Joel Dudley - Publications

2007-2011 Stanford University School of Medicine, Palo Alto, CA, United States 

161 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Sengupta PP, Shrestha S, Berthon B, Messas E, Donal E, Tison GH, Min JK, D'hooge J, Voigt JU, Dudley J, Verjans JW, Shameer K, Johnson K, Lovstakken L, Tabassian M, et al. Proposed Requirements for Cardiovascular Imaging-Related Machine Learning Evaluation (PRIME): A Checklist: Reviewed by the American College of Cardiology Healthcare Innovation Council. Jacc. Cardiovascular Imaging. 13: 2017-2035. PMID 32912474 DOI: 10.1016/j.jcmg.2020.07.015  0.36
2020 Rao G, Dwivedi SKD, Zhang Y, Dey A, Shameer K, Karthik R, Srikantan S, Hossen MN, Wren JD, Madesh M, Dudley JT, Bhattacharya R, Mukherjee P. MicroRNA-195 controls MICU1 expression and tumor growth in ovarian cancer. Embo Reports. e48483. PMID 32851774 DOI: 10.15252/embr.201948483  0.36
2020 Landi I, Glicksberg BS, Lee HC, Cherng S, Landi G, Danieletto M, Dudley JT, Furlanello C, Miotto R. Deep representation learning of electronic health records to unlock patient stratification at scale. Npj Digital Medicine. 3: 96. PMID 32699826 DOI: 10.1038/s41746-020-0301-z  0.44
2020 Readhead B, Haure-Mirande JV, Mastroeni D, Audrain M, Fanutza T, Kim SH, Blitzer RD, Gandy S, Dudley JT, Ehrlich ME. miR155 regulation of behavior, neuropathology, and cortical transcriptomics in Alzheimer's disease. Acta Neuropathologica. PMID 32666270 DOI: 10.1007/s00401-020-02185-z  0.36
2020 Lee HC, Ichikawa O, Glicksberg BS, Divaraniya AA, Becker CE, Agarwal P, Dudley JT. Identification of therapeutic targets from genetic association studies using hierarchical component analysis. Biodata Mining. 13: 6. PMID 32565911 DOI: 10.1186/s13040-020-00216-9  0.44
2020 Lesovaya EA, Savinkova AV, Morozova OV, Lylova ES, Zhidkova EM, Kulikov EP, Kirsanov KI, Klopot A, Baida G, Yakubovskaya MG, Gordon LI, Readhead B, Dudley JT, Budunova I. A novel approach to safer glucocorticoid receptor-targeted anti-lymphoma therapy via REDD1 (Regulated in development and DNA damage 1) inhibition. Molecular Cancer Therapeutics. PMID 32546661 DOI: 10.1158/1535-7163.MCT-19-1111  0.36
2020 Smith MR, Yevoo P, Sadahiro M, Readhead B, Kidd B, Dudley JT, Morishita H. Systematic Analysis of Environmental Chemicals That Dysregulate Critical Period Plasticity-Related Gene Expression Reveals Common Pathways That Mimic Immune Response to Pathogen. Neural Plasticity. 2020: 1673897. PMID 32454811 DOI: 10.1155/2020/1673897  0.36
2020 Chaudhry FF, Danieletto M, Golden E, Scelza J, Botwin G, Shervey M, De Freitas JK, Paranjpe I, Nadkarni GN, Miotto R, Glowe P, Stock G, Percha B, Zimmerman N, Dudley JT, et al. Sleep in the Natural Environment: A Pilot Study. Sensors (Basel, Switzerland). 20. PMID 32138289 DOI: 10.3390/s20051378  0.44
2020 Miotto R, Percha BL, Glicksberg BS, Lee HC, Cruz L, Dudley JT, Nabeel I. Identifying Acute Low Back Pain Episodes in Primary Care Practice From Clinical Notes: Observational Study. Jmir Medical Informatics. 8: e16878. PMID 32130159 DOI: 10.2196/16878  0.44
2020 Baida G, Agarwal S, Readhead B, Dudley JT, Budunova I. Sexual dimorphism in atrophic effects of topical glucocorticoids is driven by differential regulation of atrophogene REDD1 in male and female skin. Oncotarget. 11: 409-418. PMID 32064044 DOI: 10.18632/oncotarget.27445  0.36
2020 Lee HC, Danieletto M, Miotto R, Cherng ST, Dudley JT. Scaling structural learning with NO-BEARS to infer causal transcriptome networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 25: 391-402. PMID 31797613  0.32
2020 Vandromme M, Jun T, Perumalswami P, Dudley JT, Branch A, Li L. Automated phenotyping of patients with non-alcoholic fatty liver disease reveals clinically relevant disease subtypes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 25: 91-102. PMID 31797589  0.44
2019 Dwivedi SKD, Shameer K, Dey A, Mustafi SB, Xiong X, Bhattacharya U, Neizer-Ashun F, Rao G, Wang Y, Ivan C, Yang D, Dudley JT, Xu C, Wren JD, Mukherjee P, et al. KRCC1: A potential therapeutic target in ovarian cancer. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 31908025 DOI: 10.1096/fj.201902259R  0.36
2019 Russak AJ, Johnson KW, Halperin JL, Percha B, Dudley JT. Racial and Sex Differences in Stroke Risk in Patients With Atrial Fibrillation. Journal of the American College of Cardiology. 74: 3069-3070. PMID 31865975 DOI: 10.1016/j.jacc.2019.10.018  0.44
2019 Readhead B, Haure-Mirande JV, Ehrlich ME, Gandy S, Dudley JT. Clarifying the Potential Role of Microbes in Alzheimer's Disease. Neuron. 104: 1036-1037. PMID 31855627 DOI: 10.1016/j.neuron.2019.11.008  0.36
2019 Zouboulis CC, Nogueira da Costa A, Makrantonaki E, Hou XX, Almansouri D, Dudley JT, Edwards H, Readhead B, Balthasar O, Jemec GBE, Bonitsis NG, Nikolakis G, Trebing D, Zouboulis KC, Hossini AM. Alterations in innate immunity and epithelial cell differentiation are the molecular pillars of hidradenitis suppurativa. Journal of the European Academy of Dermatology and Venereology : Jeadv. PMID 31838778 DOI: 10.1111/jdv.16147  0.36
