan, Sajid A; Yang, Xinan; Hasselle, Michael D; Darga, Thomas E; Malik, Renuka; Fan, Hanli; Perakis, Samantha; Filippo, Matthew; Corbin, Kimberly; Lee, YoPloS one2011e2865022174856
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A cloud-based approach to medical NLP.Chard, Kyle; Russell, Michael; Lussier, Yves A; Mendonca, Eneida A; Silverstein, Jonathan CAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2011207-1622195072
Part-of-speech tagging for clinical text: wall or bridge between institutions?Fan, Jung-wei; Prasad, Rashmi; Yabut, Rommel M; Loomis, Richard M; Zisook, Daniel S; Mattison, John E; Huang, YangAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2011382-9122195091
Improving predictions in imbalanced data using Pairwise Expanded Logistic Regression.Jiang, Xiaoqian; El-Kareh, Robert; Ohno-Machado, LucilaAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2011625-3422195118
Anomaly and signature filtering improve classifier performance for detection of suspicious access to EHRs.Kim, Jihoon; Grillo, Janice M; Boxwala, Aziz A; Jiang, Xiaoqian; Mandelbaum, Rose B; Patel, Bhakti A; Mikels, Debra; Vinterbo, Staal A; Ohno-Machado, LucilaAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2011723-3122195129
The effect of reference panels and software tools on genotype imputation.Nho, Kwangsik; Shen, Li; Kim, Sungeun; Swaminathan, Shanker; Risacher, Shannon L; Saykin, Andrew J; Alzheimerýýýs Disease Neuroimaging Initiative (ADNI)AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium20111013-822195161
Qualitative analysis of workflow modifications used to generate the reference standard for the 2010 i2b2/VA challenge.South, Brett R; Shen, Shuying; Barrus, Robyn; DuVall, Scott L; Uzuner, Ozlem; Weir, CharleneAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium20111243-5122195185
Anatomic brain asymmetry in vervet monkeys.Fears, Scott C; Scheibel, Kevin; Abaryan, Zvart; Lee, Chris; Service, Susan K; Jorgensen, Matthew J; Fairbanks, Lynn A; Cantor, Rita M; Freimer, Nelson B; Woods, Roger PPloS one2011e2824322205941
Smooth isotonic regression: a new method to calibrate predictive models.Jiang, Xiaoqian; Osl, Melanie; Kim, Jihoon; Ohno-Machado, LucilaAMIA Summits on Translational Science proceedings AMIA Summit on Translational Science201116-2022211175
Ballistocardiography--a method worth revisiting.Giovangrandi, Laurent; Inan, Omer T; Wiard, Richard M; Etemadi, Mozziyar; Kovacs, Gregory T AConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20114279-8222255285
Ranking of stopping criteria for log domain diffeomorphic demons application in clinical radiation therapy.Peroni, M; Golland, P; Sharp, G C; Baroni, GConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20114884-722255433
A compressive sensing approach for glioma margin delineation using mass spectrometry.Gholami, Behnood; Agar, Nathalie Y R; Jolesz, Ferenc A; Haddad, Wassim M; Tannenbaum, Allen RConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20115682-522255629
3D Slicer as a tool for interactive brain tumor segmentation.Kikinis, Ron; Pieper, SteveConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20116982-422255945
Classification of astrocytomas and oligodendrogliomas from mass spectrometry data using sparse kernel machines.Huang, Jacob; Gholami, Behnood; Agar, Nathalie Y R; Norton, Isaiah; Haddad, Wassim M; Tannenbaum, Allen RConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20117965-822256188
A Perturbation Method for Inference on Regularized Regression Estimates.Minnier, Jessica; Tian, Lu; Cai, TianxiJournal of the American Statistical Association2011 Jan 11371-138222844171
Anisotropic conductivity of magnetic carbon nanotubes embedded in epoxy matrices.Kim, Il Tae; Tannenbaum, Allen; Tannenbaum, RinaCarbon2011 Jan54-6123019381
Efficient, Graph-based White Matter Connectivity from Orientation Distribution Functions via Multi-directional Graph Propagation.Boucharin, Alexis; Oguz, Ipek; Vachet, Clement; Shi, Yundi; Sanchez, Mar; Styner, MartinProceedings of SPIE201179620S23066452
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Interactive MRI Segmentation with Controlled Active Vision.Karasev, Peter; Kolesov, Ivan; Chudy, Karol; Muller, Grant; Xerogeanes, John; Tannenbaum, AllenProceedings of the ... IEEE Conference on Decision & Control / IEEE Control Systems Society. IEEE Conference on Decision & Control20112293-229824584213
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GLay: community structure analysis of biological networks.Su, Gang; Kuchinsky, Allan; Morris, John H; States, David J; Meng, FanBioinformatics (Oxford, England)2010 Dec 153135-721123224
An integrated approach to uncover drivers of cancer.Akavia, Uri David; Litvin, Oren; Kim, Jessica; Sanchez-Garcia, Felix; Kotliar, Dylan; Causton, Helen C; Pochanard, Panisa; Mozes, Eyal; Garraway, Levi A; Pe'er, DanaCell2010 Dec 101005-1721129771
Robust surface reconstruction via Laplace-Beltrami eigen-projection and boundary deformation.Shi, Yonggang; Lai, Rongjie; Morra, Jonathan H; Dinov, Ivo; Thompson, Paul M; Toga, Arthur WIEEE transactions on medical imaging2010 Dec2009-2220624704
Age-related changes in the corpus callosum in early-onset bipolar disorder assessed using volumetric and cross-sectional measurements.Lopez-Larson, Melissa; Breeze, Janis L; Kennedy, David N; Hodge, Steven M; Tang, Lena; Moore, Constance; Giuliano, Anthony J; Makris, Nikos; Caviness, Verne S; Frazier, Jean ABrain imaging and behavior2010 Dec220-3120686873
Using text to build semantic networks for pharmacogenomics.Coulet, Adrien; Shah, Nigam H; Garten, Yael; Musen, Mark; Altman, Russ BJournal of biomedical informatics2010 Dec1009-1920723615
The genetics of insulin resistance: Where's Waldo?Watanabe, Richard MCurrent diabetes reports2010 Dec476-8420820957
Structural, metabolic, and functional brain abnormalities as a result of prenatal exposure to drugs of abuse: evidence from neuroimaging.Roussotte, Florence; Soderberg, Lindsay; Sowell, ElizabethNeuropsychology review2010 Dec376-9720978945
Tubular surface segmentation for extracting anatomical structures from medical imagery.Mohan, Vandana; Sundaramoorthi, Ganesh; Tannenbaum, AllenIEEE transactions on medical imaging2010 Dec1945-5821118754
Salivary cortisol and prefrontal cortical thickness in middle-aged men: A twin study.Kremen, William S; O'Brien, Robert C; Panizzon, Matthew S; Prom-Wormley, Elizabeth; Eaves, Lindon J; Eisen, Seth A; Eyler, Lisa T; Hauger, Richard L; Fennema-Notestine, Christine; Fischl, Bruce; Grant, Michael D; Hellhammer, Dirk H; Jak, Amy J; Jacobson, NeuroImage2010 Nov 151093-10220156572
Voxelwise genome-wide association study (vGWAS).Stein, Jason L; Hua, Xue; Lee, Suh; Ho, April J; Leow, Alex D; Toga, Arthur W; Saykin, Andrew J; Shen, Li; Foroud, Tatiana; Pankratz, Nathan; Huentelman, Matthew J; Craig, David W; Gerber, Jill D; Allen, April N; Corneveaux, Jason J; Dechairo, Bryan M; PoNeuroImage2010 Nov 151160-7420171287
Callosal tissue loss in multiple system atrophy--a one-year follow-up study.Minnerop, Martina; Luders, Eileen; Specht, Karsten; Ruhlmann, Jurgen; Schimke, Nicole; Thompson, Paul M; Chou, Yi Y; Toga, Arthur W; Abele, Michael; Wullner, Ullrich; Klockgether, ThomasMovement disorders : official journal of the Movement Disorder Society2010 Nov 152613-2020623690
RAPID detection of gene-gene interactions in genome-wide association studies.Brinza, Dumitru; Schultz, Matthew; Tesler, Glenn; Bafna, VineetBioinformatics (Oxford, England)2010 Nov 152856-6220871107
Ontological realism: A methodology for coordinated evolution of scientific ontologies.Smith, Barry; Ceusters, WernerApplied ontology2010 Nov 15139-18821637730
A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease.Mori, Marcelo A; Liu, Manway; Bezy, Olivier; Almind, Katrine; Shapiro, Hagit; Kasif, Simon; Kahn, C RonaldDiabetes2010 Nov2960-7120713682
The contributions of disease and genetic factors towards regional cortical thinning in schizophrenia: the UCLA family study.Yang, Yaling; Nuechterlein, Keith H; Phillips, Owen; Hamilton, Liberty S; Subotnik, Kenneth L; Asarnow, Robert F; Toga, Arthur W; Narr, Katherine LSchizophrenia research2010 Nov116-2520817413
Multimodality non-rigid image registration for planning, targeting and monitoring during CT-guided percutaneous liver tumor cryoablation.Elhawary, Haytham; Oguro, Sota; Tuncali, Kemal; Morrison, Paul R; Tatli, Servet; Shyn, Paul B; Silverman, Stuart G; Hata, NobuhikoAcademic radiology2010 Nov1334-4420817574
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Visual exploration of high dimensional scalar functions.Gerber, Samuel; Bremer, Peer-Timo; Pascucci, Valerio; Whitaker, RossIEEE transactions on visualization and computer graphics2010 Nov-Dec1271-8020975167
Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers.Yang, Xinan; Lee, Younghee; Fan, Hong; Sun, Xiao; Lussier, Yves AChinese science bulletin = Kexue tongbao2010 Nov3576-358921340045
DigiWarp: a method for deformable mouse atlas warping to surface topographic data.Joshi, Anand A; Chaudhari, Abhijit J; Li, Changqing; Dutta, Joyita; Cherry, Simon R; Shattuck, David W; Toga, Arthur W; Leahy, Richard MPhysics in medicine and biology2010 Oct 216197-21420885019
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Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature.Destrieux, Christophe; Fischl, Bruce; Dale, Anders; Halgren, EricNeuroImage2010 Oct 151-1520547229
Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age.Ghosh, Satrajit S; Kakunoori, Sita; Augustinack, Jean; Nieto-Castanon, Alfonso; Kovelman, Ioulia; Gaab, Nadine; Christodoulou, Joanna A; Triantafyllou, Christina; Gabrieli, John D E; Fischl, BruceNeuroImage2010 Oct 1585-9320621657
Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.Filion, Guillaume J; van Bemmel, Joke G; Braunschweig, Ulrich; Talhout, Wendy; Kind, Jop; Ward, Lucas D; Brugman, Wim; de Castro, Ines J; Kerkhoven, Ron M; Bussemaker, Harmen J; van Steensel, BasCell2010 Oct 15212-2420888037
Plaque and tangle imaging and cognition in normal aging and Alzheimer's disease.Braskie, Meredith N; Klunder, Andrea D; Hayashi, Kiralee M; Protas, Hillary; Kepe, Vladimir; Miller, Karen J; Huang, S-C; Barrio, Jorge R; Ercoli, Linda M; Siddarth, Prabha; Satyamurthy, Nagichettiar; Liu, Jie; Toga, Arthur W; Bookheimer, Susan Y; Small, Neurobiology of aging2010 Oct1669-7819004525
Subregional hippocampal deformations in major depressive disorder.Cole, James; Toga, Arthur W; Hojatkashani, Cornelius; Thompson, Paul; Costafreda, Sergi G; Cleare, Anthony J; Williams, Steven C R; Bullmore, Edward T; Scott, Jan L; Mitterschiffthaler, Martina T; Walsh, Nicholas D; Donaldson, Catherine; Mirza, Mubeena; MJournal of affective disorders2010 Oct272-720392498
DSGeo: software tools for cross-platform analysis of gene expression data in GEO.Lacson, Ronilda; Pitzer, Erik; Kim, Jihoon; Galante, Pedro; Hinske, Christian; Ohno-Machado, LucilaJournal of biomedical informatics2010 Oct709-1520435161
A coupled global registration and segmentation framework with application to magnetic resonance prostate imagery.Gao, Yi; Sandhu, Romeil; Fichtinger, Gabor; Tannenbaum, Allen RobertIEEE transactions on medical imaging2010 Oct1781-9420529727
A generative model for image segmentation based on label fusion.Sabuncu, Mert R; Yeo, B T Thomas; Van Leemput, Koen; Fischl, Bruce; Golland, PolinaIEEE transactions on medical imaging2010 Oct1714-2920562040
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Segmentation of image ensembles via latent atlases.Riklin-Raviv, Tammy; Van Leemput, Koen; Menze, Bjoern H; Wells 3rd, William M; Golland, PolinaMedical image analysis2010 Oct654-6520580305
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Association between fine particulate matter and diabetes prevalence in the U.S.Pearson, John F; Bachireddy, Chethan; Shyamprasad, Sangameswaran; Goldfine, Allison B; Brownstein, John SDiabetes care2010 Oct2196-20120628090
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Auto-context and its application to high-level vision tasks and 3D brain image segmentation.Tu, Zhuowen; Bai, XiangIEEE transactions on pattern analysis and machine intelligence2010 Oct1744-5720724753
A molecular profile of focal segmental glomerulosclerosis from formalin-fixed, paraffin-embedded tissue.Hodgin, Jeffrey B; Borczuk, Alain C; Nasr, Samih H; Markowitz, Glen S; Nair, Viji; Martini, Sebastian; Eichinger, Felix; Vining, Courtenay; Berthier, Celine C; Kretzler, Matthias; D'Agati, Vivette DThe American journal of pathology2010 Oct1674-8620847290
Recent progress in automatically extracting information from the pharmacogenomic literature.Garten, Yael; Coulet, Adrien; Altman, Russ BPharmacogenomics2010 Oct1467-8921047206
Minimal formulation of joint motion for biomechanisms.Seth, Ajay; Sherman, Michael; Eastman, Peter; Delp, ScottNonlinear Dynamics2010 Oct 1291-30321170173
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Hierarchical evolution of the bacterial sporulation network.de Hoon, Michiel J L; Eichenberger, Patrick; Vitkup, DennisCurrent biology : CB2010 Sep 14R735-4520833318
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription.Huang, Xuhui; Wang, Dong; Weiss, Dahlia R; Bushnell, David A; Kornberg, Roger D; Levitt, MichaelProceedings of the National Academy of Sciences of the United States of America2010 Sep 715745-5020798057
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.Plata, German; Hsiao, Tzu-Lin; Olszewski, Kellen L; Llinas, Manuel; Vitkup, DennisMolecular systems biology2010 Sep 740820823846
Lifespan trajectory of myelin integrity and maximum motor speed.Bartzokis, George; Lu, Po H; Tingus, Kathleen; Mendez, Mario F; Richard, Aurore; Peters, Douglas G; Oluwadara, Bolanle; Barrall, Katherine A; Finn, J Paul; Villablanca, Pablo; Thompson, Paul M; Mintz, JimNeurobiology of aging2010 Sep1554-6218926601
The relationship between peroxisome proliferator-activated receptor-gamma and renin: a human genetics study.Underwood, Patricia C; Sun, Bei; Williams, Jonathan S; Pojoga, Luminita H; Chamarthi, Bindu; Lasky-Su, Jessica; Raby, Benjamin A; Hopkins, Paul N; Jeunemaitre, Xavier; Brown, Nancy J; Adler, Gail K; Williams, Gordon HThe Journal of clinical endocrinology and metabolism2010 SepE75-920631015
Turning limited experimental information into 3D models of RNA.Flores, Samuel Coulbourn; Altman, Russ BRNA (New York, N.Y.)2010 Sep1769-7820651028
Filtered multitensor tractography.Malcolm, James G; Shenton, Martha E; Rathi, YogeshIEEE transactions on medical imaging2010 Sep1664-7520805043
Extracting medication information from clinical text.Uzuner, Ozlem; Solti, Imre; Cadag, EithonJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct514-820819854
Community annotation experiment for ground truth generation for the i2b2 medication challenge.Uzuner, Ozlem; Solti, Imre; Xia, Fei; Cadag, EithonJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct519-2320819855
High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge.Patrick, Jon; Li, MinJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct524-720819856
Integrating existing natural language processing tools for medication extraction from discharge summaries.Doan, Son; Bastarache, Lisa; Klimkowski, Sergio; Denny, Joshua C; Xu, HuaJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct528-3120819857
Medication information extraction with linguistic pattern matching and semantic rules.Spasic, Irena; Sarafraz, Farzaneh; Keane, John A; Nenadic, GoranJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct532-520819858
Extracting Rx information from clinical narrative.Mork, James G; Bodenreider, Olivier; Demner-Fushman, Dina; Dogan, Rezarta Islamaj; Lang, Francois-Michel; Lu, Zhiyong; Neveol, Aurelie; Peters, Lee; Shooshan, Sonya E; Aronson, Alan RJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct536-920819859
Improving textual medication extraction using combined conditional random fields and rule-based systems.Tikk, Domonkos; Solt, IllesJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct540-420819860
Automatic extraction of medication information from medical discharge summaries.Yang, HuiJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct545-820819861
Extracting medical information from narrative patient records: the case of medication-related information.Deleger, Louise; Grouin, Cyril; Zweigenbaum, PierreJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct555-820819863
Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents.Meystre, Stephane M; Thibault, Julien; Shen, Shuying; Hurdle, John F; South, Brett RJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct559-6220819864
Lancet: a high precision medication event extraction system for clinical text.Li, Zuofeng; Liu, Feifan; Antieau, Lamont; Cao, Yonggang; Yu, HongJournal of the American Medical Informatics Association : JAMIA2010 Sep-Oct563-720819865
Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis.LaFramboise, Thomas; Dewal, Ninad; Wilkins, Katherine; Pe'er, Itsik; Freedman, Matthew LPLoS genetics2010 Sep20824129
Experimental approaches to the human renal transcriptome.Hodgin, Jeffrey B; Cohen, Clemens DSeminars in nephrology2010 Sep455-6721044757
A Study of Students' Learning Styles, Discipline Attitudes and Knowledge Acquisition in Technology-Enhanced Probability and Statistics Education.Christou, Nicolas; Dinov, Ivo DJournal of online learning and teaching / MERLOT2010 Sep21603097
The development of the corpus callosum in the healthy human brain.Luders, Eileen; Thompson, Paul M; Toga, Arthur WThe Journal of neuroscience : the official journal of the Society for Neuroscience2010 Aug 1810985-9020720105
Muscle contributions to support and progression during single-limb stance in crouch gait.Steele, Katherine M; Seth, Ajay; Hicks, Jennifer L; Schwartz, Michael S; Delp, Scott LJournal of biomechanics2010 Aug 102099-10520493489
Genetic and environmental contributions to neonatal brain structure: A twin study.Gilmore, John H; Schmitt, James Eric; Knickmeyer, Rebecca C; Smith, Jeffrey K; Lin, Weili; Styner, Martin; Gerig, Guido; Neale, Michael CHuman brain mapping2010 Aug1174-8220063301
Multimodal functional imaging using fMRI-informed regional EEG/MEG source estimation.Ou, Wanmei; Nummenmaa, Aapo; Ahveninen, Jyrki; Belliveau, John W; Hamalainen, Matti S; Golland, PolinaNeuroImage2010 Aug 197-10820211266
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.Lu, Xiang-Jun; Olson, Wilma K; Bussemaker, Harmen JNucleic acids research2010 Aug4868-7620223772
Electronic medical records for discovery research in rheumatoid arthritis.Liao, Katherine P; Cai, Tianxi; Gainer, Vivian; Goryachev, Sergey; Zeng-treitler, Qing; Raychaudhuri, Soumya; Szolovits, Peter; Churchill, Susanne; Murphy, Shawn; Kohane, Isaac; Karlson, Elizabeth W; Plenge, Robert MArthritis care & research2010 Aug1120-720235204
When more is less: associations between corpus callosum size and handedness lateralization.Luders, Eileen; Cherbuin, Nicolas; Thompson, Paul M; Gutman, Boris; Anstey, Kaarin J; Sachdev, Perminder; Toga, Arthur WNeuroImage2010 Aug 143-920394828
3D PIB and CSF biomarker associations with hippocampal atrophy in ADNI subjects.Apostolova, Liana G; Hwang, Kristy S; Andrawis, John P; Green, Amity E; Babakchanian, Sona; Morra, Jonathan H; Cummings, Jeffrey L; Toga, Arthur W; Trojanowski, John Q; Shaw, Leslie M; Jack Jr, Clifford R; Petersen, Ronald C; Aisen, Paul S; Jagust, WilliaNeurobiology of aging2010 Aug1284-30320538372
Point set registration via particle filtering and stochastic dynamics.Sandhu, Romeil; Dambreville, Samuel; Tannenbaum, AllenIEEE transactions on pattern analysis and machine intelligence2010 Aug1459-7320558877
Obesity is linked with lower brain volume in 700 AD and MCI patients.Ho, April J; Raji, Cyrus A; Becker, James T; Lopez, Oscar L; Kuller, Lewis H; Hua, Xue; Lee, Suh; Hibar, Derrek; Dinov, Ivo D; Stein, Jason L; Jack Jr, Clifford R; Weiner, Michael W; Toga, Arthur W; Thompson, Paul M; Cardiovascular Health Study; ADNINeurobiology of aging2010 Aug1326-3920570405
Imaging genomics.Thompson, Paul M; Martin, Nicholas G; Wright, Margaret JCurrent opinion in neurology2010 Aug368-7320581684
Sex and age differences in atrophic rates: an ADNI study with n=1368 MRI scans.Hua, Xue; Hibar, Derrek P; Lee, Suh; Toga, Arthur W; Jack Jr, Clifford R; Weiner, Michael W; Thompson, Paul M; Alzheimer's Disease Neuroimaging InitiativeNeurobiology of aging2010 Aug1463-8020620666
A Computational Model of Multidimensional Shape.Liu, Xiuwen; Shi, Yonggang; Dinov, Ivo; Mio, WashingtonInternational journal of computer vision2010 Aug 169-8321057668
A UIMA wrapper for the NCBO annotator.Roeder, Christophe; Jonquet, Clement; Shah, Nigam H; Baumgartner Jr, William A; Verspoor, Karin; Hunter, LawrenceBioinformatics (Oxford, England)2010 Jul 151800-120505005
geWorkbench: an open source platform for integrative genomics.Floratos, Aris; Smith, Kenneth; Ji, Zhou; Watkinson, John; Califano, AndreaBioinformatics (Oxford, England)2010 Jul 151779-8020511363
Splice form dependence of beta-neurexin/neuroligin binding interactions.Koehnke, Jesko; Katsamba, Phinikoula S; Ahlsen, Goran; Bahna, Fabiana; Vendome, Jeremie; Honig, Barry; Shapiro, Lawrence; Jin, XiangshuNeuron2010 Jul 1561-7420624592
Subregional hippocampal atrophy predicts Alzheimer's dementia in the cognitively normal.Apostolova, Liana G; Mosconi, Lisa; Thompson, Paul M; Green, Amity E; Hwang, Kristy S; Ramirez, Anthony; Mistur, Rachel; Tsui, Wai H; de Leon, Mony JNeurobiology of aging2010 Jul1077-8818814937
Microstructural connectivity of the arcuate fasciculus in adolescents with high-functioning autism.Fletcher, P Thomas; Whitaker, Ross T; Tao, Ran; DuBray, Molly B; Froehlich, Alyson; Ravichandran, Caitlin; Alexander, Andrew L; Bigler, Erin D; Lange, Nicholas; Lainhart, Janet ENeuroImage2010 Jul 11117-2520132894
Mesh-based spherical deconvolution: a flexible approach to reconstruction of non-negative fiber orientation distributions.Patel, Vishal; Shi, Yonggang; Thompson, Paul M; Toga, Arthur WNeuroImage2010 Jul 11071-8120206705
Subjective rating of working memory is associated with frontal lobe volume in schizophrenia.Garlinghouse, Matthew A; Roth, Robert M; Isquith, Peter K; Flashman, Laura A; Saykin, Andrew JSchizophrenia research2010 Jul71-520303715
Genetic pathway-based hierarchical clustering analysis of older adults with cognitive complaints and amnestic mild cognitive impairment using clinical and neuroimaging phenotypes.Sloan, Chantel D; Shen, Li; West, John D; Wishart, Heather A; Flashman, Laura A; Rabin, Laura A; Santulli, Robert B; Guerin, Stephen J; Rhodes, C Harker; Tsongalis, Gregory J; McAllister, Thomas W; Ahles, Tim A; Lee, Stephen L; Moore, Jason H; Saykin, AndAmerican journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics2010 Jul1060-920468060
Corpus callosum abnormalities and their association with psychotic symptoms in patients with schizophrenia.Whitford, Thomas J; Kubicki, Marek; Schneiderman, Jason S; O'Donnell, Lauren J; King, Rebecca; Alvarado, Jorge L; Khan, Usman; Markant, Douglas; Nestor, Paul G; Niznikiewicz, Margaret; McCarley, Robert W; Westin, Carl-Fredrik; Shenton, Martha EBiological psychiatry2010 Jul 170-720494336
PUDGE: a flexible, interactive server for protein structure prediction.Norel, Raquel; Petrey, Donald; Honig, BarryNucleic acids research2010 JulW550-420525783
Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma.Palanisamy, Nallasivam; Ateeq, Bushra; Kalyana-Sundaram, Shanker; Pflueger, Dorothee; Ramnarayanan, Kalpana; Shankar, Sunita; Han, Bo; Cao, Qi; Cao, Xuhong; Suleman, Khalid; Kumar-Sinha, Chandan; Dhanasekaran, Saravana M; Chen, Ying-bei; Esgueva, Raquel; Nature medicine2010 Jul793-820526349
Learning task-optimal registration cost functions for localizing cytoarchitecture and function in the cerebral cortex.Yeo, B T Thomas; Sabuncu, Mert R; Vercauteren, Tom; Holt, Daphne J; Amunts, Katrin; Zilles, Karl; Golland, Polina; Fischl, BruceIEEE transactions on medical imaging2010 Jul1424-4120529736
Tensor kernels for simultaneous fiber model estimation and tractography.Rathi, Yogesh; Malcolm, James G; Michailovich, Oleg; Westin, Carl-Fredrik; Shenton, Martha E; Bouix, SylvainMagnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine2010 Jul138-4820572129
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.Voight, Benjamin F; Scott, Laura J; Steinthorsdottir, Valgerdur; Morris, Andrew P; Dina, Christian; Welch, Ryan P; Zeggini, Eleftheria; Huth, Cornelia; Aulchenko, Yurii S; Thorleifsson, Gudmar; McCulloch, Laura J; Ferreira, Teresa; Grallert, Harald; Amin,Nature genetics2010 Jul579-8920581827
An IR-aided machine learning framework for the BioCreative II.5 Challenge.Cao, Yonggang; Li, Zuofeng; Liu, Feifan; Agarwal, Shashank; Zhang, Qing; Yu, HongIEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM2010 Jul-Sep454-6120671317
RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS.Wahlby, Carolina; Riklin-Raviv, Tammy; Ljosa, Vebjorn; Conery, Annie L; Golland, Polina; Ausubel, Frederick M; Carpenter, Anne EProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2010 Jun 21552-55521383863
Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules.Fenn, Timothy D; Schnieders, Michael J; Brunger, Axel T; Pande, Vijay SBiophysical journal2010 Jun 162984-9220550911
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.Saha, Mitul; Levitt, Michael; Chiu, WahBioinformatics (Oxford, England)2010 Jun 15i301-920529921
Protein interface conservation across structure space.Zhang, Qiangfeng Cliff; Petrey, Donald; Norel, Raquel; Honig, Barry HProceedings of the National Academy of Sciences of the United States of America2010 Jun 1510896-90120534496
Nonparametric Hierarchical Bayesian Model for Functional Brain Parcellation.Lashkari, Danial; Sridharan, Ramesh; Vul, Edward; Hsieh, Po-Jang; Kanwisher, Nancy; Golland, PolinaConference on Computer Vision and Pattern Recognition Workshops IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops2010 Jun 1315-2221841977
Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry.Atzmon, Gil; Hao, Li; Pe'er, Itsik; Velez, Christopher; Pearlman, Alexander; Palamara, Pier Francesco; Morrow, Bernice; Friedman, Eitan; Oddoux, Carole; Burns, Edward; Ostrer, HarryAmerican journal of human genetics2010 Jun 11850-920560205
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.Lefebvre, Celine; Rajbhandari, Presha; Alvarez, Mariano J; Bandaru, Pradeep; Lim, Wei Keat; Sato, Mai; Wang, Kai; Sumazin, Pavel; Kustagi, Manjunath; Bisikirska, Brygida C; Basso, Katia; Beltrao, Pedro; Krogan, Nevan; Gautier, Jean; Dalla-Favera, RiccardoMolecular systems biology2010 Jun 837720531406
ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository.Hill, James A; Smith, Bryan E; Papoulias, Panagiotis G; Andrews, Philip CJournal of proteome research2010 Jun 42809-1120356086
Atlas generation for subcortical and ventricular structures with its applications in shape analysis.Qiu, Anqi; Brown, Timothy; Fischl, Bruce; Ma, Jun; Miller, Michael IIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2010 Jun1539-4720129863
The role of mitochondria in the pathogenesis of type 2 diabetes.Patti, Mary-Elizabeth; Corvera, SilviaEndocrine reviews2010 Jun364-9520156986
Relevance vector machine learning for neonate pain intensity assessment using digital imaging.Gholami, Behnood; Haddad, Wassim M; Tannenbaum, Allen RIEEE transactions on bio-medical engineering2010 Jun1457-6620172803
Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease.Stein, Jason L; Hua, Xue; Morra, Jonathan H; Lee, Suh; Hibar, Derrek P; Ho, April J; Leow, Alex D; Toga, Arthur W; Sul, Jae Hoon; Kang, Hyun Min; Eskin, Eleazar; Saykin, Andrew J; Shen, Li; Foroud, Tatiana; Pankratz, Nathan; Huentelman, Matthew J; Craig, NeuroImage2010 Jun542-5420197096
LONI MiND: metadata in NIfTI for DWI.Patel, Vishal; Dinov, Ivo D; Van Horn, John D; Thompson, Paul M; Toga, Arthur WNeuroImage2010 Jun665-7620206274
Electrostatic interactions between arginines and the minor groove in the nucleosome.West, Sean M; Rohs, Remo; Mann, Richard S; Honig, BarryJournal of biomolecular structure & dynamics2010 Jun861-620232938
A Bayesian mixture approach to modeling spatial activation patterns in multisite fMRI data.Kim, Seyoung; Smyth, Padhraic; Stern, HalIEEE transactions on medical imaging2010 Jun1260-7420304727
Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures.Chen, James; Sam, Lee; Huang, Yong; Lee, Younghee; Li, Jianrong; Liu, Yang; Xing, H Rosie; Lussier, Yves AJournal of biomedical informatics2010 Jun385-9620350617
Network models for molecular kinetics and their initial applications to human health.Bowman, Gregory R; Huang, Xuhui; Pande, Vijay SCell research2010 Jun622-3020421891
An information-theoretic derivation of min-cut-based clustering.Raj, Anil; Wiggins, Chris HIEEE transactions on pattern analysis and machine intelligence2010 Jun988-9520431126
Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data.Yang, Xinan; Huang, Yong; Crowson, Matthew; Li, Jianrong; Maitland, Michael L; Lussier, Yves AJournal of biomedical informatics2010 Jun376-8420434586
Current methodologies for translational bioinformatics.Lussier, Yves A; Butte, Atul J; Hunter, LawrenceJournal of biomedical informatics2010 Jun355-720470899
Diffeomorphic Sulcal Shape Analysis for Cortical Surface Registration.Joshi, Shantanu H; Cabeen, Ryan P; Joshi, Anand A; Woods, Roger P; Narr, Katherine L; Toga, Arthur WProceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition2010 Jun 1475-48221076690
Contributions of muscles and passive dynamics to swing initiation over a range of walking speeds.Fox, Melanie D; Delp, Scott LJournal of biomechanics2010 May 281450-520236644
Variation of hamstrings lengths and velocities with walking speed.Agarwal-Harding, Kiran J; Schwartz, Michael H; Delp, Scott LJournal of biomechanics2010 May 281522-620381047
Automated 3D mapping of baseline and 12-month associations between three verbal memory measures and hippocampal atrophy in 490 ADNI subjects.Apostolova, Liana G; Morra, Jonathan H; Green, Amity E; Hwang, Kristy S; Avedissian, Christina; Woo, Ellen; Cummings, Jeffrey L; Toga, Arthur W; Jack Jr, Clifford R; Weiner, Michael W; Thompson, Paul M; Alzheimer's Disease Neuroimaging InitiativeNeuroImage2010 May 15488-9920083211
Evaluation of volume-based and surface-based brain image registration methods.Klein, Arno; Ghosh, Satrajit S; Avants, Brian; Yeo, B T T; Fischl, Bruce; Ardekani, Babak; Gee, James C; Mann, J J; Parsey, Ramin VNeuroImage2010 May 15214-2020123029
