Publications

* denotes equal contribution

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, Kini AS. (2017) Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes. Sci Rep. 2017 Aug 1;7(1):7001. doi: 10.1038/s41598-017-07029-7. PMID: 28765529
• 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. (2017) Necroptosis activation in Alzheimer’s disease. Nat Neurosci. 2017 Jul 24. doi: 10.1038/nn.4608. [Epub ahead of print] PMID: 28758999
• Salem Omar AM, Shameer K, Narula S, Abdel Rahman MA, Rifaie O, Narula J, Dudley JT, Sengupta PP. (2017) Artificial Intelligence-Based Assessment of Left Ventricular Filling Pressures From 2-Dimensional Cardiac Ultrasound Images. JACC Cardiovasc Imaging. 2017 Jul 13. pii: S1936-878X(17)30468-0. doi: 10.1016/j.jcmg.2017.05.003. [Epub ahead of print] PMID: 28734920
• 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. (2017) Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer’s pathology. Acta Neuropathol. 2017 Jun 13. doi: 10.1007/s00401-017-1737-3. [Epub ahead of print] PMID: 28612290 DOI: 10.1007/s00401-017-1737-3
• Miotto R, Wang F, Wang S, Jiang X, Dudley JT. Deep learning for healthcare: review, opportunities and challenges. Brief Bioinform. 2017 May 6. doi: 10.1093/bib/bbx044. [Epub ahead of print] PubMed PMID: 28481991.
• Fullard JF, Giambartolomei C, Hauberg ME, Xu K, Voloudakis G, Shao Z, Bare C, Dudley JT, Mattheisen M, Robakis NK, Haroutunian V, Roussos P. (2017) Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci. Hum Mol Genet. 2017 Mar 14. DOI: 10.1093/hmg/ddx103 PMID: 28335009.
• Chan YY, Wang P, Rogers L, Tignor N, Zweig M, Hershman SG, Genes N, Scott ER, Krock E, Badgeley M, Edgar R, Violante S, Wright R, Powell CA, Dudley JT, Schadt EE. (2017) The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit. Nat Biotechnol. 2017 Mar 13. PMID: 28288104 DOI: 10.1038/nbt.3826
• Hicks DF, Goossens N, Blas-García A, Tsuchida T, Wooden B, Wallace MC, Nieto N, Lade A, Redhead B, Cederbaum AI, Dudley JT, Fuchs BC, Lee YA, Hoshida Y, Friedman SL. (2017) Transcriptome-based repurposing of apigenin as a potential anti-fibrotic agent targeting hepatic stellate cells. Sci Rep. 2017 Mar 3. DOI: 10.1038/srep42563. PMID: 28256512.
• Horowitz CR, Shameer K, Gabrilove J, Atreja A, Shepard P, Goytia CN, Smith GW, Dudley J, Manning R, Bickell NA, Galvez MP. (2017) Accelerators: Sparking Innovation and Transdisciplinary Team Science in Disparities Research. Int J Environ Res Public Health. 2017 Feb 23. DOI: 10.3390/ijerph14030225. PMID: 28241508
• 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. (2017) Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Brief Bioinform. 2017 Feb 15. DOI: 10.1093/bib/bbw136. PMID: 28200013.
• Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT. (2017) Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. Brief Bioinform. 2017 Jan. PMID: 26876889 PMCID: PMC5221424 DOI: 10.1093/bib/bbv118.
• Lee HC, Kosoy R, Becker CE, Dudley JT, Kidd BA. (2017) Automated cell type discovery and classification through knowledge transfer. Bioinformatics. 2017 Jan 3. DOI: 10.1093/bioinformatics/btx054. PMID: 28158442.
• Di Narzo AF, Telesco SE, Brodmerkel C, Argmann C, Peters LA, Li K, Kidd B, Dudley J, Cho J, Schadt EE, Kasarskis A, Dobrin R, Hao K. (2017) High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors. PLoS Genet. 2017 Jan 27. DOI: 10.1371/journal.pgen.1006565. PMID: 28129359.
• Smith MR, Burman P, Sadahiro M, Kidd BA, Dudley JT, Morishita H. (2017) Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity. eNeuro. 2017 Jan 18. DOI: 10.1523/ENEURO.0240-16.2016. PMID: 28101530.
• 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. (2017) Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. Sci Rep. 2017 Jan 4. DOI: 10.1038/srep39487. PMID: 28051114. PMCID: PMC5209709.