2019 Glicksberg BS, Amadori L, Akers NK, Sukhavasi K, Franzén O, Li L, Belbin GM, Ayers KL, Shameer K, Badgeley MA, Johnson KW, Readhead B, Darrow BJ, Kenny EE, Betsholtz C, ... ... Dudley JT, et al. Correction to: Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. Bmc Medical Genomics. 12: 154. PMID 31684948 DOI: 10.1186/s12920-019-0573-9  0.76
2019 Zhang W, Voloudakis G, Rajagopal VM, Readhead B, Dudley JT, Schadt EE, Björkegren JLM, Kim Y, Fullard JF, Hoffman GE, Roussos P. Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits. Nature Communications. 10: 3834. PMID 31444360 DOI: 10.1038/s41467-019-11874-7  0.36
2019 Glicksberg BS, Amadori L, Akers NK, Sukhavasi K, Franzén O, Li L, Belbin GM, Akers KL, Shameer K, Badgeley MA, Johnson KW, Readhead B, Darrow BJ, Kenny EE, Betsholtz C, ... ... Dudley JT, et al. Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. Bmc Medical Genomics. 12: 108. PMID 31345219 DOI: 10.1186/s12920-019-0542-3  0.76
2019 Badgeley MA, Zech JR, Oakden-Rayner L, Glicksberg BS, Liu M, Gale W, McConnell MV, Percha B, Snyder TM, Dudley JT. Deep learning predicts hip fracture using confounding patient and healthcare variables. Npj Digital Medicine. 2: 31. PMID 31304378 DOI: 10.1038/s41746-019-0105-1  0.44
2019 Xu K, Kosoy R, Shameer K, Kumar S, Liu L, Readhead B, Belbin GM, Lee HC, Chen R, Dudley JT. Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans. Bmc Genetics. 20: 52. PMID 31266448 DOI: 10.1186/s12863-019-0758-4  0.76
2019 Lili LN, Klopot A, Readhead B, Baida G, Dudley JT, Budunova I. Transcriptomic network interactions in the human skin treated with topical glucocorticoid clobetasol propionate. The Journal of Investigative Dermatology. PMID 31247200 DOI: 10.1016/j.jid.2019.04.021  0.36
2019 Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna V, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, ... ... Dudley JT, et al. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title. Bioinformatics (Oxford, England). PMID 31214700 DOI: 10.1093/bioinformatics/btz409  0.76
2019 Liu AC, Patel K, Vunikili RD, Johnson KW, Abdu F, Belman SK, Glicksberg BS, Tandale P, Fontanez R, Mathew OK, Kasarskis A, Mukherjee P, Subramanian L, Dudley JT, Shameer K. Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses. Briefings in Bioinformatics. PMID 31190075 DOI: 10.1093/bib/bbz059  0.44
2019 Johnson KW, Glicksberg BS, Shameer K, Vengrenyuk Y, Krittanawong C, Russak AJ, Sharma SK, Narula JN, Dudley JT, Kini AS. A transcriptomic model to predict increase in fibrous cap thickness in response to high-dose statin treatment: Validation by serial intracoronary OCT imaging. Ebiomedicine. PMID 31126891 DOI: 10.1016/j.ebiom.2019.05.007  0.44
2019 Sheikhalishahi S, Miotto R, Dudley JT, Lavelli A, Rinaldi F, Osmani V. Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review. Jmir Medical Informatics. 7: e12239. PMID 31066697 DOI: 10.2196/12239  0.32
2019 Frades I, Readhead B, Amadori L, Koplev S, Talukdar HA, Crane HM, Crane PK, Kovacic JC, Dudley JT, Giannarelli C, Björkegren JLM, Peter I. Systems Pharmacology Identifies an Arterial Wall Regulatory Gene Network Mediating Coronary Artery Disease Side Effects of Antiretroviral Therapy. Circulation. Genomic and Precision Medicine. PMID 31059280 DOI: 10.1161/CIRCGEN.118.002390  0.36
2019 Percha B, Baskerville EB, Johnson M, Dudley JT, Zimmerman N. Designing Robust N-of-1 Studies for Precision Medicine: Simulation Study and Design Recommendations. Journal of Medical Internet Research. 21: e12641. PMID 30932871 DOI: 10.2196/12641  0.32
2019 Ichikawa O, Glicksberg BS, Genes N, Kidd BA, Li L, Dudley JT. Lyme Disease Patient Trajectories Learned from Electronic Medical Data for Stratification of Disease Risk and Therapeutic Response. Scientific Reports. 9: 4460. PMID 30872757 DOI: 10.1038/s41598-019-41128-x  0.44
2019 Johnson KW, De Freitas JK, Glicksberg BS, Bobe JR, Dudley JT. Evaluation of patient re-identification using laboratory test orders and mitigation via latent space variables. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 415-426. PMID 30864342  0.44
2019 Ross EG, Jung K, Dudley JT, Li L, Leeper NJ, Shah NH. Predicting Future Cardiovascular Events in Patients With Peripheral Artery Disease Using Electronic Health Record Data. Circulation. Cardiovascular Quality and Outcomes. 12: e004741. PMID 30857412 DOI: 10.1161/CIRCOUTCOMES.118.004741  0.44
2019 Glicksberg BS, Li L, Chen R, Dudley J, Chen B. Leveraging Big Data to Transform Drug Discovery. Methods in Molecular Biology (Clifton, N.J.). 1939: 91-118. PMID 30848458 DOI: 10.1007/978-1-4939-9089-4_6  0.76
2019 Agarwal S, Mirzoeva S, Readhead B, Dudley JT, Budunova I. PI3K inhibitors protect against glucocorticoid-induced skin atrophy. Ebiomedicine. PMID 30737086 DOI: 10.1016/j.ebiom.2019.01.055  0.36
2018 Miotto R, Danieletto M, Scelza JR, Kidd BA, Dudley JT. Reflecting health: smart mirrors for personalized medicine. Npj Digital Medicine. 1: 62. PMID 31304340 DOI: 10.1038/s41746-018-0068-7  0.36
2018 Laganà A, Beno I, Melnekoff D, Leshchenko V, Madduri D, Ramdas D, Sanchez L, Niglio S, Perumal D, Kidd BA, Miotto R, Shaknovich R, Chari A, Cho HJ, Barlogie B, ... ... Dudley JT, et al. Precision Medicine for Relapsed Multiple Myeloma on the Basis of an Integrative Multiomics Approach. Jco Precision Oncology. 2018. PMID 30706044 DOI: 10.1200/PO.18.00019  0.36