Mapping Alzheimer's disease progression in 1309 MRI scans: power estimates for different inter-scan intervals.Hua, Xue; Lee, Suh; Hibar, Derrek P; Yanovsky, Igor; Leow, Alex D; Toga, Arthur W; Jack Jr, Clifford R; Bernstein, Matt A; Reiman, Eric M; Harvey, Danielle J; Kornak, John; Schuff, Norbert; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M; AlzheimerNeuroImage2010 May 1563-7520139010
The construction of a Chinese MRI brain atlas: a morphometric comparison study between Chinese and Caucasian cohorts.Tang, Yuchun; Hojatkashani, Cornelius; Dinov, Ivo D; Sun, Bo; Fan, Lingzhong; Lin, Xiangtao; Qi, Hengtao; Hua, Xue; Liu, Shuwei; Toga, Arthur WNeuroImage2010 May 1533-4120152910
Improved tractography alignment using combined volumetric and surface registration.Zollei, Lilla; Stevens, Allison; Huber, Kristen; Kakunoori, Sita; Fischl, BruceNeuroImage2010 May 15206-1320153833
Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis.Chastanet, Arnaud; Vitkup, Dennis; Yuan, Guo-Cheng; Norman, Thomas M; Liu, Jun S; Losick, Richard MProceedings of the National Academy of Sciences of the United States of America2010 May 48486-9120404177
Open core control software for surgical robots.Arata, Jumpei; Kozuka, Hiroaki; Kim, Hyung Wook; Takesue, Naoyuki; Vladimirov, B; Sakaguchi, Masamichi; Tokuda, Junichi; Hata, Nobuhiko; Chinzei, Kiyoyuki; Fujimoto, HideoInternational journal of computer assisted radiology and surgery2010 May211-2020033506
Brain MRI tissue classification based on local Markov random fields.Tohka, Jussi; Dinov, Ivo D; Shattuck, David W; Toga, Arthur WMagnetic resonance imaging2010 May557-7320110151
3D comparison of low, intermediate, and advanced hippocampal atrophy in MCI.Apostolova, Liana G; Thompson, Paul M; Green, Amity E; Hwang, Kristy S; Zoumalan, Charleen; Jack Jr, Clifford R; Harvey, Danielle J; Petersen, Ronald C; Thal, Leon J; Aisen, Paul S; Toga, Arthur W; Cummings, Jeffrey L; Decarli, Charles SHuman brain mapping2010 May786-9720143386
Texture mapping via optimal mass transport.Dominitz, Ayelet; Tannenbaum, AllenIEEE transactions on visualization and computer graphics2010 May-Jun419-3320224137
Learning context-sensitive shape similarity by graph transduction.Bai, Xiang; Yang, Xingwei; Latecki, Longin Jan; Liu, Wenyu; Tu, ZhuowenIEEE transactions on pattern analysis and machine intelligence2010 May861-7420299710
Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers.Menon, Rajasree; Omenn, Gilbert SCancer research2010 May 13440-920388783
The informatics core of the Alzheimer's Disease Neuroimaging Initiative.Toga, Arthur W; Crawford, Karen L; Alzheimer's Disease Neuroimaging InitiativeAlzheimer's & dementia : the journal of the Alzheimer's Association2010 May247-5620451873
Ssecrett and NeuroTrace: interactive visualization and analysis tools for large-scale neuroscience data sets.Jeong, Wan-Ki; Beyer, Johanna; Hadwiger, Markus; Blue, Rusty; Law, Charles; Vazquez-Reina, Amelio; Reid, R Clay; Lichtman, Jeff; Pfister, HanspeterIEEE computer graphics and applications2010 May-Jun58-7020650718
HARDI DATA DENOISING USING VECTORIAL TOTAL VARIATION AND LOGARITHMIC BARRIER.Kim, Yunho; Thompson, Paul M; Vese, Luminita AInverse problems and imaging (Springfield, Mo.)2010 May 1273-31020802839
Phosphoproteomics.Ozlu, Nurhan; Akten, Bikem; Timm, Wiebke; Haseley, Nathan; Steen, Hanno; Steen, Judith A JWiley interdisciplinary reviews. Systems biology and medicine2010 May-Jun255-7620836028
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.Eastman, Peter; Pande, Vijay SJournal of computational chemistry2010 Apr 301268-7219847780
Reduced hippocampal and parahippocampal volumes in murderers with schizophrenia.Yang, Yaling; Raine, Adrian; Han, Chen-Bo; Schug, Robert A; Toga, Arthur W; Narr, Katherine LPsychiatry research2010 Apr 309-1320227253
Trajectory control of PbSe-gamma-Fe2O3 nanoplatforms under viscous flow and an external magnetic field.Etgar, Lioz; Nakhmani, Arie; Tannenbaum, Allen; Lifshitz, Efrat; Tannenbaum, RinaNanotechnology2010 Apr 3017570220368678
Hippocampal, caudate, and ventricular changes in Parkinson's disease with and without dementia.Apostolova, Liana G; Beyer, Mona; Green, Amity E; Hwang, Kristy S; Morra, Jonathan H; Chou, Yi-Yu; Avedissian, Christina; Aarsland, Dag; Janvin, Carmen C; Larsen, Jan P; Cummings, Jeffrey L; Thompson, Paul MMovement disorders : official journal of the Movement Disorder Society2010 Apr 30687-9520437538
SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs.Haque, Imran S; Pande, Vijay S; Walters, W PatrickJournal of chemical information and modeling2010 Apr 26560-420218693
Discovering structure in the space of fMRI selectivity profiles.Lashkari, Danial; Vul, Ed; Kanwisher, Nancy; Golland, PolinaNeuroImage2010 Apr 151085-9820053382
TETRAHEDRAL MESH GENERATION FOR MEDICAL IMAGES WITH MULTIPLE REGIONS USING ACTIVE SURFACES.Lederman, Carl; Joshi, Anand; Dinov, Ivo; Van Horn, John Darrell; Vese, Luminita; Toga, ArthurProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2010 Apr 14436-43921278816
Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.Voelz, Vincent A; Singh, Vijay R; Wedemeyer, William J; Lapidus, Lisa J; Pande, Vijay SJournal of the American Chemical Society2010 Apr 74702-920218718
Surface feature-guided mapping of cerebral metabolic changes in cognitively normal and mildly impaired elderly.Apostolova, Liana G; Thompson, Paul M; Rogers, Steve A; Dinov, Ivo D; Zoumalan, Charleen; Steiner, Calen A; Siu, Erin; Green, Amity E; Small, Gary W; Toga, Arthur W; Cummings, Jeffrey L; Phelps, Michael E; Silverman, Daniel HMolecular imaging and biology : MIB : the official publication of the Academy of Molecular Imaging2010 Apr218-2419636640
Deform PF-MT: particle filter with mode tracker for tracking nonaffine contour deformations.Vaswani, Namrata; Rathi, Yogesh; Yezzi, Anthony; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2010 Apr841-5719933014
Impact of breast milk on intelligence quotient, brain size, and white matter development.Isaacs, Elizabeth B; Fischl, Bruce R; Quinn, Brian T; Chong, Wui K; Gadian, David G; Lucas, AlanPediatric research2010 Apr357-6220035247
Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks.Gao, Jing; Tarcea, V Glenn; Karnovsky, Alla; Mirel, Barbara R; Weymouth, Terry E; Beecher, Christopher W; Cavalcoli, James D; Athey, Brian D; Omenn, Gilbert S; Burant, Charles F; Jagadish, H VBioinformatics (Oxford, England)2010 Apr 1971-320139469
Quantification of hemodynamics in abdominal aortic aneurysms during rest and exercise using magnetic resonance imaging and computational fluid dynamics.Les, Andrea S; Shadden, Shawn C; Figueroa, C Alberto; Park, Jinha M; Tedesco, Maureen M; Herfkens, Robert J; Dalman, Ronald L; Taylor, Charles AAnnals of biomedical engineering2010 Apr1288-31320143263
Imaging of meningioma progression by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.Agar, Nathalie Y R; Malcolm, James G; Mohan, Vandana; Yang, Hong W; Johnson, Mark D; Tannenbaum, Allen; Agar, Jeffrey N; Black, Peter MAnalytical chemistry2010 Apr 12621-520196536
FRATS: Functional Regression Analysis of DTI Tract Statistics.Zhu, Hongtu; Styner, Martin; Tang, Niansheng; Liu, Zhexing; Lin, Weili; Gilmore, John HIEEE transactions on medical imaging2010 Apr1039-4920335089
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Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.Lee, Younghee; Yang, Xinan; Huang, Yong; Fan, Hanli; Zhang, Qingbei; Wu, Youngfei; Li, Jianrong; Hasina, Rifat; Cheng, Chao; Lingen, Mark W; Gerstein, Mark B; Weichselbaum, Ralph R; Xing, H Rosie; Lussier, Yves APLoS computational biology2010 Apre100073020369013
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Differentiating prenatal exposure to methamphetamine and alcohol versus alcohol and not methamphetamine using tensor-based brain morphometry and discriminant analysis.Sowell, Elizabeth R; Leow, Alex D; Bookheimer, Susan Y; Smith, Lynne M; O'Connor, Mary J; Kan, Eric; Rosso, Carly; Houston, Suzanne; Dinov, Ivo D; Thompson, Paul MThe Journal of neuroscience : the official journal of the Society for Neuroscience2010 Mar 173876-8520237258
Putting biomedical ontologies to work.Smith, B; Brochhausen, MMethods of information in medicine2010 Mar 16135-4020135080
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A Geometric Approach to Joint 2D Region-Based Segmentation and 3D Pose Estimation Using a 3D Shape Prior.Dambreville, Samuel; Sandhu, Romeil; Yezzi, Anthony; Tannenbaum, AllenSIAM journal on imaging sciences2010 Mar 3110-13220613886
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European admixture on the Micronesian island of Kosrae: lessons from complete genetic information.Bonnen, Penelope E; Lowe, Jennifer K; Altshuler, David M; Breslow, Jan L; Stoffel, Markus; Friedman, Jeffrey M; Pe'er, ItsikEuropean journal of human genetics : EJHG2010 Mar309-1619844264
Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical records.Brownstein, John S; Murphy, Shawn N; Goldfine, Allison B; Grant, Richard W; Sordo, Margarita; Gainer, Vivian; Colecchi, Judith A; Dubey, Anil; Nathan, David M; Glaser, John P; Kohane, Isaac SDiabetes care2010 Mar526-3120009093
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Image-based modeling of blood flow and vessel wall dynamics: applications, methods and future directions: Sixth International Bio-Fluid Mechanics Symposium and Workshop, March 28-30, 2008 Pasadena, California.Taylor, Charles A; Steinman, David AAnnals of biomedical engineering2010 Mar1188-20320087775
Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2).Murphy, Shawn N; Weber, Griffin; Mendis, Michael; Gainer, Vivian; Chueh, Henry C; Churchill, Susanne; Kohane, IsaacJournal of the American Medical Informatics Association : JAMIA2010 Mar-Apr124-3020190053
Two-step adhesive binding by classical cadherins.Harrison, Oliver J; Bahna, Fabiana; Katsamba, Phini S; Jin, Xiangshu; Brasch, Julia; Vendome, Jeremie; Ahlsen, Goran; Carroll, Kilpatrick J; Price, Stephen R; Honig, Barry; Shapiro, LawrenceNature structural & molecular biology2010 Mar348-5720190754
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Visualization of image data from cells to organisms.Walter, Thomas; Shattuck, David W; Baldock, Richard; Bastin, Mark E; Carpenter, Anne E; Duce, Suzanne; Ellenberg, Jan; Fraser, Adam; Hamilton, Nicholas; Pieper, Steve; Ragan, Mark A; Schneider, Jurgen E; Tomancak, Pavel; Heriche, Jean-KarimNature methods2010 MarS26-4120195255
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Linking variants from genome-wide association analysis to function via transcriptional network analysis.Keller, Benjamin; Martini, Sebastian; Sedor, John; Kretzler, MatthiasSeminars in nephrology2010 Mar177-8420347646
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Comparison of manual and automated determination of hippocampal volumes in MCI and early AD.Shen, Li; Saykin, Andrew J; Kim, Sungeun; Firpi, Hiram A; West, John D; Risacher, Shannon L; McDonald, Brenna C; McHugh, Tara L; Wishart, Heather A; Flashman, Laura ABrain imaging and behavior2010 Mar86-9520454594
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Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.Basso, Katia; Saito, Masumichi; Sumazin, Pavel; Margolin, Adam A; Wang, Kai; Lim, Wei-Keat; Kitagawa, Yukiko; Schneider, Christof; Alvarez, Mariano J; Califano, Andrea; Dalla-Favera, RiccardoBlood2010 Feb 4975-8419965633
White matter pathology isolates the hippocampal formation in Alzheimer's disease.Salat, D H; Tuch, D S; van der Kouwe, A J W; Greve, D N; Pappu, V; Lee, S Y; Hevelone, N D; Zaleta, A K; Growdon, J H; Corkin, S; Fischl, B; Rosas, H DNeurobiology of aging2010 Feb244-5618455835
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Genetic evidence that raised sex hormone binding globulin (SHBG) levels reduce the risk of type 2 diabetes.Perry, John R B; Weedon, Michael N; Langenberg, Claudia; Jackson, Anne U; Lyssenko, Valeriya; Sparso, Thomas; Thorleifsson, Gudmar; Grallert, Harald; Ferrucci, Luigi; Maggio, Marcello; Paolisso, Giuseppe; Walker, Mark; Palmer, Colin N A; Payne, Felicity; Human molecular genetics2010 Feb 1535-4419933169
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Genetic and environmental influences on the size of specific brain regions in midlife: the VETSA MRI study.Kremen, William S; Prom-Wormley, Elizabeth; Panizzon, Matthew S; Eyler, Lisa T; Fischl, Bruce; Neale, Michael C; Franz, Carol E; Lyons, Michael J; Pacheco, Jennifer; Perry, Michele E; Stevens, Allison; Schmitt, J Eric; Grant, Michael D; Seidman, Larry J; NeuroImage2010 Jan 151213-2319786105
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Perk Station--Percutaneous surgery training and performance measurement platform.Vikal, Siddharth; U-Thainual, Paweena; Carrino, John A; Iordachita, Iulian; Fischer, Gregory S; Fichtinger, GaborComputerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society2010 Jan19-3219539446
Brain structure changes visualized in early- and late-onset blind subjects.Lepore, Natasha; Voss, Patrice; Lepore, Franco; Chou, Yi-Yu; Fortin, Madeleine; Gougoux, Frederic; Lee, Agatha D; Brun, Caroline; Lassonde, Maryse; Madsen, Sarah K; Toga, Arthur W; Thompson, Paul MNeuroImage2010 Jan 1134-4019643183
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Integrated navigation and control software system for MRI-guided robotic prostate interventions.Tokuda, Junichi; Fischer, Gregory S; DiMaio, Simon P; Gobbi, David G; Csoma, Csaba; Mewes, Philip W; Fichtinger, Gabor; Tempany, Clare M; Hata, NobuhikoComputerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society2010 Jan3-819699057
Transcriptomic analysis of human lung development.Kho, Alvin T; Bhattacharya, Soumyaroop; Tantisira, Kelan G; Carey, Vincent J; Gaedigk, Roger; Leeder, J Steven; Kohane, Isaac S; Weiss, Scott T; Mariani, Thomas JAmerican journal of respiratory and critical care medicine2010 Jan 154-6319815808
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Functional and anatomical connectivity abnormalities in left inferior frontal gyrus in schizophrenia.Jeong, Bumseok; Wible, Cynthia G; Hashimoto, Ryu-ichiro; Kubicki, MarekHuman brain mapping2009 Dec4138-5119569073
Purkinje cell loss in experimental autoimmune encephalomyelitis.MacKenzie-Graham, Allan; Tiwari-Woodruff, Seema K; Sharma, Gaurav; Aguilar, Cynthia; Vo, Kieumai T; Strickland, Lauren V; Morales, Laurie; Fubara, Boma; Martin, Melanie; Jacobs, Russell E; Johnson, G Allan; Toga, Arthur W; Voskuhl, Rhonda RNeuroImage2009 Dec637-5119589388
OpenIGTLink: an open network protocol for image-guided therapy environment.Tokuda, Junichi; Fischer, Gregory S; Papademetris, Xenophon; Yaniv, Ziv; Ibanez, Luis; Cheng, Patrick; Liu, Haiying; Blevins, Jack; Arata, Jumpei; Golby, Alexandra J; Kapur, Tina; Pieper, Steve; Burdette, Everette C; Fichtinger, Gabor; Tempany, Clare M; HThe international journal of medical robotics + computer assisted surgery : MRCAS2009 Dec423-3419621334
Elucidating a magnetic resonance imaging-based neuroanatomic biomarker for psychosis: classification analysis using probabilistic brain atlas and machine learning algorithms.Sun, Daqiang; van Erp, Theo G M; Thompson, Paul M; Bearden, Carrie E; Daley, Melita; Kushan, Leila; Hardt, Molly E; Nuechterlein, Keith H; Toga, Arthur W; Cannon, Tyrone DBiological psychiatry2009 Dec 11055-6019729150
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance.Park, Peter J; Kong, Sek Won; Tebaldi, Toma; Lai, Weil R; Kasif, Simon; Kohane, Isaac SBioinformatics (Oxford, England)2009 Dec 13121-719786482
Demographic and genetic constraints on evolution.Gomulkiewicz, Richard; Houle, DavidThe American naturalist2009 DecE218-2919821744
Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments.Lu, Hongchao; Lin, Lan; Sato, Seiko; Xing, Yi; Lee, Christopher JPLoS computational biology2009 Dece100060820019791
Computer-assisted extraction of intracranial aneurysms on 3D rotational angiograms for computational fluid dynamics modeling.Chang, Herng-Hua; Duckwiler, Gary R; Valentine, Daniel J; Chu, Woei ChynMedical physics2009 Dec5612-2120095274
Rapid equilibrium sampling initiated from nonequilibrium data.Huang, Xuhui; Bowman, Gregory R; Bacallado, Sergio; Pande, Vijay SProceedings of the National Academy of Sciences of the United States of America2009 Nov 2419765-919805023
Why sex matters: brain size independent differences in gray matter distributions between men and women.Luders, Eileen; Gaser, Christian; Narr, Katherine L; Toga, Arthur WThe Journal of neuroscience : the official journal of the Society for Neuroscience2009 Nov 1114265-7019906974
Relationships between brain activation and brain structure in normally developing children.Lu, Lisa H; Dapretto, Mirella; O'Hare, Elizabeth D; Kan, Eric; McCourt, Sarah T; Thompson, Paul M; Toga, Arthur W; Bookheimer, Susan Y; Sowell, Elizabeth RCerebral cortex (New York, N.Y. : 1991)2009 Nov2595-60419240138
Thalamo-frontal white matter alterations in chronic schizophrenia: a quantitative diffusion tractography study.Oh, Jungsu S; Kubicki, Marek; Rosenberger, Gudrun; Bouix, Sylvain; Levitt, James J; McCarley, Robert W; Westin, Carl-Fredrik; Shenton, Martha EHuman brain mapping2009 Nov3812-2519449328
DTNBP1 is associated with imaging phenotypes in schizophrenia.Narr, Katherine L; Szeszko, Philip R; Lencz, Todd; Woods, Roger P; Hamilton, Liberty S; Phillips, Owen; Robinson, Delbert; Burdick, Katherine E; DeRosse, Pamela; Kucherlapati, Raju; Thompson, Paul M; Toga, Arthur W; Malhotra, Anil K; Bilder, Robert MHuman brain mapping2009 Nov3783-9419449336
The University of Michigan Honest Broker: a Web-based service for clinical and translational research and practice.Boyd, Andrew D; Saxman, Paul R; Hunscher, Dale A; Smith, Kevin A; Morris, Timothy D; Kaston, Michelle; Bayoff, Frederick; Rogers, Bruce; Hayes, Pamela; Rajeev, Namrata; Kline-Rogers, Eva; Eagle, Kim; Clauw, Daniel; Greden, John F; Green, Lee A; Athey, BriJournal of the American Medical Informatics Association : JAMIA2009 Nov-Dec784-9119717803
Scalable and interactive segmentation and visualization of neural processes in EM datasets.Jeong, Won-Ki; Beyer, Johanna; Hadwiger, Markus; Vazquez, Amelio; Pfister, Hanspeter; Whitaker, Ross TIEEE transactions on visualization and computer graphics2009 Nov-Dec1505-1419834227
MRI signal intensity based B-spline nonrigid registration for pre- and intraoperative imaging during prostate brachytherapy.Oguro, Sota; Tokuda, Junichi; Elhawary, Haytham; Haker, Steven; Kikinis, Ron; Tempany, Clare M C; Hata, NobuhikoJournal of magnetic resonance imaging : JMRI2009 Nov1052-819856437
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.Wang, Xiao-Song; Prensner, John R; Chen, Guoan; Cao, Qi; Han, Bo; Dhanasekaran, Saravana M; Ponnala, Rakesh; Cao, Xuhong; Varambally, Sooryanarayana; Thomas, Dafydd G; Giordano, Thomas J; Beer, David G; Palanisamy, Nallasivam; Sartor, Maureen A; Omenn, GiNature biotechnology2009 Nov1005-1119881495
Looking at cerebellar malformations through text-mined interactomes of mice and humans.Iossifov, Ivan; Rodriguez-Esteban, Raul; Mayzus, Ilya; Millen, Kathleen J; Rzhetsky, AndreyPLoS computational biology2009 Nove100055919893633
Linking human diseases to animal models using ontology-based phenotype annotation.Washington, Nicole L; Haendel, Melissa A; Mungall, Christopher J; Ashburner, Michael; Westerfield, Monte; Lewis, Suzanna EPLoS biology2009 Nove100024719956802
The role of DNA shape in protein-DNA recognition.Rohs, Remo; West, Sean M; Sosinsky, Alona; Liu, Peng; Mann, Richard S; Honig, BarryNature2009 Oct 291248-5319865164
LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.Tao, Cui; Pathak, Jyotishman; Solbrig, Harold R; Wei, Wei-Qi; Chute, Christopher GCEUR workshop proceedings2009 Oct 26321804785
Accurate and robust brain image alignment using boundary-based registration.Greve, Douglas N; Fischl, BruceNeuroImage2009 Oct 1563-7219573611
Age-associated alterations in cortical gray and white matter signal intensity and gray to white matter contrast.Salat, D H; Lee, S Y; van der Kouwe, A J; Greve, D N; Fischl, B; Rosas, H DNeuroImage2009 Oct 1521-819580876
Expression differences by continent of origin point to the immortalization process.Davis, Adam R; Kohane, Isaac SHuman molecular genetics2009 Oct 153864-7519628477
Structural relationships among proteins with different global topologies and their implications for function annotation strategies.Petrey, Donald; Fischer, Markus; Honig, BarryProceedings of the National Academy of Sciences of the United States of America2009 Oct 1317377-8219805138
Triplet repeat length bias and variation in the human transcriptome.Molla, Michael; Delcher, Arthur; Sunyaev, Shamil; Cantor, Charles; Kasif, SimonProceedings of the National Academy of Sciences of the United States of America2009 Oct 617095-10019805156
Engineered myosin VI motors reveal minimal structural determinants of directionality and processivity.Liao, Jung-Chi; Elting, Mary Williard; Delp, Scott L; Spudich, James A; Bryant, ZevJournal of molecular biology2009 Oct 2862-719631216
Brain surface contraction mapped in first-episode schizophrenia: a longitudinal magnetic resonance imaging study.Sun, D; Stuart, G W; Jenkinson, M; Wood, S J; McGorry, P D; Velakoulis, D; van Erp, T G M; Thompson, P M; Toga, A W; Smith, D J; Cannon, T D; Pantelis, CMolecular psychiatry2009 Oct976-8618607377
Specializing for predicting obesity and its co-morbidities.Goldstein, Ira; Uzuner, OzlemJournal of biomedical informatics2009 Oct873-8619041423
Altered frontal-parietal functioning during verbal working memory in children and adolescents with heavy prenatal alcohol exposure.O'Hare, Elizabeth D; Lu, Lisa H; Houston, Suzanne M; Bookheimer, Susan Y; Mattson, Sarah N; O'Connor, Mary J; Sowell, Elizabeth RHuman brain mapping2009 Oct3200-819263420
Using generalized ensemble simulations and Markov state models to identify conformational states.Bowman, Gregory R; Huang, Xuhui; Pande, Vijay SMethods (San Diego, Calif.)2009 Oct197-20119410002
Increased sensitivity to effects of normal aging and Alzheimer's disease on cortical thickness by adjustment for local variability in gray/white contrast: a multi-sample MRI study.Westlye, Lars T; Walhovd, Kristine B; Dale, Anders M; Espeseth, Thomas; Reinvang, Ivar; Raz, Naftali; Agartz, Ingrid; Greve, Douglas N; Fischl, Bruce; Fjell, Anders MNeuroImage2009 Oct 11545-5719501655
Comparing registration methods for mapping brain change using tensor-based morphometry.Yanovsky, Igor; Leow, Alex D; Lee, Suh; Osher, Stanley J; Thompson, Paul MMedical image analysis2009 Oct679-70019631572
Widespread cortical thinning is a robust anatomical marker for attention-deficit/hyperactivity disorder.Narr, Katherine L; Woods, Roger P; Lin, James; Kim, John; Phillips, Owen R; Del'Homme, Melissa; Caplan, Rochelle; Toga, Arthur W; McCracken, James T; Levitt, Jennifer GJournal of the American Academy of Child and Adolescent Psychiatry2009 Oct1014-2219730275
Different gene regulation strategies revealed by analysis of binding motifs.Wunderlich, Zeba; Mirny, Leonid ATrends in genetics : TIG2009 Oct434-4019815308
In vivo deformation of the human abdominal aorta and common iliac arteries with hip and knee flexion: implications for the design of stent-grafts.Choi, Gilwoo; Shin, Lewis K; Taylor, Charles A; Cheng, Christopher PJournal of endovascular therapy : an official journal of the International Society of Endovascular Specialists2009 Oct531-819842734
Spectral solutions to stochastic models of gene expression with bursts and regulation.Mugler, Andrew; Walczak, Aleksandra M; Wiggins, Chris HPhysical review. E, Statistical, nonlinear, and soft matter physics2009 Oct04192119905356
Spectral solutions to stochastic models of gene expression with bursts and regulation.Mugler, Andrew; Walczak, Aleksandra M; Wiggins, Chris HPhysical review. E, Statistical, nonlinear, and soft matter physics2009 Oct4192119905356
Laplace-Beltrami Eigenvalues and Topological Features of Eigenfunctions for Statistical Shape Analysis.Reuter, Martin; Franz-Erichwolter; Shenton, Martha; Niethammer, MarcComputer aided design2009 Oct 1739-75520161035
Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.Yang, Chao-Yie; Sun, Haiying; Chen, Jianyong; Nikolovska-Coleska, Zaneta; Wang, ShaomengJournal of the American Chemical Society2009 Sep 3013709-2119736924
Progress and challenges in the automated construction of Markov state models for full protein systems.Bowman, Gregory R; Beauchamp, Kyle A; Boxer, George; Pande, Vijay SThe Journal of chemical physics2009 Sep 2812410119791846
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation.Fei, Jingyi; Bronson, Jonathan E; Hofman, Jake M; Srinivas, Rathi L; Wiggins, Chris H; Gonzalez Jr, Ruben LProceedings of the National Academy of Sciences of the United States of America2009 Sep 1515702-719717422
The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories.Weber, Griffin M; Murphy, Shawn N; McMurry, Andrew J; Macfadden, Douglas; Nigrin, Daniel J; Churchill, Susanne; Kohane, Isaac SJournal of the American Medical Informatics Association : JAMIA2009 Sep-Oct624-3019567788
Adjusted exponentially tilted likelihood with applications to brain morphology.Zhu, Hongtu; Zhou, Haibo; Chen, Jiahua; Li, Yimei; Lieberman, Jeffrey; Styner, MartinBiometrics2009 Sep919-2718945269
High consistency of regional cortical thinning in aging across multiple samples.Fjell, Anders M; Westlye, Lars T; Amlien, Inge; Espeseth, Thomas; Reinvang, Ivar; Raz, Naftali; Agartz, Ingrid; Salat, David H; Greve, Doug N; Fischl, Bruce; Dale, Anders M; Walhovd, Kristine BCerebral cortex (New York, N.Y. : 1991)2009 Sep2001-1219150922
Image-driven population analysis through mixture modeling.Sabuncu, Mert R; Balci, Serdar K; Shenton, Martha E; Golland, PolinaIEEE transactions on medical imaging2009 Sep1473-8719336293
Robotics-based synthesis of human motion.Khatib, O; Demircan, E; De Sapio, V; Sentis, L; Besier, T; Delp, SJournal of physiology, Paris2009 Sep-Dec211-919665552
Novel opportunities for computational biology and sociology in drug discovery.Yao, Lixia; Evans, James A; Rzhetsky, AndreyTrends in biotechnology2009 Sep531-4019674801
Localization of deformations within the amygdala in individuals with psychopathy.Yang, Yaling; Raine, Adrian; Narr, Katherine L; Colletti, Patrick; Toga, Arthur WArchives of general psychiatry2009 Sep986-9419736355
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.Wang, Kai; Saito, Masumichi; Bisikirska, Brygida C; Alvarez, Mariano J; Lim, Wei Keat; Rajbhandari, Presha; Shen, Qiong; Nemenman, Ilya; Basso, Katia; Margolin, Adam A; Klein, Ulf; Dalla-Favera, Riccardo; Califano, AndreaNature biotechnology2009 Sep829-3919741643
Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics.Parker, David; Bryant, Zev; Delp, Scott LCellular and molecular bioengineering2009 Sep 1366-37420428469
Nonparametric Mixture Models for Supervised Image Parcellation.Sabuncu, Mert R; Yeo, B T Thomas; Van Leemput, Koen; Fischl, Bruce; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009 Sep 1301-31320814584
Quantifying evolvability in small biological networks.Mugler, A; Ziv, E; Nemenman, I; Wiggins, C HIET systems biology2009 Sep379-8721028928
Lack of relationship between psychological denial and unawareness of illness in schizophrenia-spectrum disorders.Kruck, Carrie L; Flashman, Laura A; Roth, Robert M; Koven, Nancy S; McAllister, Thomas W; Saykin, Andrew JPsychiatry research2009 Aug 3033-819616309
Adsorption of poly(methyl methacrylate) on concave Al2O3 surfaces in nanoporous membranes.Nunnery, Grady; Hershkovits, Eli; Tannenbaum, Allen; Tannenbaum, RinaLangmuir : the ACS journal of surfaces and colloids2009 Aug 189157-6319415910
Total brain volume and corpus callosum size in medication-naive adolescents and young adults with autism spectrum disorder.Freitag, Christine M; Luders, Eileen; Hulst, Hanneke E; Narr, Katherine L; Thompson, Paul M; Toga, Arthur W; Krick, Christoph; Konrad, CarstenBiological psychiatry2009 Aug 15316-919409535
MRI RESOLUTION ENHANCEMENT USING TOTAL VARIATION REGULARIZATION.Joshi, Shantanu H; Marquina, Antonio; Osher, Stanley J; Dinov, Ivo; Van Horn, John D; Toga, Arthur WProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2009 Aug 7161-16421113426
Conflict monitoring in early frontotemporal dementia.Krueger, C E; Bird, A C; Growdon, M E; Jang, J Y; Miller, B L; Kramer, J HNeurology2009 Aug 4349-5519652138
MicroRNA expression changes in lymphoblastoid cell lines in response to lithium treatment.Chen, Haiming; Wang, Nulang; Burmeister, Margit; McInnis, Melvin GThe international journal of neuropsychopharmacology / official scientific journal of the Collegium Internationale Neuropsychopharmacologicum (CINP)2009 Aug975-8119254429
Performance measure characterization for evaluating neuroimage segmentation algorithms.Chang, Herng-Hua; Zhuang, Audrey H; Valentino, Daniel J; Chu, Woei-ChynNeuroImage2009 Aug 1122-3519345740
Predicting the location of entorhinal cortex from MRI.Fischl, Bruce; Stevens, Allison A; Rajendran, Niranjini; Yeo, B T Thomas; Greve, Douglas N; Van Leemput, Koen; Polimeni, Jonathan R; Kakunoori, Sita; Buckner, Randy L; Pacheco, Jennifer; Salat, David H; Melcher, Jennifer; Frosch, Matthew P; Hyman, BradleyNeuroImage2009 Aug 18-1719376238
Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription.Chen, Yili; Lin, Grace; Huo, Jeffrey S; Barney, Deborah; Wang, Zhenni; Livshiz, Tamara; States, David J; Qin, Zhaohui S; Schwartz, JessicaEndocrinology2009 Aug3645-5419406940
Active fibers: matching deformable tract templates to diffusion tensor images.Eckstein, Ilya; Shattuck, David W; Stein, Jason L; McMahon, Katie L; de Zubicaray, Greig; Wright, Margaret J; Thompson, Paul M; Toga, Arthur WNeuroImage2009 AugT82-919457360
Using genome-wide measurements for computational prediction of SH2-peptide interactions.Wunderlich, Zeba; Mirny, Leonid ANucleic acids research2009 Aug4629-4119502496
Multisite neuroimaging trials.Van Horn, John Darrell; Toga, Arthur WCurrent opinion in neurology2009 Aug370-819506479
New resource for the computation of cartilage biphasic material properties with the interpolant response surface method.Keenan, Kathryn E; Kourtis, Lampros C; Besier, Thor F; Lindsey, Derek P; Gold, Garry E; Delp, Scott L; Beaupre, Gary SComputer methods in biomechanics and biomedical engineering2009 Aug415-2219675978
The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain.Zhao, Xudong; D' Arca, Domenico; Lim, Wei Keat; Brahmachary, Manisha; Carro, Maria Stella; Ludwig, Thomas; Cardo, Carlos Cordon; Guillemot, Francois; Aldape, Ken; Califano, Andrea; Iavarone, Antonio; Lasorella, AnnaDevelopmental cell2009 Aug210-2119686682
