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Privacy-Preserving Methods for Feature Engineering Using Blockchain: Review, Evaluation, and Proof of Concept.

Jones M, Johnson M, Shervey M, Dudley JT, Zimmerman N.

J Med Internet Res. 2019 Aug 14;21(8):e13600. doi: 10.2196/13600.


Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits.

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, Ermel R, Skogsberg J, Ruusalepp A, Schadt EE, Dudley JT, Ren H, Kovacic JC, Giannarelli C, Li SD, Björkegren JLM, Chen R.

BMC Med Genomics. 2019 Jul 25;12(Suppl 6):108. doi: 10.1186/s12920-019-0542-3.


Deep learning predicts hip fracture using confounding patient and healthcare variables.

Badgeley MA, Zech JR, Oakden-Rayner L, Glicksberg BS, Liu M, Gale W, McConnell MV, Percha B, Snyder TM, Dudley JT.

NPJ Digit Med. 2019 Apr 30;2:31. doi: 10.1038/s41746-019-0105-1. eCollection 2019.


Reflecting health: smart mirrors for personalized medicine.

Miotto R, Danieletto M, Scelza JR, Kidd BA, Dudley JT.

NPJ Digit Med. 2018 Nov 8;1:62. doi: 10.1038/s41746-018-0068-7. eCollection 2018. Review.


Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans.

Xu K, Kosoy R, Shameer K, Kumar S, Liu L, Readhead B, Belbin GM, Lee HC, Chen R, Dudley JT.

BMC Genet. 2019 Jul 2;20(1):52. doi: 10.1186/s12863-019-0758-4.


Transcriptomic Network Interactions in Human Skin Treated with Topical Glucocorticoid Clobetasol Propionate.

Lili LN, Klopot A, Readhead B, Baida G, Dudley JT, Budunova I.

J Invest Dermatol. 2019 Jun 25. pii: S0022-202X(19)31629-X. doi: 10.1016/j.jid.2019.04.021. [Epub ahead of print]


PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.

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, Israni S, Larsen R, Percha B, Li L, Dudley JT, Tatonetti NP, Butte AJ.

Bioinformatics. 2019 Jun 19. pii: btz409. doi: 10.1093/bioinformatics/btz409. [Epub ahead of print]


Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses.

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.

Brief Bioinform. 2019 Jun 11. pii: bbz059. doi: 10.1093/bib/bbz059. [Epub ahead of print]


A transcriptomic model to predict increase in fibrous cap thickness in response to high-dose statin treatment: Validation by serial intracoronary OCT imaging.

Johnson KW, Glicksberg BS, Shameer K, Vengrenyuk Y, Krittanawong C, Russak AJ, Sharma SK, Narula JN, Dudley JT, Kini AS.

EBioMedicine. 2019 Jun;44:41-49. doi: 10.1016/j.ebiom.2019.05.007. Epub 2019 May 22.


Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review.

Sheikhalishahi S, Miotto R, Dudley JT, Lavelli A, Rinaldi F, Osmani V.

JMIR Med Inform. 2019 Apr 27;7(2):e12239. doi: 10.2196/12239. Review.


Systems Pharmacology Identifies an Arterial Wall Regulatory Gene Network Mediating Coronary Artery Disease Side Effects of Antiretroviral Therapy.

Frades I, Readhead B, Amadori L, Koplev S, Talukdar HA, Crane HM, Crane PK, Kovacic JC, Dudley JT, Giannarelli C, Björkegren JLM, Peter I.

Circ Genom Precis Med. 2019 Jun;12(6):e002390. doi: 10.1161/CIRCGEN.118.002390. Epub 2019 May 6.


Designing Robust N-of-1 Studies for Precision Medicine: Simulation Study and Design Recommendations.

Percha B, Baskerville EB, Johnson M, Dudley JT, Zimmerman N.

J Med Internet Res. 2019 Apr 1;21(4):e12641. doi: 10.2196/12641.


Lyme Disease Patient Trajectories Learned from Electronic Medical Data for Stratification of Disease Risk and Therapeutic Response.

Ichikawa O, Glicksberg BS, Genes N, Kidd BA, Li L, Dudley JT.

Sci Rep. 2019 Mar 14;9(1):4460. doi: 10.1038/s41598-019-41128-x.


Evaluation of patient re-identification using laboratory test orders and mitigation via latent space variables.

Johnson KW, De Freitas JK, Glicksberg BS, Bobe JR, Dudley JT.

Pac Symp Biocomput. 2019;24:415-426.


Predicting Future Cardiovascular Events in Patients With Peripheral Artery Disease Using Electronic Health Record Data.

Ross EG, Jung K, Dudley JT, Li L, Leeper NJ, Shah NH.

Circ Cardiovasc Qual Outcomes. 2019 Mar;12(3):e004741. doi: 10.1161/CIRCOUTCOMES.118.004741.


PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

Agarwal S, Mirzoeva S, Readhead B, Dudley JT, Budunova I.

EBioMedicine. 2019 Mar;41:526-537. doi: 10.1016/j.ebiom.2019.01.055. Epub 2019 Feb 5.


Precision Medicine for Relapsed Multiple Myeloma on the Basis of an Integrative Multiomics Approach.

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, Jagannath S, Dudley JT, Parekh S.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.18.00019. Epub 2018 Aug 8.


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.

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, Van Zandt M, Reckard A, Reich CG, Weaver J, Schuemie MJ, Ryan PB, Callahan A, Shah NH.

JAMA Netw Open. 2018 Aug 3;1(4):e181755. doi: 10.1001/jamanetworkopen.2018.1755.


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.

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.

Mol Psychiatry. 2019 Mar;24(3):472. doi: 10.1038/s41380-018-0301-4.


Author Correction: Expression-based drug screening of neural progenitor cells from individuals with schizophrenia.

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.

Nat Commun. 2018 Nov 19;9(1):4926. doi: 10.1038/s41467-018-07326-3.


Critical period plasticity-related transcriptional aberrations in schizophrenia and bipolar disorder.

Smith MR, Readhead B, Dudley JT, Morishita H.

Schizophr Res. 2019 May;207:12-21. doi: 10.1016/j.schres.2018.10.021. Epub 2018 Nov 12.


Deletion of the glucocorticoid receptor chaperone FKBP51 prevents glucocorticoid-induced skin atrophy.

Baida G, Bhalla P, Yemelyanov A, Stechschulte LA, Shou W, Readhead B, Dudley JT, Sánchez ER, Budunova I.

Oncotarget. 2018 Oct 5;9(78):34772-34783. doi: 10.18632/oncotarget.26194. eCollection 2018 Oct 5.


Integrative bioinformatics identifies postnatal lead (Pb) exposure disrupts developmental cortical plasticity.

Smith MR, Yevoo P, Sadahiro M, Austin C, Amarasiriwardena C, Awawda M, Arora M, Dudley JT, Morishita H.

Sci Rep. 2018 Nov 6;8(1):16388. doi: 10.1038/s41598-018-34592-4.


Expression-based drug screening of neural progenitor cells from individuals with schizophrenia.

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.

Nat Commun. 2018 Oct 24;9(1):4412. doi: 10.1038/s41467-018-06515-4. Erratum in: Nat Commun. 2018 Nov 19;9(1):4926.


CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis.

Badgeley MA, Liu M, Glicksberg BS, Shervey M, Zech J, Shameer K, Lehar J, Oermann EK, McConnell MV, Snyder TM, Dudley JT.

Bioinformatics. 2019 May 1;35(9):1610-1612. doi: 10.1093/bioinformatics/bty855.


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.

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.

Mol Psychiatry. 2019 Mar;24(3):431-446. doi: 10.1038/s41380-018-0255-6. Epub 2018 Oct 3. Erratum in: Mol Psychiatry. 2018 Nov 21;:.


Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining.

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, Kasarskis A, Tatonetti NP, Dudley JT.

BMC Med Inform Decis Mak. 2018 Sep 14;18(Suppl 3):79. doi: 10.1186/s12911-018-0653-3.


MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data.

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, Butte AJ.

Cell Rep. 2018 Jul 31;24(5):1377-1388. doi: 10.1016/j.celrep.2018.07.003.


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. 2018 Jun 29. doi: 10.1093/hmg/ddy229. [Epub ahead of print] No abstract available.


The whole is greater than the sum of its parts: combining classical statistical and machine intelligence methods in medicine.

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

Heart. 2018 Jul;104(14):1228. doi: 10.1136/heartjnl-2018-313377. No abstract available.


Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus.

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.

Neuron. 2018 Jul 11;99(1):64-82.e7. doi: 10.1016/j.neuron.2018.05.023. Epub 2018 Jun 21.


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 Aug 1;35(8):2015-2025. doi: 10.1093/molbev/msy107.


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. Review.


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 Sep;138(9):1935-1944. doi: 10.1016/j.jid.2018.02.045. Epub 2018 Mar 27.


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 Sep;138(9):2033-2040. doi: 10.1016/j.jid.2018.02.038. Epub 2018 Mar 13.


Machine learning in cardiovascular medicine: are we there yet?

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

Heart. 2018 Jul;104(14):1156-1164. doi: 10.1136/heartjnl-2017-311198. Epub 2018 Jan 19. 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.


Enabling Precision Cardiology Through Multiscale Biology and Systems Medicine.

Johnson KW, Shameer K, Glicksberg BS, Readhead B, Sengupta PP, Björkegren JLM, Kovacic JC, Dudley JT.

JACC Basic Transl Sci. 2017 Jun 26;2(3):311-327. doi: 10.1016/j.jacbts.2016.11.010. eCollection 2017 Jun. Review.

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