2018 Vashisht R, Jung K, Schuler A, Banda JM, Park RW, Jin S, Li L, Dudley JT, Johnson KW, Shervey MM, Xu H, Wu Y, Natrajan K, Hripcsak G, Jin P, et al. Association of Hemoglobin A1c Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With Metformin: Analysis From the Observational Health Data Sciences and Informatics Initiative. Jama Network Open. 1: e181755. PMID 30646124 DOI: 10.1001/jamanetworkopen.2018.1755  0.44
2018 Haure-Mirande JV, Wang M, Audrain M, Fanutza T, Kim SH, Heja S, Readhead B, Dudley JT, Blitzer RD, Schadt EE, Zhang B, Gandy S, Ehrlich ME. Correction: Integrative approach to sporadic Alzheimer's disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden. Molecular Psychiatry. PMID 30464330 DOI: 10.1038/s41380-018-0301-4  0.36
2018 Readhead B, Hartley BJ, Eastwood BJ, Collier DA, Evans D, Farias R, He C, Hoffman G, Sklar P, Dudley JT, Schadt EE, Savić R, Brennand KJ. Author Correction: Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nature Communications. 9: 4926. PMID 30451900 DOI: 10.1038/s41467-018-07326-3  0.36
2018 Smith MR, Readhead B, Dudley JT, Morishita H. Critical period plasticity-related transcriptional aberrations in schizophrenia and bipolar disorder. Schizophrenia Research. PMID 30442475 DOI: 10.1016/j.schres.2018.10.021  0.36
2018 Baida G, Bhalla P, Yemelyanov A, Stechschulte LA, Shou W, Readhead B, Dudley JT, Sánchez ER, Budunova I. Deletion of the glucocorticoid receptor chaperone FKBP51 prevents glucocorticoid-induced skin atrophy. Oncotarget. 9: 34772-34783. PMID 30410676 DOI: 10.18632/oncotarget.26194  0.36
2018 Badgeley MA, Liu M, Glicksberg BS, Shervey M, Zech J, Shameer K, Lehar J, Oermann EK, McConnell MV, Snyder TM, Dudley JT. CANDI: an R package and Shiny app for annotating radiographs and evaluating Computer-Aided Diagnosis. Bioinformatics (Oxford, England). PMID 30304439 DOI: 10.1093/bioinformatics/bty855  0.44
2018 Haure-Mirande JV, Wang M, Audrain M, Fanutza T, Kim SH, Heja S, Readhead B, Dudley JT, Blitzer RD, Schadt EE, Zhang B, Gandy S, Ehrlich ME. Integrative approach to sporadic Alzheimer's disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden. Molecular Psychiatry. PMID 30283032 DOI: 10.1038/s41380-018-0255-6  0.36
2018 Shameer K, Perez-Rodriguez MM, Bachar R, Li L, Johnson A, Johnson KW, Glicksberg BS, Smith MR, Readhead B, Scarpa J, Jebakaran J, Kovatch P, Lim S, Goodman W, Reich DL, ... ... Dudley JT, et al. Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining. Bmc Medical Informatics and Decision Making. 18: 79. PMID 30255805 DOI: 10.1186/s12911-018-0653-3  0.44
2018 Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, et al. MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data. Cell Reports. 24: 1377-1388. PMID 30067990 DOI: 10.1016/j.celrep.2018.07.003  0.76
2018 Fullard JF, Giambartolomei C, Hauberg ME, Xu K, Voloudakis G, Shao Z, Bare C, Dudley JT, Mattheisen M, Robakis NK, Haroutunian V, Roussos P. Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci. Human Molecular Genetics. PMID 29982455 DOI: 10.1093/hmg/ddy229  0.32
2018 Shameer K, Johnson KW, Glicksberg BS, Dudley JT, Sengupta PP. The whole is greater than the sum of its parts: combining classical statistical and machine intelligence methods in medicine. Heart (British Cardiac Society). 104: 1228. PMID 29945951 DOI: 10.1136/heartjnl-2018-313377  0.44
2018 Readhead B, Haure-Mirande JV, Funk CC, Richards MA, Shannon P, Haroutunian V, Sano M, Liang WS, Beckmann ND, Price ND, Reiman EM, Schadt EE, Ehrlich ME, Gandy S, Dudley JT. Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus. Neuron. PMID 29937276 DOI: 10.1016/j.neuron.2018.05.023  0.36
2018 Johnson KW, Dudley JT, Bobe JR. A 72-Year-Old Patient with Longstanding, Untreated Familial Hypercholesterolemia but no Coronary Artery Calcification: A Case Report. Cureus. 10: e2452. PMID 29888156 DOI: 10.7759/cureus.2452  0.44
2018 Shameer K, Dow G, Glicksberg BS, Johnson KW, Ze Y, Tomlinson MS, Readhead B, Dudley JT, Kullo IJ. A Network-Biology Informed Computational Drug Repositioning Strategy to Target Disease Risk Trajectories and Comorbidities of Peripheral Artery Disease. Amia Joint Summits On Translational Science Proceedings. Amia Joint Summits On Translational Science. 2017: 108-117. PMID 29888052  0.44
2018 Johnson KW, Torres Soto J, Glicksberg BS, Shameer K, Miotto R, Ali M, Ashley E, Dudley JT. Artificial Intelligence in Cardiology. Journal of the American College of Cardiology. 71: 2668-2679. PMID 29880128 DOI: 10.1016/j.jacc.2018.03.521  0.44
2018 Sullivan T, Ichikawa O, Dudley J, Li L, Aberg J. The Rapid Prediction of Carbapenem Resistance in Patients With Bacteremia Using Electronic Medical Record Data. Open Forum Infectious Diseases. 5: ofy091. PMID 29876366 DOI: 10.1093/ofid/ofy091  0.44
2018 Patel R, Scheinfeldt LB, Sanderford MD, Lanham TR, Tamura K, Platt A, Glicksberg BS, Xu K, Dudley JT, Kumar S. Adaptive landscape of protein variation in human exomes. Molecular Biology and Evolution. PMID 29846678 DOI: 10.1093/molbev/msy107  0.44