Survey of modular ontology techniques and their applications in the biomedical domain.Pathak, Jyotishman; Johnson, Thomas M; Chute, Christopher GIntegrated computer-aided engineering2009 Aug225-24221686030
Obstetric complications and risk for conversion to psychosis among individuals at high clinical risk.Mittal, Vijay A; Willhite, Rachael; Daley, Melita; Bearden, Carrie E; Niendam, Tara; Ellman, Lauren M; Cannon, Tyrone DEarly intervention in psychiatry2009 Aug226-3022640387
Chimeric transcript discovery by paired-end transcriptome sequencing.Maher, Christopher A; Palanisamy, Nallasivam; Brenner, John C; Cao, Xuhong; Kalyana-Sundaram, Shanker; Luo, Shujun; Khrebtukova, Irina; Barrette, Terrence R; Grasso, Catherine; Yu, Jindan; Lonigro, Robert J; Schroth, Gary; Kumar-Sinha, Chandan; ChinnaiyanProceedings of the National Academy of Sciences of the United States of America2009 Jul 2812353-819592507
Pattern of hippocampal shape and volume differences in blind subjects.Lepore, Natasha; Shi, Yonggang; Lepore, Franco; Fortin, Madeline; Voss, Patrice; Chou, Yi-Yu; Lord, Catherine; Lassonde, Maryse; Dinov, Ivo D; Toga, Arthur W; Thompson, Paul MNeuroImage2009 Jul 15949-5719285559
Regional gray matter variation in male-to-female transsexualism.Luders, Eileen; Sanchez, Francisco J; Gaser, Christian; Toga, Arthur W; Narr, Katherine L; Hamilton, Liberty S; Vilain, EricNeuroImage2009 Jul 15904-719341803
Improving structure-based function prediction using molecular dynamics.Glazer, Dariya S; Radmer, Randall J; Altman, Russ BStructure (London, England : 1993)2009 Jul 15919-2919604472
Minute effects of sex on the aging brain: a multisample magnetic resonance imaging study of healthy aging and Alzheimer's disease.Fjell, Anders M; Westlye, Lars T; Amlien, Inge; Espeseth, Thomas; Reinvang, Ivar; Raz, Naftali; Agartz, Ingrid; Salat, David H; Greve, Doug N; Fischl, Bruce; Dale, Anders M; Walhovd, Kristine BThe Journal of neuroscience : the official journal of the Society for Neuroscience2009 Jul 88774-8319587284
Collaborative computational anatomy: an MRI morphometry study of the human brain via diffeomorphic metric mapping.Miller, Michael I; Priebe, Carey E; Qiu, Anqi; Fischl, Bruce; Kolasny, Anthony; Brown, Timothy; Park, Youngser; Ratnanather, J Tilak; Busa, Evelina; Jovicich, Jorge; Yu, Peng; Dickerson, Bradford C; Buckner, Randy L; Morphometry BIRNHuman brain mapping2009 Jul2132-4118781592
New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites.Lee, Inhan; Ajay, Subramanian S; Yook, Jong In; Kim, Hyun Sil; Hong, Su Hyung; Kim, Nam Hee; Dhanasekaran, Saravana M; Chinnaiyan, Arul M; Athey, Brian DGenome research2009 Jul1175-8319336450
Recognizing obesity and comorbidities in sparse data.Uzuner, OzlemJournal of the American Medical Informatics Association : JAMIA2009 Jul-Aug561-7019390096
Predicting outcomes of rectus femoris transfer surgery.Reinbolt, Jeffrey A; Fox, Melanie D; Schwartz, Michael H; Delp, Scott LGait & posture2009 Jul100-519411175
Elevated triglycerides correlate with progression of diabetic neuropathy.Wiggin, Timothy D; Sullivan, Kelli A; Pop-Busui, Rodica; Amato, Antonino; Sima, Anders A F; Feldman, Eva LDiabetes2009 Jul1634-4019411614
Overlapping pools for high-throughput targeted resequencing.Prabhu, Snehit; Pe'er, ItsikGenome research2009 Jul1254-6119447964
BioPortal: ontologies and integrated data resources at the click of a mouse.Noy, Natalya F; Shah, Nigam H; Whetzel, Patricia L; Dai, Benjamin; Dorf, Michael; Griffith, Nicholas; Jonquet, Clement; Rubin, Daniel L; Storey, Margaret-Anne; Chute, Christopher G; Musen, Mark ANucleic acids research2009 JulW170-319483092
How to build a tight but permeable glomerular junction.Martini, Sebastian; Kretzler, MatthiasJournal of the American Society of Nephrology : JASN2009 Jul1420-119520750
Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer.Lin, Biaoyang; White, James T; Wu, Jian; Lele, Shashikant; Old, Lloyd J; Hood, Leroy; Odunsi, KunleProteomics. Clinical applications2009 Jul 1853-86120559449
Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes.Pantazatos, Spiro P; Li, Jianrong; Pavlidis, Paul; Lussier, Yves ACancer informatics2009 Jun 875-9420495688
Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma.Compagno, Mara; Lim, Wei Keat; Grunn, Adina; Nandula, Subhadra V; Brahmachary, Manisha; Shen, Qiong; Bertoni, Francesco; Ponzoni, Maurilio; Scandurra, Marta; Califano, Andrea; Bhagat, Govind; Chadburn, Amy; Dalla-Favera, Riccardo; Pasqualucci, LauraNature2009 Jun 4717-2119412164
Encoding probabilistic brain atlases using Bayesian inference.Van Leemput, KoenIEEE transactions on medical imaging2009 Jun822-3719068424
Is protein classification necessary? Toward alternative approaches to function annotation.Petrey, Donald; Honig, BarryCurrent opinion in structural biology2009 Jun363-819269161
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.Kim, You Jung; Teletia, Nikhil; Ruotti, Victor; Maher, Christopher A; Chinnaiyan, Arul M; Stewart, Ron; Thomson, James A; Patel, Jignesh MBioinformatics (Oxford, England)2009 Jun 11424-519351619
Target-specific contrast agents for magnetic resonance microscopy.Blackwell, Megan L; Farrar, Christian T; Fischl, Bruce; Rosen, Bruce RNeuroImage2009 Jun382-9319385012
Automated segmentation of hippocampal subfields from ultra-high resolution in vivo MRI.Van Leemput, Koen; Bakkour, Akram; Benner, Thomas; Wiggins, Graham; Wald, Lawrence L; Augustinack, Jean; Dickerson, Bradford C; Golland, Polina; Fischl, BruceHippocampus2009 Jun549-5719405131
Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus.Shen, Li; Firpi, Hiram A; Saykin, Andrew J; West, John DHippocampus2009 Jun588-9519405146
Genome-wide association study identifies eight loci associated with blood pressure.Newton-Cheh, Christopher; Johnson, Toby; Gateva, Vesela; Tobin, Martin D; Bochud, Murielle; Coin, Lachlan; Najjar, Samer S; Zhao, Jing Hua; Heath, Simon C; Eyheramendy, Susana; Papadakis, Konstantinos; Voight, Benjamin F; Scott, Laura J; Zhang, Feng; FarrNature genetics2009 Jun666-7619430483
Disease classification with hippocampal shape invariants.Gutman, Boris; Wang, Yalin; Morra, Jonathan; Toga, Arthur W; Thompson, Paul MHippocampus2009 Jun572-819437498
Range of motion after computed tomography-based simulation of intertrochanteric corrective osteotomy in cases of slipped capital femoral epiphysis: comparison of uniplanar flexion osteotomy and multiplanar flexion, valgisation, and rotational osteotomies.Mamisch, Tallal Charles; Kim, Young-Jo; Richolt, Jens; Zilkens, Christoph; Kikinis, Ron; Millis, Michael; Kordelle, JensJournal of pediatric orthopedics2009 Jun336-4019461373
Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.Khan, Aly A; Betel, Doron; Miller, Martin L; Sander, Chris; Leslie, Christina S; Marks, Debora SNature biotechnology2009 Jun549-5519465925
Effects of prenatal methamphetamine exposure on verbal memory revealed with functional magnetic resonance imaging.Lu, Lisa H; Johnson, Arianne; O'Hare, Elizabeth D; Bookheimer, Susan Y; Smith, Lynne M; O'Connor, Mary J; Sowell, Elizabeth RJournal of developmental and behavioral pediatrics : JDBP2009 Jun185-9219525715
Gene regulatory networks in embryonic stem cells and brain development.Ghosh, Dhimankrishna; Yan, Xiaowei; Tian, QiangBirth defects research. Part C, Embryo today : reviews2009 Jun182-9119530135
Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data.Shah, Abhik; Woolf, PeterJournal of machine learning research : JMLR2009 Jun 1159-16220161541
Relationship Between White Matter Integrity, Attention, and Memory in Schizophrenia: A Diffusion Tensor Imaging Study.Kubicki, Marek; Niznikiewicz, Margaret; Connor, Elizabeth; Nestor, Paul; Bouix, Sylvain; Dreusicke, Mark; Kikinis, Ron; McCarley, Robert; Shenton, MarthaBrain imaging and behavior2009 Jun 1191-20120556231
Optimization of Landmark Selection for Cortical Surface Registration.Joshi, Anand; Pantazis, Dimitrios; Damasio, Hanna; Shattuck, David; Li, Quanzheng; Leahy, RichardProceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition2009 Jun 1699-70620717476
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.Wang, Dong; Bushnell, David A; Huang, Xuhui; Westover, Kenneth D; Levitt, Michael; Kornberg, Roger DScience (New York, N.Y.)2009 May 291203-619478184
The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation.Kelley, Nicholas W; Huang, Xuhui; Tam, Stephen; Spiess, Christoph; Frydman, Judith; Pande, Vijay SJournal of molecular biology2009 May 22919-2719361448
Knee muscle forces during walking and running in patellofemoral pain patients and pain-free controls.Besier, Thor F; Fredericson, Michael; Gold, Garry E; Beaupre, Gary S; Delp, Scott LJournal of biomechanics2009 May 11898-90519268945
Using real-time MRI to quantify altered joint kinematics in subjects with patellofemoral pain and to evaluate the effects of a patellar brace or sleeve on joint motion.Draper, Christine E; Besier, Thor F; Santos, Juan M; Jennings, Fabio; Fredericson, Michael; Gold, Garry E; Beaupre, Gary S; Delp, Scott LJournal of orthopaedic research : official publication of the Orthopaedic Research Society2009 May571-718985690
Automated semantic indexing of figure captions to improve radiology image retrieval.Kahn Jr, Charles E; Rubin, Daniel LJournal of the American Medical Informatics Association : JAMIA2009 May-Jun380-619261938
Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using electronic medical records.Himes, Blanca E; Dai, Yi; Kohane, Isaac S; Weiss, Scott T; Ramoni, Marco FJournal of the American Medical Informatics Association : JAMIA2009 May-Jun371-919261943
Shape abnormalities of caudate nucleus in schizotypal personality disorder.Levitt, James J; Styner, Martin; Niethammer, Marc; Bouix, Sylvain; Koo, Min-Seong; Voglmaier, Martina M; Dickey, Chandlee C; Niznikiewicz, Margaret A; Kikinis, Ron; McCarley, Robert W; Shenton, Martha ESchizophrenia research2009 May127-3919328654
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Diffusion tensor imaging detects abnormalities in the corticospinal tracts of neonates with infantile Krabbe disease.Escolar, M L; Poe, M D; Smith, J K; Gilmore, J H; Kurtzberg, J; Lin, W; Styner, MAJNR. American journal of neuroradiology2009 May1017-2119386732
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Widespread reductions of cortical thickness in schizophrenia and spectrum disorders and evidence of heritability.Goldman, Aaron L; Pezawas, Lukas; Mattay, Venkata S; Fischl, Bruce; Verchinski, Beth A; Chen, Qiang; Weinberger, Daniel R; Meyer-Lindenberg, AndreasArchives of general psychiatry2009 May467-7719414706
Targeting stem cells-clinical implications for cancer therapy.Tu, Lan Chun; Foltz, Greg; Lin, Edward; Hood, Leroy; Tian, QiangCurrent stem cell research & therapy2009 May147-5319442199
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Accelerating molecular dynamic simulation on graphics processing units.Friedrichs, Mark S; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L; Ensign, Daniel L; Bruns, Christopher M; Pande, Vijay SJournal of computational chemistry2009 Apr 30864-7219191337
The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations.Ensign, Daniel L; Pande, Vijay SBiophysical journal2009 Apr 22L53-519383445
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Tract-based morphometry for white matter group analysis.O'Donnell, Lauren J; Westin, Carl-Fredrik; Golby, Alexandra JNeuroImage2009 Apr 15832-4419154790
The underlying anatomical correlates of long-term meditation: larger hippocampal and frontal volumes of gray matter.Luders, Eileen; Toga, Arthur W; Lepore, Natasha; Gaser, ChristianNeuroImage2009 Apr 15672-819280691
Computer science. Automating science.Waltz, David; Buchanan, Bruce GScience (New York, N.Y.)2009 Apr 343-419342574
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Exact and efficient inference procedure for meta-analysis and its application to the analysis of independent 2 x 2 tables with all available data but without artificial continuity correction.Tian, Lu; Cai, Tianxi; Pfeffer, Marc A; Piankov, Nikita; Cremieux, Pierre-Yves; Wei, L JBiostatistics (Oxford, England)2009 Apr275-8118922759
Online resource for validation of brain segmentation methods.Shattuck, David W; Prasad, Gautam; Mirza, Mubeena; Narr, Katherine L; Toga, Arthur WNeuroImage2009 Apr 1431-919073267
Combined volumetric and surface registration.Postelnicu, Gheorghe; Zollei, Lilla; Fischl, BruceIEEE transactions on medical imaging2009 Apr508-2219273000
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Circumferential and longitudinal cyclic strain of the human thoracic aorta: age-related changes.Morrison, Tina M; Choi, Gilwoo; Zarins, Christopher K; Taylor, Charles AJournal of vascular surgery : official publication, the Society for Vascular Surgery [and] International Society for Cardiovascular Surgery, North American Chapter2009 Apr1029-3619341890
SOCR Analyses: Implementation and Demonstration of a New Graphical Statistics Educational Toolkit.Chu, Annie; Cui, Jenny; Dinov, Ivo DJournal of statistical software2009 Apr 11-1921666874
Mechanisms of improved knee flexion after rectus femoris transfer surgery.Fox, Melanie D; Reinbolt, Jeffrey A; Ounpuu, Sylvia; Delp, Scott LJournal of biomechanics2009 Mar 26614-919217109
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis.Hur, Junguk; Schuyler, Adam D; States, David J; Feldman, Eva LBioinformatics (Oxford, England)2009 Mar 15838-4019188191
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Transcriptome sequencing to detect gene fusions in cancer.Maher, Christopher A; Kumar-Sinha, Chandan; Cao, Xuhong; Kalyana-Sundaram, Shanker; Han, Bo; Jing, Xiaojun; Sam, Lee; Barrette, Terrence; Palanisamy, Nallasivam; Chinnaiyan, Arul MNature2009 Mar 597-10119136943
Identifying heritable brain phenotypes in an extended pedigree of vervet monkeys.Fears, Scott C; Melega, William P; Service, Susan K; Lee, Chris; Chen, Kelly; Tu, Zhuowen; Jorgensen, Matthew J; Fairbanks, Lynn A; Cantor, Rita M; Freimer, Nelson B; Woods, Roger PThe Journal of neuroscience : the official journal of the Society for Neuroscience2009 Mar 42867-7519261882
An MRI-based method for measuring volume, thickness and surface area of entorhinal, perirhinal, and posterior parahippocampal cortex.Feczko, Eric; Augustinack, Jean C; Fischl, Bruce; Dickerson, Bradford CNeurobiology of aging2009 Mar420-3117850926
Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area.Dickerson, Bradford C; Feczko, Eric; Augustinack, Jean C; Pacheco, Jenni; Morris, John C; Fischl, Bruce; Buckner, Randy LNeurobiology of aging2009 Mar432-4017869384
Group analysis of DTI fiber tract statistics with application to neurodevelopment.Goodlett, Casey B; Fletcher, P Thomas; Gilmore, John H; Gerig, GuidoNeuroImage2009 MarS133-4219059345
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Increased diffusivity in superior temporal gyrus in patients with schizophrenia: a Diffusion Tensor Imaging study.Lee, KangUk; Yoshida, Takeshi; Kubicki, Marek; Bouix, Sylvain; Westin, Carl-Fredrik; Kindlmann, Gordon; Niznikiewicz, Margaret; Cohen, Adam; McCarley, Robert W; Shenton, Martha ESchizophrenia research2009 Mar33-4019135872
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Optimal estimation of dynamically consistent kinematics and kinetics for forward dynamic simulation of gait.Remy, C David; Thelen, Darryl GJournal of biomechanical engineering2009 Mar03100519154064
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BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.Bryan Jr, Allen W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan L; Berger, BonniePLoS computational biology2009 Mare100033319325876
Anterior cruciate ligament reconstruction in the skeletally immature: an anatomical study utilizing 3-dimensional magnetic resonance imaging reconstructions.Kercher, Jim; Xerogeanes, John; Tannenbaum, Allen; Al-Hakim, Ramsey; Black, James C; Zhao, JohnJournal of pediatric orthopedics2009 Mar124-919352236
Creating a controlled vocabulary for the ethics of human research: towards a biomedical ethics ontology.Koepsell, David; Arp, Robert; Fostel, Jennifer; Smith, BarryJournal of empirical research on human research ethics : JERHRE2009 Mar43-5819374479
Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation.Voelz, Vincent A; Luttmann, Edgar; Bowman, Gregory R; Pande, Vijay SInternational journal of molecular sciences2009 Mar1013-3019399235
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Probabilistic white matter fiber tracking using particle filtering and von Mises-Fisher sampling.Zhang, Fan; Hancock, Edwin R; Goodlett, Casey; Gerig, GuidoMedical image analysis2009 Feb5-1818602332
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Molecular dynamics/order parameter extrapolation for bionanosystem simulations.Miao, Yinglong; Ortoleva, Peter JJournal of computational chemistry2009 Feb423-3718636559
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Choice of in vivo versus idealized velocity boundary conditions influences physiologically relevant flow patterns in a subject-specific simulation of flow in the human carotid bifurcation.Wake, Amanda K; Oshinski, John N; Tannenbaum, Allen R; Giddens, Don PJournal of biomechanical engineering2009 Feb02101319102572
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.Jonikas, Magdalena A; Radmer, Randall J; Laederach, Alain; Das, Rhiju; Pearlman, Samuel; Herschlag, Daniel; Altman, Russ BRNA (New York, N.Y.)2009 Feb189-9919144906
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Loss of myotubularin function results in T-tubule disorganization in zebrafish and human myotubular myopathy.Dowling, James J; Vreede, Andrew P; Low, Sean E; Gibbs, Elizabeth M; Kuwada, John Y; Bonnemann, Carsten G; Feldman, Eva LPLoS genetics2009 Febe100037219197364
Accelerating molecular dynamic simulation on the cell processor and Playstation 3.Luttmann, Edgar; Ensign, Daniel L; Vaidyanathan, Vishal; Houston, Mike; Rimon, Noam; Oland, Jeppe; Jayachandran, Guha; Friedrichs, Mark; Pande, Vijay SJournal of computational chemistry2009 Jan 30268-7418615421
Mean diffusivity: a biomarker for CSF-related disease and genetic liability effects in schizophrenia.Narr, Katherine L; Hageman, Nathan; Woods, Roger P; Hamilton, Liberty S; Clark, Kristi; Phillips, Owen; Shattuck, David W; Asarnow, Robert F; Toga, Arthur W; Nuechterlein, Keith HPsychiatry research2009 Jan 3020-3219081707
Can morphing methods predict intermediate structures?Weiss, Dahlia R; Levitt, MichaelJournal of molecular biology2009 Jan 16665-7418996395
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Detecting brain growth patterns in normal children using tensor-based morphometry.Hua, Xue; Leow, Alex D; Levitt, Jennifer G; Caplan, Rochelle; Thompson, Paul M; Toga, Arthur WHuman brain mapping2009 Jan209-1918064588
Spiny versus stubby: 3D reconstruction of human myenteric (type I) neurons.Lindig, Tobias M; Kumar, Vinod; Kikinis, Ron; Pieper, Steve; Schrodl, Falk; Neuhuber, Winfried L; Brehmer, AxelHistochemistry and cell biology2009 Jan1-1218807064
Integrating and annotating the interactome using the MiMI plugin for cytoscape.Gao, Jing; Ade, Alex S; Tarcea, V Glenn; Weymouth, Terry E; Mirel, Barbara R; Jagadish, H V; States, David JBioinformatics (Oxford, England)2009 Jan 1137-818812364
Decreased callosal thickness in attention-deficit/hyperactivity disorder.Luders, Eileen; Narr, Katherine L; Hamilton, Liberty S; Phillips, Owen R; Thompson, Paul M; Valle, Jessica S; Del'Homme, Melissa; Strickland, Tony; McCracken, James T; Toga, Arthur W; Levitt, Jennifer GBiological psychiatry2009 Jan 184-818842255
Machine learning and rule-based approaches to assertion classification.Uzuner, Ozlem; Zhang, Xiaoran; Sibanda, TawandaJournal of the American Medical Informatics Association : JAMIA2009 Jan-Feb109-1518952931
Michigan molecular interactions r2: from interacting proteins to pathways.Tarcea, V Glenn; Weymouth, Terry; Ade, Alex; Bookvich, Aaron; Gao, Jing; Mahavisno, Vasudeva; Wright, Zach; Chapman, Adriane; Jayapandian, Magesh; Ozgur, Arzucan; Tian, Yuanyuan; Cavalcoli, Jim; Mirel, Barbara; Patel, Jignesh; Radev, Dragomir; Athey, BriaNucleic acids research2009 JanD642-618978014
Methods for quantifying three-dimensional deformation of arteries due to pulsatile and nonpulsatile forces: implications for the design of stents and stent grafts.Choi, Gilwoo; Cheng, Christopher P; Wilson, Nathan M; Taylor, Charles AAnnals of biomedical engineering2009 Jan14-3319002584
Fiber tractography reveals disruption of temporal lobe white matter tracts in schizophrenia.Phillips, Owen R; Nuechterlein, Keith H; Clark, Kristi A; Hamilton, Liberty S; Asarnow, Robert F; Hageman, Nathan S; Toga, Arthur W; Narr, Katherine LSchizophrenia research2009 Jan30-819028423
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Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.Menon, Rajasree; Zhang, Qing; Zhang, Yan; Fermin, Damian; Bardeesy, Nabeel; DePinho, Ronald A; Lu, Chunxia; Hanash, Samir M; Omenn, Gilbert S; States, David JCancer research2009 Jan 1300-919118015
A role for self-gravity at multiple length scales in the process of star formation.Goodman, Alyssa A; Rosolowsky, Erik W; Borkin, Michelle A; Foster, Jonathan B; Halle, Michael; Kauffmann, Jens; Pineda, Jaime ENature2009 Jan 163-619122636
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Dissecting the interface between signaling and transcriptional regulation in human B cells.Wang, Kai; Alvarez, Mariano J; Bisikirska, Brygida C; Linding, Rune; Basso, Katia; Dalla Favera, Riccardo; Califano, AndreaPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2009264-7519209707
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GAGE: generally applicable gene set enrichment for pathway analysis.Luo, Weijun; Friedman, Michael S; Shedden, Kerby; Hankenson, Kurt D; Woolf, Peter JBMC bioinformatics200916119473525
Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor.Lin, Biaoyang; Wang, Jun; Hong, Xu; Yan, Xiaowei; Hwang, Daehee; Cho, Ji-Hoon; Yi, Danielle; Utleg, Angelita G; Fang, Xuefeng; Schones, Dustin E; Zhao, Keji; Omenn, Gilbert S; Hood, LeroyPloS one2009e658919668381
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Genephony: a knowledge management tool for genome-wide research.Nuzzo, Angelo; Riva, AlbertoBMC bioinformatics200927819728881
Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers.Dreyfuss, Jonathan M; Johnson, Mark D; Park, Peter JMolecular cancer20097119732454
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Network analysis of genes regulated in renal diseases: implications for a molecular-based classification.Bhavnani, Suresh K; Eichinger, Felix; Martini, Sebastian; Saxman, Paul; Jagadish, H V; Kretzler, MatthiasBMC bioinformatics2009S319761573
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Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.Vellaichamy, Adaikkalam; Sreekumar, Arun; Strahler, John R; Rajendiran, Theckelnaycke; Yu, Jindan; Varambally, Sooryanarayana; Li, Yong; Omenn, Gilbert S; Chinnaiyan, Arul M; Nesvizhskii, Alexey IPloS one2009e707519763266
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Harnessing gene expression to identify the genetic basis of drug resistance.Chen, Bo-Juen; Causton, Helen C; Mancenido, Denesy; Goddard, Noel L; Perlstein, Ethan O; Pe'er, DanaMolecular systems biology200931019888205
Agitation and pain assessment using digital imaging.Gholami, Behnood; Haddad, Wassim M; Tannenbaum, Allen RConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference20092176-919963539
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On the manifold structure of the space of brain images.Gerber, Samuel; Tasdizen, Tolga; Joshi, Sarang; Whitaker, RossMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009305-1220426001
Constrained data decomposition and regression for analyzing healthy aging from fiber tract diffusion properties.Gouttard, Sylvain; Prastawa, Marcel; Bullitt, Elizabeth; Lin, Weili; Goodlett, Casey; Gerig, GuidoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009321-820426003
Multivariate tensor-based brain anatomical surface morphometry via holomorphic one-forms.Wang, Yalin; Chan, Tony F; Toga, Arthur W; Thompson, Paul MMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009337-4420426005
Local white matter geometry indices from diffusion tensor gradients.Savadjiev, Peter; Kindlmann, Gordon; Bouix, Sylvain; Shenton, Martha E; Westin, Carl-FredrikMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009345-5220426006
Asymmetric image-template registration.Sabuncu, Mert R; Yeo, B T Thomas; Van Leemput, Koen; Vercauteren, Tom; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009565-7320426033
Task-optimal registration cost functions.Yeo, B T Thomas; Sabuncu, Mert; Golland, Polina; Fischl, BruceMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009598-60620426037
Two-tensor tractography using a constrained filter.Malcolm, James G; Shenton, Martha E; Rathi, YogeshMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009894-90220426073
Modeling adaptation effects in fMRI analysis.Ou, Wanmei; Raij, Tommi; Lin, Fa-Hsuan; Golland, Polina; Hamalainen, MattiMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention20091009-1720426087
Teichmoller shape space theory and its application to brain morphometry.Wang, Yalin; Dai, Wei; Gu, Xianfeng; Chan, Tony F; Yau, Shing-Tung; Toga, Arthur W; Thompson, Paul MMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009133-4020426105
Particle based shape regression of open surfaces with applications to developmental neuroimaging.Datar, Manasi; Cates, Joshua; Fletcher, P Thomas; Gouttard, Sylvain; Gerig, Guido; Whitaker, RossMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009167-7420426109
Intrinsic regression models for manifold-valued data.Shi, Xiaoyan; Styner, Martin; Lieberman, Jeffrey; Ibrahim, Joseph G; Lin, Weili; Zhu, HongtuMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009192-920426112
Cortical shape analysis in the Laplace-Beltrami feature space.Shi, Yonggang; Dinov, Ivo; Toga, Arthur WMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009208-1520426114
Lossless online ensemble learning (LOEL) and its application to subcortical segmentation.Morra, Jonathan H; Tu, Zhuowen; Toga, Arthur W; Thompson, Paul MMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009432-4020426141
Atlas-based improved prediction of magnetic field inhomogeneity for distortion correction of EPI data.Poynton, Clare; Jenkinson, Mark; Wells 3rd, WilliamMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2009951-920426203
Supervised nonparametric image parcellation.Sabuncu, Mert R; Yeo, B T Thomas; Van Leemput, Koen; Fischl, Bruce; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention20091075-8320426218
Consistency Clustering: A Robust Algorithm for Group-wise Registration, Segmentation and Automatic Atlas Construction in Diffusion MRI.Ziyan, Ulas; Sabuncu, Mert R; Grimson, W Eric L; Westin, Carl-FredrikInternational journal of computer vision2009279-29020442792
Edge-Enhanced Image Reconstruction Using (TV) Total Variation and Bregman Refinement.Joshi, Shantanu H; Marquina, Antonio; Osher, Stanley J; Dinov, Ivo; Van Horn, John D; Toga, Arthur WLecture notes in computer science2009 Jan 1389-40021113387
VOXEL-WISE GROUP ANALYSIS OF DTI.Liu, Zhexing; Zhu, Hongtu; Marks, Bonita L; Katz, Laurence M; Goodlett, Casey B; Gerig, Guido; Styner, MartinProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2009807-81023703686
Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach.Kelley, Nicholas W; Vishal, V; Krafft, Grant A; Pande, Vijay SThe Journal of chemical physics2008 Dec 721470719063575
Aging elevates metabolic gene expression in brain cholinergic neurons.Baskerville, Karen A; Kent, Caroline; Personett, David; Lai, Weil R; Park, Peter J; Coleman, Paul; McKinney, MichaelNeurobiology of aging2008 Dec1874-9317560690
The influence of femoral internal and external rotation on cartilage stresses within the patellofemoral joint.Besier, Thor F; Gold, Garry E; Delp, Scott L; Fredericson, Michael; Beaupre, Gary SJournal of orthopaedic research : official publication of the Orthopaedic Research Society2008 Dec1627-3518524000
Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.Martini, Sebastian; Eichinger, Felix; Nair, Viji; Kretzler, MatthiasReviews in endocrine & metabolic disorders2008 Dec267-7418704688
An integrated system for planning, navigation and robotic assistance for skull base surgery.Xia, Tian; Baird, Clint; Jallo, George; Hayes, Kathryn; Nakajima, Nobuyuki; Hata, Nobuhiko; Kazanzides, PeterThe international journal of medical robotics + computer assisted surgery : MRCAS2008 Dec321-3018803337
Regional patterns and clinical correlates of basal ganglia morphology in non-medicated schizophrenia.Ballmaier, Martina; Schlagenhauf, Florian; Toga, Arthur W; Gallinat, Jurgen; Koslowski, Michael; Zoli, Michele; Hojatkashani, Cornelius; Narr, Katherine L; Heinz, AndreasSchizophrenia research2008 Dec140-718818054
Reduced interhemispheric connectivity in schizophrenia-tractography based segmentation of the corpus callosum.Kubicki, M; Styner, M; Bouix, S; Gerig, G; Markant, D; Smith, K; Kikinis, R; McCarley, R W; Shenton, M ESchizophrenia research2008 Dec125-3118829262
A bioinformatics analysis of the cell line nomenclature.Sarntivijai, Sirarat; Ade, Alexander S; Athey, Brian D; States, David JBioinformatics (Oxford, England)2008 Dec 12760-618849319
Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene.Wang, Qi; Barr, Ian; Guo, Feng; Lee, ChristopherRNA (New York, N.Y.)2008 Dec2478-8818974280
MRI-based anatomical model of the human head for specific absorption rate mapping.Makris, Nikos; Angelone, Leonardo; Tulloch, Seann; Sorg, Scott; Kaiser, Jonathan; Kennedy, David; Bonmassar, GiorgioMedical & biological engineering & computing2008 Dec1239-5118985401
Segmentation of tracking sequences using dynamically updated adaptive learning.Michailovich, Oleg; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2008 Dec2403-1219004712
Grey and white matter loss along cerebral midline structures in myotonic dystrophy type 2.Minnerop, Martina; Luders, Eileen; Specht, Karsten; Ruhlmann, Jurgen; Schneider-Gold, Christiane; Schroder, Rolf; Thompson, Paul M; Toga, Arthur W; Klockgether, Thomas; Kornblum, CorneliaJournal of neurology2008 Dec1904-919224318
Reduced white matter integrity in attention-deficit hyperactivity disorder.Hamilton, Liberty S; Levitt, Jennifer G; O'Neill, Joseph; Alger, Jeffry R; Luders, Eileen; Phillips, Owen R; Caplan, Rochelle; Toga, Arthur W; McCracken, James; Narr, Katherine LNeuroreport2008 Nov 191705-818841089
