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A Network-Biology Informed Computational Drug Repositioning Strategy to Target Disease Risk Trajectories and Comorbidities of Peripheral Artery Disease.

Shameer K, Dow G, Glicksberg BS, Johnson KW, Ze Y, Tomlinson MS, Readhead B, Dudley JT, Kullo IJ.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:108-117. eCollection 2018.


Artificial Intelligence in Cardiology.

Johnson KW, Torres Soto J, Glicksberg BS, Shameer K, Miotto R, Ali M, Ashley E, Dudley JT.

J Am Coll Cardiol. 2018 Jun 12;71(23):2668-2679. doi: 10.1016/j.jacc.2018.03.521. Review.


Adaptive landscape of protein variation in human exomes.

Patel R, Scheinfeldt LB, Sanderford MD, Lanham TR, Tamura K, Platt A, Glicksberg BS, Xu K, Dudley JT, Kumar S.

Mol Biol Evol. 2018 May 28. doi: 10.1093/molbev/msy107. [Epub ahead of print]


The next generation of precision medicine: observational studies, electronic health records, biobanks and continuous monitoring.

Glicksberg BS, Johnson KW, Dudley JT.

Hum Mol Genet. 2018 May 1;27(R1):R56-R62. doi: 10.1093/hmg/ddy114.


Rapamycin Modulates Glucocorticoid Receptor Function, Blocks Atrophogene REDD1, and Protects Skin from Steroid Atrophy.

Lesovaya E, Agarwal S, Readhead B, Vinokour E, Baida G, Bhalla P, Kirsanov K, Yakubovskaya M, Platanias LC, Dudley JT, Budunova I.

J Invest Dermatol. 2018 Mar 27. pii: S0022-202X(18)31809-8. doi: 10.1016/j.jid.2018.02.045. [Epub ahead of print]


Isolation and Identification of the Follicular Microbiome: Implications for Acne Research.

Hall JB, Cong Z, Imamura-Kawasawa Y, Kidd BA, Dudley JT, Thiboutot DM, Nelson AM.

J Invest Dermatol. 2018 Mar 13. pii: S0022-202X(18)30224-0. doi: 10.1016/j.jid.2018.02.038. [Epub ahead of print]


Machine learning in cardiovascular medicine: are we there yet?

Shameer K, Johnson KW, Glicksberg BS, Dudley JT, Sengupta PP.

Heart. 2018 Jan 19. pii: heartjnl-2017-311198. doi: 10.1136/heartjnl-2017-311198. [Epub ahead of print] Review.


Causal inference on electronic health records to assess blood pressure treatment targets: an application of the parametric g formula.

Johnson KW, Glicksberg BS, Hodos RA, Shameer K, Dudley JT.

Pac Symp Biocomput. 2018;23:180-191.


Automated disease cohort selection using word embeddings from Electronic Health Records.

Glicksberg BS, Miotto R, Johnson KW, Shameer K, Li L, Chen R, Dudley JT.

Pac Symp Biocomput. 2018;23:145-156.


Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders.

Smith MR, Glicksberg BS, Li L, Chen R, Morishita H, Dudley JT.

Pac Symp Biocomput. 2018;23:68-79.


Regulatory T-cell Genes Drive Altered Immune Microenvironment in Adult Solid Cancers and Allow for Immune Contextual Patient Subtyping.

Brouwer-Visser J, Cheng WY, Bauer-Mehren A, Maisel D, Lechner K, Andersson E, Dudley JT, Milletti F.

Cancer Epidemiol Biomarkers Prev. 2018 Jan;27(1):103-112. doi: 10.1158/1055-9965.EPI-17-0461. Epub 2017 Nov 13.


Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.

Wang Z, Li L, Glicksberg BS, Israel A, Dudley JT, Ma'ayan A.

J Biomed Inform. 2017 Dec;76:59-68. doi: 10.1016/j.jbi.2017.11.003. Epub 2017 Nov 4.


Uncovering exposures responsible for birth season - disease effects: a global study.

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, Hripcsak G, Gentine P, Tatonetti NP.

J Am Med Inform Assoc. 2017 Sep 28. doi: 10.1093/jamia/ocx105. [Epub ahead of print]


Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells.

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.