2018 Polubriaginof FCG, Vanguri R, Quinnies K, Belbin GM, Yahi A, Salmasian H, Lorberbaum T, Nwankwo V, Li L, Shervey MM, Glowe P, Ionita-Laza I, Simmerling M, Hripcsak G, Bakken S, ... ... Dudley J, et al. Disease Heritability Inferred from Familial Relationships Reported in Medical Records. Cell. PMID 29779949 DOI: 10.1016/j.cell.2018.04.032  0.44
2018 Glicksberg BS, Johnson KW, Dudley JT. The next generation of precision medicine: observational studies, electronic health records, biobanks, and continuous monitoring. Human Molecular Genetics. PMID 29659828 DOI: 10.1093/hmg/ddy114  0.44
2018 Lesovaya E, Agarwal S, Readhead B, Vinokour E, Baida G, Bhalla P, Kirsanov K, Yakubovskaya M, Platanias LC, Dudley JT, Budunova I. Rapamycin modulates glucocorticoid receptor function, blocks atrophogene REDD1, and protects skin from steroid atrophy. The Journal of Investigative Dermatology. PMID 29596905 DOI: 10.1016/j.jid.2018.02.045  0.36
2018 Shameer K, Johnson KW, Glicksberg BS, Dudley JT, Sengupta PP. Machine learning in cardiovascular medicine: are we there yet? Heart (British Cardiac Society). PMID 29352006 DOI: 10.1136/heartjnl-2017-311198  0.44
2018 Johnson KW, Glicksberg BS, Hodos RA, Shameer K, Dudley JT. Causal inference on electronic health records to assess blood pressure treatment targets: an application of the parametric g formula. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 180-191. PMID 29218880  0.44
2018 Hodos R, Zhang P, Lee HC, Duan Q, Wang Z, Clark NR, Ma'ayan A, Wang F, Kidd B, Hu J, Sontag D, Dudley J. Cell-specific prediction and application of drug-induced gene expression profiles. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 23: 32-43. PMID 29218867  0.36
2017 Johnson KW, Shameer K, Glicksberg BS, Readhead B, Sengupta PP, Björkegren JLM, Kovacic JC, Dudley JT. Enabling Precision Cardiology Through Multiscale Biology and Systems Medicine. Jacc. Basic to Translational Science. 2: 311-327. PMID 30062151 DOI: 10.1016/j.jacbts.2016.11.010  0.44
2017 Brouwer-Visser J, Cheng WY, Bauer-Mehren A, Maisel D, Lechner K, Andersson E, Dudley JT, Milletti F. Regulatory T-cell genes drive altered immune microenvironment in adult solid cancers and allow for immune contextual patient subtyping. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. PMID 29133367 DOI: 10.1158/1055-9965.EPI-17-0461  0.32
2017 Wang Z, Li L, Glicksberg BS, Israel A, Dudley JT, Ma'ayan A. Predicting Age by Mining Electronic Medical Records with Deep Learning Characterizes Differences between Chronological and Physiological Age. Journal of Biomedical Informatics. PMID 29113935 DOI: 10.1016/j.jbi.2017.11.003  0.44
2017 Boland MR, Parhi P, Li L, Miotto R, Carroll R, Iqbal U, Nguyen PA, Schuemie M, You SC, Smith D, Mooney S, Ryan P, Li YJ, Park RW, Denny J, ... Dudley JT, et al. Uncovering exposures responsible for birth season - disease effects: a global study. Journal of the American Medical Informatics Association : Jamia. PMID 29036387 DOI: 10.1093/jamia/ocx105  0.44
2017 Scott SA, Obeng AO, Botton MR, Yang Y, Scott ER, Ellis SB, Wallsten R, Kaszemacher T, Zhou X, Chen R, Nicoletti P, Naik H, Kenny EE, Vega A, Waite E, ... ... Dudley J, et al. Institutional profile: translational pharmacogenomics at the Icahn School of Medicine at Mount Sinai. Pharmacogenomics. PMID 28982267 DOI: 10.2217/pgs-2017-0137  0.76
2017 Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Tran N, Rittenhouse CA, Simone A, Ruderfer DM, Johnson J, Readhead B, Hadas Y, Gochman PA, Wang YC, Shah H, ... ... Dudley JT, et al. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Reports. 20: 2525. PMID 28877483 DOI: 10.1016/j.celrep.2017.08.073  0.36
2017 Chamaria S, Johnson KW, Vengrenyuk Y, Baber U, Shameer K, Divaraniya AA, Glicksberg BS, Li L, Bhatheja S, Moreno P, Maehara A, Mehran R, Dudley JT, Narula J, Sharma SK, et al. Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes. Scientific Reports. 7: 7001. PMID 28765529 DOI: 10.1038/s41598-017-07029-7  0.44
2017 Caccamo A, Branca C, Piras IS, Ferreira E, Huentelman MJ, Liang WS, Readhead B, Dudley JT, Spangenberg EE, Green KN, Belfiore R, Winslow W, Oddo S. Necroptosis activation in Alzheimer's disease. Nature Neuroscience. PMID 28758999 DOI: 10.1038/nn.4608  0.36
2017 Salem Omar AM, Shameer K, Narula S, Abdel Rahman MA, Rifaie O, Narula J, Dudley JT, Sengupta PP. Artificial Intelligence-Based Assessment of Left Ventricular Filling Pressures From 2-Dimensional Cardiac Ultrasound Images. Jacc. Cardiovascular Imaging. PMID 28734920 DOI: 10.1016/j.jcmg.2017.05.003  0.36
2017 Laganà A, Perumal D, Melnekoff D, Readhead B, Kidd BA, Leshchenko V, Kuo PY, Keats J, DeRome M, Yesil J, Auclair D, Lonial S, Chari A, Cho HJ, Barlogie B, ... ... Dudley JT, et al. Integrative network analysis identifies novel drivers of pathogenesis and progression in newly diagnosed multiple myeloma. Leukemia. PMID 28642592 DOI: 10.1038/leu.2017.197  0.36
2017 Haure-Mirande JV, Audrain M, Fanutza T, Kim SH, Klein WL, Glabe C, Readhead B, Dudley JT, Blitzer RD, Wang M, Zhang B, Schadt EE, Gandy S, Ehrlich ME. Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer's pathology. Acta Neuropathologica. PMID 28612290 DOI: 10.1007/s00401-017-1737-3  0.36