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, Ma’ayan A. (2016) L1000CDS2: LINCS L1000 characteristic direction signatures search engine. NPJ Syst Biol Appl. 2016 Aug 4. PMID: 28413689. PMCID: PMC5389891. DOI: 10.1038/npjsba.2016.15.
• 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, Mahajan M, Moreno P, Mehran R, Kovacic JC, Baber U, Dudley JT, Narula J, Sharma S. (2016) Intracoronary Imaging, Cholesterol Efflux, and Transcriptomes after Intensive Statin Treatment: The YELLOW II study. J Am Coll Cardiol. 2016 Oct 27. DOI: 10.1016/j.jacc.2016.10.029 PMID: 27989886
• 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. (2016) Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis. J Am Soc Nephrol. 2016 Dec 7. DOI: 10.1681/ASN.2016020238 PMID: 27927780
• 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, Pinney S, Dudley JT. (2016) Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort. Pac Symp Biocomput. 2016;22:276-287. PMID: 27896982
• Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE. (2016) Exploring The Reproducibility of Probabilistic Causal Molecular Network Models. Pac Symp Biocomput. 2016;22:120-131. PMID: 27896968
• Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP. (2016) Machine-Learning Algorithms to Automate Morphological and Functional Assessments in 2D Echocardiography. J Am Coll Cardiol. 2016 Nov 29;68(21):2287-2295. doi: 10.1016/j.jacc.2016.08.062.
• Kosoy R, Agashe C, Grishin A, Leung DY, Wood RA, Sicherer SH, Jones SM, Burks AW, Davidson WF, Lindblad RW, Dawson P, Merad M, Kidd BA, Dudley JT, Sampson HA, Berin MC. (2016) Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype. PLoS One. 2016 Oct 27. doi: 10.1371/journal.pone.0163831.
• 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, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YC, Mahajan MC, Derry JM, Dudley JT, Hemby SE, Logsdon BA, Talbot K, Raj T, Bennett DA, De Jager PL, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu LA, Mangravite LM, Toyoshiba H, Gur RE, Hahn CG, Lewis DA, Haroutunian V, Peters MA, Lipska BK, Buxbaum JD, Schadt EE, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B, Sklar P. (2016) Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nat Neurosci. 2016 September. doi: 10.1038/nn.
• Karim S, NourEldin HF, Abusamra H, Salem N, Alhathli E, Dudley J, Sanderford M, Scheinfeldt LB, Kumar S. (2016) e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations. BMC Genomics. 2016 Oct 17. PMID:27766955
• 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. (2016) Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. ACS Nano. 2016 Oct 19. PMID:27758098
• Nead KT, Gaskin G, Chester C, Swisher-McClure S, Dudley JT, Leeper NJ, Shah NH. (2016) Influence of age on androgen deprivation therapy-associated Alzheimer’s disease. Sci Rep. 2016 Oct 18. PMID:27752112
• Li L, Boland MR, Miotto R, Tatonetti NP, Dudley JT. (2016) Replicating Cardiovascular Condition-Birth Month Associations. Sci Rep. 2016 September. doi: 10.1038/srep33166
• Ruderfer DM, Dudley JT. (2016) Deep phenotyping predicts Huntington’s genotype. Nature Biotechnology. 2016 August. doi: 10.1038/nbt.3648
• Scarpa JR, Jiang P, Losic B, Readhead B, Gao VD, Dudley JT, Vitaterna MH, Turek FW, Kasarskis A. (2016) Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington’s Disease. PLoS Genet. 2016 July. doi: 10.1371/journal.pgen.1006137
• 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. (2016) Evaluation of direct-to-consumer low-volume lab tests in healthy adults. Journal of Clinical Investigation. 2016 July. doi: 10.1172/JCI88464
• Di Narzo AF, Peters LA, Argmann C, Stojmirovic A, Perrigoue J, Li K, Telesco S, Kidd B, Walker J, Dudley J, Cho J, Schadt EE, Kasarskis A, Curran M, Dobrin R, Hao K. (2016) Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn’s Disease Cohort Inform IBD Genetic Association Loci. Clinical and Translational Gastroenterology. 2016 June. doi: 10.1038/ctg.2016.34
