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Items: 42

1.

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.

2.

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.

3.

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]

PMID:
31214700
4.

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]

PMID:
31190075
5.

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.

6.

Evaluating cell lines as models for metastatic breast cancer through integrative analysis of genomic data.

Liu K, Newbury PA, Glicksberg BS, Zeng WZD, Paithankar S, Andrechek ER, Chen B.

Nat Commun. 2019 May 15;10(1):2138. doi: 10.1038/s41467-019-10148-6.

7.

Confronting data sparsity to identify potential sources of Zika virus spillover infection among primates.

Han BA, Majumdar S, Calmon FP, Glicksberg BS, Horesh R, Kumar A, Perer A, von Marschall EB, Wei D, Mojsilović A, Varshney KR.

Epidemics. 2019 Jun;27:59-65. doi: 10.1016/j.epidem.2019.01.005. Epub 2019 Mar 19.

8.

Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis.

Norgeot B, Glicksberg BS, Trupin L, Lituiev D, Gianfrancesco M, Oskotsky B, Schmajuk G, Yazdany J, Butte AJ.

JAMA Netw Open. 2019 Mar 1;2(3):e190606. doi: 10.1001/jamanetworkopen.2019.0606.

9.

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.

10.

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.

11.

Leveraging Big Data to Transform Drug Discovery.

Glicksberg BS, Li L, Chen R, Dudley J, Chen B.

Methods Mol Biol. 2019;1939:91-118. doi: 10.1007/978-1-4939-9089-4_6.

PMID:
30848458
12.

Selecting precise reference normal tissue samples for cancer research using a deep learning approach.

Zeng WZD, Glicksberg BS, Li Y, Chen B.

BMC Med Genomics. 2019 Jan 31;12(Suppl 1):21. doi: 10.1186/s12920-018-0463-6.

13.

A call for deep-learning healthcare.

Norgeot B, Glicksberg BS, Butte AJ.

Nat Med. 2019 Jan;25(1):14-15. doi: 10.1038/s41591-018-0320-3. No abstract available.

PMID:
30617337
14.

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.

15.

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.

16.

Robust prediction of clinical outcomes using cytometry data.

Hu Z, Glicksberg BS, Butte AJ.

Bioinformatics. 2019 Apr 1;35(7):1197-1203. doi: 10.1093/bioinformatics/bty768.

17.

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.

PMID:
29945951
18.

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.

19.

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.

20.

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.

21.

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS.

Dobbyn A, Huckins LM, Boocock J, Sloofman LG, Glicksberg BS, Giambartolomei C, Hoffman GE, Perumal TM, Girdhar K, Jiang Y, Raj T, Ruderfer DM, Kramer RS, Pinto D; CommonMind Consortium, Akbarian S, Roussos P, Domenici E, Devlin B, Sklar P, Stahl EA, Sieberts SK.

Am J Hum Genet. 2018 Jun 7;102(6):1169-1184. doi: 10.1016/j.ajhg.2018.04.011. Epub 2018 May 24.

22.

Melanocortin 4 Receptor Pathway Dysfunction in Obesity: Patient Stratification Aimed at MC4R Agonist Treatment.

Ayers KL, Glicksberg BS, Garfield AS, Longerich S, White JA, Yang P, Du L, Chittenden TW, Gulcher JR, Roy S, Fiedorek F, Gottesdiener K, Cohen S, North KE, Schadt EE, Li SD, Chen R, Van der Ploeg LHT.

J Clin Endocrinol Metab. 2018 Jul 1;103(7):2601-2612. doi: 10.1210/jc.2018-00258.

PMID:
29726959
23.

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.

PMID:
29659828
24.

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.

PMID:
29352006
25.

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.

26.

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.

27.

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.

28.

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.

29.

Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system.

Belbin GM, Odgis J, Sorokin EP, Yee MC, Kohli S, Glicksberg BS, Gignoux CR, Wojcik GL, Van Vleck T, Jeff JM, Linderman M, Schurmann C, Ruderfer D, Cai X, Merkelson A, Justice AE, Young KL, Graff M, North KE, Peters U, James R, Hindorff L, Kornreich R, Edelmann L, Gottesman O, Stahl EE, Cho JH, Loos RJ, Bottinger EP, Nadkarni GN, Abul-Husn NS, Kenny EE.

Elife. 2017 Sep 12;6. pii: e25060. doi: 10.7554/eLife.25060.

30.

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.

31.

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.

32.

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. 2018 Jul 20;19(4):656-678. doi: 10.1093/bib/bbw136.

33.

IDENTIFY CANCER DRIVER GENES THROUGH SHARED MENDELIAN DISEASE PATHOGENIC VARIANTS AND CANCER SOMATIC MUTATIONS.

Ma M, Wang C, Glicksberg BS, Schadt EE, Li SD, Chen R.

Pac Symp Biocomput. 2017;22:473-484. doi: 10.1142/9789813207813_0044.

34.

A loss of function variant in CASP7 protects against Alzheimer's disease in homozygous APOE ε4 allele carriers.

Ayers KL, Mirshahi UL, Wardeh AH, Murray MF, Hao K, Glicksberg BS, Li S, Carey DJ, Chen R.

BMC Genomics. 2016 Jun 23;17 Suppl 2:445. doi: 10.1186/s12864-016-2725-z.

35.

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.

36.

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.

37.

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.

38.

EHDViz: clinical dashboard development using open-source technologies.

Badgeley MA, Shameer K, Glicksberg BS, Tomlinson MS, Levin MA, McCormick PJ, Kasarskis A, Reich DL, Dudley JT.

BMJ Open. 2016 Mar 24;6(3):e010579. doi: 10.1136/bmjopen-2015-010579.

39.

Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams.

Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT.

Brief Bioinform. 2017 Jan;18(1):105-124. doi: 10.1093/bib/bbv118. Epub 2016 Feb 14.

40.

Identification of type 2 diabetes subgroups through topological analysis of patient similarity.

Li L, Cheng WY, Glicksberg BS, Gottesman O, Tamler R, Chen R, Bottinger EP, Dudley JT.

Sci Transl Med. 2015 Oct 28;7(311):311ra174. doi: 10.1126/scitranslmed.aaa9364.

41.

Disease-associated variants in different categories of disease located in distinct regulatory elements.

Ma M, Ru Y, Chuang LS, Hsu NY, Shi LS, Hakenberg J, Cheng WY, Uzilov A, Ding W, Glicksberg BS, Chen R.

BMC Genomics. 2015;16 Suppl 8:S3. doi: 10.1186/1471-2164-16-S8-S3. Epub 2015 Jun 18.

42.

An integrative pipeline for multi-modal discovery of disease relationships.

Glicksberg BS, Li L, Cheng WY, Shameer K, Hakenberg J, Castellanos R, Ma M, Shi L, Shah H, Dudley JT, Chen R.

Pac Symp Biocomput. 2015:407-18.

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