2017 Miotto R, Wang F, Wang S, Jiang X, Dudley JT. Deep learning for healthcare: review, opportunities and challenges. Briefings in Bioinformatics. PMID 28481991 DOI: 10.1093/bib/bbx044  0.32
2017 Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP. Reply: Deep Learning With Unsupervised Feature in Echocardiographic Imaging. Journal of the American College of Cardiology. 69: 2101-2102. PMID 28427589 DOI: 10.1016/j.jacc.2017.01.062  0.36
2017 Karim S, Nour Eldin HF, Abusamra H, Salem N, Alhathli E, Dudley J, Sanderford M, Scheinfeldt LB, Chaudhary AG, Al-Qahtani MH, Kumar S. Erratum to: e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations. Bmc Genomics. 18: 281. PMID 28385147 DOI: 10.1186/s12864-017-3647-0  0.32
2017 Fullard JF, Giambartolomei C, Hauberg ME, Xu K, Voloudakis G, Shao Z, Bare C, Dudley JT, Mattheisen M, Robakis NK, Haroutunian V, Roussos P. Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci. Human Molecular Genetics. PMID 28335009 DOI: 10.1093/hmg/ddx103  0.32
2017 Horowitz CR, Shameer K, Gabrilove J, Atreja A, Shepard P, Goytia CN, Smith GW, Dudley J, Manning R, Bickell NA, Galvez MP. Accelerators: Sparking Innovation and Transdisciplinary Team Science in Disparities Research. International Journal of Environmental Research and Public Health. 14. PMID 28241508 DOI: 10.3390/ijerph14030225  0.36
2017 Shameer K, Glicksberg BS, Hodos R, Johnson KW, Badgeley MA, Readhead B, Tomlinson MS, O'Connor T, Miotto R, Kidd BA, Chen R, Ma'ayan A, Dudley JT. Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings in Bioinformatics. PMID 28200013 DOI: 10.1093/bib/bbw136  0.76
2017 Li L, Greene I, Readhead B, Menon MC, Kidd BA, Uzilov AV, Wei C, Philippe N, Schroppel B, He JC, Chen R, Dudley JT, Murphy B. Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. Scientific Reports. 7: 39487. PMID 28051114 DOI: 10.1038/srep39487  0.76
2016 Duan Q, Reid SP, Clark NR, Wang Z, Fernandez NF, Rouillard AD, Readhead B, Tritsch SR, Hodos R, Hafner M, Niepel M, Sorger PK, Dudley JT, Bavari S, Panchal RG, et al. L1000CDS(2): LINCS L1000 characteristic direction signatures search engine. Npj Systems Biology and Applications. 2. PMID 28413689 DOI: 10.1038/npjsba.2016.15  0.36
2016 Kini AS, Vengrenyuk Y, Shameer K, Maehara A, Purushothaman M, Yoshimura T, Matsumura M, Aquino M, Haider N, Johnson KW, Readhead B, Kidd BA, Feig JE, Krishnan P, Sweeny J, ... ... Dudley JT, et al. Intracoronary Imaging, Cholesterol Efflux, and Transcriptomes after Intensive Statin Treatment: The YELLOW II study. Journal of the American College of Cardiology. PMID 27989886 DOI: 10.1016/j.jacc.2016.10.029  0.44
2016 Wei C, Li L, Menon MC, Zhang W, Fu J, Kidd B, Keung KL, Woytovich C, Greene I, Xiao W, Salem F, Yi Z, He JC, Dudley JT, Murphy B. Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis. Journal of the American Society of Nephrology : Jasn. PMID 27927780 DOI: 10.1681/ASN.2016020238  0.44
2016 Shameer K, Johnson KW, Yahi A, Miotto R, Li LI, Ricks D, Jebakaran J, Kovatch P, Sengupta PP, Gelijns S, Moskovitz A, Darrow B, David DL, Kasarskis A, Tatonetti NP, ... ... Dudley JT, et al. PREDICTIVE MODELING OF HOSPITAL READMISSION RATES USING ELECTRONIC MEDICAL RECORD-WIDE MACHINE LEARNING: A CASE-STUDY USING MOUNT SINAI HEART FAILURE COHORT. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 276-287. PMID 27896982  0.44
2016 Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP. Machine-Learning Algorithms to Automate Morphological and Functional Assessments in 2D Echocardiography. Journal of the American College of Cardiology. 68: 2287-2295. PMID 27884247 DOI: 10.1016/j.jacc.2016.08.062  0.36
2016 Karim S, NourEldin HF, Abusamra H, Salem N, Alhathli E, Dudley J, Sanderford M, Scheinfeldt LB, Kumar S. e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations. Bmc Genomics. 17: 770. PMID 27766955 DOI: 10.1186/s12864-016-3088-1  0.32
2016 Saha S, Xiong X, Chakraborty PK, Shameer K, Arvizo RR, Kudgus RA, Dwivedi SK, Hossen MN, Gillies EM, Robertson JD, Dudley JT, Urrutia RA, Postier RG, Bhattacharya R, Mukherjee P. Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. Acs Nano. PMID 27758098 DOI: 10.1021/acsnano.6b02231  0.36
2016 Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, Klei LL, Kramer R, Pinto D, Gümüş ZH, Cicek AE, ... ... Dudley JT, et al. Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nature Neuroscience. PMID 27668389 DOI: 10.1038/nn.4399  0.64
2016 Li L, Boland MR, Miotto R, Tatonetti NP, Dudley JT. Replicating Cardiovascular Condition-Birth Month Associations. Scientific Reports. 6: 33166. PMID 27624541 DOI: 10.1038/srep33166  0.44
2016 Scarpa JR, Jiang P, Losic B, Readhead B, Gao VD, Dudley JT, Vitaterna MH, Turek FW, Kasarskis A. Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington's Disease. Plos Genetics. 12: e1006137. PMID 27390852 DOI: 10.1371/journal.pgen.1006137  0.36
2016 Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT. Evaluation of direct-to-consumer low-volume lab tests in healthy adults. The Journal of Clinical Investigation. 126: 2773. PMID 27367185 DOI: 10.1172/JCI88464  0.44