• 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. (2016) Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinformatics. 2016 June. doi: 10.1093/bioinformatics/btw282
• Nead KT, Gaskin G, Chester C, Swisher-McClure S, Dudley JT, Leeper NJ, Shah NH. (2016) Reply to R.L. Bowen et al, M. Froehner et al, J.L. Leow et al, and C. Brady et al. Journal of Clinical Oncology. 2016 August. doi: 10.1200/JCO.2016.67.9449
• Kishibe M, Baida G, Bhalla P, Lavker RM, Schlosser B, Iinuma S, Yoshida S, Dudley JT, Budunova I. (2016) Important role of kallikrein 6 for the development of keratinocyte proliferative resistance to topical glucocorticoids. Oncotarget. 2016 June. doi: 10.18632/oncotarget.9926
• Sengupta PP, Huang YM, Bansal M, Ashrafi A, Fisher M, Shameer K, Gall W, Dudley JT. (2016) Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy. Circ Cardiovasc Imaging. 2016 June. pii: e00433
• MetaSUB International Consortium. (2016) The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium Inaugural Meeting Report. Microbiome. 2016 June. doi: 10.1186/s40168-016-0168-z
• 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, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R. (2016) Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Med. 2016 Jun 1;8(1):62. doi: 10.1186
• Li L, Lee NJ, Glicksberg BS, Radbill BD, Dudley JT. (2016) Data-Driven Identification of Risk Factors of Patient Satisfaction at a Large Urban Academic Medical Center. PLoS One. 2016 May 26;11(5):e0156076. doi: 10.1371
• Miotto R, Li L, Kidd BA, Dudley JT. (2016) Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records. Sci Rep. 2016 May 17;6:26094. doi: 10.1038/srep26094.
• Yadav KK, Khader S, Readhead B, Yadav SS, Li L, Kasarksis A, Tewari AK, Dudley JT. (2016) Systems Medicine approaches to improving understanding, treatment, and clinical management of Neuroendocrine Prostate Cancer. Curr Pharm Des. 2016 May 13. [Epub ahead of print]
• 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, Skogsberg J, Michoel T, Björkegren JL. (2016) Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease. Cell Syst. doi: 10.1016/j.cels.2016.02.002. Epub 2016 Mar 3.
• 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, Cagney G, Rapoport J, Gage FH, Dudley JT, Sklar P, Mattheisen M, Cotter D, Fang G, Brennand KJ. (2016) Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. Cell Rep. 2016 Apr 21. pii: S2211-1247(16)30396-5. Epub ahead of print.
• Hodos RA, Kidd BA, Shameer K, Readhead BP, Dudley JT. (2016) In Silico Methods for Drug Repurposing and Pharmacology. Wiley Interdiscip Rev Syst Biol Med. 2016 Apr 15. doi: 10.1002. Epub ahead of print.
• 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. (2016) Evaluation of direct-to-consumer low-volume lab tests in healthy adults. Journal of Clinical Investigation. pii: 86318. doi: 10.1172
• Badgeley MA, Shameer K, Glicksberg BS, Tomlinson MS, Levin MA, McCormick PJ, Kasarskis A, Reich DL, Dudley JT. (2016) EHDViz: Clinical Dashboard Development Using Open-Source Technologies. BMJ Open. doi: 10.1136.
• 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. (2016) Polygenic Overlap Between Schizophrenia Risk and Antipsychotic Response: A Genomic Medicine Approach. The Lancet. Epub.
• Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush JF, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC. (2016) Toward Clinical Genomics in Everyday Medicine: Perspectives and Recommendations. Expert Review of Molecular Diagnostics. Epub
• Nead KT, Gaskin G, Chester C, Swisher-McClure S, Dudley JT, Leeper NJ, Shah NH. (2016) Androgen Deprivation Therapy and Future Alzheimer’s Disease Risk. Journal of Clinical Oncology. 34(6):566-71.
• Kidd BA*, Wroblewska A*, Boland MR, Agudo J, Merad M, Tatonetti NP, Brown BD*, Dudley JT*. (2016) Mapping the Effects of Drugs on the Immune System. Nature Biotechnology. 34 (1), 47-54