Muscle function may depend on model selection in forward simulation of normal walking.Xiao, Ming; Higginson, Jill SJournal of biomechanics2008 Nov 143236-4218804767
Muscle contributions to support and progression over a range of walking speeds.Liu, May Q; Anderson, Frank C; Schwartz, Michael H; Delp, Scott LJournal of biomechanics2008 Nov 143243-5218822415
The intrinsic shape of human and macaque primary visual cortex.Hinds, Oliver; Polimeni, Jonathan R; Rajendran, Niranjini; Balasubramanian, Mukund; Wald, Lawrence L; Augustinack, Jean C; Wiggins, Graham; Rosas, H Diana; Fischl, Bruce; Schwartz, Eric LCerebral cortex (New York, N.Y. : 1991)2008 Nov2586-9518308709
HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.Flores, Samuel C; Keating, Kevin S; Painter, Jay; Morcos, Faruck; Nguyen, Khang; Merritt, Ethan A; Kuhn, Leslie A; Gerstein, Mark BProteins2008 Nov 1299-31918433058
Gene-environment interaction and covariation in schizophrenia: the role of obstetric complications.Mittal, Vijay A; Ellman, Lauren M; Cannon, Tyrone DSchizophrenia bulletin2008 Nov1083-9418635675
Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes.Gaulton, Kyle J; Willer, Cristen J; Li, Yun; Scott, Laura J; Conneely, Karen N; Jackson, Anne U; Duren, William L; Chines, Peter S; Narisu, Narisu; Bonnycastle, Lori L; Luo, Jingchun; Tong, Maurine; Sprau, Andrew G; Pugh, Elizabeth W; Doheny, Kimberly F; Diabetes2008 Nov3136-4418678618
The effect of intron length on exon creation ratios during the evolution of mammalian genomes.Roy, Meenakshi; Kim, Namshin; Xing, Yi; Lee, ChristopherRNA (New York, N.Y.)2008 Nov2261-7318796579
Localizing region-based active contours.Lankton, Shawn; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2008 Nov2029-3918854247
Focal reversible deactivation of cerebral metabolism affects water diffusion.Khachaturian, Mark H; Arsenault, John; Ekstrom, Leeland B; Tuch, David S; Vanduffel, WimMagnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine2008 Nov1178-8918958855
A predictive model of the oxygen and heme regulatory network in yeast.Kundaje, Anshul; Xin, Xiantong; Lan, Changgui; Lianoglou, Steve; Zhou, Mei; Zhang, Li; Leslie, ChristinaPLoS computational biology2008 Nove100022419008939
Hypermutable non-synonymous sites are under stronger negative selection.Schmidt, Steffen; Gerasimova, Anna; Kondrashov, Fyodor A; Adzhubei, Ivan A; Adzuhbei, Ivan A; Kondrashov, Alexey S; Sunyaev, ShamilPLoS genetics2008 Nove100028119043566
Murine lung responses to ambient particulate matter: genomic analysis and influence on airway hyperresponsiveness.Wang, Ting; Moreno-Vinasco, Liliana; Huang, Yong; Lang, Gabriel D; Linares, Jered D; Goonewardena, Sascha N; Grabavoy, Alayna; Samet, Jonathan M; Geyh, Alison S; Breysse, Patrick N; Lussier, Yves A; Natarajan, Viswanathan; Garcia, Joe G NEnvironmental health perspectives2008 Nov1500-819057703
Computer simulations of isolated conductors in electrostatic equilibrium.Chang, Herng-HuaPhysical review. E, Statistical, nonlinear, and soft matter physics2008 Nov05670419113234
Side-chain recognition and gating in the ribosome exit tunnel.Petrone, Paula M; Snow, Christopher D; Lucent, Del; Pande, Vijay SProceedings of the National Academy of Sciences of the United States of America2008 Oct 2816549-5418946046
Glial reactions and degeneration of myelinated processes in spinal cord gray matter in chronic experimental autoimmune encephalomyelitis.Wu, J; Ohlsson, M; Warner, E A; Loo, K K; Hoang, T X; Voskuhl, R R; Havton, L ANeuroscience2008 Oct 15586-9618718511
Optimal screening for promising genes in 2-stage designs.Moerkerke, B; Goetghebeur, EBiostatistics (Oxford, England)2008 Oct700-1418349035
Rosiglitazone treatment reduces diabetic neuropathy in streptozotocin-treated DBA/2J mice.Wiggin, Timothy D; Kretzler, Matthias; Pennathur, Subramaniam; Sullivan, Kelli A; Brosius, Frank C; Feldman, Eva LEndocrinology2008 Oct4928-3718583417
Neurodevelopmental changes in verbal working memory load-dependency: an fMRI investigation.O'Hare, Elizabeth D; Lu, Lisa H; Houston, Suzanne M; Bookheimer, Susan Y; Sowell, Elizabeth RNeuroImage2008 Oct 11678-8518586110
Effects of registration regularization and atlas sharpness on segmentation accuracy.Yeo, B T Thomas; Sabuncu, Mert R; Desikan, Rahul; Fischl, Bruce; Golland, PolinaMedical image analysis2008 Oct603-1518667352
Caenorhabditis elegans mutant allele identification by whole-genome sequencing.Sarin, Sumeet; Prabhu, Snehit; O'Meara, M Maggie; Pe'er, Itsik; Hobert, OliverNature methods2008 Oct865-718677319
Restoration of DWI data using a Rician LMMSE estimator.Aja-Fernandez, Santiago; Niethammer, Marc; Kubicki, Marek; Shenton, Martha E; Westin, Carl-FredrikIEEE transactions on medical imaging2008 Oct1389-40318815091
Wagner and Dollo: a stochastic duet by composing two parsimonious solos.Alekseyenko, Alexander V; Lee, Christopher J; Suchard, Marc ASystematic biology2008 Oct772-8418853363
Efficient algorithms to explore conformation spaces of flexible protein loops.Yao, Peggy; Dhanik, Ankur; Marz, Nathan; Propper, Ryan; Kou, Charles; Liu, Guanfeng; van den Bedem, Henry; Latombe, Jean-Claude; Halperin-Landsberg, Inbal; Altman, Russ BiagioIEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM2008 Oct-Dec534-4518989041
Reconstruction Using Witness Complexes.Guibas, Leonidas J; Oudot, Steve YDiscrete & computational geometry2008 Oct 1325-35621643440
Chemical denaturants inhibit the onset of dewetting.England, Jeremy L; Pande, Vijay S; Haran, GiladJournal of the American Chemical Society2008 Sep 1011854-518707183
Mapping the relationship between cortical convolution and intelligence: effects of gender.Luders, Eileen; Narr, Katherine L; Bilder, Robert M; Szeszko, Philip R; Gurbani, Mala N; Hamilton, Liberty; Toga, Arthur W; Gaser, ChristianCerebral cortex (New York, N.Y. : 1991)2008 Sep2019-2618089578
Neural phenotypes of common and rare genetic variants.Bearden, Carrie E; Glahn, David C; Lee, Agatha D; Chiang, Ming-Chang; van Erp, Theo G M; Cannon, Tyrone D; Reiss, Allan L; Toga, Arthur W; Thompson, Paul MBiological psychology2008 Sep43-5718395317
The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.Bug, William J; Ascoli, Giorgio A; Grethe, Jeffrey S; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R; Larson, Stephen D; Rubin, Daniel; Shepherd, Gordon M; Turner, Jessica A; Martone, Maryann ENeuroinformatics2008 Sep175-9418975148
Prediction of Successful Memory Encoding from fMRI Data.Balci, S K; Sabuncu, M R; Yoo, J; Ghosh, S S; Whitfield-Gabrieli, S; Gabrieli, J D E; Golland, PMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008 Sep 197-10420401334
Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources.Pathak, Jyotishman; Jiang, Guoqian; Dwarkanath, Sridhar O; Buntrock, James D; Chute, Christopher GProceedings / IEEE International Conference on Semantic Computing ... ICSC. IEEE International Conference on Semantic Computing2008 Aug 12460-46721625412
Importance of preswing rectus femoris activity in stiff-knee gait.Reinbolt, Jeffrey A; Fox, Melanie D; Arnold, Allison S; Ounpuu, Sylvia; Delp, Scott LJournal of biomechanics2008 Aug 72362-918617180
Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins.Miloushev, Vesselin Z; Bahna, Fabiana; Ciatto, Carlo; Ahlsen, Goran; Honig, Barry; Shapiro, Lawrence; Palmer 3rd, Arthur GStructure (London, England : 1993)2008 Aug 61195-20518682221
Modular Ontology Techniques and their Applications in the Biomedical Domain.Pathak, Jyotishman; Johnson, Thomas M; Chute, Christopher GProceedings of the ... IEEE International Conference on Information Reuse and Integration. IEEE International Conference on Information Reuse and Integration2008 Aug 5351-35621625409
Cortical folding patterns and predicting cytoarchitecture.Fischl, Bruce; Rajendran, Niranjini; Busa, Evelina; Augustinack, Jean; Hinds, Oliver; Yeo, B T Thomas; Mohlberg, Hartmut; Amunts, Katrin; Zilles, KarlCerebral cortex (New York, N.Y. : 1991)2008 Aug1973-8018079129
Provenance in neuroimaging.Mackenzie-Graham, Allan J; Van Horn, John D; Woods, Roger P; Crawford, Karen L; Toga, Arthur WNeuroImage2008 Aug 1178-9518519166
A framework for image segmentation using shape models and kernel space shape priors.Dambreville, Samuel; Rathi, Yogesh; Tannenbaum, AllenIEEE transactions on pattern analysis and machine intelligence2008 Aug1385-9918566493
The Simbios National Center: Systems Biology in Motion.Schmidt, Jeanette P; Delp, Scott L; Sherman, Michael A; Taylor, Charles A; Pande, Vijay S; Altman, Russ BProceedings of the IEEE. Institute of Electrical and Electronics Engineers2008 Aug 11266-128020107615
Structural insight into RNA hairpin folding intermediates.Bowman, Gregory R; Huang, Xuhui; Yao, Yuan; Sun, Jian; Carlsson, Gunnar; Guibas, Leonidas J; Pande, Vijay SJournal of the American Chemical Society2008 Jul 309676-818593120
Cardiorespiratory fitness and brain atrophy in early Alzheimer disease.Burns, J M; Cronk, B B; Anderson, H S; Donnelly, J E; Thomas, G P; Harsha, A; Brooks, W M; Swerdlow, R HNeurology2008 Jul 15210-618625967
Modeling of Anatomical Information in Clustering of White Matter Fiber Trajectories Using Dirichlet Distribution.Maddah, Mahnaz; Zollei, Lilla; Grimson, W Eric L; Wells, William MProceedings / sponsored by IEEE Computer Society Technical Committee on Pattern Analysis and Machine Intelligence. Workshop on Mathematical Methods in Biomedical Image Analysis2008 Jul 151-721625356
Family-based SNP association study on 8q24 in bipolar disorder.Zandi, Peter P; Zollner, Sebastian; Avramopoulos, Dimitrios; Willour, Virginia L; Chen, Yi; Qin, Zhaohui S; Burmeister, Margit; Miao, Kuangyi; Gopalakrishnan, Shyam; McEachin, Richard; Potash, James B; Depaulo Jr, J Raymond; McInnis, Melvin GAmerican journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics2008 Jul 5612-818163389
Characterization of coherent structures in the cardiovascular system.Shadden, Shawn C; Taylor, Charles AAnnals of biomedical engineering2008 Jul1152-6218437573
Two-way coupled SPH and particle level set fluid simulation.Losasso, Frank; Talton, Jerry; Kwatra, Nipun; Fedkiw, RonaldIEEE transactions on visualization and computer graphics2008 Jul-Aug797-80418467755
Age-related deficits in fronto-temporal connections in schizophrenia: a diffusion tensor imaging study.Rosenberger, Gudrun; Kubicki, Marek; Nestor, Paul G; Connor, Erin; Bushell, Georgia B; Markant, Douglas; Niznikiewicz, Margaret; Westin, Carl-Fredrik; Kikinis, Ron; J Saykin, Andrew; McCarley, Robert W; Shenton, Martha ESchizophrenia research2008 Jul181-818504117
Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels.Chen, Wei-Min; Erdos, Michael R; Jackson, Anne U; Saxena, Richa; Sanna, Serena; Silver, Kristi D; Timpson, Nicholas J; Hansen, Torben; Orru, Marco; Grazia Piras, Maria; Bonnycastle, Lori L; Willer, Cristen J; Lyssenko, Valeriya; Shen, Haiqing; Kuusisto, JThe Journal of clinical investigation2008 Jul2620-818521185
Feasibility of using real-time MRI to measure joint kinematics in 1.5T and open-bore 0.5T systems.Draper, Christine E; Santos, Juan M; Kourtis, Lampros C; Besier, Thor F; Fredericson, Michael; Beaupre, Gary S; Gold, Garry E; Delp, Scott LJournal of magnetic resonance imaging : JMRI2008 Jul158-6618581329
Cartilage imaging at 3.0T with gradient refocused acquisition in the steady-state (GRASS) and IDEAL fat-water separation.Kijowski, Richard; Tuite, Michael; Passov, Leo; Shimakawa, Ann; Yu, Huanzhou; Hu, Huanzhou; Reeder, Scott BJournal of magnetic resonance imaging : JMRI2008 Jul167-7418581337
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.Ward, Lucas D; Bussemaker, Harmen JBioinformatics (Oxford, England)2008 Jul 1i165-7118586710
Identifying gene-disease associations using centrality on a literature mined gene-interaction network.Ozgur, Arzucan; Vu, Thuy; Erkan, Gunes; Radev, Dragomir RBioinformatics (Oxford, England)2008 Jul 1i277-8518586725
Central Limit Theorem: New SOCR Applet and Demonstration Activity.Dinov, Ivo D; Christou, Nicolas; Sanchez, JuanaJournal of statistics education : an international journal on the teaching and learning of statistics2008 Jul 11-1521833159
Bayesian approach to network modularity.Hofman, Jake M; Wiggins, Chris HPhysical review letters2008 Jun 2725870118643711
Cytoscape ESP: simple search of complex biological networks.Ashkenazi, Maital; Bader, Gary D; Kuchinsky, Allan; Moshelion, Menachem; States, David JBioinformatics (Oxford, England)2008 Jun 151465-618445605
Mapping callosal morphology in early- and late-onset elderly depression: an index of distinct changes in cortical connectivity.Ballmaier, Martina; Kumar, Anand; Elderkin-Thompson, Virginia; Narr, Katherine L; Luders, Eileen; Thompson, Paul M; Hojatkashani, Cornelius; Pham, Daniel; Heinz, Andreas; Toga, Arthur WNeuropsychopharmacology : official publication of the American College of Neuropsychopharmacology2008 Jun1528-3617712348
Geometric observers for dynamically evolving curves.Niethammer, Marc; Vela, Patricio A; Tannenbaum, AllenIEEE transactions on pattern analysis and machine intelligence2008 Jun1093-10818421113
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis.Mitra, Somdeb; Shcherbakova, Inna V; Altman, Russ B; Brenowitz, Michael; Laederach, AlainNucleic acids research2008 June6318477638
Dynamic denoising of tracking sequences.Michailovich, Oleg; Tannenbaum, AllenIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2008 Jun847-5618482881
Thinning of sensorimotor cortices in children with Tourette syndrome.Sowell, Elizabeth R; Kan, Eric; Yoshii, June; Thompson, Paul M; Bansal, Ravi; Xu, Dongrong; Toga, Arthur W; Peterson, Bradley SNature neuroscience2008 Jun637-918488025
The role of SPINK1 in ETS rearrangement-negative prostate cancers.Tomlins, Scott A; Rhodes, Daniel R; Yu, Jianjun; Varambally, Sooryanarayana; Mehra, Rohit; Perner, Sven; Demichelis, Francesca; Helgeson, Beth E; Laxman, Bharathi; Morris, David S; Cao, Qi; Cao, Xuhong; Andren, Ove; Fall, Katja; Johnson, Laura; Wei, John Cancer cell2008 Jun519-2818538735
Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.Huang, Xuhui; Bowman, Gregory R; Pande, Vijay SThe Journal of chemical physics2008 May 2820510618513049
Adsorption of Block Copolymers from Selective Solvents on Curved Surfaces.Hershkovits, Eli; Tannenbaum, Allen; Tannenbaum, RinaMacromolecules2008 May 133190-319820976029
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?Posy, Shoshana; Shapiro, Lawrence; Honig, BarryJournal of molecular biology2008 May 9954-6818395225
Estimation of the multiple testing burden for genomewide association studies of nearly all common variants.Pe'er, Itsik; Yelensky, Roman; Altshuler, David; Daly, Mark JGenetic epidemiology2008 May381-518348202
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.Zeggini, Eleftheria; Scott, Laura J; Saxena, Richa; Voight, Benjamin F; Marchini, Jonathan L; Hu, Tianle; de Bakker, Paul I W; Abecasis, Goncalo R; Almgren, Peter; Andersen, Gitte; Ardlie, Kristin; Bostrom, Kristina Bengtsson; Bergman, Richard N; BonnycasNature genetics2008 May638-4518372903
Self-repelling snakes for topology-preserving segmentation models.Le Guyader, Carole; Vese, Luminita AIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2008 May767-7918390381
Scaling aspects of block co-polymer adsorption on curved surfaces from nonselective solvents.Hershkovits, Eli; Tannenbaum, Allen; Tannenbaum, RinaThe journal of physical chemistry. B2008 May 15317-2618399678
Hamilton-Jacobi skeleton on cortical surfaces.Shi, Y; Thompson, P M; Dinov, I; Toga, A WIEEE transactions on medical imaging2008 May664-7318450539
Introduction to the special section on computer vision for intravascular and intracardiac imaging.Unal, Gozde; Slabaugh, Greg; Kakadiaris, Ioannis A; Tannenbaum, AllenIEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society2008 May273-618693494
Genomic assessment of a multikinase inhibitor, sorafenib, in a rodent model of pulmonary hypertension.Moreno-Vinasco, Liliana; Gomberg-Maitland, Mardi; Maitland, Michael L; Desai, Ankit A; Singleton, Patrick A; Sammani, Saad; Sam, Lee; Liu, Yang; Husain, Aliya N; Lang, Roberto M; Ratain, Mark J; Lussier, Yves A; Garcia, Joe G NPhysiological genomics2008 Apr 22278-9118303084
Age effects on hippocampal structural changes in old men: the HAAS.Xu, Yuan; Valentino, Daniel J; Scher, Ann I; Dinov, Ivo; White, Lon R; Thompson, Paul M; Launer, Lenore J; Toga, Arthur WNeuroImage2008 Apr 151003-1518280181
Normal mode partitioning of Langevin dynamics for biomolecules.Sweet, Christopher R; Petrone, Paula; Pande, Vijay S; Izaguirre, Jesus AThe Journal of chemical physics2008 Apr 1414510118412479
Colon polyp detection using smoothed shape operators: preliminary results.Sundaram, P; Zomorodian, A; Beaulieu, C; Napel, SMedical image analysis2008 Apr99-11917910934
Evidence of interaction between PPARG2 and HNF4A contributing to variation in insulin sensitivity in Mexican Americans.Black, Mary Helen; Fingerlin, Tasha E; Allayee, Hooman; Zhang, Weiming; Xiang, Anny H; Trigo, Enrique; Hartiala, Jaana; Lehtinen, Allison B; Haffner, Steven M; Bergman, Richard N; McEachin, Richard C; Kjos, Siri L; Lawrence, Jean M; Buchanan, Thomas A; WaDiabetes2008 Apr1048-5618162503
A prototype symbolic model of canonical functional neuroanatomy of the motor system.Talos, Ion-Florin; Rubin, Daniel L; Halle, Michael; Musen, Mark; Kikinis, RonJournal of biomedical informatics2008 Apr251-6318164666
A unified framework for clustering and quantitative analysis of white matter fiber tracts.Maddah, Mahnaz; Grimson, W Eric L; Warfield, Simon K; Wells, William MMedical image analysis2008 Apr191-20218180197
Brain morphometry with multiecho MPRAGE.van der Kouwe, Andre J W; Benner, Thomas; Salat, David H; Fischl, BruceNeuroImage2008 Apr 1559-6918242102
Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes.Lee, Hyunju; Kong, Sek Won; Park, Peter JBioinformatics (Oxford, England)2008 Apr 1889-9618263644
Brain anatomical structure segmentation by hybrid discriminative/generative models.Tu, Z; Narr, K L; Dollar, P; Dinov, I; Thompson, P M; Toga, A WIEEE transactions on medical imaging2008 Apr495-50818390346
Structural inference of native and partially folded RNA by high-throughput contact mapping.Das, Rhiju; Kudaravalli, Madhuri; Jonikas, Magdalena; Laederach, Alain; Fong, Robert; Schwans, Jason P; Baker, David; Piccirilli, Joseph A; Altman, Russ B; Herschlag, DanielProceedings of the National Academy of Sciences of the United States of America2008 Mar 184144-918322008
How hydrophobic buckminsterfullerene affects surrounding water structure.Weiss, Dahlia R; Raschke, Tanya M; Levitt, MichaelThe journal of physical chemistry. B2008 Mar 132981-9018275178
Fast approximate surface evolution in arbitrary dimension.Malcolm, James; Rathi, Yogesh; Yezzi, Anthony; Tannenbaum, AllenProceedings of SPIE2008 Mar 11NULL24392194
Using the wild bootstrap to quantify uncertainty in diffusion tensor imaging.Whitcher, Brandon; Tuch, David S; Wisco, Jonathan J; Sorensen, A Gregory; Wang, LiqunHuman brain mapping2008 Mar346-6217455199
Heritability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study.Goldman, Aaron L; Pezawas, Lukas; Mattay, Venkata S; Fischl, Bruce; Verchinski, Beth A; Zoltick, Brad; Weinberger, Daniel R; Meyer-Lindenberg, AndreasBiological psychiatry2008 Mar 1475-8317727823
Humoral response profiling reveals pathways to prostate cancer progression.Taylor, Barry S; Pal, Manoj; Yu, Jianjun; Laxman, Bharathi; Kalyana-Sundaram, Shanker; Zhao, Rong; Menon, Anjana; Wei, John T; Nesvizhskii, Alexey I; Ghosh, Debashis; Omenn, Gilbert S; Lubman, David M; Chinnaiyan, Arul M; Sreekumar, ArunMolecular & cellular proteomics : MCP2008 Mar600-1118077443
Finsler active contours.Melonakos, John; Pichon, Eric; Angenent, Sigurd; Tannenbaum, AllenIEEE transactions on pattern analysis and machine intelligence2008 Mar412-2318195436
Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).Lee, Inhan; Ajay, Subramanian S; Chen, Haiming; Maruyama, Atsushi; Wang, Nulang; McInnis, Melvin G; Athey, Brian DNucleic acids research2008 Mare2718208839
On the construction of invertible filter banks on the 2-sphere.Yeo, Boon Thye Thomas; Ou, Wanmei; Golland, PolinaIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2008 Mar283-30018270119
The effect of early human diet on caudate volumes and IQ.Isaacs, Elizabeth B; Gadian, David G; Sabatini, Stuart; Chong, Wui K; Quinn, Brian T; Fischl, Bruce R; Lucas, AlanPediatric research2008 Mar308-1418287970
Neuropsychological disturbance in schizophrenia: a diffusion tensor imaging study.Nestor, Paul G; Kubicki, Marek; Niznikiewicz, Margaret; Gurrera, Ronald J; McCarley, Robert W; Shenton, Martha ENeuropsychology2008 Mar246-5418331167
Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4.Koehnke, Jesko; Jin, Xiangshu; Trbovic, Nikola; Katsamba, Phinikoula S; Brasch, Julia; Ahlsen, Goran; Scheiffele, Peter; Honig, Barry; Palmer 3rd, Arthur G; Shapiro, LawrenceStructure (London, England : 1993)2008 Mar410-2118334216
Integrated, Multidisciplinary and Technology-Enhanced Science Education: The Next Frontier.Dinov, Ivo DJournal of online learning and teaching / MERLOT2008 Mar 184-9321552453
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models.Qian, Yuntao; Murphy, Robert FBioinformatics (Oxford, England)2008 Feb 15569-7618033795
Accurate prediction of V1 location from cortical folds in a surface coordinate system.Hinds, Oliver P; Rajendran, Niranjini; Polimeni, Jonathan R; Augustinack, Jean C; Wiggins, Graham; Wald, Lawrence L; Diana Rosas, H; Potthast, Andreas; Schwartz, Eric L; Fischl, BruceNeuroImage2008 Feb 151585-9918055222
Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2.Koehnke, Jesko; Jin, Xiangshu; Budreck, Elaine C; Posy, Shoshana; Scheiffele, Peter; Honig, Barry; Shapiro, LawrenceProceedings of the National Academy of Sciences of the United States of America2008 Feb 121873-818250328
Mapping white matter integrity and neurobehavioral correlates in children with fetal alcohol spectrum disorders.Sowell, Elizabeth R; Johnson, Arianne; Kan, Eric; Lu, Lisa H; Van Horn, John Darrell; Toga, Arthur W; O'Connor, Mary J; Bookheimer, Susan YThe Journal of neuroscience : the official journal of the Society for Neuroscience2008 Feb 61313-918256251
Hippocampal morphology and distinguishing late-onset from early-onset elderly depression.Ballmaier, Martina; Narr, Katherine L; Toga, Arthur W; Elderkin-Thompson, Virginia; Thompson, Paul M; Hamilton, Liberty; Haroon, Ebrahim; Pham, Daniel; Heinz, Andreas; Kumar, AnandThe American journal of psychiatry2008 Feb229-3717986679
Construction of a 3D probabilistic atlas of human cortical structures.Shattuck, David W; Mirza, Mubeena; Adisetiyo, Vitria; Hojatkashani, Cornelius; Salamon, Georges; Narr, Katherine L; Poldrack, Russell A; Bilder, Robert M; Toga, Arthur WNeuroImage2008 Feb 11064-8018037310
Automatic independent component labeling for artifact removal in fMRI.Tohka, Jussi; Foerde, Karin; Aron, Adam R; Tom, Sabrina M; Toga, Arthur W; Poldrack, Russell ANeuroImage2008 Feb 11227-4518042495
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data.Stoyanovich, Julia; Pe'er, ItsikBioinformatics (Oxford, England)2008 Feb 1440-218048395
MR-guided prostate interventions.Tempany, Clare; Straus, Sarah; Hata, Nobuhiko; Haker, StevenJournal of magnetic resonance imaging : JMRI2008 Feb356-6718219689
A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer.Laxman, Bharathi; Morris, David S; Yu, Jianjun; Siddiqui, Javed; Cao, Jie; Mehra, Rohit; Lonigro, Robert J; Tsodikov, Alex; Wei, John T; Tomlins, Scott A; Chinnaiyan, Arul MCancer research2008 Feb 1645-918245462
On approximation of smooth functions from samples of partial derivatives with application to phase unwrapping.Michailovich, Oleg; Tannenbaum, AllenIEEE transactions on signal processing : a publication of the IEEE Signal Processing Society2008 Feb 1358-37420046803
Evidence for deficient modulation of amygdala response by prefrontal cortex in bipolar mania.Foland, Lara C; Altshuler, Lori L; Bookheimer, Susan Y; Eisenberger, Naomi; Townsend, Jennifer; Thompson, Paul MPsychiatry research2008 Jan 1527-3718063349
Abnormal cortical thickness and brain-behavior correlation patterns in individuals with heavy prenatal alcohol exposure.Sowell, Elizabeth R; Mattson, Sarah N; Kan, Eric; Thompson, Paul M; Riley, Edward P; Toga, Arthur WCerebral cortex (New York, N.Y. : 1991)2008 Jan136-4417443018
3D mapping of language networks in clinical and pre-clinical Alzheimer's disease.Apostolova, Liana G; Lu, Po; Rogers, Steve; Dutton, Rebecca A; Hayashi, Kiralee M; Toga, Arthur W; Cummings, Jeffrey L; Thompson, Paul MBrain and language2008 Jan33-4117485107
Apathy and the processing of novelty in schizophrenia.Roth, Robert M; Koven, Nancy S; Pendergrass, Jo Cara; Flashman, Laura A; McAllister, Thomas W; Saykin, Andrew JSchizophrenia research2008 Jan232-817884352
An electrostatic deformable model for medical image segmentation.Chang, Herng-Hua; Valentino, Daniel JComputerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society2008 Jan22-3517933492
Detection of cortical thickness correlates of cognitive performance: Reliability across MRI scan sessions, scanners, and field strengths.Dickerson, B C; Fenstermacher, E; Salat, D H; Wolk, D A; Maguire, R P; Desikan, R; Pacheco, J; Quinn, B T; Van der Kouwe, A; Greve, D N; Blacker, D; Albert, M S; Killiany, R J; Fischl, BNeuroImage2008 Jan 110-817942325
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors.Foat, Barrett C; Tepper, Ronald G; Bussemaker, Harmen JNucleic acids research2008 JanD125-3117947326
Identifying patient smoking status from medical discharge records.Uzuner, Ozlem; Goldstein, Ira; Luo, Yuan; Kohane, IsaacJournal of the American Medical Informatics Association : JAMIA2008 Jan-Feb14-2417947624
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.Sprague, Judy; Bayraktaroglu, Leyla; Bradford, Yvonne; Conlin, Tom; Dunn, Nathan; Fashena, David; Frazer, Ken; Haendel, Melissa; Howe, Douglas G; Knight, Jonathan; Mani, Prita; Moxon, Sierra A T; Pich, Christian; Ramachandran, Sridhar; Schaper, Kevin; SegNucleic acids research2008 JanD768-7217991680
Impulse-based control of joints and muscles.Weinstein, Rachel; Guendelman, Eran; Fedkiw, RonaldIEEE transactions on visualization and computer graphics2008 Jan-Feb37-4617993700
A de-identifier for medical discharge summaries.Uzuner, Ozlem; Sibanda, Tawanda C; Luo, Yuan; Szolovits, PeterArtificial intelligence in medicine2008 Jan13-3518053696
Biomedical ontologies: a functional perspective.Rubin, Daniel L; Shah, Nigam H; Noy, Natalya FBriefings in bioinformatics2008 Jan75-9018077472
Lowering the barriers inherent in translating advances in neuroimage analysis to clinical research applications.Pujol, Sonia; Kikinis, Ron; Gollub, RandyAcademic radiology2008 Jan114-818078914
Combining molecular dynamics and machine learning to improve protein function recognition.Glazer, Dariya S; Radmer, Randall J; Altman, Russ BPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2008332-4318229697
A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival.Yu, Jianjun; Yu, Jindan; Cordero, Kevin E; Johnson, Michael D; Ghosh, Debashis; Rae, James M; Chinnaiyan, Arul M; Lippman, Marc ENeoplasia (New York, N.Y.)2008 Jan79-8818231641
A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas.Mani, Kartik M; Lefebvre, Celine; Wang, Kai; Lim, Wei Keat; Basso, Katia; Dalla-Favera, Riccardo; Califano, AndreaMolecular systems biology200816918277385
Crouched postures reduce the capacity of muscles to extend the hip and knee during the single-limb stance phase of gait.Hicks, Jennifer L; Schwartz, Michael H; Arnold, Allison S; Delp, Scott LJournal of biomechanics2008960-718291404
Mapping progressive brain structural changes in early Alzheimer's disease and mild cognitive impairment.Apostolova, Liana G; Thompson, Paul MNeuropsychologia20081597-61218395760
Gene Ontology annotations: what they mean and where they come from.Hill, David P; Smith, Barry; McAndrews-Hill, Monica S; Blake, Judith ABMC bioinformatics2008S218460184
iTools: a framework for classification, categorization and integration of computational biology resources.Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; AltmaPloS one2008e226518509477
Automatic localization of anatomical point landmarks for brain image processing algorithms.Neu, Scott C; Toga, Arthur WNeuroinformatics2008135-4818512163
poolHiTS: a shifted transversal design based pooling strategy for high-throughput drug screening.Kainkaryam, Raghunandan M; Woolf, Peter JBMC bioinformatics200825618513431
Bioinformatics detection of alternative splicing.Kim, Namshin; Lee, ChristopherMethods in molecular biology (Clifton, N.J.)2008179-9718566765
Reconstruction of full-length isoforms from splice graphs.Xing, Yi; Lee, ChristopherMethods in molecular biology (Clifton, N.J.)2008199-20518566766
Translating the Foundational Model of Anatomy into OWL.Noy, Natalya F; Rubin, Daniel LWeb semantics (Online)2008133-13618688289
Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.Boorsma, Andre; Lu, Xiang-Jun; Zakrzewska, Anna; Klis, Frans M; Bussemaker, Harmen JPloS one2008e311218769540
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments.Laederach, Alain; Das, Rhiju; Vicens, Quentin; Pearlman, Samuel M; Brenowitz, Michael; Herschlag, Daniel; Altman, Russ BNature protocols20081395-40118772866
ConTrack: finding the most likely pathways between brain regions using diffusion tractography.Sherbondy, Anthony J; Dougherty, Robert F; Ben-Shachar, Michal; Napel, Sandy; Wandell, Brian AJournal of vision200815.1-1618831651
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications.Halperin, Inbal; Glazer, Dariya S; Wu, Shirley; Altman, Russ BBMC genomics2008S218831785
Introducing meta-services for biomedical information extraction.Leitner, Florian; Krallinger, Martin; Rodriguez-Penagos, Carlos; Hakenberg, Jorg; Plake, Conrad; Kuo, Cheng-Ju; Hsu, Chun-Nan; Tsai, Richard Tzong-Han; Hung, Hsi-Chuan; Lau, William W; Johnson, Calvin A; Saetre, Rune; Yoshida, Kazuhiro; Chen, Yan Hua; KimGenome biology2008S618834497
A distributed spatio-temporal EEG/MEG inverse solver.Ou, Wanmei; Golland, Polina; Hamalainen, MattiMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention200826-3418979728
Model-based segmentation of hippocampal subfields in ultra-high resolution in vivo MRI.Van Leemput, Koen; Bakkour, Akram; Benner, Thomas; Wiggins, Graham; Wald, Lawrence L; Augustinack, Jean; Dickerson, Bradford C; Golland, Polina; Fischl, BruceMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008235-4318979753
Joint segmentation of thalamic nuclei from a population of diffusion tensor MR images.Ziyan, Ulas; Westin, Carl-FredrikMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008279-8618979758