2016 Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, ... Dudley JT, et al. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinformatics (Oxford, England). 32: i101-i110. PMID 27307606 DOI: 10.1093/bioinformatics/btw282  0.76
2016 Sengupta PP, Huang YM, Bansal M, Ashrafi A, Fisher M, Shameer K, Gall W, Dudley JT. Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy. Circulation. Cardiovascular Imaging. 9. PMID 27266599 DOI: 10.1161/CIRCIMAGING.115.004330  0.36
2016 Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, ... ... Dudley JT, et al. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Medicine. 8: 62. PMID 27245685 DOI: 10.1186/s13073-016-0313-0  0.76
2016 Li L, Lee NJ, Glicksberg BS, Radbill BD, Dudley JT. Data-Driven Identification of Risk Factors of Patient Satisfaction at a Large Urban Academic Medical Center. Plos One. 11: e0156076. PMID 27228056 DOI: 10.1371/journal.pone.0156076  0.44
2016 Miotto R, Li L, Kidd BA, Dudley JT. Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records. Scientific Reports. 6: 26094. PMID 27185194 DOI: 10.1038/srep26094  0.44
2016 Yadav KK, Khader S, Readhead B, Yadav SS, Li L, Kasarksis A, Tewari AK, Dudley JT. Systems Medicine approaches to improving understanding, treatment, and clinical management of Neuroendocrine Prostate Cancer. Current Pharmaceutical Design. PMID 27174811  0.44
2016 Talukdar HA, Foroughi Asl H, Jain RK, Ermel R, Ruusalepp A, Franzén O, Kidd BA, Readhead B, Giannarelli C, Kovacic JC, Ivert T, Dudley JT, Civelek M, Lusis AJ, Schadt EE, et al. Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease. Cell Systems. 2: 196-208. PMID 27135365 DOI: 10.1016/j.cels.2016.02.002  0.36
2016 Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Tran N, Rittenhouse CA, Simone A, Ruderfer DM, Johnson J, Readhead B, Hadas Y, Gochman PA, Wang YC, Shah H, ... ... Dudley JT, et al. Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Reports. PMID 27117414 DOI: 10.1016/j.celrep.2016.03.090  0.36
2016 Hodos RA, Kidd BA, Shameer K, Readhead BP, Dudley JT. In silico methods for drug repurposing and pharmacology. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 27080087 DOI: 10.1002/wsbm.1337  0.64
2016 Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT. Evaluation of direct-to-consumer low-volume lab tests in healthy adults. The Journal of Clinical Investigation. PMID 27018593 DOI: 10.1172/JCI86318  0.44
2016 Badgeley MA, Shameer K, Glicksberg BS, Tomlinson MS, Levin MA, McCormick PJ, Kasarskis A, Reich DL, Dudley JT. EHDViz: clinical dashboard development using open-source technologies. Bmj Open. 6: e010579. PMID 27013597 DOI: 10.1136/bmjopen-2015-010579  0.64
2016 Ruderfer DM, Charney AW, Readhead B, Kidd BA, Kähler AK, Kenny PJ, Keiser MJ, Moran JL, Hultman CM, Scott SA, Sullivan PF, Purcell SM, Dudley JT, Sklar P. Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. The Lancet. Psychiatry. PMID 26915512 DOI: 10.1016/S2215-0366(15)00553-2  0.64
2016 Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT. Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. Briefings in Bioinformatics. PMID 26876889 DOI: 10.1093/bib/bbv118  0.44
2016 Readhead B, Haure-Mirande JV, Zhang B, Haroutunian V, Gandy S, Schadt EE, Dudley JT, Ehrlich ME. Molecular systems evaluation of oligomerogenic APPE693Q and fibrillogenic APPKM670/671NL/PSEN1?exon9 mouse models identifies shared features with human Alzheimer’s brain molecular pathology Molecular Psychiatry. DOI: 10.1038/mp.2015.215  0.36
2015 Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT. Integrative network modeling approaches to personalized cancer medicine. Personalized Medicine. 12: 245-257. PMID 27019658 DOI: 10.2217/pme.14.87  0.64
2015 Kidd BA, Wroblewska A, Boland MR, Agudo J, Merad M, Tatonetti NP, Brown BD, Dudley JT. Mapping the effects of drugs on the immune system. Nature Biotechnology. PMID 26619012 DOI: 10.1038/nbt.3367  0.64
2015 Dincer A, Gavin DP, Xu K, Zhang B, Dudley JT, Schadt EE, Akbarian S. Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain. Translational Psychiatry. 5: e679. PMID 26575220 DOI: 10.1038/tp.2015.169  0.32
2015 Readhead B, Haure-Mirande JV, Zhang B, Haroutunian V, Gandy S, Schadt EE, Dudley JT, Ehrlich ME. Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(Δexon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. Molecular Psychiatry. PMID 26552589 DOI: 10.1038/mp.2015.167  0.36
2015 Li L, Cheng WY, Glicksberg BS, Gottesman O, Tamler R, Chen R, Bottinger EP, Dudley JT. Identification of type 2 diabetes subgroups through topological analysis of patient similarity. Science Translational Medicine. 7: 311ra174. PMID 26511511 DOI: 10.1126/scitranslmed.aaa9364  0.64
2015 Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. Briefings in Bioinformatics. PMID 26494363 DOI: 10.1093/bib/bbv084  0.36
2015 Brohl AS, Li L, Andikyan V, Običan SG, Cioffi A, Hao K, Dudley JT, Ascher-Walsh C, Kasarskis A, Maki RG. Age-stratified risk of unexpected uterine sarcoma following surgery for presumed benign leiomyoma. The Oncologist. 20: 433-9. PMID 25765878 DOI: 10.1634/theoncologist.2014-0361  0.44