2015

• Readhead B*, Haure-Mirande JV*, Zhang B, Haroutunian V, Gandy S, Schadt EE, Dudley JT*, Ehrlich ME*. (2015) Molecular Systems Evaluation of Oligomerogenic APPE693Q and Fibrillogenic APPKM670/671NL/PSEN1Δexon9 Mouse Models Identifies Shared Features with Human Alzheimer’s Brain Molecular Pathology. Molecular Psychiatry. (advances online access)
• Dincer A, Gavin DP, Xu K, B Zhang, 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 (11), e679.
• Li L, Cheng WY, Glicksberg BS, Gottesman O, Tamler R, Chen R, Bottinger EP, Dudley JT. (2015) Identification of Type 2 Diabetes Subgroups Through Topological Analysis of Patient Similarity. Science Translational Medicine. 7 (311), 311ra174-311ra174.
• Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R. (2015) Interpreting Functional Effects of Coding Variants: Challenges in Proteome-Scale Prediction, Annotation and Assessment. Briefings in Bioinformatics. bbv084.
• Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT. (2015) Integrative network modeling approaches to personalized cancer medicine. Personalized Medicine. Vol. 12, No. 3, Pages 245-257
• Brohl AS, Li L, Andikyan V, Običan SG, Cioffi A, Hao K, Dudley JT, Ascher-Walsh C, Kasarskis A, Maki RG. (2015) Age-Stratified Risk of Unexpected Uterine Sarcoma Following Surgery for Presumed Benign Leiomyoma. Oncologist. 2015 Apr;20(4):433-9
• Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. (2015) Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. Molecular Biology and Evolution. 2015 Feb 12. pii: msv031.
• Björkegren JLM, Kovacic JC, Dudley JT, Schadt EE. (2015) Genome-Wide Significant Loci: How Important Are They?: Systems Genetics to Understand Heritability of Coronary Artery Disease and Other Common Complex Disorders. Journal of the American College of Cardiology. 2015;65(8):830-845.
• 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, Rabadan R, Silva JM, Hoshida Y, Lowe SW, Cordon-Cardo C, Domingo-Domenech J. (2015) A Targetable GATA2-IGF2 Axis Confers Aggressiveness in Lethal Prostate Cancer. Cancer Cell. 2015 Feb 9;27(2):223-39.
• Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis S-O, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE (2015) Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Systems. (Available online 7 February 2015)
• Shameer K, Readhead B, Dudley JT. (2015) Computational and experimental advances in drug repositioning for accelerated therapeutic stratification. Current Topics in Medicinal Chemistry. 2015;15(1):5-20.
• Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R. (2015) An integrative pipeline for multi-modal discovery of disease relationships. Pacific Symposium on Biocomputing. 2015;20:407-18.
• Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. (2015) Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine. Pacific Symposium on Biocomputing. 2015;20:342-6.