Cell Rep. 2017 Sep 5;20(10):2525. doi: 10.1016/j.celrep.2017.08.073. No abstract available.


Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes.

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.

Sci Rep. 2017 Aug 1;7(1):7001. doi: 10.1038/s41598-017-07029-7.


Necroptosis activation in Alzheimer's disease.

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.

Nat Neurosci. 2017 Sep;20(9):1236-1246. doi: 10.1038/nn.4608. Epub 2017 Jul 24.


Artificial Intelligence-Based Assessment of Left Ventricular Filling Pressures From 2-Dimensional Cardiac Ultrasound Images.

Salem Omar AM, Shameer K, Narula S, Abdel Rahman MA, Rifaie O, Narula J, Dudley JT, Sengupta PP.

JACC Cardiovasc Imaging. 2018 Mar;11(3):509-510. doi: 10.1016/j.jcmg.2017.05.003. Epub 2017 Jul 19. No abstract available.


Integrative network analysis identifies novel drivers of pathogenesis and progression in newly diagnosed multiple myeloma.

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, Jagannath S, Dudley JT, Parekh S.

Leukemia. 2018 Jan;32(1):120-130. doi: 10.1038/leu.2017.197. Epub 2017 Jun 23.


Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer's pathology.

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.

Acta Neuropathol. 2017 Nov;134(5):769-788. doi: 10.1007/s00401-017-1737-3. Epub 2017 Jun 13.


Deep learning for healthcare: review, opportunities and challenges.

Miotto R, Wang F, Wang S, Jiang X, Dudley JT.

Brief Bioinform. 2017 May 6. doi: 10.1093/bib/bbx044. [Epub ahead of print]


Reply: Deep Learning With Unsupervised Feature in Echocardiographic Imaging.

Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP.

J Am Coll Cardiol. 2017 Apr 25;69(16):2101-2102. doi: 10.1016/j.jacc.2017.01.062. No abstract available.


Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci.

Fullard JF, Giambartolomei C, Hauberg ME, Xu K, Voloudakis G, Shao Z, Bare C, Dudley JT, Mattheisen M, Robakis NK, Haroutunian V, Roussos P.

Hum Mol Genet. 2017 May 15;26(10):1942-1951. doi: 10.1093/hmg/ddx103.


The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit.

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.

Nat Biotechnol. 2017 Apr;35(4):354-362. doi: 10.1038/nbt.3826. Epub 2017 Mar 13.


Transcriptome-based repurposing of apigenin as a potential anti-fibrotic agent targeting hepatic stellate cells.

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.

Sci Rep. 2017 Mar 3;7:42563. doi: 10.1038/srep42563.


Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.

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.

Brief Bioinform. 2017 Feb 15. doi: 10.1093/bib/bbw136. [Epub ahead of print]


Automated cell type discovery and classification through knowledge transfer.

Lee HC, Kosoy R, Becker CE, Dudley JT, Kidd BA.

Bioinformatics. 2017 Jun 1;33(11):1689-1695. doi: 10.1093/bioinformatics/btx054.


Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity.

Smith MR, Burman P, Sadahiro M, Kidd BA, Dudley JT, Morishita H.

eNeuro. 2017 Jan 18;3(6). pii: ENEURO.0240-16.2016. doi: 10.1523/ENEURO.0240-16.2016. eCollection 2016 Nov-Dec.


Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach.

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.

Sci Rep. 2017 Jan 4;7:39487. doi: 10.1038/srep39487.


Intracoronary Imaging, Cholesterol Efflux, and Transcriptomes After Intensive Statin Treatment: The YELLOW II Study.

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, Milind M, Moreno P, Mehran R, Kovacic JC, Baber U, Dudley JT, Narula J, Sharma S.

J Am Coll Cardiol. 2017 Feb 14;69(6):628-640. doi: 10.1016/j.jacc.2016.10.029. Epub 2016 Oct 29.


Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis.

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.

J Am Soc Nephrol. 2017 May;28(5):1385-1393. doi: 10.1681/ASN.2016020238. Epub 2016 Dec 7.



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.

Pac Symp Biocomput. 2017;22:276-287. doi: 10.1142/9789813207813_0027.



Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE.

Pac Symp Biocomput. 2017;22:120-131. doi: 10.1142/9789813207813_0013.