2015 Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. Molecular Biology and Evolution. 32: 1148-60. PMID 25681384 DOI: 10.1093/molbev/msv031  0.32
2015 Vidal SJ, Rodriguez-Bravo V, Quinn SA, Rodriguez-Barrueco R, Lujambio A, Williams E, Sun X, de la Iglesia-Vicente J, Lee A, Readhead B, Chen X, Galsky M, Esteve B, Petrylak DP, Dudley JT, et al. A targetable GATA2-IGF2 axis confers aggressiveness in lethal prostate cancer. Cancer Cell. 27: 223-39. PMID 25670080 DOI: 10.1016/j.ccell.2014.11.013  0.36
2015 Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R. An integrative pipeline for multi-modal discovery of disease relationships. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 407-18. PMID 25592600  0.76
2015 Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 342-6. PMID 25592594  0.64
2015 Shameer K, Readhead B, Dudley JT. Computational and experimental advances in drug repositioning for accelerated therapeutic stratification. Current Topics in Medicinal Chemistry. 15: 5-20. PMID 25579574  0.36
2015 Baida G, Bhalla P, Kirsanov K, Lesovaya E, Yakubovskaya M, Yuen K, Guo S, Lavker RM, Readhead B, Dudley JT, Budunova I. REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids. Embo Molecular Medicine. 7: 42-58. PMID 25504525 DOI: 10.15252/emmm.201404601  0.36
2015 Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions Molecular Biology and Evolution. 32: 1148-1160. DOI: 10.1093/molbev/msv031  0.64
2014 Dudley J. The promise of genomics-based drug repurposing Clinical Advances in Hematology and Oncology. 12: 601-603. PMID 25654481  0.64
2014 Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ. Disease risk factors identified through shared genetic architecture and electronic medical records. Science Translational Medicine. 6: 234ra57. PMID 24786325 DOI: 10.1126/scitranslmed.3007191  0.76
2014 Jung K, LePendu P, Chen WS, Iyer SV, Readhead B, Dudley JT, Shah NH. Automated detection of off-label drug use. Plos One. 9: e89324. PMID 24586689 DOI: 10.1371/journal.pone.0089324  0.64
2014 Karczewski KJ, Fernald GH, Martin AR, Snyder M, Tatonetti NP, Dudley JT. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud. Plos One. 9: e84860. PMID 24454756 DOI: 10.1371/journal.pone.0084860  0.64
2014 Kidd BA, Peters LA, Schadt EE, Dudley JT. Unifying immunology with informatics and multiscale biology. Nature Immunology. 15: 118-27. PMID 24448569 DOI: 10.1038/ni.2787  0.64
2013 Readhead B, Dudley J. Translational Bioinformatics Approaches to Drug Development. Advances in Wound Care. 2: 470-489. PMID 24527359 DOI: 10.1089/wound.2012.0422  0.36
2013 Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos AF, Vaka D, Tran KQ, Zhou M, Krasinska K, Riess JW, Neal JW, Khatri P, Park KS, et al. A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discovery. 3: 1364-77. PMID 24078773 DOI: 10.1158/2159-8290.CD-13-0183  0.64
2013 Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M. Systematic functional regulatory assessment of disease-associated variants. Proceedings of the National Academy of Sciences of the United States of America. 110: 9607-12. PMID 23690573 DOI: 10.1073/pnas.1219099110  0.76
2012 Haeberle H, Dudley JT, Liu JT, Butte AJ, Contag CH. Identification of cell surface targets through meta-analysis of microarray data. Neoplasia (New York, N.Y.). 14: 666-9. PMID 22904683 DOI: 10.1593/neo.12634  0.64
2012 Chen R, Dudley JT, Ruau D, Butte AJ. Quantifying multi-ethnic representation in genetic studies of high mortality diseases. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2012: 11-8. PMID 22779041  0.76
2012 Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS. Integrative approach to pain genetics identifies pain sensitivity loci across diseases. Plos Computational Biology. 8: e1002538. PMID 22685391 DOI: 10.1371/journal.pcbi.1002538  0.64
2012 Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human genomic disease variants: a neutral evolutionary explanation. Genome Research. 22: 1383-94. PMID 22665443 DOI: 10.1101/gr.133702.111  0.64
2012 Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. Plos Genetics. 8: e1002621. PMID 22511877 DOI: 10.1371/journal.pgen.1002621  0.76
2012 Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, ... ... Dudley JT, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 148: 1293-307. PMID 22424236 DOI: 10.1016/j.cell.2012.02.009  0.64
2012 Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S. Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Molecular Biology and Evolution. 29: 2087-94. PMID 22389448 DOI: 10.1093/molbev/mss079  0.64
2012 Karczewski KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, Salari K, Snyder M, Altman RB, Kim SK. Interpretome: a freely available, modular, and secure personal genome interpretation engine. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 339-50. PMID 22174289  0.64
2011 Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinformatics (Oxford, England). 27: 3317-8. PMID 21967760 DOI: 10.1093/bioinformatics/btr548  0.64
2011 Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, et al. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. Plos Genetics. 7: e1002280. PMID 21935354 DOI: 10.1371/journal.pgen.1002280  0.76