2014

• Baida G, Bhalla P, Kirsanov K, Lesovaya E, Yakubovskaya M, Yuen K, Guo S, Lavker RM, Readhead B, Dudley JT, Budunova I. (2014) REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids. EMBO Molecular Medicine. 2014 Dec 11;7(1):42-58.
• Shineman DW, Alam J, Anderson M, Black SE, Carman AJ, Cummings JL, Dacks PA, Dudley JT, Frail DE, Green A, Lane RF, Lappin D, Simuni T, Stefanacci RG, Sherer T, Fillit HM (2014) Overcoming obstacles to repurposing for neurodegenerative disease. Annals of Clinical and Translational Neurology. Advanced online access.
• Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ (2014) Disease Risk Factors Identified Through Shared Genetic Architecture and Electronic Medical Records. Science Translational Medicine. 30 April 2014 6:234ra57.
• Kidd BA, Peters LA, Schadt EE, Dudley JT (2014) Unifying immunology with informatics and multiscale biology. Nature Immunology Jan 21;15(2):118-27.
• Karczewski KJ, Martin A, Fernald GH, Tatonetti NP, Snyder M, Dudley JT (2014) STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud. PLoS ONE 9(1): e84860.
• Jung K, LePendu P, Chen WS, Iyer SV, Readhead B, Dudley JT, Shah NH (2014) Automated Detection of Off-Label Drug Use. PLoS ONE 9(2): e89324.
• Avitzur Y, Guo C, Mastropaolo LA, Bahrami E, Chen H, Zhao Z, Elkadri A, Dhillon S, Murchie R, Fattouh R, Huynh H, Walker JL, Wales PW, Cutz E, Kakuta Y, Dudley J, Kammermeier J, Powrie F, Shah N, Walz C, Nathrath M, Kotlarz D, Puchaka J, Krieger J, Racek T, Kirchner T, Walters TD, Brumell JH, Griffiths AM, Rezaei N, Rashtian P, Najafi M, Monajemzadeh M, Pelsue S, McGovern DPB, Uhlig HH, Schadt EE, Klein C, Snapper SB, Muise AM (2014) Mutations in Tetratricopeptide Repeat Domain 7A Result in a Severe Form of Very Early Onset Inflammatory Bowel Disease. Gastroenterology Apr;146(4):1028-39.

2013

• Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos AF, Vaka D, Tran KQT, Zhou M, Krasinska K, Riess JW, Neal JW, Khatri P, Park KS, Butte AJ, Sage J (2013) A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors. Cancer Discovery Dec;3(12):1364-77.
• Readhead B, Dudley JT (2013) Translational Bioinformatics Approaches to Drug Development. Advances in Wound Care Nov; 2(9): 470–489.
• Karczewski KJ*, Dudley JT*, Kaburka K, Chen R, Montgomery S, Butte AJ, Snyder M (2013) Systematic functional regulatory assessment of disease-associated variants. Proceedings of the National Academy of Sciences (USA) Jun 4;110(23):9607-12.

2012

• Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S (2012) Human genomic disease variants: A neutral evolutionary explanation. Genome Research 22(8):1383-94. Epub Jun 4.
• Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS (2012) Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases. PLoS Computational Biology 8(6): e1002538.
• Chen R, Dudley JT, Ruau D, Butte AJ (2012) Quantifying multi-ethnic representation in genetic studies of high mortality diseases. AMIA Summits Transl Sci Proc. 11-8. Epub Mar 19.
• Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S (2012) Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery. Molecular Biology and Evolution 29(9):2087-94.
• Karczewski KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, Salari K, Snyder M, Altman RB, Kim SK (2012) Interpretome: a freely available, modular, and secure personal genome interpretation engine. Pacific Symposium on Biocomputing 2012:339-350.
• Haeberle H, Dudley JT, Butte AJ, Contag C (2012) Identification of Cell Surface Targets through Meta-analysis of Microarray Data. Neoplasia 14(7):666-9.
• 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, O’Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. (2012) Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148(6): 1293-1307.
• Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD et al. (2012) Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases. PLoS Genetics 8(4): e1002621.