Machine-Learning Algorithms to Automate Morphological and Functional Assessments in 2D Echocardiography.

Narula S, Shameer K, Salem Omar AM, Dudley JT, Sengupta PP.

J Am Coll Cardiol. 2016 Nov 29;68(21):2287-2295. doi: 10.1016/j.jacc.2016.08.062.


Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype.

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.

PLoS One. 2016 Oct 27;11(10):e0163831. doi: 10.1371/journal.pone.0163831. eCollection 2016.


Gene expression elucidates functional impact of polygenic risk for schizophrenia.

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.

Nat Neurosci. 2016 Nov;19(11):1442-1453. doi: 10.1038/nn.4399. Epub 2016 Sep 26.


Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth.

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.

ACS Nano. 2016 Dec 27;10(12):10636-10651. doi: 10.1021/acsnano.6b02231. Epub 2016 Oct 19.


Influence of age on androgen deprivation therapy-associated Alzheimer's disease.

Nead KT, Gaskin G, Chester C, Swisher-McClure S, Dudley JT, Leeper NJ, Shah NH.

Sci Rep. 2016 Oct 18;6:35695. doi: 10.1038/srep35695.


Replicating Cardiovascular Condition-Birth Month Associations.

Li L, Boland MR, Miotto R, Tatonetti NP, Dudley JT.

Sci Rep. 2016 Sep 14;6:33166. doi: 10.1038/srep33166.


Deep phenotyping predicts Huntington's genotype.

Ruderfer DM, Dudley JT.

Nat Biotechnol. 2016 Aug 9;34(8):823-4. doi: 10.1038/nbt.3648. No abstract available.


Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington's Disease.

Scarpa JR, Jiang P, Losic B, Readhead B, Gao VD, Dudley JT, Vitaterna MH, Turek FW, Kasarskis A.

PLoS Genet. 2016 Jul 8;12(7):e1006137. doi: 10.1371/journal.pgen.1006137. eCollection 2016 Jul.


Evaluation of direct-to-consumer low-volume lab tests in healthy adults.

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.

J Clin Invest. 2016 Jul 1;126(7):2773. doi: 10.1172/JCI88464. Epub 2016 Jul 1. No abstract available.


Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

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.

Bioinformatics. 2016 Jun 15;32(12):i101-i110. doi: 10.1093/bioinformatics/btw282.


Reply to R.L. Bowen et al, M. Froehner et al, J.L. Leow et al, and C. Brady et al.

Nead KT, Gaskin G, Chester C, Swisher-McClure S, Dudley JT, Leeper NJ, Shah NH.

J Clin Oncol. 2016 Aug 10;34(23):2804-5. doi: 10.1200/JCO.2016.67.9449. Epub 2016 Jun 13. No abstract available.


Important role of kallikrein 6 for the development of keratinocyte proliferative resistance to topical glucocorticoids.

Kishibe M, Baida G, Bhalla P, Lavker RM, Schlosser B, Iinuma S, Yoshida S, Dudley JT, Budunova I.

Oncotarget. 2016 Oct 25;7(43):69479-69488. doi: 10.18632/oncotarget.9926.


Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy.

Sengupta PP, Huang YM, Bansal M, Ashrafi A, Fisher M, Shameer K, Gall W, Dudley JT.

Circ Cardiovasc Imaging. 2016 Jun;9(6). pii: e004330. doi: 10.1161/CIRCIMAGING.115.004330.


Development and clinical application of an integrative genomic approach to personalized cancer therapy.

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.

Genome Med. 2016 Jun 1;8(1):62. doi: 10.1186/s13073-016-0313-0.


Data-Driven Identification of Risk Factors of Patient Satisfaction at a Large Urban Academic Medical Center.

Li L, Lee NJ, Glicksberg BS, Radbill BD, Dudley JT.

PLoS One. 2016 May 26;11(5):e0156076. doi: 10.1371/journal.pone.0156076. eCollection 2016.


Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records.

Miotto R, Li L, Kidd BA, Dudley JT.

Sci Rep. 2016 May 17;6:26094. doi: 10.1038/srep26094.


Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer.

Yadav KK, Shameer K, Readhead B, Yadav SS, Li L, Kasarskis A, Tewari AK, Dudley JT.

Curr Pharm Des. 2016;22(34):5234-5248. Review.


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