2011 Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Science Translational Medicine. 3: 96ra77. PMID 21849665 DOI: 10.1126/scitranslmed.3001318  0.64
2011 Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Science Translational Medicine. 3: 96ra76. PMID 21849664 DOI: 10.1126/scitranslmed.3002648  0.64
2011 Kumar S, Dudley JT, Filipski A, Liu L. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics : Tig. 27: 377-86. PMID 21764165 DOI: 10.1016/j.tig.2011.06.004  0.64
2011 Dudley JT, Deshpande T, Butte AJ. Exploiting drug-disease relationships for computational drug repositioning. Briefings in Bioinformatics. 12: 303-11. PMID 21690101 DOI: 10.1093/bib/bbr013  0.64
2011 Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ. Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. Journal of Biomedical Informatics. 44: S39-43. PMID 21420508 DOI: 10.1016/j.jbi.2011.03.007  0.76
2011 Sharaf RN, Butte AJ, Montgomery KD, Pai R, Dudley JT, Pasricha PJ. Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes. Bmc Gastroenterology. 11: 5. PMID 21251264 DOI: 10.1186/1471-230X-11-5  0.64
2011 Dudley JT, Chen R, Butte AJ. Matching cancer genomes to established cell lines for personalized oncology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 243-52. PMID 21121052  0.76
2010 Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. Content-based microarray search using differential expression profiles. Bmc Bioinformatics. 11: 603. PMID 21172034 DOI: 10.1186/1471-2105-11-603  0.64
2010 Dudley JT, Butte AJ. In silico research in the era of cloud computing. Nature Biotechnology. 28: 1181-5. PMID 21057489 DOI: 10.1038/nbt1110-1181  0.76
2010 Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB. An integrative method for scoring candidate genes from association studies: application to warfarin dosing. Bmc Bioinformatics. 11: S9. PMID 21044367 DOI: 10.1186/1471-2105-11-S9-S9  0.76
2010 Chen DP, Dudley JT, Butte AJ. Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. Bmc Bioinformatics. 11: S4. PMID 21044362 DOI: 10.1186/1471-2105-11-S9-S4  0.64
2010 Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. Plos Computational Biology. 6. PMID 20885780 DOI: 10.1371/journal.pcbi.1000940  0.64
2010 Corona E, Dudley JT, Butte AJ. Extreme evolutionary disparities seen in positive selection across seven complex diseases. Plos One. 5: e12236. PMID 20808933 DOI: 10.1371/journal.pone.0012236  0.64
2010 Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Translational bioinformatics in the cloud: an affordable alternative. Genome Medicine. 2: 51. PMID 20691073 DOI: 10.1186/gm172  0.64
2010 Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. Journal of Cardiovascular Translational Research. 3: 438-47. PMID 20677029 DOI: 10.1007/s12265-010-9214-6  0.76
2010 Dudley JT, Butte AJ. Biomarker and drug discovery for gastroenterology through translational bioinformatics. Gastroenterology. 139: 735-41, 741.e1. PMID 20650279 DOI: 10.1053/j.gastro.2010.07.024  0.76
2010 Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, et al. Clinical assessment incorporating a personal genome. Lancet (London, England). 375: 1525-35. PMID 20435227 DOI: 10.1016/S0140-6736(10)60452-7  0.76
2010 Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ. Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. Plos Computational Biology. 6: e1000662. PMID 20140234 DOI: 10.1371/journal.pcbi.1000662  0.64
2010 Morgan AA, Dudley JT, Deshpande T, Butte AJ. Dynamism in gene expression across multiple studies. Physiological Genomics. 40: 128-40. PMID 19920211 DOI: 10.1152/physiolgenomics.90403.2008  0.64
2009 Dudley JT, Butte AJ. A quick guide for developing effective bioinformatics programming skills. Plos Computational Biology. 5: e1000589. PMID 20041221 DOI: 10.1371/journal.pcbi.1000589  0.76
2009 Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Molecular Systems Biology. 5: 307. PMID 19756046 DOI: 10.1038/msb.2009.66  0.64
2009 Dudley JT, Butte AJ. Identification of discriminating biomarkers for human disease using integrative network biology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27-38. PMID 19209693  0.76
2008 Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biology. 9: R170. PMID 19061490 DOI: 10.1186/gb-2008-9-12-r170  0.64
2008 Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics. 9: 299-306. PMID 18417537 DOI: 10.1093/bib/bbn017  0.64
2008 Dudley J, Butte AJ. Enabling integrative genomic analysis of high-impact human diseases through text mining Pacific Symposium On Biocomputing 2008, Psb 2008. 580-591. PMID 18229717  0.64
2007 Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-9. PMID 17488738 DOI: 10.1093/molbev/msm092  0.64
2007 Kumar S, Dudley J. Bioinformatics software for biologists in the genomics era Bioinformatics. 23: 1713-1717. PMID 17485425 DOI: 10.1093/bioinformatics/btm239  0.64
2006 Hedges SB, Dudley J, Kumar S. TimeTree: A public knowledge-base of divergence times among organisms Bioinformatics. 22: 2971-2972. PMID 17021158 DOI: 10.1093/bioinformatics/btl505  0.64
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