Shape analysis with overcomplete spherical wavelets.Yeo, B T Thomas; Yu, Peng; Grant, P Ellen; Fischl, Bruce; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008468-7618979780
Particle-based shape analysis of multi-object complexes.Cates, Joshua; Fletcher, P Thomas; Styner, Martin; Hazlett, Heather Cody; Whitaker, RossMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008477-8518979781
Spherical demons: fast surface registration.Yeo, B T Thomas; Sabuncu, Mert; Vercauteren, Tom; Ayache, Nicholas; Fischl, Bruce; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008745-5318979813
Findings in schizophrenia by tract-oriented DT-MRI analysis.Maddah, Mahnaz; Kubicki, Marek; Wells, William M; Westin, Carl-Fredrik; Shenton, Martha E; Grimson, W Eric LMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008917-2418979833
Discovering structure in the space of activation profiles in fMRI.Lashkari, Danial; Vul, Ed; Kanwisher, Nancy; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention20081016-2418979845
Group statistics of DTI fiber bundles using spatial functions of tensor measures.Goodlett, Casey B; Fletcher, P Thomas; Gilmore, John H; Gerig, GuidoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention20081068-7518979851
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information.Luo, Weijun; Hankenson, Kurt D; Woolf, Peter JBMC bioinformatics200846718980677
Harmonic surface mapping with Laplace-Beltrami eigenmaps.Shi, Yonggang; Lai, Rongjie; Kern, Kyle; Sicotte, Nancy; Dinov, Ivo; Toga, Arthur WMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008147-5418982600
Assessment of reliability of multi-site neuroimaging via traveling phantom study.Gouttard, Sylvain; Styner, Martin; Prastawa, Marcel; Piven, Joseph; Gerig, GuidoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008263-7018982614
Fieldmap-free retrospective registration and distortion correction for EPI-based functional imaging.Poynton, Clare; Jenkinson, Mark; Whalen, Stephen; Golby, Alexandra J; Wells 3rd, WilliamMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008271-918982615
Discovering modes of an image population through mixture modeling.Sabuncu, Mert R; Balci, Serdar K; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008381-918982628
Models of normal variation and local contrasts in hippocampal anatomy.Liu, Xinyang; Mio, Washington; Shi, Yonggang; Dinov, Ivo; Liu, Xiuwen; Lepore, Natasha; Lepore, Franco; Fortin, Madeleine; Voss, Patrice; Lassonde, Maryse; Thompson, Paul MMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008407-1518982631
Label space: a coupled multi-shape representation.Malcolm, James; Rathi, Yogesh; Shenton, Martha E; Tannenbaum, AllenMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008416-2418982632
Software strategy for robotic transperineal prostate therapy in closed-bore MRI.Tokuda, Junichi; Fischer, Gregory S; Csoma, Csaba; DiMaio, Simon P; Gobbi, David G; Fichtinger, Gabor; Tempany, Clare M; Hata, NobuhikoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2008701-918982666
UMLS-Query: a perl module for querying the UMLS.Shah, Nigam H; Shah, Nigam; Muse, Mark A; Musen, MarkAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2008652-618998805
Second i2b2 workshop on natural language processing challenges for clinical records.Uzuner, OzlemAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium20081252-318998924
An interactive tool for visualizing design heterogeneity in clinical trials.Hernandez, Maria-Elena; Carini, Simona; Storey, Margaret-Anne; Sim, IdaAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2008298-30218998925
Integrating outside modules into the i2b2 architecture.Mendis, Michael; Phillips, Lori C; Kuttan, Rajesh; Pan, Wensong; Gainer, Vivian; Kohane, Isaac; Murphy, Shawn NAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2008105418999021
Characterization of patients who suffer asthma exacerbations using data extracted from electronic medical records.Himes, Blanca E; Kohane, Isaac S; Ramoni, Marco F; Weiss, Scott TAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2008308-1218999057
Identification and extraction of family history information from clinical reports.Goryachev, Sergey; Kim, Hyeoneui; Zeng-Treitler, QingAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2008247-5118999129
Comparison of ontology-based semantic-similarity measures.Lee, Wei-Nchih; Shah, Nigam; Sundlass, Karanjot; Musen, MarkAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2008384-818999312
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.Mo, Fan; Hong, Xu; Gao, Feng; Du, Lin; Wang, Jun; Omenn, Gilbert S; Lin, BiaoyangBMC bioinformatics200853719087293
Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing.Shen, Yufeng; Sarin, Sumeet; Liu, Ye; Hobert, Oliver; Pe'er, ItsikPloS one2008e401219107202
A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI Analysis.Maddah, Mahnaz; Zollei, Lilla; Grimson, W Eric L; Westin, Carl-Fredrik; Wells, William MProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2008105-10819212449
Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.Noy, Natalya F; de Coronado, Sherri; Solbrig, Harold; Fragoso, Gilberto; Hartel, Frank W; Musen, Mark AApplied ontology2008 Jan 1173-19019789731
Adapting Clinical Ontologies in Real-World Environments.Stenzhorn, Holger; Schulz, Stefan; Boeker, Martin; Smith, BarryJournal of universal computer science : J. UCS20083767-378020390048
AUTOMATED COMPARISON OF PROTEIN SUBCELLULAR LOCATION PATTERNS BETWEEN IMAGES OF NORMAL AND CANCEROUS TISSUES.Glory, Estelle; Newberg, Justin; Murphy, Robert FProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2008304-30720628549
TRACKING THROUGH CHANGES IN SCALE.Lankton, Shawn; Malcolm, James; Nakhmani, Arie; Tannenbaum, AllenProceedings / ICIP ... International Conference on Image Processing2008241-24423645076
Localized Statistics for DW-MRI Fiber Bundle Segmentation.Lankton, Shawn; Melonakos, John; Malcolm, James; Dambreville, Samuel; Tannenbaum, AllenProceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition20081-823652079
KERNEL-BASED HIGH-DIMENSIONAL HISTOGRAM ESTIMATION FOR VISUAL TRACKING.Karasev, Peter; Malcolm, James; Tannenbaum, AllenProceedings / ICIP ... International Conference on Image Processing20082728-273123666258
A Graph Cut Approach to Image Segmentation in Tensor Space.Malcolm, James; Rathi, Yogesh; Tannenbaum, AllenProceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition20081-823680693
Hierarchical tree snipping: clustering guided by prior knowledge.Dotan-Cohen, Dikla; Melkman, Avraham A; Kasif, SimonBioinformatics (Oxford, England)2007 Dec 153335-4217989094
Negative findings in electronic health records and biomedical ontologies: a realist approach.Ceusters, Werner; Elkin, Peter; Smith, BarryInternational journal of medical informatics2007 DecS326-3317369081
Distinct regional atrophy in the corpus callosum of patients with temporal lobe epilepsy.Weber, Bernd; Luders, Eileen; Faber, Jennifer; Richter, Sabine; Quesada, Carlos M; Urbach, Horst; Thompson, Paul M; Toga, Arthur W; Elger, Christian E; Helmstaedter, ChristophBrain : a journal of neurology2007 Dec3149-5417728360
Mouse models of diabetic neuropathy.Sullivan, Kelli A; Hayes, John M; Wiggin, Timothy D; Backus, Carey; Su Oh, Sang; Lentz, Stephen I; Brosius 3rd, Frank; Feldman, Eva LNeurobiology of disease2007 Dec276-8517804249
Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data.David, Lawrence A; Wiggins, Chris HAnnals of the New York Academy of Sciences2007 Dec90-10117925346
Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol.Spirin, Victor; Schmidt, Steffen; Pertsemlidis, Alexander; Cooper, Richard S; Cohen, Jonathan C; Sunyaev, Shamil RAmerican journal of human genetics2007 Dec1298-30317952847
Automated learning of generative models for subcellular location: building blocks for systems biology.Zhao, Ting; Murphy, Robert FCytometry. Part A : the journal of the International Society for Analytical Cytology2007 Dec978-9017972315
Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution.Schroder, Gunnar F; Brunger, Axel T; Levitt, MichaelStructure (London, England : 1993)2007 Dec1630-4118073112
Analysis of sequence conservation at nucleotide resolution.Asthana, Saurabh; Roytberg, Mikhail; Stamatoyannopoulos, John; Sunyaev, ShamilPLoS computational biology2007 Dece25418166073
Global analysis of alternative splicing differences between humans and chimpanzees.Calarco, John A; Xing, Yi; Caceres, Mario; Calarco, Joseph P; Xiao, Xinshu; Pan, Qun; Lee, Christopher; Preuss, Todd M; Blencowe, Benjamin JGenes & development2007 Nov 152963-7517978102
Predicting allosteric communication in myosin via a pathway of conserved residues.Tang, Susan; Liao, Jung-Chi; Dunn, Alexander R; Altman, Russ B; Spudich, James A; Schmidt, Jeanette PJournal of molecular biology2007 Nov 91361-7317900617
Functional specificity of a Hox protein mediated by the recognition of minor groove structure.Joshi, Rohit; Passner, Jonathan M; Rohs, Remo; Jain, Rinku; Sosinsky, Alona; Crickmore, Michael A; Jacob, Vinitha; Aggarwal, Aneel K; Honig, Barry; Mann, Richard SCell2007 Nov 2530-4317981120
Protege: a tool for managing and using terminology in radiology applications.Rubin, Daniel L; Noy, Natalya F; Musen, Mark AJournal of digital imaging : the official journal of the Society for Computer Applications in Radiology2007 Nov34-4617687607
Topological analysis of large-scale biomedical terminology structures.Bales, Michael E; Lussier, Yves A; Johnson, Stephen BJournal of the American Medical Informatics Association : JAMIA2007 Nov-Dec788-9717712094
Interactive visualization of volumetric white matter connectivity in DT-MRI using a parallel-hardware Hamilton-Jacobi solver.Jeong, Won-Ki; Fletcher, P Thomas; Tao, Ran; Whitaker, RossIEEE transactions on visualization and computer graphics2007 Nov-Dec1480-717968100
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.Smith, Barry; Ashburner, Michael; Rosse, Cornelius; Bard, Jonathan; Bug, William; Ceusters, Werner; Goldberg, Louis J; Eilbeck, Karen; Ireland, Amelia; Mungall, Christopher J; OBI Consortium; Leontis, Neocles; Rocca-Serra, Philippe; Ruttenberg, Alan; SansNature biotechnology2007 Nov1251-517989687
OpenSim: open-source software to create and analyze dynamic simulations of movement.Delp, Scott L; Anderson, Frank C; Arnold, Allison S; Loan, Peter; Habib, Ayman; John, Chand T; Guendelman, Eran; Thelen, Darryl GIEEE transactions on bio-medical engineering2007 Nov1940-5018018689
Diffusion tensor analysis with invariant gradients and rotation tangents.Kindlmann, Gordon; Ennis, Daniel B; Whitaker, Ross T; Westin, Carl-FredrikIEEE transactions on medical imaging2007 Nov1483-9918041264
Corpus callosum abnormalities in women with borderline personality disorder and comorbid attention-deficit hyperactivity disorder.Rusch, Nicolas; Luders, Eileen; Lieb, Klaus; Zahn, Roland; Ebert, Dieter; Thompson, Paul M; Toga, Arthur W; van Elst, Ludger TebartzJournal of psychiatry & neuroscience : JPN2007 Nov417-2218043765
Global Medical Shape Analysis Using the Volumetric Laplace Spectrum.Reuter, Martin; Niethammer, Marc; Wolter, Franz-Erich; Bouix, Sylvain; Shenton, MarthaLecture notes in computer science2007 Oct 24417-42620046537
Event-related functional magnetic resonance imaging of response inhibition in obsessive-compulsive disorder.Roth, Robert M; Saykin, Andrew J; Flashman, Laura A; Pixley, Heather S; West, John D; Mamourian, Alexander CBiological psychiatry2007 Oct 15901-917511967
Frontal connections and cognitive changes in normal aging rhesus monkeys: a DTI study.Makris, Nikos; Papadimitriou, George M; van der Kouwe, Andre; Kennedy, David N; Hodge, Steven M; Dale, Anders M; Benner, Thomas; Wald, Lawrence L; Wu, Ona; Tuch, David S; Caviness, Verne S; Moore, Tara L; Killiany, Ronald J; Moss, Mark B; Rosene, Douglas Neurobiology of aging2007 Oct1556-6716962214
The effect of excessive tibial torsion on the capacity of muscles to extend the hip and knee during single-limb stance.Hicks, Jennifer; Arnold, Allison; Anderson, Frank; Schwartz, Michael; Delp, ScottGait & posture2007 Oct546-5217229573
Positive correlations between corpus callosum thickness and intelligence.Luders, Eileen; Narr, Katherine L; Bilder, Robert M; Thompson, Paul M; Szeszko, Philip R; Hamilton, Liberty; Toga, Arthur WNeuroImage2007 Oct 11457-6417689267
Using the logarithm of odds to define a vector space on probabilistic atlases.Pohl, Kilian M; Fisher, John; Bouix, Sylvain; Shenton, Martha; McCarley, Robert W; Grimson, W Eric L; Kikinis, Ron; Wells, William MMedical image analysis2007 Oct465-7717698403
What is where and why it is important.Toga, Arthur W; Thompson, Paul MNeuroImage2007 Oct 11045-9; discussion 1066-817720552
Atlas stratification.Blezek, Daniel J; Miller, James VMedical image analysis2007 Oct443-5717765003
Early postnatal development of corpus callosum and corticospinal white matter assessed with quantitative tractography.Gilmore, J H; Lin, W; Corouge, I; Vetsa, Y S K; Smith, J K; Kang, C; Gu, H; Hamer, R M; Lieberman, J A; Gerig, GAJNR. American journal of neuroradiology2007 Oct1789-9517923457
Three-dimensional gray matter atrophy mapping in mild cognitive impairment and mild Alzheimer disease.Apostolova, Liana G; Steiner, Calen A; Akopyan, Gohar G; Dutton, Rebecca A; Hayashi, Kiralee M; Toga, Arthur W; Cummings, Jeffrey L; Thompson, Paul MArchives of neurology2007 Oct1489-9517923632
Segmentation of brain MR images using a charged fluid model.Chang, Herng-Hua; Valentino, Daniel J; Duckwiler, Gary R; Toga, Arthur WIEEE transactions on bio-medical engineering2007 Oct1798-81317926678
Asymmetries of cortical thickness: effects of handedness, sex, and schizophrenia.Hamilton, Liberty S; Narr, Katherine L; Luders, Eileen; Szeszko, Philip R; Thompson, Paul M; Bilder, Robert M; Toga, Arthur WNeuroreport2007 Sep 171427-3117712268
Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish.Mabee, Paula M; Arratia, Gloria; Coburn, Miles; Haendel, Melissa; Hilton, Eric J; Lundberg, John G; Mayden, Richard L; Rios, Nelson; Westerfield, MonteJournal of experimental zoology. Part B, Molecular and developmental evolution2007 Sep 15655-6817599725
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis.Xiang, Zuoshuang; Minter, Rebecca M; Bi, Xiaoming; Woolf, Peter J; He, YongqunBioinformatics (Oxford, England)2007 Sep 152423-3217644819
Medline search engine for finding genetic markers with biological significance.Xuan, Weijian; Wang, Pinglang; Watson, Stanley J; Meng, FanBioinformatics (Oxford, England)2007 Sep 152477-8417823133
Acceleration of cerebral ventricular expansion in the Cardiovascular Health Study.Carmichael, Owen T; Kuller, L H; Lopez, O L; Thompson, P M; Dutton, R A; Lu, A; Lee, S E; Lee, J Y; Aizenstein, H J; Meltzer, C C; Liu, Y; Toga, A W; Becker, J TNeurobiology of aging2007 Sep1316-2116875759
Reduced neocortical thickness and complexity mapped in mesial temporal lobe epilepsy with hippocampal sclerosis.Lin, Jack J; Salamon, Noriko; Lee, Agatha D; Dutton, Rebecca A; Geaga, Jennifer A; Hayashi, Kiralee M; Luders, Eileen; Toga, Arthur W; Engel Jr, Jerome; Thompson, Paul MCerebral cortex (New York, N.Y. : 1991)2007 Sep2007-1817088374
Relationships between IQ and regional cortical gray matter thickness in healthy adults.Narr, Katherine L; Woods, Roger P; Thompson, Paul M; Szeszko, Philip; Robinson, Delbert; Dimtcheva, Teodora; Gurbani, Mala; Toga, Arthur W; Bilder, Robert MCerebral cortex (New York, N.Y. : 1991)2007 Sep2163-7117118969
QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments.Kim, Namshin; Lee, ChristopherBioinformatics (Oxford, England)2007 Sep 12331-317599926
Evaluating the state-of-the-art in automatic de-identification.Uzuner, Ozlem; Luo, Yuan; Szolovits, PeterJournal of the American Medical Informatics Association : JAMIA2007 Sep-Oct550-6317600094
Informatics challenges in structured RNA.Laederach, AlainBriefings in bioinformatics2007 Sep294-30317611237
Direct mapping of hippocampal surfaces with intrinsic shape context.Shi, Yonggang; Thompson, Paul M; de Zubicaray, Greig I; Rose, Stephen E; Tu, Zhuowen; Dinov, Ivo; Toga, Arthur WNeuroImage2007 Sep 1792-80717625918
Regional cortical thinning in subjects with violent antisocial personality disorder or schizophrenia.Narayan, Veena M; Narr, Katherine L; Kumari, Veena; Woods, Roger P; Thompson, Paul M; Toga, Arthur W; Sharma, TonmoyThe American journal of psychiatry2007 Sep1418-2717728428
Transparent rendering of intraluminal contrast for 3D polyp visualization at CT colonography.Shi, Rong; Napel, Sandy; Rosenberg, Jarrett K; Shin, Lewis K; Walsh, Cynthia F; Mogensen, Monique A; Joshi, Ajay Jayant; Pankhudi, Pankhudi; Beaulieu, Christopher FJournal of computer assisted tomography2007 Sep-Oct773-917895791
A hierarchical algorithm for MR brain image parcellation.Pohl, Kilian M; Bouix, Sylvain; Nakamura, Motoaki; Rohlfing, Torsten; McCarley, Robert W; Kikinis, Ron; Grimson, W Eric L; Shenton, Martha E; Wells, William MIEEE transactions on medical imaging2007 Sep1201-1217896593
Distribution Metrics and Image Segmentation.Georgiou, Tryphon; Michailovich, Oleg; Rathi, Yogesh; Malcolm, James; Tannenbaum, AllenLinear algebra and its applications2007 Sep 1663-67218769529
A package for exact kinetic data structures and sweepline algorithms.Russel, Daniel; Karavelas, Menelaos I; Guibas, Leonidas JComputational geometry : theory and applications2007 Sep 1111-12721165159
Polymer Adsorption on Curved Surfaces: A Geometric Approach.Hershkovits, Eli; Tannenbaum, Allen; Tannenbaum, RinaThe journal of physical chemistry. C, Nanomaterials and interfaces2007 Aug 2312369-1237523710263
Web-based GeneChip analysis system for large-scale collaborative projects.Dai, Manhong; Wang, Pinglang; Jakupovic, Elvis; Watson, Stanley J; Meng, FanBioinformatics (Oxford, England)2007 Aug 152185-717586830
Reduced microstructural integrity of the white matter underlying anterior cingulate cortex is associated with increased saccadic latency in schizophrenia.Manoach, Dara S; Ketwaroo, G Avinash; Polli, Frida E; Thakkar, Katharine N; Barton, Jason J S; Goff, Donald C; Fischl, Bruce; Vangel, Mark; Tuch, David SNeuroImage2007 Aug 15599-61017590354
Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain.Dauguet, Julien; Peled, Sharon; Berezovskii, Vladimir; Delzescaux, Thierry; Warfield, Simon K; Born, Richard; Westin, Carl-FredrikNeuroImage2007 Aug 15530-817604650
Abnormal cortical folding patterns within Broca's area in schizophrenia: evidence from structural MRI.Wisco, Jonathan J; Kuperberg, Gina; Manoach, Dara; Quinn, Brian T; Busa, Evelina; Fischl, Bruce; Heckers, Stephan; Sorensen, A GregorySchizophrenia research2007 Aug317-2717490861
Tracking deforming objects using particle filtering for geometric active contours.Rathi, Yogesh; Vaswani, Namrata; Tannenbaum, Allen; Yezzi, AnthonyIEEE transactions on pattern analysis and machine intelligence2007 Aug1470-517568149
Increased anterior abdominal aortic wall motion: possible role in aneurysm pathogenesis and design of endovascular devices.Goergen, Craig J; Johnson, Bonnie L; Greve, Joan M; Taylor, Charles A; Zarins, Christopher KJournal of endovascular therapy : an official journal of the International Society of Endovascular Specialists2007 Aug574-8417696635
Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism.Lee, Jong-Min; Ivanova, Elena V; Seong, Ihn Sik; Cashorali, Tanya; Kohane, Isaac; Gusella, James F; MacDonald, Marcy EPLoS genetics2007 Auge13517708681
A Novel Representation for Riemannian Analysis of Elastic Curves in ýýýJoshi, Shantanu H; Klassen, Eric; Srivastava, Anuj; Jermyn, IanProceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition2007 Jul 161-721311729
Persistent voids: a new structural metric for membrane fusion.Kasson, Peter M; Zomorodian, Afra; Park, Sanghyun; Singhal, Nina; Guibas, Leonidas J; Pande, Vijay SBioinformatics (Oxford, England)2007 Jul 151753-917488753
OBO to OWL: a protege OWL tab to read/save OBO ontologies.Moreira, Dilvan A; Musen, Mark ABioinformatics (Oxford, England)2007 Jul 151868-7017496317
Volumetric cerebral characteristics of children exposed to opiates and other substances in utero.Walhovd, K B; Moe, V; Slinning, K; Due-Tonnessen, P; Bjornerud, A; Dale, A M; van der Kouwe, A; Quinn, B T; Kosofsky, B; Greve, D; Fischl, BNeuroImage2007 Jul 151331-4417513131
On evaluating brain tissue classifiers without a ground truth.Bouix, Sylvain; Martin-Fernandez, Marcos; Ungar, Lida; Nakamura, Motoaki; Koo, Min-Seong; McCarley, Robert W; Shenton, Martha ENeuroImage2007 Jul 151207-2417532646
Probing genetic overlap among complex human phenotypes.Rzhetsky, Andrey; Wajngurt, David; Park, Naeun; Zheng, TianProceedings of the National Academy of Sciences of the United States of America2007 Jul 1011694-917609372
Phase maps reveal cortical architecture.Fischl, Bruce; Wald, Lawrence LProceedings of the National Academy of Sciences of the United States of America2007 Jul 1011513-417609374
Sex differences in cortical thickness mapped in 176 healthy individuals between 7 and 87 years of age.Sowell, Elizabeth R; Peterson, Bradley S; Kan, Eric; Woods, Roger P; Yoshii, June; Bansal, Ravi; Xu, Dongrong; Zhu, Hongtu; Thompson, Paul M; Toga, Arthur WCerebral cortex (New York, N.Y. : 1991)2007 Jul1550-6016945978
Differential effects of typical and atypical antipsychotics on brain myelination in schizophrenia.Bartzokis, George; Lu, Po H; Nuechterlein, Keith H; Gitlin, Michael; Doi, Clarissa; Edwards, Nancy; Lieu, Christopher; Altshuler, Lori L; Mintz, JimSchizophrenia research2007 Jul13-2217407804
Phenotype ontologies: the bridge between genomics and evolution.Mabee, Paula M; Ashburner, Michael; Cronk, Quentin; Gkoutos, Georgios V; Haendel, Melissa; Segerdell, Erik; Mungall, Chris; Westerfield, MonteTrends in ecology & evolution2007 Jul345-5017416439
Using surface envelopes to constrain molecular modeling.Dugan, Jonathan M; Altman, Russ BProtein science : a publication of the Protein Society2007 Jul1266-7317586766
Brain mapping as a tool to study neurodegeneration.Apostolova, Liana G; Thompson, Paul MNeurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics2007 Jul387-40017599704
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks.Lim, Wei Keat; Wang, Kai; Lefebvre, Celine; Califano, AndreaBioinformatics (Oxford, England)2007 Jul 1i282-817646307
Information theory applied to the sparse gene ontology annotation network to predict novel gene function.Tao, Ying; Sam, Lee; Li, Jianrong; Friedman, Carol; Lussier, Yves ABioinformatics (Oxford, England)2007 Jul 1i529-3817646340
Automated image analysis of protein localization in budding yeast.Chen, Shann-Ching; Zhao, Ting; Gordon, Geoffrey J; Murphy, Robert FBioinformatics (Oxford, England)2007 Jul 1i66-7117646347
Strategies for identifying statistically significant dense regions in microarray data.Yip, Andy M; Ng, Michael K; Wu, Edmond H; Chan, Tony FIEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM2007 Jul-Sep415-2917666761
The Release 5.1 annotation of Drosophila melanogaster heterochromatin.Smith, Christopher D; Shu, Shengqiang; Mungall, Christopher J; Karpen, Gary HScience (New York, N.Y.)2007 Jun 151586-9117569856
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.Alekseyenko, Alexander V; Lee, Christopher JBioinformatics (Oxford, England)2007 Jun 11386-9317234640
Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model.Zheng, Wenjun; Liao, Jung-Chi; Brooks, Bernard R; Doniach, SebastianProteins2007 Jun 1886-9617373706
Direct cortical mapping via solving partial differential equations on implicit surfaces.Shi, Yonggang; Thompson, Paul M; Dinov, Ivo; Osher, Stanley; Toga, Arthur WMedical image analysis2007 Jun207-2317379568
Cortical mapping of genotype-phenotype relationships in schizophrenia.Bearden, Carrie E; van Erp, Theo G M; Thompson, Paul M; Toga, Arthur W; Cannon, Tyrone DHuman brain mapping2007 Jun519-3217437284
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.Scott, Laura J; Mohlke, Karen L; Bonnycastle, Lori L; Willer, Cristen J; Li, Yun; Duren, William L; Erdos, Michael R; Stringham, Heather M; Chines, Peter S; Jackson, Anne U; Prokunina-Olsson, Ludmila; Ding, Chia-Jen; Swift, Amy J; Narisu, Narisu; Hu, TianScience (New York, N.Y.)2007 Jun 11341-517463248
Statistical group comparison of diffusion tensors via multivariate hypothesis testing.Whitcher, Brandon; Wisco, Jonathan J; Hadjikhani, Nouchine; Tuch, David SMagnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine2007 Jun1065-7417534902
Computational analysis of non-adherence and non-attendance using the text of narrative physician notes in the electronic medical record.Turchin, Alexander; Kolatkar, Nikheel S; Pendergrass, Merri L; Kohane, Isaac SMedical informatics and the Internet in medicine2007 Jun93-10217541859
Network-based analysis of affected biological processes in type 2 diabetes models.Liu, Manway; Liberzon, Arthur; Kong, Sek Won; Lai, Weil R; Park, Peter J; Kohane, Isaac S; Kasif, SimonPLoS genetics2007 June9617571924
Statistical properties of Jacobian maps and the realization of unbiased large-deformation nonlinear image registration.Leow, Alex D; Yanovsky, Igor; Chiang, Ming-Chang; Lee, Agatha D; Klunder, Andrea D; Lu, Allen; Becker, James T; Davis, Simon W; Toga, Arthur W; Thompson, Paul MIEEE transactions on medical imaging2007 Jun822-3217679333
Brain surface conformal parameterization using Riemann surface structure.Wang, Yalin; Lui, Lok Ming; Gu, Xianfeng; Hayashi, Kiralee M; Chan, Tony F; Toga, Arthur W; Thompson, Paul M; Yau, Shing-TungIEEE transactions on medical imaging2007 Jun853-6517679336
CSF sub-compartments in relation to plasma osmolality in healthy controls and in patients with first episode schizophrenia.Gunduz-Bruce, Handan; Narr, Katherine L; Gueorguieva, Ralitza; Toga, Arthur W; Szeszko, Philip R; Ashtari, Manzar; Robinson, Delbert G; Sevy, Serge; Kane, John M; Bilder, Robert MPsychiatry research2007 May 1557-6617398079
Integrating biomedical knowledge to model pathways of prostate cancer progression.Morris, David S; Tomlins, Scott A; Rhodes, Daniel R; Mehra, Rohit; Shah, Rajal B; Chinnaiyan, Arul MCell cycle (Georgetown, Tex.)2007 May 151177-8717495538
Functional magnetic resonance imaging of verbal learning in children with heavy prenatal alcohol exposure.Sowell, Elizabeth R; Lu, Lisa H; O'Hare, Elizabeth D; McCourt, Sarah T; Mattson, Sarah N; O'Connor, Mary J; Bookheimer, Susan YNeuroreport2007 May 7635-917426589
Normal developmental changes in inferior frontal gray matter are associated with improvement in phonological processing: a longitudinal MRI analysis.Lu, Lh; Leonard, Cm; Thompson, Pm; Kan, E; Jolley, J; Welcome, Se; Toga, Aw; Sowell, ErCerebral cortex (New York, N.Y. : 1991)2007 May1092-916782757
Coplanar and coaxial orientations of RNA bases and helices.Laederach, Alain; Chan, Joseph M; Schwartzman, Armin; Willgohs, Eric; Altman, Russ BRNA (New York, N.Y.)2007 May643-5017339576
Occipital lobe gray matter volume in male patients with chronic schizophrenia: A quantitative MRI study.Onitsuka, Toshiaki; McCarley, Robert W; Kuroki, Noriomi; Dickey, Chandlee C; Kubicki, Marek; Demeo, Susan S; Frumin, Melissa; Kikinis, Ron; Jolesz, Ferenc A; Shenton, Martha ESchizophrenia research2007 May197-20617350226
Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes.Alekseyenko, Alexander V; Kim, Namshin; Lee, Christopher JRNA (New York, N.Y.)2007 May661-7017369312
White matter fiber tractography and color mapping of the normal human cerebellum with diffusion tensor imaging.Salamon, N; Sicotte, N; Drain, A; Frew, A; Alger, J R; Jen, J; Perlman, S; Salamon, GJournal of neuroradiology. Journal de neuroradiologie2007 May115-2817481730
Genetic algorithms for finite mixture model based voxel classification in neuroimaging.Tohka, Jussi; Krestyannikov, Evgeny; Dinov, Ivo D; Graham, Allan MacKenzie; Shattuck, David W; Ruotsalainen, Ulla; Toga, Arthur WIEEE transactions on medical imaging2007 May696-71117518064
Genetic criteria for Huntington's disease pathogenesis.Gusella, James F; Macdonald, MarcyBrain research bulletin2007 Apr 3078-8217352930
Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding.Laederach, Alain; Shcherbakova, Inna; Jonikas, Magdalena A; Altman, Russ B; Brenowitz, MichaelProceedings of the National Academy of Sciences of the United States of America2007 Apr 247045-5017438287
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.Sosinsky, Alona; Honig, Barry; Mann, Richard S; Califano, AndreaProceedings of the National Academy of Sciences of the United States of America2007 Apr 106305-1017395715
Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function.Chen, Yili; Blackwell, Thomas W; Chen, Ji; Gao, Jing; Lee, Angel W; States, David JPLoS computational biology2007 Apr 6e6317411336
Longitudinal in vivo reproducibility of cartilage volume and surface in osteoarthritis of the knee.Brem, M H; Pauser, J; Yoshioka, H; Brenning, A; Stratmann, J; Hennig, F F; Kikinis, R; Duryea, J; Winalski, C S; Lang, PSkeletal radiology2007 Apr315-2017219231
Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells.Tu, Lan Chun; Yan, Xiaowei; Hood, Leroy; Lin, BiaoyangMolecular & cellular proteomics : MCP2007 Apr575-8817220478
Local RNA structural changes induced by crystallization are revealed by SHAPE.Vicens, Quentin; Gooding, Anne R; Laederach, Alain; Cech, Thomas RRNA (New York, N.Y.)2007 Apr536-4817299128
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies.Kryukov, Gregory V; Pennacchio, Len A; Sunyaev, Shamil RAmerican journal of human genetics2007 Apr727-3917357078
Atlas renormalization for improved brain MR image segmentation across scanner platforms.Han, Xiao; Fischl, BruceIEEE transactions on medical imaging2007 Apr479-8617427735
Geometrically accurate topology-correction of cortical surfaces using nonseparating loops.Segonne, Florent; Pacheco, Jenni; Fischl, BruceIEEE transactions on medical imaging2007 Apr518-2917427739
Automated extraction of the cortical sulci based on a supervised learning approach.Tu, Zhuowen; Zheng, Songfeng; Yuille, Alan L; Reiss, Allan L; Dutton, Rebecca A; Lee, Agatha D; Galaburda, Albert M; Dinov, Ivo; Thompson, Paul M; Toga, Arthur WIEEE transactions on medical imaging2007 Apr541-5217427741
Cortical surface shape analysis based on spherical wavelets.Yu, Peng; Grant, P Ellen; Qi, Yuan; Han, Xiao; Segonne, Florent; Pienaar, Rudolph; Busa, Evelina; Pacheco, Jenni; Makris, Nikos; Buckner, Randy L; Golland, Polina; Fischl, BruceIEEE transactions on medical imaging2007 Apr582-9717427744
Multiscale 3-D shape representation and segmentation using spherical wavelets.Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, AllenIEEE transactions on medical imaging2007 Apr598-61817427745