Prior to 2012

• Dudley JT*, Sirota M*, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ (2011) Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Science Translational Medicine 3(96): 96ra76.
• Sirota M*, Dudley JT*, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ (2011) Discovery and preclinical validation of drug indications using compendia of public gene expression data. Science Translational Medicine 3(96): 96ra77.
• Sharaf RN, Butte AJ, Montgomery KD, Pai R, Dudley JT, Pasricha PJ (2011) Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes. BMC Gastroenterology 11: 5.
• Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ (2011) Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. Journal of Biomedical Informatics 44 Suppl 1: S39-43.
• Kumar S, Dudley JT, Filipski A, Liu L (2011) Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics 27(9): 377-386.
• Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ (2011) ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinformatics 27(23): 3317-3318.
• Dudley JT, Deshpande T, Butte AJ (2011) Exploiting drug-disease relationships for computational drug repositioning. Briefings in Bioinformatics 12(4): 303-311.
• Dudley JT, Chen R, Butte AJ (2011) Matching cancer genomes to established cell lines for personalized oncology. Pacific Symposium on Biocomputing 2011: 243-252.
• Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK et al. (2011) Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genetics 7(9): e1002280.
• Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB (2010) An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinformatics 11 Suppl 9: S9.
• Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ (2010) Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Computational Biology 6(2): e1000662.
• Morgan AA, Dudley JT, Deshpande T, Butte AJ (2010) Dynamism in gene expression across multiple studies. Physiological Genomics 40(3): 128-140.
• Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ (2010) Content-based microarray search using differential expression profiles. BMC Bioinformatics 11: 603.
• Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E (2010) Drug discovery in a multidimensional world: systems, patterns, and networks. Journal of Cardiovascular Translational Research 3(5): 438-447.
• Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ (2010) Translational bioinformatics in the cloud: an affordable alternative. Genome Medicine 2(8): 51.
• Dudley JT, Butte AJ (2010) In silico research in the era of cloud computing. Nature Biotechnology 28(11): 1181-1185.
• Dudley JT, Butte AJ (2010) Biomarker and drug discovery for gastroenterology through translational bioinformatics. Gastroenterology 139(3): 735-741, 741 e731.
• Corona E, Dudley JT, Butte AJ (2010) Extreme evolutionary disparities seen in positive selection across seven complex diseases. PLoS One 5(8): e12236.
• Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA et al (2010) Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Computational Biology 6(9).
• Chen DP*, Dudley JT*, Butte AJ (2010) Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. BMC Bioinformatics 11 Suppl 9: S4.
• Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA et al (2010) Clinical assessment incorporating a personal genome. Lancet 375(9725): 1525-1535.
• Dudley JT, Tibshirani R, Deshpande T, Butte AJ (2009) Disease signatures are robust across tissues and experiments. Molecular Systems Biology 5: 307.
• Dudley JT, Butte AJ (2009) A quick guide for developing effective bioinformatics programming skills. PLoS Computational Biology 5(12): e1000589.
• Dudley JT, Butte AJ (2009) Identification of discriminating biomarkers for human disease using integrative network biology. Pacific Symposium on Biocomputing 2009: 27-38.
• Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9(4): 299-306.
• Dudley J, Chen D, Butte A (2008) Using SNOMED-CT for Translational Genomics Data Integration. Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008).
• Dudley J, Butte AJ (2008) Enabling integrative genomic analysis of high-impact human diseases through text mining. Pacific Symposium on Biocomputing 2008: 580-591.
• Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ (2008) FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biology 9(12): R170.
• Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24(8): 1596-1599.
• Kumar S, Dudley J (2007) Bioinformatics software for biologists in the genomics era. Bioinformatics 23(14): 1713-1717.
• Hedges SB, Dudley J, Kumar S (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22(23): 2971-2972.