Feature selection and molecular classification of cancer using genetic programming.Yu, Jianjun; Yu, Jindan; Almal, Arpit A; Dhanasekaran, Saravana M; Ghosh, Debashis; Worzel, William P; Chinnaiyan, Arul MNeoplasia (New York, N.Y.)2007 Apr292-30317460773
STATISTICAL SHAPE ANALYSIS OF BRAIN STRUCTURES USING SPHERICAL WAVELETS.Nain, D; Styner, M; Niethammer, M; Levitt, J J; Shenton, M E; Gerig, G; Bobick, A; Tannenbaum, AProceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging2007 Apr 1209-21219888446
Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location.Inaoka, Hidenori; Fukuoka, Yutaka; Kohane, Isaac SProceedings of the National Academy of Sciences of the United States of America2007 Mar 205020-517360362
Interictal alterations of the trigeminal somatosensory pathway and periaqueductal gray matter in migraine.DaSilva, Alexandre F M; Granziera, Cristina; Tuch, David S; Snyder, Josh; Vincent, Maurice; Hadjikhani, NouchineNeuroreport2007 Mar 5301-517435592
Semi-Automatic Parcellation of the Corpus Striatum.Al-Hakim, Ramsey; Nain, Delphine; Levitt, James; Shenton, Martha; Tannenbaum, AllenProceedings of SPIE2007 Mar 565123624511366
Tissue Tracking: Applications for Brain MRI Classification.Melonakos, John; Gao, Yi; Tannenbaum, AllenProceedings of SPIE2007 Mar 3NULL24392193
Ventricular volume and dementia progression in the Cardiovascular Health Study.Carmichael, Owen T; Kuller, Lewis H; Lopez, Oscar L; Thompson, Paul M; Dutton, Rebecca A; Lu, Allen; Lee, Sharon E; Lee, Jessica Y; Aizenstein, Howard J; Meltzer, Carolyn Cidis; Liu, Yanxi; Toga, Arthur W; Becker, James TNeurobiology of aging2007 Mar389-9716504345
Fracturing rigid materials.Bao, Zhaosheng; Hong, Jeong-Mo; Teran, Joseph; Fedkiw, RonaldIEEE transactions on visualization and computer graphics2007 Mar-Apr370-817218752
Candidate mechanisms for chemotherapy-induced cognitive changes.Ahles, Tim A; Saykin, Andrew JNature reviews. Cancer2007 Mar192-20117318212
Altered orbitofrontal sulcogyral pattern in schizophrenia.Nakamura, Motoaki; Nestor, Paul G; McCarley, Robert W; Levitt, James J; Hsu, Lillian; Kawashima, Toshiro; Niznikiewicz, Margaret; Shenton, Martha EBrain : a journal of neurology2007 Mar693-70717347256
Cavum septum pellucidum in schizophrenia: clinical and neuropsychological correlates.Flashman, Laura A; Roth, Robert M; Pixley, Heather S; Cleavinger, Howard B; McAllister, Thomas W; Vidaver, Robert; Saykin, Andrew JPsychiatry research2007 Feb 28147-5517291728
Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways.Liao, Jung-Chi; Spudich, James A; Parker, David; Delp, Scott LProceedings of the National Academy of Sciences of the United States of America2007 Feb 273171-617360624
Callosal morphology in Williams syndrome: a new evaluation of shape and thickness.Luders, Eileen; Di Paola, Margherita; Tomaiuolo, Francesco; Thompson, Paul M; Toga, Arthur W; Vicari, Stefano; Petrides, Michael; Caltagirone, CarloNeuroreport2007 Feb 12203-717314657
The uncinate fasciculus and extraversion in schizotypal personality disorder: a diffusion tensor imaging study.Gurrera, Ronald J; Nakamura, Motoaki; Kubicki, Marek; Dickey, Chandlee C; Niznikiewicz, Margaret A; Voglmaier, Martina M; McCarley, Robert W; Shenton, Martha E; Westin, Carl-Fredrik; Maier, Stephan E; Seidman, Larry JSchizophrenia research2007 Feb360-217126532
Asymmetries of cortical shape: Effects of handedness, sex and schizophrenia.Narr, Katherine L; Bilder, Robert M; Luders, Eileen; Thompson, Paul M; Woods, Roger P; Robinson, Delbert; Szeszko, Philip R; Dimtcheva, Teodora; Gurbani, Mala; Toga, Arthur WNeuroImage2007 Feb 1939-4817166743
Boosting the sampling efficiency of q-Ball imaging using multiple wavevector fusion.Khachaturian, Mark H; Wisco, Jonathan J; Tuch, David SMagnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine2007 Feb289-9617260358
Image-based musculoskeletal modeling: applications, advances, and future opportunities.Blemker, Silvia S; Asakawa, Deanna S; Gold, Garry E; Delp, Scott LJournal of magnetic resonance imaging : JMRI2007 Feb441-5117260405
Localisation of increased prefrontal white matter in pathological liars.Yang, Yaling; Raine, Adrian; Narr, Katherine L; Lencz, Todd; LaCasse, Lori; Colletti, Patrick; Toga, Arthur WThe British journal of psychiatry : the journal of mental science2007 Feb174-517267937
Iterative regularization and nonlinear inverse scale space applied to wavelet-based denoising.Xu, Jinjun; Osher, StanleyIEEE transactions on image processing : a publication of the IEEE Signal Processing Society2007 Feb534-4417269645
Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements.Lee, Ji-Ann; Xing, Yi; Nguyen, David; Xie, Jiuyong; Lee, Christopher J; Black, Douglas LPLoS biology2007 Febe4017298178
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.Rhodes, Daniel R; Kalyana-Sundaram, Shanker; Mahavisno, Vasudeva; Varambally, Radhika; Yu, Jianjun; Briggs, Benjamin B; Barrette, Terrence R; Anstet, Matthew J; Kincead-Beal, Colleen; Kulkarni, Prakash; Varambally, Sooryanaryana; Ghosh, Debashis; ChinnaiyNeoplasia (New York, N.Y.)2007 Feb166-8017356713
Tracking Alzheimer's disease.Thompson, Paul M; Hayashi, Kiralee M; Dutton, Rebecca A; Chiang, Ming-Chang; Leow, Alex D; Sowell, Elizabeth R; De Zubicaray, Greig; Becker, James T; Lopez, Oscar L; Aizenstein, Howard J; Toga, Arthur WAnnals of the New York Academy of Sciences2007 Feb183-21417413023
SAGA: a subgraph matching tool for biological graphs.Tian, Yuanyuan; McEachin, Richard C; Santos, Carlos; States, David J; Patel, Jignesh MBioinformatics (Oxford, England)2007 Jan 15232-917110368
Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics.Sun, Bingyun; Ranish, Jeffrey A; Utleg, Angelita G; White, James T; Yan, Xiaowei; Lin, Biaoyang; Hood, LeroyMolecular & cellular proteomics : MCP2007 Jan141-917074749
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.Kim, Namshin; Alekseyenko, Alexander V; Roy, Meenakshi; Lee, ChristopherNucleic acids research2007 JanD93-817108355
The HIV positive selection mutation database.Pan, Calvin; Kim, Joseph; Chen, Lamei; Wang, Qi; Lee, ChristopherNucleic acids research2007 JanD371-517108357
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together.Jayapandian, Magesh; Chapman, Adriane; Tarcea, V Glenn; Yu, Cong; Elkiss, Aaron; Ianni, Angela; Liu, Bin; Nandi, Arnab; Santos, Carlos; Andrews, Philip; Athey, Brian; States, David; Jagadish, H VNucleic acids research2007 JanD566-7117130145
Integrative molecular concept modeling of prostate cancer progression.Tomlins, Scott A; Mehra, Rohit; Rhodes, Daniel R; Cao, Xuhong; Wang, Lei; Dhanasekaran, Saravana M; Kalyana-Sundaram, Shanker; Wei, John T; Rubin, Mark A; Pienta, Kenneth J; Shah, Rajal B; Chinnaiyan, Arul MNature genetics2007 Jan41-5117173048
Computational approaches to phenotyping: high-throughput phenomics.Lussier, Yves A; Liu, YangProceedings of the American Thoracic Society2007 Jan18-2517202287
A gel-based proteomic comparison of human cerebrospinal fluid between inflicted and non-inflicted pediatric traumatic brain injury.Gao, Wei-Min; Chadha, Mandeep S; Berger, Rachel P; Omenn, Gilbert S; Allen, David L; Pisano, Michael; Adelson, P David; Clark, Robert S B; Jenkins, Larry W; Kochanek, Patrick MJournal of neurotrauma2007 Jan43-5317263669
Predictive modeling of genome-wide mRNA expression: from modules to molecules.Bussemaker, Harmen J; Foat, Barrett C; Ward, Lucas DAnnual review of biophysics and biomolecular structure2007329-4717311525
Cerebral ventricular changes associated with transitions between normal cognitive function, mild cognitive impairment, and dementia.Carmichael, Owen T; Kuller, Lewis H; Lopez, Oscar L; Thompson, Paul M; Dutton, Rebecca A; Lu, Allen; Lee, Sharon E; Lee, Jessica Y; Aizenstein, Howard J; Meltzer, Carolyn C; Liu, Yanxi; Toga, Arthur W; Becker, James TAlzheimer disease and associated disorders2007 Jan-Mar14-2417334268
Hippocampal volume and shape analysis in an older adult population.McHugh, Tara L; Saykin, Andrew J; Wishart, Heather A; Flashman, Laura A; Cleavinger, Howard B; Rabin, Laura A; Mamourian, Alexander C; Shen, LiThe Clinical neuropsychologist2007 Jan130-4517366281
Evolutionary-conserved gene expression response profiles across mammalian tissues.Chen, Ji; Blackwell, Thomas W; Fermin, Damian; Menon, Rajasree; Chen, Yili; Gao, Jing; Lee, Angel W; States, David JOmics : a journal of integrative biology200796-11517411398
Evaluation of high-throughput functional categorization of human disease genes.Chen, James L; Liu, Yang; Sam, Lee T; Li, Jianrong; Lussier, Yves ABMC bioinformatics2007S717493290
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Structural correlates of apathy in Alzheimer's disease.Apostolova, Liana G; Akopyan, Gohar G; Partiali, Negar; Steiner, Calen A; Dutton, Rebecca A; Hayashi, Kiralee M; Dinov, Ivo D; Toga, Arthur W; Cummings, Jeffrey L; Thompson, Paul MDementia and geriatric cognitive disorders200791-717570907
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Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization.Kim, Namshin; Lee, ChristopherBMC bioinformatics200721317584922
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Challenges in image-guided therapy system design.Dimaio, Simon; Kapur, Tina; Cleary, Kevin; Aylward, Stephen; Kazanzides, Peter; Vosburgh, Kirby; Ellis, Randy; Duncan, James; Farahani, Keyvan; Lemke, Heinz; Peters, Terry; Lorensen, William Bill; Gobbi, David; Haller, John; Clarke, Laurence Larry; Pizer,NeuroImage2007S144-5117644360
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Tract-based morphometry.O'Donnell, Lauren J; Westin, Carl-Fredrik; Golby, Alexandra JMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2007161-818044565
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MCMC curve sampling for image segmentation.Fan, Ayres C; Fisher 3rd, John W; Wells 3rd, William M; Levitt, James J; Willsky, Alan SMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2007477-8518044603
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Quantification of measurement error in DTI: theoretical predictions and validation.Goodlett, Casey; Fletcher, P Thomas; Lin, Weili; Gerig, GuidoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention200710-718051038
Finsler tractography for white matter connectivity analysis of the cingulum bundle.Melonakos, John; Mohan, Vandana; Niethammer, Marc; Smith, Kate; Kubicki, Marek; Tannenbaum, AllenMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention200736-4318051041
Detection of spatial activation patterns as unsupervised segmentation of fMRI data.Golland, Polina; Golland, Yulia; Malach, RafaelMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2007110-818051050
Outlier rejection for diffusion weighted imaging.Niethammer, Marc; Bouix, Sylvain; Aja-Fernandez, Santiago; Westin, Carl-Fredrik; Shenton, Martha EMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2007161-818051055
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Application of open source image guided therapy software in MR-guided therapies.Hata, Nobuhiko; Piper, Steve; Jolesz, Ferenc A; Tempany, Clare M C; Black, Peter McL; Morikawa, Shigehiro; Iseki, Horoshi; Hashizume, Makoto; Kikinis, RonMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2007491-818051095
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Global medical shape analysis using the Laplace-Beltrami spectrum.Niethammer, Marc; Reuter, Martin; Wolter, Franz-Erich; Bouix, Sylvain; Peinecke, Niklas; Koo, Min-Seong; Shenton, Martha EMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2007850-718051138
Detection and segmentation of pathological structures by the extended graph-shifts algorithm.Corso, Jason J; Yuille, Alan; Sicotte, Nancy L; Toga, ArthurMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2007985-9318051154
Brain atlases and neuroanatomic imaging.MacKenzie-Graham, Allan; Boline, Jyl; Toga, Arthur WMethods in molecular biology (Clifton, N.J.)2007183-9418368367
Relating alternative splicing to proteome complexity and genome evolution.Xing, Yi; Lee, ChristopherAdvances in experimental medicine and biology200736-4918380339
Interpretation errors related to the GO annotation file format.Moreira, Dilvan A; Shah, Nigam H; Musen, Mark AAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2007538-4218693894
Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside.Murphy, Shawn N; Mendis, Michael; Hackett, Kristel; Kuttan, Rajesh; Pan, Wensong; Phillips, Lori C; Gainer, Vivian; Berkowicz, David; Glaser, John P; Kohane, Isaac; Chueh, Henry CAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2007548-5218693896
Integration of Hive and cell software in the i2b2 architecture.Mendis, Michael; Wattanasin, Nich; Kuttan, Rajesh; Pan, Wensong; Philips, Lori; Hackett, Kristel; Gainer, Vivian; Chueh, Henry C; Murphy, ShawnAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2007104818694146
Prioritizing Disease Genes by Analysis of Common Elements (PDG-ACE).McEachin, Richard C; Keller, Benjamin J; Zandi, Peter P; Almani, Mohsen; McInnis, Melvin GAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2007106818694166
Structural integrity of the uncinate fasciculus in geriatric depression: Relationship with age of onset.Taylor, Warren D; MacFall, James R; Gerig, Guido; Krishnan, Ranga RNeuropsychiatric disease and treatment2007669-7419300596
Free-Form B-spline Deformation Model for Groupwise Registration.Balci, Serdar K; Golland, Polina; Shenton, Martha; Wells, William MMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention200723-3020224762
Joint Registration and Clustering of Images.Sabuncu, Mert R; Shenton, Martha E; Golland, PolinaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention200747-5420224763
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Removing Shape-Preserving Transformations in Square-Root Elastic (SRE) Framework for Shape Analysis of Curves.Joshi, Shantanu H; Klassen, Eric; Srivastava, Anuj; Jermyn, IanProceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition2007387-39821738385
Locally-Constrained Region-Based Methods for DW-MRI Segmentation.Melonakos, John; Niethammer, Marc; Mohan, Vandana; Kubicki, Marek; Miller, James V; Tannenbaum, AllenProceedings / IEEE International Conference on Computer Vision. IEEE International Conference on Computer Vision20078-Jan23857521
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Middle and inferior temporal gyrus gray matter volume abnormalities in first-episode schizophrenia: an MRI study.Kuroki, Noriomi; Shenton, Martha E; Salisbury, Dean F; Hirayasu, Yoshio; Onitsuka, Toshiaki; Ersner-Hershfield, Hal; Yurgelun-Todd, Deborah; Kikinis, Ron; Jolesz, Ferenc A; McCarley, Robert WThe American journal of psychiatry2006 Dec2103-1017151161
NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth.Palomero, Teresa; Lim, Wei Keat; Odom, Duncan T; Sulis, Maria Luisa; Real, Pedro J; Margolin, Adam; Barnes, Kelly C; O'Neil, Jennifer; Neuberg, Donna; Weng, Andrew P; Aster, Jon C; Sigaux, Francois; Soulier, Jean; Look, A Thomas; Young, Richard A; CalifanProceedings of the National Academy of Sciences of the United States of America2006 Nov 2818261-617114293
Detection and mapping of hippocampal abnormalities in autism.Nicolson, Rob; DeVito, Timothy J; Vidal, Christine N; Sui, Yihong; Hayashi, Kiralee M; Drost, Dick J; Williamson, Peter C; Rajakumar, Nagalingam; Toga, Arthur W; Thompson, Paul MPsychiatry research2006 Nov 2211-2117056234
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.Liu, Yang; Li, Jianrong; Sam, Lee; Goh, Chern-Sing; Gerstein, Mark; Lussier, Yves APLoS computational biology2006 Nov 17e15917112314
A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma.Liu, Fenghua; Park, Peter J; Lai, Weil; Maher, Elizabeth; Chakravarti, Arnab; Durso, Laura; Jiang, Xiuli; Yu, Yi; Brosius, Amanda; Thomas, Meredith; Chin, Lynda; Brennan, Cameron; DePinho, Ronald A; Kohane, Isaac; Carroll, Rona S; Black, Peter M; Johnson,Cancer research2006 Nov 1510815-2317090523
3D comparison of hippocampal atrophy in amnestic mild cognitive impairment and Alzheimer's disease.Apostolova, Liana G; Dinov, Ivo D; Dutton, Rebecca A; Hayashi, Kiralee M; Toga, Arthur W; Cummings, Jeffrey L; Thompson, Paul MBrain : a journal of neurology2006 Nov2867-7317018552
Selecting "significant" differentially expressed genes from the combined perspective of the null and the alternative.Moerkerke, B; Goetghebeur, EJournal of computational biology : a journal of computational molecular cell biology2006 Nov1513-3117147475
The paradoxical behavior of a highly structured misfolded intermediate in RNA folding.Russell, Rick; Das, Rhiju; Suh, Hyejean; Travers, Kevin J; Laederach, Alain; Engelhardt, Mark A; Herschlag, DanielJournal of molecular biology2006 Oct 20531-4416963081
Increased local gyrification mapped in Williams syndrome.Gaser, Christian; Luders, Eileen; Thompson, Paul M; Lee, Agatha D; Dutton, Rebecca A; Geaga, Jennifer A; Hayashi, Kiralee M; Bellugi, Ursula; Galaburda, Albert M; Korenberg, Julie R; Mills, Debra L; Toga, Arthur W; Reiss, Allan LNeuroImage2006 Oct 1546-5416901723
Regional brain atrophy in cognitively intact adults with a single APOE epsilon4 allele.Wishart, H A; Saykin, A J; McAllister, T W; Rabin, L A; McDonald, B C; Flashman, L A; Roth, R M; Mamourian, A C; Tsongalis, G J; Rhodes, C HNeurology2006 Oct 101221-417030756
Bio-Ontology and text: bridging the modeling gap.Friedman, Carol; Borlawsky, Tara; Shagina, Lyudmila; Xing, H Rosie; Lussier, Yves ABioinformatics (Oxford, England)2006 Oct 12421-916870928
A multivariate approach for integrating genome-wide expression data and biological knowledge.Kong, Sek Won; Pu, William T; Park, Peter JBioinformatics (Oxford, England)2006 Oct 12373-8016877751
Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.Corouge, Isabelle; Fletcher, P Thomas; Joshi, Sarang; Gouttard, Sylvain; Gerig, GuidoMedical image analysis2006 Oct786-9816926104
Integral invariants for shape matching.Manay, Siddharth; Cremers, Daniel; Hong, Byung-Woo; Yezzi Jr, Anthony J; Soatto, StefanoIEEE transactions on pattern analysis and machine intelligence.2006 Oct1602-1816986542
Strategies for plasma proteomic profiling of cancers.Omenn, Gilbert SProteomics2006 Oct5662-7316991194
Characterizing the shape of anatomical structures with Poisson's equation.Haidar, Haissam; Bouix, Sylvain; Levitt, James J; McCarley, Robert W; Shenton, Martha E; Soul, Janet SIEEE transactions on medical imaging2006 Oct1249-5717024829
3D mapping of mini-mental state examination performance in clinical and preclinical Alzheimer disease.Apostolova, Liana G; Lu, Po H; Rogers, Steve; Dutton, Rebecca A; Hayashi, Kiralee M; Toga, Arthur W; Cummings, Jeffrey L; Thompson, Paul MAlzheimer disease and associated disorders2006 Oct-Dec224-3117132966
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Older adults with cognitive complaints show brain atrophy similar to that of amnestic MCI.Saykin, A J; Wishart, H A; Rabin, L A; Santulli, R B; Flashman, L A; West, J D; McHugh, T L; Mamourian, A CNeurology.2006 Sep 12834-4216966547
Imitating manual curation of text-mined facts in biomedicine.Rodriguez-Esteban, Raul; Iossifov, Ivan; Rzhetsky, AndreyPLoS computational biology2006 Sep 8e11816965176
Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis.MacKenzie-Graham, Allan; Tinsley, Matthew R; Shah, Kaanan P; Aguilar, Cynthia; Strickland, Lauren V; Boline, Jyl; Martin, Melanie; Morales, Laurie; Shattuck, David W; Jacobs, Russell E; Voskuhl, Rhonda R; Toga, Arthur WNeuroImage.2006 Sep1016-2316806982
Huntington's disease: seeing the pathogenic process through a genetic lens.Gusella, James F; MacDonald, Marcy ETrends in biochemical sciences2006 Sep533-4016829072
Standards for plasma and serum proteomics in early cancer detection: a needs assessment report from the national institute of standards and technology--National Cancer Institute Standards, Methods, Assays, Reagents and Technologies Workshop, August 18-19,Barker, Peter E; Wagner, Paul D; Stein, Stephen E; Bunk, David M; Srivastava, Sudhir; Omenn, Gilbert SClinical chemistry2006 Sep1669-7416840585
A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers.Carter, Scott L; Eklund, Aron C; Kohane, Isaac S; Harris, Lyndsay N; Szallasi, ZoltanNature genetics2006 Sep1043-816921376
Association of transcription factor 7-like 2 (TCF7L2) variants with type 2 diabetes in a Finnish sample.Scott, Laura J; Bonnycastle, Lori L; Willer, Cristen J; Sprau, Andrew G; Jackson, Anne U; Narisu, Narisu; Duren, William L; Chines, Peter S; Stringham, Heather M; Erdos, Michael R; Valle, Timo T; Tuomilehto, Jaakko; Bergman, Richard N; Mohlke, Karen L; CoDiabetes2006 Sep2649-5316936217
Damage to the human cerebellum from prenatal alcohol exposure: the anatomy of a simple biometrical explanation.Bookstein, Fred L; Streissguth, Ann P; Connor, Paul D; Sampson, Paul DAnatomical record. Part B, New anatomist2006 Sep195-20916955499
Image-guided neurosurgery at Brigham and Women's Hospital.Dimaio, Simon P; Archip, Neculai; Hata, Nobuhiko; Talos, Ion-Florin; Warfield, Simon K; Majumdar, Amit; Mcdannold, Nathan; Hynynen, Kullervo; Morrison, Paul R; Wells 3rd, William M; Kacher, Daniel F; Ellis, Randy E; Golby, Alexandra J; Black, Peter M; JolIEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society2006 Sep-Oct67-7317020201
Referent tracking for treatment optimisation in schizophrenic patients: A case study in applying philosophical ontology to diagnostic algorithms.Ceusters, Werner; Smith, BarryWeb semantics (Online)2006 Sep 1229-23623459504
A susceptible-infected model of early detection of respiratory infection outbreaks on a background of influenza.Mohtashemi, Mojdeh; Szolovits, Peter; Dunyak, James; Mandl, Kenneth DJournal of theoretical biology2006 Aug 21954-6316556450
White matter abnormalities in dystonia normalize after botulinum toxin treatment.Blood, Anne J; Tuch, David S; Makris, Nikos; Makhlouf, Miriam L; Sudarsky, Lewis R; Sharma, NutanNeuroreport2006 Aug 211251-516951564
Hemispheric asymmetries in cortical thickness.Luders, E; Narr, K L; Thompson, P M; Rex, D E; Jancke, L; Toga, A WCerebral cortex (New York, N.Y. : 1991) 2006 Aug1232-816267139
Skull-stripping magnetic resonance brain images using a model-based level set.Zhuang, Audrey H; Valentino, Daniel J; Toga, Arthur WNeuroImage.2006 Aug 179-9216697666
Coronary vessel trees from 3D imagery: a topological approach.Szymczak, Andrzej; Stillman, Arthur; Tannenbaum, Allen; Mischaikow, KonstantinMedical image analysis2006 Aug548-5916798058
Deformable spanners and applications.Gao, Jie; Guibas, Leonidas J; Nguyen, AnComputational geometry : theory and applications2006 Aug 12-1921165161
Functional magnetic resonance imaging of executive control in bipolar disorder.Roth, Robert M; Koven, Nancy S; Randolph, John J; Flashman, Laura A; Pixley, Heather S; Ricketts, Sarah M; Wishart, Heather A; Saykin, Andrew JNeuroreport.2006 Jul 311085-916837832
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.Foat, Barrett C; Morozov, Alexandre V; Bussemaker, Harmen JBioinformatics (Oxford, England)2006 Jul 15e141-916873464
SNP Function Portal: a web database for exploring the function implication of SNP alleles.Wang, Pinglang; Dai, Manhong; Xuan, Weijian; McEachin, Richard C; Jackson, Anne U; Scott, Laura J; Athey, Brian; Watson, Stanley J; Meng, FanBioinformatics (Oxford, England)2006 Jul 15e523-916873516
The incidentalome: a threat to genomic medicine.Kohane, Isaac S; Masys, Daniel R; Altman, Russ BJAMA : the journal of the American Medical Association2006 Jul 12212-516835427
Lobar distribution of lesion volumes in late-life depression: the Biomedical Informatics Research Network (BIRN).MacFall, James R; Taylor, Warren D; Rex, David E; Pieper, Steve; Payne, Martha E; McQuoid, Douglas R; Steffens, David C; Kikinis, Ron; Toga, Arthur W; Krishnan, K Ranga RamaNeuropsychopharmacology : official publication of the American College of Neuropsychopharmacology2006 Jul1500-716341022
Fornix integrity and hippocampal volume in male schizophrenic patients.Kuroki, Noriomi; Kubicki, Marek; Nestor, Paul G; Salisbury, Dean F; Park, Hae-Jeong; Levitt, James J; Woolston, Sophie; Frumin, Melissa; Niznikiewicz, Margaret; Westin, Carl-Fredrik; Maier, Stephan E; McCarley, Robert W; Shenton, Martha EBiological psychiatry2006 Jul 122-3116406249
Effect of acute aldosterone administration on gene expression profile in the heart.Turchin, Alexander; Guo, Christine Z; Adler, Gail K; Ricchiuti, Vincent; Kohane, Isaac S; Williams, Gordon HEndocrinology2006 Jul3183-916601137
Evolutionary divergence of exon flanks: a dissection of mutability and selection.Xing, Yi; Wang, Qi; Lee, ChristopherGenetics2006 Jul1787-9116702427
White matter alterations in cerebral amyloid angiopathy measured by diffusion tensor imaging.Salat, David H; Smith, Eric E; Tuch, David S; Benner, Thomas; Pappu, Vasanth; Schwab, Kristin M; Gurol, M Edip; Rosas, H Diana; Rosand, Jonathan; Greenberg, Steven MStroke; a journal of cerebral circulation.2006 Jul1759-6416763176
Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.Liu, Hongye; Kho, Alvin T; Kohane, Isaac S; Sun, YaoPLoS medicine2006 Jule23216800721
Of mice and men: cancer gene discovery using comparative oncogenomics.Tomlins, Scott A; Chinnaiyan, Arul MCancer cell2006 Jul2-416843259
Normal variants of Microcephalin and ASPM do not account for brain size variability.Woods, Roger P; Freimer, Nelson B; De Young, Joseph A; Fears, Scott C; Sicotte, Nancy L; Service, Susan K; Valentino, Daniel J; Toga, Arthur W; Mazziotta, John CHuman molecular genetics.2006 Jun 152025-916687438
LONI visualization environment.Dinov, Ivo D; Valentino, Daniel; Shin, Bae Cheol; Konstantinidis, Fotios; Hu, Guogang; MacKenzie-Graham, Allan; Lee, Erh-Fang; Shattuck, David; Ma, Jeff; Schwartz, Craig; Toga, Arthur WJournal of digital imaging : the official journal of the Society for Computer Applications in Radiology2006 Jun148-5816598642
CT colonography: influence of 3D viewing and polyp candidate features on interpretation with computer-aided detection.Shi, Rong; Schraedley-Desmond, Pamela; Napel, Sandy; Olcott, Eric W; Jeffrey Jr, R Brooke; Yee, Judy; Zalis, Michael E; Margolis, Daniel; Paik, David S; Sherbondy, Anthony J; Sundaram, Padmavathi; Beaulieu, Christopher FRadiology.2006 Jun768-7616714460
Adaptive reproducing kernel particle method for extraction of the cortical surface.Xu, Meihe; Thompson, Paul M; Toga, Arthur WIEEE transactions on medical imaging.2006 Jun755-6716768240
A Bayesian model for joint segmentation and registration.Pohl, Kilian M; Fisher, John; Grimson, W Eric L; Kikinis, Ron; Wells, William MNeuroImage.2006 May 15228-3916466677
Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule.Laederach, Alain; Shcherbakova, Inna; Liang, Mike P; Brenowitz, Michael; Altman, Russ BJournal of molecular biology.2006 May 121179-9016574145
Dynamic simulation of articulated rigid bodies with contact and collision.Weinstein, Rachel; Teran, Joseph; Fedkiw, RonIEEE transactions on visualization and computer graphics.2006 May-Jun365-7416640250
Conversion of mild cognitive impairment to Alzheimer disease predicted by hippocampal atrophy maps.Apostolova, Liana G; Dutton, Rebecca A; Dinov, Ivo D; Hayashi, Kiralee M; Toga, Arthur W; Cummings, Jeffrey L; Thompson, Paul MArchives of neurology2006 May693-916682538
A method for clustering white matter fiber tracts.O'Donnell, L J; Kubicki, M; Shenton, M E; Dreusicke, M H; Grimson, W E L; Westin, C FAJNR. American journal of neuroradiology2006 May1032-616687538
Gender effects on cortical thickness and the influence of scaling.Luders, E; Narr, K L; Thompson, P M; Rex, D E; Woods, R P; Deluca, H; Jancke, L; Toga, A WHuman brain mapping2006 Apr314-2416124013
Parasagittal asymmetries of the corpus callosum.Luders, E; Narr, K L; Zaidel, E; Thompson, P M; Jancke, L; Toga, A WCerebral cortex (New York, N.Y. : 1991)2006 Mar346-5415901651
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Mapping brain maturation.Toga, Arthur W; Thompson, Paul M; Sowell, Elizabeth RTrends in neurosciences2006 Mar148-5916472876
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A Web-based telemedicine system for diabetic retinopathy screening using digital fundus photography.Wei, Jack C; Valentino, Daniel J; Bell, Douglas S; Baker, Richard STelemedicine journal and e-health : the official journal of the American Telemedicine Association.2006 Feb50-716478413
Rectus femoris and vastus intermedius fiber excursions predicted by three-dimensional muscle models.Blemker, Silvia S; Delp, Scott LJournal of biomechanics.20061383-9115972213
Three-dimensional patterns of hippocampal atrophy in mild cognitive impairment.Becker, James T; Davis, Simon W; Hayashi, Kiralee M; Meltzer, Carolyn Cidis; Toga, Arthur W; Lopez, Oscar L; Thompson, Paul M; Imaging Methods and Analysis in Geriatrics Research GroupArchives of neurology2006 Jan97-10116401741
Creation and implications of a phenome-genome network.Butte, Atul J; Kohane, Isaac SNature biotechnology2006 Jan55-6216404398
Despeckling of medical ultrasound images.Michailovich, Oleg V; Tannenbaum, AllenIEEE transactions on ultrasonics, ferroelectrics, and frequency control2006 Jan64-7816471433
Mapping heritability and molecular genetic associations with cortical features using probabilistic brain atlases: methods and applications to schizophrenia.Cannon, Tyrone D; Thompson, Paul M; van Erp, Theo G M; Huttunen, Matti; Lonnqvist, Jouko; Kaprio, Jaakko; Toga, Arthur WNeuroinformatics.20065-1916595856
Imaging phenotypes and genotypes in schizophrenia.Turner, Jessica A; Smyth, Padhraic; Macciardi, Fabio; Fallon, James H; Kennedy, James L; Potkin, Steven GNeuroinformatics.200621-4916595857
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.Fermin, Damian; Allen, Baxter B; Blackwell, Thomas W; Menon, Rajasree; Adamski, Marcin; Xu, Yin; Ulintz, Peter; Omenn, Gilbert S; States, David JGenome biology2006R3516646984
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs.Xing, Yi; Yu, Tianwei; Wu, Ying Nian; Roy, Meenakshi; Kim, Joseph; Lee, ChristopherNucleic acids research.20063150-6016757580
Dynamic mapping of normal human hippocampal development.Gogtay, Nitin; Nugent 3rd, Tom F; Herman, David H; Ordonez, Anna; Greenstein, Deanna; Hayashi, Kiralee M; Clasen, Liv; Toga, Arthur W; Giedd, Jay N; Rapoport, Judith L; Thompson, Paul MHippocampus2006664-7216826559
Detecting transcriptionally active regions using genomic tiling arrays.Halasz, Gabor; van Batenburg, Marinus F; Perusse, Joelle; Hua, Sujun; Lu, Xiang-Jun; White, Kevin P; Bussemaker, Harmen JGenome biology2006R5916859498
Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system.Zeng, Qing T; Goryachev, Sergey; Weiss, Scott; Sordo, Margarita; Murphy, Shawn N; Lazarus, RossBMC medical informatics and decision making [electronic resource].20063016872495
National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge.Rubin, Daniel L; Lewis, Suzanna E; Mungall, Chris J; Misra, Sima; Westerfield, Monte; Ashburner, Michael; Sim, Ida; Chute, Christopher G; Solbrig, Harold; Storey, Margaret-Anne; Smith, Barry; Day-Richter, John; Noy, Natalya F; Musen, Mark AOmics : a journal of integrative biology2006185-9816901225
Development of FuGO: an ontology for functional genomics investigations.Whetzel, Patricia L; Brinkman, Ryan R; Causton, Helen C; Fan, Liju; Field, Dawn; Fostel, Jennifer; Fragoso, Gilberto; Gray, Tanya; Heiskanen, Mervi; Hernandez-Boussard, Tina; Morrison, Norman; Parkinson, Helen; Rocca-Serra, Philippe; Sansone, Susanna-AssuOmics : a journal of integrative biology2006199-20416901226
A framework for protein structure classification and identification of novel protein structures.Kim, You Jung; Patel, Jignesh MBMC bioinformatics200645617042958
Statistical analysis of RNA backbone.Hershkovitz, Eli; Sapiro, Guillermo; Tannenbaum, Allen; Williams, Loren DeanIEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM2006 Jan-Mar33-4617048391
Absolute enrichment: gene set enrichment analysis for homeostatic systems.Saxena, Vishal; Orgill, Dennis; Kohane, IsaacNucleic acids research2006e15117130162
Biological context networks: a mosaic view of the interactome.Rachlin, John; Cohen, Dikla Dotan; Cantor, Charles; Kasif, SimonMolecular systems biology20066617130868
An unsupervised classification method for inferring original case locations from low-resolution disease maps.Brownstein, John S; Cassa, Christopher A; Kohane, Isaac S; Mandl, Kenneth DInternational journal of health geographics20065617156451
Finding temporal order in discharge summaries.Bramsen, Philip; Deshpande, Pawan; Lee, Yoong Keok; Barzilay, ReginaAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium200681-517238307
Syntactically-informed semantic category recognition in discharge summaries.Sibanda, Tawanda; He, Tian; Szolovits, Peter; Uzuner, OzlemAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2006714-817238434
Mapping tool for maintaining vocabulary relationships.Hackett, Kristel L; Kohane, Isaac S; Chueh, Henry C; Murphy, Shawn NAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium200693917238558
Integration of clinical and genetic data in the i2b2 architecture.Murphy, Shawn N; Mendis, Michael E; Berkowitz, David A; Kohane, Isaac; Chueh, Henry CAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2006104017238659
A nonparametric bayesian approach to detecting spatial activation patterns in fMRI data.Kim, Seyoung; Smyth, Padhraic; Stern, HalMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006217-2417354775
High-dimensional white matter atlas generation and group analysis.O'Donnell, Lauren; Westin, Carl-FredrikMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006243-5117354778
Fiber bundle estimation and parameterization.Niethammer, Marc; Bouix, Sylvain; Westin, Carl-Fredrik; Shenton, Martha EMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006252-917354779
Improved correspondence for DTI population studies via unbiased atlas building.Goodlett, Casey; Davis, Brad; Jean, Remi; Gilmore, John; Gerig, GuidoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006260-717354780
A method for registering diffusion weighted magnetic resonance images.Tao, Xiaodong; Miller, James VMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006594-60217354821
Segmentation of thalamic nuclei from DTI using spectral clustering.Ziyan, Ulas; Tuch, David; Westin, Carl-FredrikMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006807-1417354847
Logarithm odds maps for shape representation.Pohl, Kilian M; Fisher, John; Shenton, Martha; McCarley, Robert W; Grimson, W Eric L; Kikinis, Ron; Wells, William MMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006955-6317354865
Shape-driven 3D segmentation using spherical wavelets.Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, AllenMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention200666-7417354875
3D histological reconstruction of fiber tracts and direct comparison with diffusion tensor MRI tractography.Dauguet, Julien; Peled, Sharon; Berezovskii, Vladimir; Delzescaux, Thierry; Warfield, Simon K; Born, Richard; Westin, Carl-FredrikMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006109-1617354880
Rician noise removal in diffusion tensor MRI.Basu, Saurav; Fletcher, Thomas; Whitaker, RossMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006117-2517354881
A learning based algorithm for automatic extraction of the cortical sulci.Zheng, Songfeng; Tu, Zhuowen; Yuille, Alan L; Reiss, Allan L; Dutton, Rebecca A; Lee, Agatha D; Galaburda, Albert M; Thompson, Paul M; Dinov, Ivo; Toga, Arthur WMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006695-70317354951
Atlas stratification.Blezek, Daniel J; Miller, James VMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2006712-917354953
On diffusion tensor estimation.Niethammer, Marc; San Jose Estepar, Raul; Bouix, Sylvain; Shenton, Martha; Westin, Carl-FredrikConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20062622-517946125
Flattening the abdominal aortic tree for effective visualization.Won, Joong Ho; Rubin, Geoffrey D; Napel, SandyConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20063345-817946176
3D modeling of patient-specific geometries of portal veins using MR images.Yang, Yan; George, Stephanie; Martin, Diego R; Tannenbaum, Allen R; Giddens, Don PConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20065290-317946691
On diffusion tensor estimation.Niethammer, Marc; Estepar, Raul San Jose; Bouix, Sylvain; Shenton, Martha; Westin, Carl-FredrikConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20066707-1017959492
Combining Web-based Searching with Latent Semantic Analysis to Discover Similarity Between Phrases.Falconer, Sean M; Maslov, Dmitri; Storey, Margaret-AnneLecture notes in computer science20061075-109118714367
Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM.Styner, Martin; Oguz, Ipek; Xu, Shun; Brechbuhler, Christian; Pantazis, Dimitrios; Levitt, James J; Shenton, Martha E; Gerig, GuidoThe insight journal2006242-25021941375
MATHEMATICAL METHODS IN MEDICAL IMAGE PROCESSING.Angenent, Sigurd; Pichon, Eric; Tannenbaum, AllenBulletin (new series) of the American Mathematical Society2006365-39623645963
Shape-Based Approach to Robust Image Segmentation using Kernel PCA.Dambreville, Samuel; Rathi, Yogesh; Tannenbaum, AllenProceedings / CVPR, IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society Conference on Computer Vision and Pattern Recognition2006977-98423685633
Dynamic Active Contours for Visual Tracking.Niethammer, Marc; Tannenbaum, Allen; Angenent, SigurdIEEE transactions on automatic control2006562-57923729836
Computational biology for visualization of brain structure.Toga, Arthur WAnatomy and embryology.2005 Dec433-816177906
The human cerebral cortex on MRI: value of the coronal plane.Salamon, N; Sicotte, N; Mongkolwat, P; Shattuck, D; Salamon, GSurgical and radiologic anatomy : SRA.2005 Dec431-4316307199
Standard atlas space for C57BL/6J neonatal mouse brain.Lee, Erh-Fang; Jacobs, Russell E; Dinov, Ivo; Leow, Alex; Toga, Arthur WAnatomy and embryology.2005 Nov245-6316228227
Atlas-based hippocampus segmentation in Alzheimer's disease and mild cognitive impairment.Carmichael, Owen T; Aizenstein, Howard A; Davis, Simon W; Becker, James T; Thompson, Paul M; Meltzer, Carolyn Cidis; Liu, YanxiNeuroImage2005 Oct 1979-9015990339
Assessing the application of Ka/Ks ratio test to alternatively spliced exons.Xing, Yi; Lee, ChristopherBioinformatics (Oxford, England) 2005 Oct 13701-316091412
Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.Xing, Yi; Lee, ChristopherProceedings of the National Academy of Sciences of the United States of America. 2005 Sep 2013526-3116157889
Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study.Nakamura, Motoaki; McCarley, Robert W; Kubicki, Marek; Dickey, Chandlee C; Niznikiewicz, Margaret A; Voglmaier, Martina M; Seidman, Larry J; Maier, Stephan E; Westin, Carl-Fredrik; Kikinis, Ron; Shenton, Martha EBiological psychiatry2005 Sep 15468-7815978550
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.Wolfe, Cecily J; Kohane, Isaac S; Butte, Atul JBMC bioinformatics [electronic resource]. 2005 Sep 1422716162296
Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing.Xing, Yi; Lee, Christopher JPLoS genetics2005 Sepe3416170410
Choice reaction time performance correlates with diffusion anisotropy in white matter pathways supporting visuospatial attention.Tuch, David S; Salat, David H; Wisco, Jonathan J; Zaleta, Alexandra K; Hevelone, Nathanael D; Rosas, H DianaProceedings of the National Academy of Sciences of the United States of America2005 Aug 2312212-716103359
Small fitness effect of mutations in highly conserved non-coding regions.Kryukov, Gregory V; Schmidt, Steffen; Sunyaev, ShamilHuman molecular genetics. 2005 Aug 12221-915994173
GEMS: a web server for biclustering analysis of expression data.Wu, Chang-Jiun; Kasif, SimonNucleic acids research. 2005 Jul 1W596-915980544
Meshless Animation of Fracturing Solids.Pauly, Mark; Keiser, Richard; Adams, Bart; Dutre, Philip; Gross, Markus; Guibas, Leonidas JACM transactions on graphics2005 Jul 1957-96421165160
Determining the Mg2+ stoichiometry for folding an RNA metal ion core.Das, Rhiju; Travers, Kevin J; Bai, Yu; Herschlag, DanielJournal of the American Chemical Society2005 Jun 158272-315941246
Flux driven automatic centerline extraction.Bouix, Sylvain; Siddiqi, Kaleem; Tannenbaum, AllenMedical image analysis2005 Jun209-2115854842
A model of the upper extremity for simulating musculoskeletal surgery and analyzing neuromuscular control.Holzbaur, Katherine R S; Murray, Wendy M; Delp, Scott LAnnals of biomedical engineering. 2005 Jun829-4016078622
Q-ball imaging of macaque white matter architecture.Tuch, David S; Wisco, Jonathan J; Khachaturian, Mark H; Ekstrom, Leeland B; Kotter, Rolf; Vanduffel, WimPhilosophical transactions of the Royal Society of London. Series B, Biological sciences. 2005 May 29869-7916087432
Detection of entorhinal layer II using 7Tesla [corrected] magnetic resonance imaging.Augustinack, Jean C; van der Kouwe, Andre J W; Blackwell, Megan L; Salat, David H; Wiggins, Christopher J; Frosch, Matthew P; Wiggins, Graham C; Potthast, Andreas; Wald, Lawrence L; Fischl, Bruce RAnnals of neurology2005 Apr489-9415786476
Brain structural mapping using a novel hybrid implicit/explicit framework based on the level-set method.Leow, A; Yu, C L; Lee, S J; Huang, S C; Protas, H; Nicolson, R; Hayashi, K M; Toga, A W; Thompson, P MNeuroImage. 2005 Feb 1910-2715652325
Flattening maps for the visualization of multibranched vessels.Zhu, Lei; Haker, Steven; Tannenbaum, AllenIEEE transactions on medical imaging2005 Feb191-815707245
Automated diagnosis of brain tumours astrocytomas using probabilistic neural network clustering and support vector machines.Glotsos, Dimitris; Tohka, Jussi; Ravazoula, Panagiota; Cavouras, Dionisis; Nikiforidis, GeorgeInternational journal of neural systems. 2005 Feb-Apr1-1115912578
Genetics of brain structure and intelligence.Toga, Arthur W; Thompson, Paul MAnnual review of neuroscience20051-2315651931
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements.Carter, Scott L; Eklund, Aron C; Mecham, Brigham H; Kohane, Isaac S; Szallasi, ZoltanBMC bioinformatics200510715850491
Implementing electronic medical record systems in developing countries.Fraser, Hamish S F; Biondich, Paul; Moodley, Deshen; Choi, Sharon; Mamlin, Burke W; Szolovits, PeterInformatics in primary care200583-9515992493
Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms.Roy, Meenakshi; Xu, Qiang; Lee, ChristopherNucleic acids research. 20055026-3316147986
Structural MRI and brain development.Thompson, Paul M; Sowell, Elizabeth R; Gogtay, Nitin; Giedd, Jay N; Vidal, Christine N; Hayashi, Kiralee M; Leow, Alex; Nicolson, Rob; Rapoport, Judith L; Toga, Arthur WInternational review of neurobiology2005285-32316291026
Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.Lee, Soohyun; Kohane, Isaac; Kasif, SimonBMC genomics [electronic resource]. 200516816309559
Brain atlases of normal and diseased populations.Toga, Arthur W; Thompson, Paul MInternational review of neurobiology20051-5416387199
Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.Corouge, Isabelle; Fletcher, P Thomas; Joshi, Sarang; Gilmore, John H; Gerig, GuidoMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005131-916685838
White matter tract clustering and correspondence in populations.O'Donnell, Lauren; Westin, Carl-FredrikMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005140-716685839
A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography.Pichon, Eric; Westin, Carl-Fredrik; Tannenbaum, Allen RMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005180-716685844
Automated atlas-based clustering of white matter fiber tracts from DTMRI.Maddah, Mahnaz; Mewes, Andrea U J; Haker, Steven; Grimson, W Eric L; Warfield, Simon KMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005188-9516685845
A unifying approach to registration, segmentation, and intensity correction.Pohl, Kilian M; Fisher, John; Levitt, James J; Shenton, Martha E; Kikinis, Ron; Grimson, W Eric L; Wells, William MMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005310-816685860
Parametric response surface models for analysis of multi-site fMRI data.Kim, Seyoung; Smyth, Padhraic; Stern, Hal; Turner, JessicaMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005352-916685865
Harmonic skeleton guided evaluation of stenoses in human coronary arteries.Yang, Yan; Zhu, Lei; Haker, Steven; Tannenbaum, Allen R; Giddens, Don PMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005490-716685882
Two methods for validating brain tissue classifiers.Martin-Fernandez, Marcos; Bouix, Sylvain; Ungar, Lida; McCarley, Robert W; Shenton, Martha EMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005515-2216685885
Mass preserving registration for heart MR images.Zhu, Lei; Haker, Steven; Tannenbaum, AllenMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005147-5416685954
Multiscale 3D shape analysis using spherical wavelets.Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen RMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention2005459-6716685992
Copy fees and patients' rights to obtain a copy of their medical records: from law to reality.Fioriglio, Gianluigi; Szolovits, PeterAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2005251-516779040
DITTO - a tool for identification of patient cohorts from the text of physician notes in the electronic medical record.Turchin, Alexander; Pendergrass, Merri L; Kohane, Isaac SAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium2005744-816779139
From spatial regularization to anatomical priors in fMRI analysis.Ou, Wanmei; Golland, PolinaInformation processing in medical imaging : proceedings of the ... conference200588-10017354687
The 3D structure of real polymer foams.Montminy, Matthew D; Tannenbaum, Allen R; Macosko, Christopher WJournal of colloid and interface science2004 Dec 1202-1115476791

Building Blocks, Biological Pathways, and Networks (949)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman, Dina; Sali, Andrej; Rout, Michael P; Chait, Brian TMolecular & cellular proteomics : MCP2014 Aug 26NULL25161197
Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B; Sauder, J Michael; Burley, Stephen K; Almo, Steven C; Rout, Michael; SaMolecular & cellular proteomics : MCP2014 Aug 19NULL25139911
Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.Algret, Romain; Fernandez-Martinez, Javier; Shi, Yi; Kim, Seung Joong; Pellarin, Riccardo; Cimermancic, Peter; Cochet, Emilie; Sali, Andrej; Chait, Brian T; Rout, Michael P; Dokudovskaya, SvetlanaMolecular & cellular proteomics : MCP2014 Jul 29NULL25073740
Fluorogen-activating scFv biosensors target surface markers on live cells via streptavidin or single-chain avidin.Gallo, Eugenio; Jarvik, JonathanMolecular biotechnology2014 Jul585-9024562573
Imaging mass spectrometry of diversified cardiolipin molecular species in the brain.Amoscato, A A; Sparvero, L J; He, R R; Watkins, S; Bayir, H; Kagan, V EAnalytical chemistry2014 Jul 16587-9524949523
Functional annotation of proteome encoded by human chromosome 22.Pinto, Sneha M; Manda, Srikanth S; Kim, Min-Sik; Taylor, KyOnese; Selvan, Lakshmi Dhevi Nagarajha; Balakrishnan, Lavanya; Subbannayya, Tejaswini; Yan, Fangfei; Prasad, T S Keshava; Gowda, Harsha; Lee, Charles; Hancock, William S; Pandey, AkhileshJournal of proteome research2014 Jun 62749-6024669763
A draft map of the human proteome.Kim, Min-Sik; Pinto, Sneha M; Getnet, Derese; Nirujogi, Raja Sekhar; Manda, Srikanth S; Chaerkady, Raghothama; Madugundu, Anil K; Kelkar, Dhanashree S; Isserlin, Ruth; Jain, Shobhit; Thomas, Joji K; Muthusamy, Babylakshmi; Leal-Rojas, Pamela; Kumar, PraveNature2014 May 29575-8124870542
Self-Checking Cell-Based Assays for GPCR Desensitization and Resensitization.Fisher, Gregory W; Fuhrman, Margaret H; Adler, Sally A; Szent-Gyorgyi, Christopher; Waggoner, Alan S; Jarvik, Jonathan WJournal of biomolecular screening2014 May 12NULL24820110
Increased glucose metabolism and glycerolipid formation by fatty acids and GPR40 receptor signaling underlies the fatty acid potentiation of insulin secretion.El-Azzouny, Mahmoud; Evans, Charles R; Treutelaar, Mary K; Kennedy, Robert T; Burant, Charles FThe Journal of biological chemistry2014 May 913575-8824675078
Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity.Holden, Jennifer M; Koreny, Ludek; Obado, Samson; Ratushny, Alexander V; Chen, Wei-Ming; Chiang, Jung-Hsien; Kelly, Steven; Chait, Brian T; Aitchison, John D; Rout, Michael P; Field, Mark CMolecular biology of the cell2014 May1421-3624600046
A Selective Phenelzine Analogue Inhibitor of Histone Demethylase LSD1.Prusevich, Polina; Kalin, Jay H; Ming, Shonoi A; Basso, Manuela; Givens, Jeffrey; Li, Xin; Hu, Jianfei; Taylor, Martin S; Cieniewicz, Anne M; Hsiao, Po-Yuan; Huang, Rong; Roberson, Heather; Adejola, Nkosi; Avery, Lindsay B; Casero Jr, Robert A; Taverna, SACS chemical biology2014 Apr 7NULL24707965
An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.Wurtmann, Elisabeth J; Ratushny, Alexander V; Pan, Min; Beer, Karlyn D; Aitchison, John D; Baliga, Nitin SMolecular microbiology2014 Apr369-8224612392
Lysine glutarylation is a protein posttranslational modification regulated by SIRT5.Tan, Minjia; Peng, Chao; Anderson, Kristin A; Chhoy, Peter; Xie, Zhongyu; Dai, Lunzhi; Park, Jeongsoon; Chen, Yue; Huang, He; Zhang, Yi; Ro, Jennifer; Wagner, Gregory R; Green, Michelle F; Madsen, Andreas S; Schmiesing, Jessica; Peterson, Brett S; Xu, GuoCell metabolism2014 Apr 1605-1724703693
Human cytomegalovirus pUL37x1-induced calcium flux activates PKC*, inducing altered cell shape and accumulation of cytoplasmic vesicles.Sharon-Friling, Ronit; Shenk, ThomasProceedings of the National Academy of Sciences of the United States of America2014 Mar 25E1140-824616524
The multifunctional nuclear pore complex: a platform for controlling gene expression.Ptak, Christopher; Aitchison, John D; Wozniak, Richard WCurrent opinion in cell biology2014 Mar 2046-5324657998
Improved spatial resolution of matrix-assisted laser desorption/ionization imaging of lipids in the brain by alkylated derivatives of 2,5-dihydroxybenzoic acid.Stoyanovsky, D A; Sparvero, L J; Amoscato, A A; He, R R; Watkins, S; Pitt, B R; Bayir, H; Kagan, V ERapid communications in mass spectrometry : RCM2014 Mar 15403-1224497278
Twist1-induced dissemination preserves epithelial identity and requires E-cadherin.Shamir, Eliah R; Pappalardo, Elisa; Jorgens, Danielle M; Coutinho, Kester; Tsai, Wen-Ting; Aziz, Khaled; Auer, Manfred; Tran, Phuoc T; Bader, Joel S; Ewald, Andrew JThe Journal of cell biology2014 Mar 3839-5624590176
Novel approach in LC-MS/MS using MRM to generate a full profile of acyl-CoAs: discovery of acyl-dephospho-CoAs.Li, Qingling; Zhang, Shenghui; Berthiaume, Jessica M; Simons, Brigitte; Zhang, Guo-FangJournal of lipid research2014 Mar592-60224367045
Glutathionylated 4-hydroxy-2-(E)-alkenal enantiomers in rat organs and their contributions toward the disposal of 4-hydroxy-2-(E)-nonenal in rat liver.Sadhukhan, Sushabhan; Han, Yong; Jin, Zhicheng; Tochtrop, Gregory P; Zhang, Guo-FangFree radical biology & medicine2014 Feb 1878-8524556413
Circadian clocks and feeding time regulate the oscillations and levels of hepatic triglycerides.Adamovich, Yaarit; Rousso-Noori, Liat; Zwighaft, Ziv; Neufeld-Cohen, Adi; Golik, Marina; Kraut-Cohen, Judith; Wang, Miao; Han, Xianlin; Asher, GadCell metabolism2014 Feb 4319-3024506873
Molecular mechanisms of system responses to novel stimuli are predictable from public data.Danziger, Samuel A; Ratushny, Alexander V; Smith, Jennifer J; Saleem, Ramsey A; Wan, Yakun; Arens, Christina E; Armstrong, Abraham M; Sitko, Katherine; Chen, Wei-Ming; Chiang, Jung-Hsien; Reiss, David J; Baliga, Nitin S; Aitchison, John DNucleic acids research2014 Feb1442-6024185701
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.Zhang, Xiaojun; Dantas Machado, Ana Carolina; Ding, Yuan; Chen, Yongheng; Lu, Yan; Duan, Yankun; Tham, Kenneth W; Chen, Lin; Rohs, Remo; Qin, Peter ZNucleic acids research2014 Feb2789-9724293651
Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin.Lan, Li; Nakajima, Satoshi; Wei, Leizhen; Sun, Luxi; Hsieh, Ching-Lung; Sobol, Robert W; Bruchez, Marcel; Van Houten, Bennett; Yasui, Akira; Levine, Arthur SNucleic acids research2014 Feb2330-4524293652
Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.Schoggins, John W; MacDuff, Donna A; Imanaka, Naoko; Gainey, Maria D; Shrestha, Bimmi; Eitson, Jennifer L; Mar, Katrina B; Richardson, R Blake; Ratushny, Alexander V; Litvak, Vladimir; Dabelic, Rea; Manicassamy, Balaji; Aitchison, John D; Aderem, Alan; ElNature2014 Jan 30691-524284630
Loss of TRPML1 promotes production of reactive oxygen species: is oxidative damage a factor in mucolipidosis type IV?Coblentz, Jessica; St Croix, Claudette; Kiselyov, KirillThe Biochemical journal2014 Jan 15361-824192042
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A human proteome microarray identifies that the heterogeneous nuclear ribonucleoprotein K (hnRNP K) recognizes the 5' terminal sequence of the hepatitis C virus RNA.Fan, Baochang; Lu, Kuan-Yi; Reymond Sutandy, F X; Chen, Yi-Wen; Konan, Kouacou; Zhu, Heng; Kao, C Cheng; Chen, Chien-ShengMolecular & cellular proteomics : MCP2014 Jan84-9224113282
Modeling of proteins and their assemblies with the Integrative Modeling Platform.Webb, Benjamin; Lasker, Keren; Velazquez-Muriel, Javier; Schneidman-Duhovny, Dina; Pellarin, Riccardo; Bonomi, Massimiliano; Greenberg, Charles; Raveh, Barak; Tjioe, Elina; Russel, Daniel; Sali, AndrejMethods in molecular biology (Clifton, N.J.)2014277-9524203340
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Plasma Proteome Database as a resource for proteomics research: 2014 update.Nanjappa, Vishalakshi; Thomas, Joji Kurian; Marimuthu, Arivusudar; Muthusamy, Babylakshmi; Radhakrishnan, Aneesha; Sharma, Rakesh; Ahmad Khan, Aafaque; Balakrishnan, Lavanya; Sahasrabuddhe, Nandini A; Kumar, Satwant; Jhaveri, Binit Nitinbhai; Sheth, KaushNucleic acids research2014 JanD959-6524304897
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TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling.Zhong, Jun; Sharma, Jyoti; Raju, Rajesh; Palapetta, Shyam Mohan; Prasad, T S Keshava; Huang, Tai-Chung; Yoda, Akinori; Tyner, Jeffrey W; van Bodegom, Diederik; Weinstock, David M; Ziegler, Steven F; Pandey, AkhileshDatabase : the journal of biological databases and curation2014bau00724573880
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Intracellular pH Measurements Using Perfluorocarbon Nanoemulsions.Patrick, Michael J; Janjic, Jelena M; Teng, Haibing; O'Hear, Meredith R; Brown, Cortlyn W; Stokum, Jesse A; Schmidt, Brigitte F; Ahrens, Eric T; Waggoner, Alan SJournal of the American Chemical Society2013 Dec 1118445-5724266634
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Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition.Taylor, Martin S; Lacava, John; Mita, Paolo; Molloy, Kelly R; Huang, Cheng Ran Lisa; Li, Donghui; Adney, Emily M; Jiang, Hua; Burns, Kathleen H; Chait, Brian T; Rout, Michael P; Boeke, Jef D; Dai, LixinCell2013 Nov 211034-4824267889
Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces.Szent-Gyorgyi, Chris; Stanfield, Robyn L; Andreko, Susan; Dempsey, Alison; Ahmed, Mushtaq; Capek, Sarah; Waggoner, Alan S; Wilson, Ian A; Bruchez, Marcel PJournal of molecular biology2013 Nov 154595-61323978698
Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase.Taylor, Martin S; Ruch, Travis R; Hsiao, Po-Yuan; Hwang, Yousang; Zhang, Pingfeng; Dai, Lixin; Huang, Cheng Ran Lisa; Berndsen, Christopher E; Kim, Min-Sik; Pandey, Akhilesh; Wolberger, Cynthia; Marmorstein, Ronen; Machamer, Carolyn; Boeke, Jef D; Cole, PThe Journal of biological chemistry2013 Nov 832211-2824045953
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Localization Microscopy using Noncovalent Fluorogen Activation by Genetically Encoded Fluorogen-Activating Proteins.Yan, Qi; Schwartz, Samantha L; Maji, Suvrajit; Huang, Fang; Szent-Gyorgyi, Chris; Lidke, Diane S; Lidke, Keith A; Bruchez, Marcel PChemphyschem : a European journal of chemical physics and physical chemistry2013 Nov 5NULL24194371
Kinetochore function and chromosome segregation rely on critical residues in histones h3 and h4 in budding yeast.Ng, Tessie M; Lenstra, Tineke L; Duggan, Nicole; Jiang, Shuangying; Ceto, Steven; Holstege, Frank C P; Dai, Junbiao; Boeke, Jef D; Biggins, SueGenetics2013 Nov795-80724037263
Pretreatment with pyridoxamine mitigates isolevuglandin-associated retinal effects in mice exposed to bright light.Charvet, Casey D; Saadane, Aicha; Wang, Meiyao; Salomon, Robert G; Brunengraber, Henri; Turko, Illarion V; Pikuleva, Irina AThe Journal of biological chemistry2013 Oct 1129267-8023970548
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Selective inhibition of p300 HAT blocks cell cycle progression, induces cellular senescence, and inhibits the DNA damage response in melanoma cells.Yan, Gai; Eller, Mark S; Elm, Courtney; Larocca, Cecilia A; Ryu, Byungwoo; Panova, Izabela P; Dancy, Beverley M; Bowers, Erin M; Meyers, David; Lareau, Lisa; Cole, Philip A; Taverna, Sean D; Alani, Rhoda MThe Journal of investigative dermatology2013 Oct2444-5223698071
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.Chen, Wei-Ming; Danziger, Samuel A; Chiang, Jung-Hsien; Aitchison, John DBioinformatics (Oxford, England)2013 Oct 12435-4423832245
The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress.Baker, Lindsey A; Ueberheide, Beatrix M; Dewell, Scott; Chait, Brian T; Zheng, Deyou; Allis, C DavidMolecular and cellular biology2013 Oct3735-4823878396
Fatty acidomics: global analysis of lipid species containing a carboxyl group with a charge-remote fragmentation-assisted approach.Wang, Miao; Han, Rowland H; Han, XianlinAnalytical chemistry2013 Oct 19312-2023971716
Single cell metabolic profiling of tumor mimics.Keithley, Richard B; Weaver, Eric M; Rosado, Andrea M; Metzinger, Mark P; Hummon, Amanda B; Dovichi, Norman JAnalytical chemistry2013 Oct 18910-824011091
VirD: a virion display array for profiling functional membrane proteins.Hu, Shaohui; Feng, Yingzhu; Henson, Brandon; Wang, Bochu; Huang, Xiaofang; Li, Min; Desai, Prashant; Zhu, HengAnalytical chemistry2013 Sep 38046-5423941274
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Accurate SAXS profile computation and its assessment by contrast variation experiments.Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A; Sali, AndrejBiophysical journal2013 Aug 20962-7423972848
Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA.Mitchell, Leslie A; Cai, Yizhi; Taylor, Martin; Noronha, Anne Marie; Chuang, James; Dai, Lixin; Boeke, Jef DACS synthetic biology2013 Aug 16473-723654272
Superimposed topographic and chemical cues synergistically guide neurite outgrowth.Kundu, Arnab; Micholt, Liesbeth; Friedrich, Sarah; Rand, Danielle R; Bartic, Carmen; Braeken, Dries; Levchenko, AndreLab on a chip2013 Aug 73070-8123752939
Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer's mouse model.Steele, J W; Lachenmayer, M L; Ju, S; Stock, A; Liken, J; Kim, S H; Delgado, L M; Alfaro, I E; Bernales, S; Verdile, G; Bharadwaj, P; Gupta, V; Barr, R; Friss, A; Dolios, G; Wang, R; Ringe, D; Fraser, P; Westaway, D; St George-Hyslop, P H; Szabo, P; RelkiMolecular psychiatry2013 Aug889-9722850627
Latrepirdine stimulates autophagy and reduces accumulation of *-synuclein in cells and in mouse brain.Steele, J W; Ju, S; Lachenmayer, M L; Liken, J; Stock, A; Kim, S H; Delgado, L M; Alfaro, I E; Bernales, S; Verdile, G; Bharadwaj, P; Gupta, V; Barr, R; Friss, A; Dolios, G; Wang, R; Ringe, D; Protter, A A; Martins, R N; Ehrlich, M E; Yue, Z; Petsko, G A;Molecular psychiatry2013 Aug882-822869031
Molecular crowding shapes gene expression in synthetic cellular nanosystems.Tan, Cheemeng; Saurabh, Saumya; Bruchez, Marcel P; Schwartz, Russell; Leduc, PhilipNature nanotechnology2013 Aug602-823851358
Manipulating ionic strength to improve single cell electrophoretic separations.Keithley, Richard B; Metzinger, Mark P; Rosado, Andrea M; Dovichi, Norman JTalanta2013 Jul 15206-1423622546
Directed evolution of a fluorogen-activating single chain antibody for function and enhanced brightness in the cytoplasm.Yates, Bradley P; Peck, Michelle A; Berget, Peter BMolecular biotechnology2013 Jul829-4123242633
Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms.Xu, Min; Alber, FrankBioinformatics (Oxford, England)2013 Jul 1i274-8223812994
SIRT5-Mediated Lysine Desuccinylation Impacts Diverse Metabolic Pathways.Park, Jeongsoon; Chen, Yue; Tishkoff, Daniel X; Peng, Chao; Tan, Minjia; Dai, Lunzhai; Xie, Zhongyu; Zhang, Yi; Zwaans, Bernadette M M; Skinner, Mary E; Lombard, David B; Zhao, YingmingMolecular cell2013 Jun 27919-3023806337
Using glycinylation, a chemical derivatization technique, for the quantitation of ubiquitinated proteins.Fiedler, Katherine L; Cotter, Robert JAnalytical chemistry2013 Jun 185827-3423682733
Differential regulation of glucose transport activity in yeast by specific cAMP signatures.Bermejo, Clara; Haerizadeh, Farzad; Sadoine, Mayuri S C; Chermak, Diane; Frommer, Wolf BThe Biochemical journal2013 Jun 15489-9723495665
Regulated recycling of mutant CFTR is partially restored by pharmacological treatment.Holleran, John P; Zeng, Jianxin; Frizzell, Raymond A; Watkins, Simon CJournal of cell science2013 Jun 152692-70323572510
Automated imaging system for fast quantitation of neurons, cell morphology and neurite morphometry in vivo and in vitro.Tapias, Victor; Greenamyre, J Timothy; Watkins, Simon CNeurobiology of disease2013 Jun158-6823220621
In vivo biochemistry: applications for small molecule biosensors in plant biology.Jones, Alexander M; Grossmann, Guido; Danielson, Jonas Ah; Sosso, Davide; Chen, Li-Qing; Ho, Cheng-Hsun; Frommer, Wolf BCurrent opinion in plant biology2013 Jun389-9523587939
Population-expression models of immune response.Stromberg, Sean P; Antia, Rustom; Nemenman, IlyaPhysical biology2013 Jun3501023735782
The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence.Hansen, Anne-Marie; Chaerkady, Raghothama; Sharma, Jyoti; Diaz-Mejia, J Javier; Tyagi, Nidhi; Renuse, Santosh; Jacob, Harrys K C; Pinto, Sneha M; Sahasrabuddhe, Nandini A; Kim, Min-Sik; Delanghe, Bernard; Srinivasan, Narayanaswamy; Emili, Andrew; Kaper, JPLoS pathogens2013 June100340323785281
Detection and correction of interference in SRM analysis.Bao, Y; Waldemarson, S; Zhang, G; Wahlander, A; Ueberheide, B; Myung, S; Reed, B; Molloy, K; Padovan, J C; Eriksson, J; Neubert, T A; Chait, B T; Fenyo, DMethods (San Diego, Calif.)2013 May 2323707623
Engineering fluorogen activating proteins into self-assembling materials.Saunders, Matthew J; Liu, Wen; Szent-Gyorgyi, Christopher; Wen, Yi; Drennen, Zachary; Waggoner, Alan S; Meng, Wilson SBioconjugate chemistry2013 May 15803-1023573960
4-Hydroxy-2(E)-nonenal (HNE) catabolism and formation of HNE adducts are modulated by ýý oxidation of fatty acids in the isolated rat heart.Li, Qingling; Sadhukhan, Sushabhan; Berthiaume, Jessica M; Ibarra, Rafael A; Tang, Hui; Deng, Shuang; Hamilton, Eric; Nagy, Laura E; Tochtrop, Gregory P; Zhang, Guo-FangFree radical biology & medicine2013 May35-4423328733
Global analysis of condition-specific subcellular protein distribution and abundance.Jung, Sunhee; Smith, Jennifer J; von Haller, Priska D; Dilworth, David J; Sitko, Katherine A; Miller, Leslie R; Saleem, Ramsey A; Goodlett, David R; Aitchison, John DMolecular & cellular proteomics : MCP2013 May1421-3523349476
Spatiotemporal resolution of BDNF neuroprotection against glutamate excitotoxicity in cultured hippocampal neurons.Melo, C V; Okumoto, S; Gomes, J R; Baptista, M S; Bahr, B A; Frommer, W B; Duarte, C BNeuroscience2013 May 166-8623384605
NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink.Ulanovskaya, Olesya A; Zuhl, Andrea M; Cravatt, Benjamin FNature chemical biology2013 May300-623455543
A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants.Fiedler, Katherine L; Bheda, Poonam; Dai, Junbiao; Boeke, Jef D; Wolberger, Cynthia; Cotter, Robert JJournal of mass spectrometry : JMS2013 May608-1523674285
Saturated very long chain Fatty acids are required for the production of infectious human cytomegalovirus progeny.Koyuncu, Emre; Purdy, John G; Rabinowitz, Joshua D; Shenk, ThomasPLoS pathogens2013 Maye100333323696731
Evolution of modular intraflagellar transport from a coatomer-like progenitor.van Dam, Teunis J P; Townsend, Matthew J; Turk, Martin; Schlessinger, Avner; Sali, Andrej; Field, Mark C; Huynen, Martijn AProceedings of the National Academy of Sciences of the United States of America2013 Apr 236943-823569277
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Signaling through purinergic receptors for ATP induces human cutaneous innate and adaptive Th17 responses: implications in the pathogenesis of psoriasis.Killeen, Meaghan E; Ferris, Laura; Kupetsky, Erine A; Falo Jr, Louis; Mathers, Alicia RJournal of immunology (Baltimore, Md. : 1950)2013 Apr 154324-3623479230
Metabolome response to glucose in the ýý-cell line INS-1 832/13.Lorenz, Matthew A; El Azzouny, Mahmoud A; Kennedy, Robert T; Burant, Charles FThe Journal of biological chemistry2013 Apr 1210923-3523426361
Postage for the messenger: designating routes for nuclear mRNA export.Natalizio, Barbara J; Wente, Susan RTrends in cell biology2013 Apr 11NULL23583578
Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.Sampathkumar, Parthasarathy; Kim, Seung Joong; Upla, Paula; Rice, William J; Phillips, Jeremy; Timney, Benjamin L; Pieper, Ursula; Bonanno, Jeffrey B; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Ketaren, Natalia E; Matsui, Tsutomu; Weiss, Thomas M; SStructure (London, England : 1993)2013 Apr 2560-7123499021
Simulation of triacylglycerol ion profiles: bioinformatics for interpretation of triacylglycerol biosynthesis.Han, Rowland H; Wang, Miao; Fang, Xiaoling; Han, XianlinJournal of lipid research2013 Apr1023-3223365150
Inhibition of ghrelin O-acyltransferase attenuates food deprivation-induced increases in ingestive behavior.Teubner, Brett J W; Garretson, John T; Hwang, Yousang; Cole, Philip A; Bartness, Timothy JHormones and behavior2013 Apr667-7323399323
New centromere autoantigens identified in systemic sclerosis using centromere protein microarrays.Song, Guang; Hu, Chaojun; Zhu, Heng; Wang, Li; Zhang, Fengchun; Li, Yongzhe; Wu, LinThe Journal of rheumatology2013 Apr461-823418382
Determining target engagement in living systems.Simon, Gabriel M; Niphakis, Micah J; Cravatt, Benjamin FNature chemical biology2013 Apr200-523508173
Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry.Nemes, Peter; Rubakhin, Stanislav S; Aerts, Jordan T; Sweedler, Jonathan VNature protocols2013 Apr783-9923538882
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Improved native isolation of endogenous Protein A-tagged protein complexes.LaCava, John; Chandramouli, Nagarajan; Jiang, Hua; Rout, Michael PBioTechniques2013 Apr213-623581468
Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry.Nemes, Peter; Rubakhin, Stanislav S; Aerts, Jordan T; Sweedler, Jonathan VNature protocols2013 Apr783-9923589938
Global analysis of phosphorylation networks in humans.Hu, Jianfei; Rho, Hee-Sool; Newman, Robert H; Hwang, Woochang; Neiswinger, John; Zhu, Heng; Zhang, Jin; Qian, JiangBiochimica et biophysica acta2013 Mar 2123524292
Global analysis of phosphorylation networks in humans.Hu, Jianfei; Rho, Hee-Sool; Newman, Robert H; Hwang, Woochang; Neiswinger, John; Zhu, Heng; Zhang, Jin; Qian, JiangBiochimica et biophysica acta2013 Mar 21NULL23524292
Combining small-volume metabolomic and transcriptomic approaches for assessing brain chemistry.Knolhoff, Ann M; Nautiyal, Katherine M; Nemes, Peter; Kalachikov, Sergey; Morozova, Irina; Silver, Rae; Sweedler, Jonathan VAnalytical chemistry2013 Mar 193136-4323409944
Uncovering nuclear pore complexity with innovation.Adams, Rebecca L; Wente, Susan RCell2013 Mar 141218-2123498931
Examining post-translational modification-mediated protein-protein interactions using a chemical proteomics approach.Li, Xiang; Foley, Emily A; Kawashima, Shigehiro A; Molloy, Kelly R; Li, Yinyin; Chait, Brian T; Kapoor, Tarun MProtein science : a publication of the Protein Society2013 Mar287-9523281010
Network motifs provide signatures that characterize metabolism.Shellman, Erin R; Burant, Charles F; Schnell, SantiagoMolecular bioSystems2013 Mar352-6023287894
Proteome-wide mapping of cholesterol-interacting proteins in mammalian cells.Hulce, Jonathan J; Cognetta, Armand B; Niphakis, Micah J; Tully, Sarah E; Cravatt, Benjamin FNature methods2013 Mar259-6423396283
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A role for the nucleoporin Nup170p in chromatin structure and gene silencing.Van de Vosse, David W; Wan, Yakun; Lapetina, Diego L; Chen, Wei-Ming; Chiang, Jung-Hsien; Aitchison, John D; Wozniak, Richard WCell2013 Feb 28969-8323452847
Metabolomics and mass isotopomer analysis as a strategy for pathway discovery: pyrrolyl and cyclopentenyl derivatives of the pro-drug of abuse, levulinate.Harris, Stephanie R; Zhang, Guo-Fang; Sadhukhan, Sushabhan; Wang, Hua; Shi, Chuan; Puchowicz, Michelle A; Anderson, Vernon E; Salomon, Robert G; Tochtrop, Gregory P; Brunengraber, HenriChemical research in toxicology2013 Feb 18213-2023171137
Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching.Di Virgilio, Michela; Callen, Elsa; Yamane, Arito; Zhang, Wenzhu; Jankovic, Mila; Gitlin, Alexander D; Feldhahn, Niklas; Resch, Wolfgang; Oliveira, Thiago Y; Chait, Brian T; Nussenzweig, Andre; Casellas, Rafael; Robbiani, Davide F; Nussenzweig, Michel CScience (New York, N.Y.)2013 Feb 8711-523306439
Proteomics for understanding miRNA biology.Huang, Tai-Chung; Pinto, Sneha M; Pandey, AkhileshProteomics2013 Feb558-6723125164
Quantitative peptidomics for discovery of circadian-related peptides from the rat suprachiasmatic nucleus.Lee, Ji Eun; Zamdborg, Leonid; Southey, Bruce R; Atkins Jr, Norman; Mitchell, Jennifer W; Li, Mingxi; Gillette, Martha U; Kelleher, Neil L; Sweedler, Jonathan VJournal of proteome research2013 Feb 1585-9323256577
High-throughput flow cytometry compatible biosensor based on fluorogen activating protein technology.Wu, Yang; Tapia, Phillip H; Fisher, Gregory W; Waggoner, Alan S; Jarvik, Jonathan; Sklar, Larry ACytometry. Part A : the journal of the International Society for Analytical Cytology2013 Feb220-623303704
Neuronal metabolomics by ion mobility mass spectrometry: cocaine effects on glucose and selected biogenic amine metabolites in the frontal cortex, striatum, and thalamus of the rat.Kaplan, Kimberly A; Chiu, Veronica M; Lukus, Peter A; Zhang, Xing; Siems, William F; Schenk, James O; Hill Jr, Herbert HAnalytical and bioanalytical chemistry2013 Feb1959-6823314481
Interactome mapping: using protein microarray technology to reconstruct diverse protein networks.Uzoma, Ijeoma; Zhu, HengGenomics, proteomics & bioinformatics2013 Feb18-2823395178
Quantitative LC-MS/MS analysis of arachidonoyl amino acids in mouse brain with treatment of FAAH inhibitor.Han, Bingnan; Wright, Rachel; Kirchhoff, Aaron M; Chester, Julia A; Cooper, Bruce R; Davisson, Vincent Jo; Barker, EricAnalytical biochemistry2013 Jan 1574-8123044255
Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule.Shank, Nathaniel I; Pham, Ha H; Waggoner, Alan S; Armitage, Bruce AJournal of the American Chemical Society2013 Jan 9242-5123252842
Capillary electrophoresis with three-color fluorescence detection for the analysis of glycosphingolipid metabolism.Keithley, Richard B; Rosenthal, Alison S; Essaka, David C; Tanaka, Hidenori; Yoshimura, Yayoi; Palcic, Monica M; Hindsgaul, Ole; Dovichi, Norman JThe Analyst2013 Jan 7164-7023154386
Metallochaperones regulate intracellular copper levels.Pang, W Lee; Kaur, Amardeep; Ratushny, Alexander V; Cvetkovic, Aleksandar; Kumar, Sunil; Pan, Min; Arkin, Adam P; Aitchison, John D; Adams, Michael W W; Baliga, Nitin SPLoS computational biology2013e100288023349626
Separation and purification of multiply acetylated proteins using cation-exchange chromatography.Papazyan, Romeo; Taverna, Sean DMethods in molecular biology (Clifton, N.J.)2013103-1323381856
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A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells.San Martin, Alejandro; Ceballo, Sebastian; Ruminot, Ivan; Lerchundi, Rodrigo; Frommer, Wolf B; Barros, Luis FelipePloS one2013e5771223469056
Construction of human activity-based phosphorylation networks.Newman, Robert H; Hu, Jianfei; Rho, Hee-Sool; Xie, Zhi; Woodard, Crystal; Neiswinger, John; Cooper, Christopher; Shirley, Matthew; Clark, Hillary M; Hu, Shaohui; Hwang, Woochang; Jeong, Jun Seop; Wu, George; Lin, Jimmy; Gao, Xinxin; Ni, Qiang; Goel, Renu;Molecular systems biology201365523549483
Construction of human activity-based phosphorylation networks.Newman, Robert H; Hu, Jianfei; Rho, Hee-Sool; Xie, Zhi; Woodard, Crystal; Neiswinger, John; Cooper, Christopher; Shirley, Matthew; Clark, Hillary M; Hu, Shaohui; Hwang, Woochang; Jeong, Jun Seop; Wu, George; Lin, Jimmy; Gao, Xinxin; Ni, Qiang; Goel, Renu; Xia, Shuli; Ji, Hongkai; Dalby, Kevin N; Birnbaum, Morris J; Cole, Philip A; Knapp, Stefan; Ryazanov, Alexey G; Zack, Donald J; Blackshaw, Seth; Pawson, Tony; Gingras, Anne-Claude; Desiderio, Stephen; Pandey, Akhilesh; Turk, Benjamin E; Zhang, Jin; Zhu, Heng; Qian, JiangMolecular systems biology201365523549483
Proteomic strategies to characterize signaling pathways.Harsha, H C; Pinto, Sneha M; Pandey, AkhileshMethods in molecular biology (Clifton, N.J.)2013359-7723666735
SILAC-based quantification of Sirt1-responsive lysine acetylome.Chen, Yue; Colak, Gozde; Zhao, YingmingMethods in molecular biology (Clifton, N.J.)2013105-2024014402
Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling.Woodard, Crystal L; Goodwin, C Rory; Wan, Jun; Xia, Shuli; Newman, Robert; Hu, Jianfei; Zhang, Jin; Hayward, S Diane; Qian, Jiang; Laterra, John; Zhu, HengPloS one2013e7267124023761
Elastic coupling of nascent apCAM adhesions to flowing actin networks.Mejean, Cecile O; Schaefer, Andrew W; Buck, Kenneth B; Kress, Holger; Shundrovsky, Alla; Merrill, Jason W; Dufresne, Eric R; Forscher, PaulPloS one2013e7338924039928
Integrated proteomic and metabolic analysis of breast cancer progression.Shaw, Patrick G; Chaerkady, Raghothama; Wang, Tao; Vasilatos, Shauna; Huang, Yi; Van Houten, Bennett; Pandey, Akhilesh; Davidson, Nancy EPloS one2013e7622024086712
Recycling of kinesin-1 motors by diffusion after transport.Blasius, T Lynne; Reed, Nathan; Slepchenko, Boris M; Verhey, Kristen JPloS one2013e7608124098765
A role for cytosolic isocitrate dehydrogenase as a negative regulator of glucose signaling for insulin secretion in pancreatic ýý-cells.Guay, Claudiane; Joly, Erik; Pepin, Emilie; Barbeau, Annie; Hentsch, Lisa; Pineda, Marco; Madiraju, S R Murthy; Brunengraber, Henri; Prentki, MarcPloS one2013e7709724130841
A method for integrative structure determination of protein-protein complexes.Schneidman-Duhovny, Dina; Rossi, Andrea; Avila-Sakar, Agustin; Kim, Seung Joong; Velazquez-Muriel, Javier; Strop, Pavel; Liang, Hong; Krukenberg, Kristin A; Liao, Maofu; Kim, Ho Min; Sobhanifar, Solmaz; Dotsch, Volker; Rajpal, Arvind; Pons, Jaume; Agard, Bioinformatics (Oxford, England)2012 Dec 153282-923093611
RNF4-dependent hybrid SUMO-ubiquitin chains are signals for RAP80 and thereby mediate the recruitment of BRCA1 to sites of DNA damage.Guzzo, Catherine M; Berndsen, Christopher E; Zhu, Jianmei; Gupta, Vibhor; Datta, Ajit; Greenberg, Roger A; Wolberger, Cynthia; Matunis, Michael JScience signaling2012 Dec 4ra8823211528
Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics.Zhu, Heng; Cox, Eric; Qian, JiangProteomics. Clinical applications2012 Dec548-6223027439
Three-dimensional cultures modeling premalignant progression of human breast epithelial cells: role of cysteine cathepsins.Mullins, Stefanie R; Sameni, Mansoureth; Blum, Galia; Bogyo, Matthew; Sloane, Bonnie F; Moin, KamiarBiological chemistry2012 Dec1405-1623667900
Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.Velazquez-Muriel, Javier; Lasker, Keren; Russel, Daniel; Phillips, Jeremy; Webb, Benjamin M; Schneidman-Duhovny, Dina; Sali, AndrejProceedings of the National Academy of Sciences of the United States of America2012 Nov 1318821-623112201
Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs).Kim, Min-Sik; Kuppireddy, Sarada V; Sakamuri, Sruthi; Singal, Mukul; Getnet, Derese; Harsha, H C; Goel, Renu; Balakrishnan, Lavanya; Jacob, Harrys K C; Kashyap, Manoj K; Tankala, Shantal G; Maitra, Anirban; Iacobuzio-Donahue, Christine A; Jaffee, ElizabetJournal of proteome research2012 Nov 25556-6322985314
Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin.Ren, Yunzhao R; Chaerkady, Raghothama; Hu, Shaohui; Wan, Jun; Qian, Jiang; Zhu, Heng; Pandey, Akhilesh; Kern, Scott EJournal of proteome research2012 Nov 25301-1023025254
Profiling lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays.Lu, Kuan-Yi; Tao, Sheng-Ce; Yang, Tzu-Ching; Ho, Yu-Hsuan; Lee, Chia-Hsien; Lin, Chen-Ching; Juan, Hsueh-Fen; Huang, Hsuan-Cheng; Yang, Chin-Yu; Chen, Ming-Shuo; Lin, Yu-Yi; Lu, Jin-Ying; Zhu, Heng; Chen, Chien-ShengMolecular & cellular proteomics : MCP2012 Nov1177-9022843995
Telomeres, tethers and trypanosomes.Field, Mark C; Horn, David; Alsford, Sam; Koreny, Ludek; Rout, Michael PNucleus (Austin, Tex.)2012 Nov-Dec478-8622992703
Systems biology. How information theory handles cell signaling and uncertainty.Brennan, Matthew D; Cheong, Raymond; Levchenko, AndreScience (New York, N.Y.)2012 Oct 19334-523087235
A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.Litvak, Vladimir; Ratushny, Alexander V; Lampano, Aaron E; Schmitz, Frank; Huang, Albert C; Raman, Ayush; Rust, Alistair G; Bergthaler, Andreas; Aitchison, John D; Aderem, AlanNature2012 Oct 18421-522982991
Single-cell metabolomics: changes in the metabolome of freshly isolated and cultured neurons.Nemes, Peter; Knolhoff, Ann M; Rubakhin, Stanislav S; Sweedler, Jonathan VACS chemical neuroscience2012 Oct 17782-9223077722
Differences in signaling through the B-cell leukemia oncoprotein CRLF2 in response to TSLP and through mutant JAK2.van Bodegom, Diederik; Zhong, Jun; Kopp, Nadja; Dutta, Chaitali; Kim, Min-Sik; Bird, Liat; Weigert, Oliver; Tyner, Jeffrey; Pandey, Akhilesh; Yoda, Akinori; Weinstock, David MBlood2012 Oct 42853-6322915648
Constructing the angiome: a global angiogenesis protein interaction network.Chu, Liang-Hui; Rivera, Corban G; Popel, Aleksander S; Bader, Joel SPhysiological genomics2012 Oct 2915-2422911453
A targeted enzyme approach to sensitization of tyrosine kinase inhibitor-resistant breast cancer cells.Giordano, Courtney R; Mueller, Kelly L; Terlecky, Laura J; Krentz, Kendra A; Bollig-Fischer, Aliccia; Terlecky, Stanley R; Boerner, Julie LExperimental cell research2012 Oct 12014-2122687878
Discovery of regulators of receptor internalization with high-throughput flow cytometry.Wu, Yang; Tapia, Phillip H; Fisher, Gregory W; Simons, Peter C; Strouse, J Jacob; Foutz, Terry; Waggoner, Alan S; Jarvik, Jonathan; Sklar, Larry AMolecular pharmacology2012 Oct645-5722767611
Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways.Chen, Yue; Zhao, Wenhui; Yang, Jeong Soo; Cheng, Zhongyi; Luo, Hao; Lu, Zhike; Tan, Minjia; Gu, Wei; Zhao, YingmingMolecular & cellular proteomics : MCP2012 Oct1048-6222826441
Zooming in on genome organization.Zhou, Xianghong Jasmine; Alber, FrankNature methods2012 Oct961-323018997
Live-cell studies of p300/CBP histone acetyltransferase activity and inhibition.Dancy, Beverley M; Crump, Nicholas T; Peterson, Daniel J; Mukherjee, Chandrani; Bowers, Erin M; Ahn, Young-Hoon; Yoshida, Minoru; Zhang, Jin; Mahadevan, Louis C; Meyers, David J; Boeke, Jef D; Cole, Philip AChembiochem : a European journal of chemical biology2012 Sep 242113-2122961914
UCSF Chimera, MODELLER, and IMP: an integrated modeling system.Yang, Zheng; Lasker, Keren; Schneidman-Duhovny, Dina; Webb, Ben; Huang, Conrad C; Pettersen, Eric F; Goddard, Thomas D; Meng, Elaine C; Sali, Andrej; Ferrin, Thomas EJournal of structural biology2012 Sep269-7821963794
Identification of new autoantigens for primary biliary cirrhosis using human proteome microarrays.Hu, Chao-Jun; Song, Guang; Huang, Wei; Liu, Guo-Zhen; Deng, Chui-Wen; Zeng, Hai-Pan; Wang, Li; Zhang, Feng-Chun; Zhang, Xuan; Jeong, Jun Seop; Blackshaw, Seth; Jiang, Li-Zhi; Zhu, Heng; Wu, Lin; Li, Yong-ZheMolecular & cellular proteomics : MCP2012 Sep669-8022647870
Cell Adhesion on Micro-Structured Fibronectin Gradients Fabricated by Multiphoton Excited Photochemistry.Chen, Xiyi; Su, Yuan-Deng; Ajeti, Visar; Chen, Shean-Jen; Campagnola, Paul JCellular and molecular bioengineering2012 Sep307-31923710258
Proteomics on the rims: insights into the biology of the nuclear envelope and flagellar pocket of trypanosomes.Field, Mark C; Adung'a, Vincent; Obado, Samson; Chait, Brian T; Rout, Michael PParasitology2012 Aug1158-6722309600
Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.Sampathkumar, Parthasarathy; Kim, Seung Joong; Manglicmot, Danalyn; Bain, Kevin T; Gilmore, Jeremiah; Gheyi, Tarun; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D; Matsui, Tsutomu; Tsuruta, Hiro; Atwell, Shane; Thompson, DevProteins2012 Aug2110-622544723
Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase.Grady, Sarah L; Hwang, Jesse; Vastag, Livia; Rabinowitz, Joshua D; Shenk, ThomasJournal of virology2012 Aug8259-6822623791
Serotonin of mast cell origin contributes to hippocampal function.Nautiyal, Katherine M; Dailey, Christopher A; Jahn, Jaquelyn L; Rodriquez, Elizabeth; Son, Nguyen Hong; Sweedler, Jonathan V; Silver, RaeThe European journal of neuroscience2012 Aug2347-5922632453
The BECN1 coiled coil domain: an "imperfect" homodimer interface that facilitates ATG14 and UVRAG binding.Li, Xiaohua; He, Liqiang; Zhang, Mingjie; Yue, Zhenyu; Zhao, YanxiangAutophagy2012 Aug1258-6022647755
The application of information theory to biochemical signaling systems.Rhee, Alex; Cheong, Raymond; Levchenko, AndrePhysical biology2012 Aug04501122872091
Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics.Ye, Yu; Stahley, Mary R; Xu, Jianqing; Friedman, Joshua I; Sun, Yan; McKnight, Jeffrey N; Gray, Jeffrey J; Bowman, Gregory D; Stivers, James TBiochemistry2012 Jul 316028-3822784353
ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus.Byrum, Stephanie D; Raman, Ana; Taverna, Sean D; Tackett, Alan JCell reports2012 Jul 26198-20522840409
Thiogalactopyranosides are resistant to hydrolysis by ýý-galactosidases.Adlercreutz, Dietlind; Yoshimura, Yayoi; Mannerstedt, Karin; Wakarchuk, Warren W; Bennett, Eric P; Dovichi, Norman J; Hindsgaul, Ole; Palcic, Monica MChembiochem : a European journal of chemical biology2012 Jul 231673-922740420
Genetically targetable and color-switching fluorescent probe.Yushchenko, Dmytro A; Zhang, Ming; Yan, Qi; Waggoner, Alan S; Bruchez, Marcel PChembiochem : a European journal of chemical biology2012 Jul 231564-822777954
High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization.Xu, Min; Alber, FrankBMC systems biology2012 Jul 16S1823046491
Sampling techniques for single-cell electrophoresis.Cecala, Christine; Sweedler, Jonathan VThe Analyst2012 Jul 72922-922288071
A hyphenated optical trap capillary electrophoresis laser induced native fluorescence system for single-cell chemical analysis.Cecala, Christine; Rubakhin, Stanislav S; Mitchell, Jennifer W; Gillette, Martha U; Sweedler, Jonathan VThe Analyst2012 Jul 72965-7222543409
Fluorogen activating proteins in flow cytometry for the study of surface molecules and receptors.Saunders, Matthew J; Szent-Gyorgyi, Christopher; Fisher, Gregory W; Jarvik, Jonathan W; Bruchez, Marcel P; Waggoner, Alan SMethods (San Diego, Calif.)2012 Jul308-1722366230
Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.Tjong, Harianto; Gong, Ke; Chen, Lin; Alber, FrankGenome research2012 Jul1295-30522619363
Identification of n-hydroxy acid metabolites in electron impact ionization mass spectrometry.Li, Qingling; Zhang, Guo-FangRapid communications in mass spectrometry : RCM2012 Jun 151355-6222555929
Global tumor protein p53/p63 interactome: making a case for cisplatin chemoresistance.Huang, Yiping; Jeong, Jun Seop; Okamura, Jun; Sook-Kim, Myoung; Zhu, Heng; Guerrero-Preston, Rafael; Ratovitski, Edward ACell cycle (Georgetown, Tex.)2012 Jun 152367-7922672905
How networks change with time.Park, Yongjin; Bader, Joel SBioinformatics (Oxford, England)2012 Jun 15i40-822689777
Quantitative imaging with fluorescent biosensors.Okumoto, Sakiko; Jones, Alexander; Frommer, Wolf BAnnual review of plant biology2012 Jun 2663-70622404462
Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.Jeong, Jun Seop; Jiang, Lizhi; Albino, Edisa; Marrero, Josean; Rho, Hee Sool; Hu, Jianfei; Hu, Shaohui; Vera, Carlos; Bayron-Poueymiroy, Diane; Rivera-Pacheco, Zully Ann; Ramos, Leonardo; Torres-Castro, Cecil; Qian, Jiang; Bonaventura, Joseph; Boeke, Jef Molecular & cellular proteomics : MCP2012 JunO111.01625322307071
TSLP signaling network revealed by SILAC-based phosphoproteomics.Zhong, Jun; Kim, Min-Sik; Chaerkady, Raghothama; Wu, Xinyan; Huang, Tai-Chung; Getnet, Derese; Mitchell, Christopher J; Palapetta, Shyam M; Sharma, Jyoti; O'Meally, Robert N; Cole, Robert N; Yoda, Akinori; Moritz, Albrecht; Loriaux, Marc M; Rush, John; WeMolecular & cellular proteomics : MCP2012 JunM112.01776422345495
To the pore and through the pore: a story of mRNA export kinetics.Oeffinger, Marlene; Zenklusen, DanielBiochimica et biophysica acta2012 Jun494-50622387213
Single cell ganglioside catabolism in primary cerebellar neurons and glia.Essaka, David C; Prendergast, Jillian; Keithley, Richard B; Hindsgaul, Ole; Palcic, Monica M; Schnaar, Ronald L; Dovichi, Norman JNeurochemical research2012 Jun1308-1422407243
Metabolism of ýý-hydroxybutyrate in perfused rat livers.Zhang, Guo-Fang; Sadhukhan, Sushabhan; Ibarra, Rafael A; Lauden, Stephanie M; Chuang, Chia-Ying; Sushailo, Sophia; Chatterjee, Priya; Anderson, Vernon E; Tochtrop, Gregory P; Brunengraber, HenriThe Biochemical journal2012 Jun 1333-4122428548
A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.Frazier, Zachary; Alber, FrankJournal of computational biology : a journal of computational molecular cell biology2012 Jun606-1822697237
Scp160-dependent mRNA trafficking mediates pheromone gradient sensing and chemotropism in yeast.Gelin-Licht, Rita; Paliwal, Saurabh; Conlon, Patrick; Levchenko, Andre; Gerst, Jeffrey ECell reports2012 May 31483-9422832273
Stoichiometry of Nck-dependent actin polymerization in living cells.Ditlev, Jonathon A; Michalski, Paul J; Huber, Greg; Rivera, Gonzalo M; Mohler, William A; Loew, Leslie M; Mayer, Bruce JThe Journal of cell biology2012 May 28643-5822613834
Shotgun lipidomics analysis of 4-hydroxyalkenal species directly from lipid extracts after one-step in situ derivatization.Wang, Miao; Fang, Huafeng; Han, XianlinAnalytical chemistry2012 May 154580-622500579
Genetically encoded pH sensor for tracking surface proteins through endocytosis.Grover, Anmol; Schmidt, Brigitte F; Salter, Russell D; Watkins, Simon C; Waggoner, Alan S; Bruchez, Marcel PAngewandte Chemie (International ed. in English)2012 May 144838-4222461279
Nucleocytoplasmic transport: a role for nonspecific competition in karyopherin-nucleoporin interactions.Tetenbaum-Novatt, Jaclyn; Hough, Loren E; Mironska, Roxana; McKenney, Anna Sophia; Rout, Michael PMolecular & cellular proteomics : MCP2012 May31-4622357553
A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening.Shamay, Meir; Liu, Jianyong; Li, Renfeng; Liao, Gangling; Shen, Li; Greenway, Melanie; Hu, Shaohui; Zhu, Jian; Xie, Zhi; Ambinder, Richard F; Qian, Jiang; Zhu, Heng; Hayward, S DianeJournal of virology2012 May5179-9122379092
SUMO binding by the Epstein-Barr virus protein kinase BGLF4 is crucial for BGLF4 function.Li, Renfeng; Wang, Leyao; Liao, Gangling; Guzzo, Catherine M; Matunis, Michael J; Zhu, Heng; Hayward, S DianeJournal of virology2012 May5412-2122398289
High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching.Xu, Min; Beck, Martin; Alber, FrankJournal of structural biology2012 May152-6422420977
Identification of protein SUMOylation sites by mass spectrometry using combined microwave-assisted aspartic acid cleavage and tryptic digestion.Osula, Omoruyi; Swatkoski, Stephen; Cotter, Robert JJournal of mass spectrometry : JMS2012 May644-5422576878
Two steps forward--one step back: advances in affinity purification mass spectrometry of macromolecular complexes.Oeffinger, MarleneProteomics2012 May1591-60822592981
Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels.Domanski, Michal; Molloy, Kelly; Jiang, Hua; Chait, Brian T; Rout, Michael P; Jensen, Torben Heick; LaCava, JohnBioTechniques2012 May1-622668517
Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2.Bheda, Poonam; Swatkoski, Stephen; Fiedler, Katherine L; Boeke, Jef D; Cotter, Robert J; Wolberger, CynthiaProceedings of the National Academy of Sciences of the United States of America2012 Apr 17E916-2522474337
Ciliary and nuclear transport: different places, similar routes?Obado, Samson O; Rout, Michael PDevelopmental cell2012 Apr 17693-422516195
Regulation of lipid metabolism by Dicer revealed through SILAC mice.Huang, Tai-Chung; Sahasrabuddhe, Nandini A; Kim, Min-Sik; Getnet, Derese; Yang, Yi; Peterson, Jonathan M; Ghosh, Bidyut; Chaerkady, Raghothama; Leach, Steven D; Marchionni, Luigi; Wong, G William; Pandey, AkhileshJournal of proteome research2012 Apr 62193-20522313051
A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red.Senutovitch, Nina; Stanfield, Robyn L; Bhattacharyya, Shantanu; Rule, Gordon S; Wilson, Ian A; Armitage, Bruce A; Waggoner, Alan S; Berget, Peter BBiochemistry2012 Mar 272471-8522390683
Azalysine analogues as probes for protein lysine deacetylation and demethylation.Dancy, Blair C R; Ming, Shonoi A; Papazyan, Romeo; Jelinek, Christine A; Majumdar, Ananya; Sun, Yan; Dancy, Beverley M; Drury 3rd, William J; Cotter, Robert J; Taverna, Sean D; Cole, Philip AJournal of the American Chemical Society2012 Mar 215138-4822352831
Competitive activity-based protein profiling identifies aza-ýý-lactams as a versatile chemotype for serine hydrolase inhibition.Zuhl, Andrea M; Mohr, Justin T; Bachovchin, Daniel A; Niessen, Sherry; Hsu, Ku-Lung; Berlin, Jacob M; Dochnahl, Maximilian; Lopez-Alberca, Maria P; Fu, Gregory C; Cravatt, Benjamin FJournal of the American Chemical Society2012 Mar 215068-7122400490
Metabolic cytometry: capillary electrophoresis with two-color fluorescence detection for the simultaneous study of two glycosphingolipid metabolic pathways in single primary neurons.Essaka, David C; Prendergast, Jillian; Keithley, Richard B; Palcic, Monica M; Hindsgaul, Ole; Schnaar, Ronald L; Dovichi, Norman JAnalytical chemistry2012 Mar 202799-80422400492
Preparation and electrophoretic separation of Bodipy-Fl-labeled glycosphingolipids.Sarver, Scott A; Keithley, Richard B; Essaka, David C; Tanaka, Hidenori; Yoshimura, Yayoi; Palcic, Monica M; Hindsgaul, Ole; Dovichi, Norman JJournal of chromatography. A2012 Mar 16268-7322321948
Dietary regulation of catabolic disposal of 4-hydroxynonenal analogs in rat liver.Li, Qingling; Tomcik, Kristyen; Zhang, Shenghui; Puchowicz, Michelle A; Zhang, Guo-FangFree radical biology & medicine2012 Mar 151043-5322245097
Single-molecule imaging of translational output from individual RNA granules in neurons.Tatavarty, Vedakumar; Ifrim, Marius F; Levin, Mikhail; Korza, George; Barbarese, Elisa; Yu, Ji; Carson, John HMolecular biology of the cell2012 Mar918-2922219377
Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis.Tarrant, Mary Katherine; Rho, Hee-Sool; Xie, Zhi; Jiang, Yu Lin; Gross, Christopher; Culhane, Jeffrey