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Items: 42

1.

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network.

Shang N, Liu C, Rasmussen LV, Ta CN, Caroll RJ, Benoit B, Lingren T, Dikilitas O, Mentch FD, Carrell DS, Wei WQ, Luo Y, Gainer VS, Kullo IJ, Pacheco JA, Hakonarson H, Walunas TL, Denny JC, Wiley K, Murphy SN, Hripcsak G, Weng C.

J Biomed Inform. 2019 Nov;99:103293. doi: 10.1016/j.jbi.2019.103293. Epub 2019 Sep 19.

PMID:
31542521
2.

Use of Narrative Concepts in Electronic Health Records to Validate Associations Between Genetic Factors and Response to Treatment of Inflammatory Bowel Diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Savova G, Shaw SY, Churchill S, Burke KE, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ.

Clin Gastroenterol Hepatol. 2019 Aug 9. pii: S1542-3565(19)30861-4. doi: 10.1016/j.cgh.2019.08.005. [Epub ahead of print]

PMID:
31404664
3.

Facilitating phenotype transfer using a common data model.

Hripcsak G, Shang N, Peissig PL, Rasmussen LV, Liu C, Benoit B, Carroll RJ, Carrell DS, Denny JC, Dikilitas O, Gainer VS, Howell KM, Klann JG, Kullo IJ, Lingren T, Mentch FD, Murphy SN, Natarajan K, Pacheco JA, Wei WQ, Wiley K, Weng C.

J Biomed Inform. 2019 Aug;96:103253. doi: 10.1016/j.jbi.2019.103253. Epub 2019 Jul 17.

PMID:
31325501
4.

A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments.

Pacheco JA, Rasmussen LV, Kiefer RC, Campion TR, Speltz P, Carroll RJ, Stallings SC, Mo H, Ahuja M, Jiang G, LaRose ER, Peissig PL, Shang N, Benoit B, Gainer VS, Borthwick K, Jackson KL, Sharma A, Wu AY, Kho AN, Roden DM, Pathak J, Denny JC, Thompson WK.

J Am Med Inform Assoc. 2018 Nov 1;25(11):1540-1546. doi: 10.1093/jamia/ocy101.

5.

Natural Language Processing Accurately Calculates Adenoma and Sessile Serrated Polyp Detection Rates.

Nayor J, Borges LF, Goryachev S, Gainer VS, Saltzman JR.

Dig Dis Sci. 2018 Jul;63(7):1794-1800. doi: 10.1007/s10620-018-5078-4. Epub 2018 Apr 26.

PMID:
29696479
6.

Antihyperglycemic Agents Are Inversely Associated With Intracranial Aneurysm Rupture.

Can A, Castro VM, Yu S, Dligach D, Finan S, Gainer VS, Shadick NA, Savova G, Murphy S, Cai T, Weiss ST, Du R.

Stroke. 2018 Jan;49(1):34-39. doi: 10.1161/STROKEAHA.117.019249. Epub 2017 Dec 4.

PMID:
29203688
7.

Enabling phenotypic big data with PheNorm.

Yu S, Ma Y, Gronsbell J, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Liao KP, Cai T.

J Am Med Inform Assoc. 2018 Jan 1;25(1):54-60. doi: 10.1093/jamia/ocx111.

8.

Phenome-Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis.

Liao KP, Sparks JA, Hejblum BP, Kuo IH, Cui J, Lahey LJ, Cagan A, Gainer VS, Liu W, Cai TT, Sokolove J, Cai T.

Arthritis Rheumatol. 2017 Apr;69(4):742-749. doi: 10.1002/art.39974.

9.

Surrogate-assisted feature extraction for high-throughput phenotyping.

Yu S, Chakrabortty A, Liao KP, Cai T, Ananthakrishnan AN, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T.

J Am Med Inform Assoc. 2017 Apr 1;24(e1):e143-e149. doi: 10.1093/jamia/ocw135.

10.

Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Kohane I, Liao KP, Murphy SN.

Inflamm Bowel Dis. 2016 Apr;22(4):880-5. doi: 10.1097/MIB.0000000000000754.

11.

The Biobank Portal for Partners Personalized Medicine: A Query Tool for Working with Consented Biobank Samples, Genotypes, and Phenotypes Using i2b2.

Gainer VS, Cagan A, Castro VM, Duey S, Ghosh B, Goodson AP, Goryachev S, Metta R, Wang TD, Wattanasin N, Murphy SN.

J Pers Med. 2016 Feb 26;6(1). pii: E11. doi: 10.3390/jpm6010011.

12.

Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I.

Clin Gastroenterol Hepatol. 2016 Jul;14(7):973-9. doi: 10.1016/j.cgh.2016.02.017. Epub 2016 Feb 22.

13.

Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I.

Inflamm Bowel Dis. 2016 Jan;22(1):151-8. doi: 10.1097/MIB.0000000000000580.

14.

Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts.

Liao KP, Ananthakrishnan AN, Kumar V, Xia Z, Cagan A, Gainer VS, Goryachev S, Chen P, Savova GK, Agniel D, Churchill S, Lee J, Murphy SN, Plenge RM, Szolovits P, Kohane I, Shaw SY, Karlson EW, Cai T.

PLoS One. 2015 Aug 24;10(8):e0136651. doi: 10.1371/journal.pone.0136651. eCollection 2015.

15.

Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ.

Inflamm Bowel Dis. 2015 Nov;21(11):2507-14. doi: 10.1097/MIB.0000000000000524.

16.

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources.

Yu S, Liao KP, Shaw SY, Gainer VS, Churchill SE, Szolovits P, Murphy SN, Kohane IS, Cai T.

J Am Med Inform Assoc. 2015 Sep;22(5):993-1000. doi: 10.1093/jamia/ocv034. Epub 2015 Apr 29.

17.

Development of phenotype algorithms using electronic medical records and incorporating natural language processing.

Liao KP, Cai T, Savova GK, Murphy SN, Karlson EW, Ananthakrishnan AN, Gainer VS, Shaw SY, Xia Z, Szolovits P, Churchill S, Kohane I.

BMJ. 2015 Apr 24;350:h1885. doi: 10.1136/bmj.h1885. No abstract available.

18.

Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

Aliment Pharmacol Ther. 2015 Jun;41(11):1141-8. doi: 10.1111/apt.13195. Epub 2015 Apr 13.

19.

Mode of childbirth and long-term outcomes in women with inflammatory bowel diseases.

Ananthakrishnan AN, Cheng A, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

Dig Dis Sci. 2015 Feb;60(2):471-7. doi: 10.1007/s10620-014-3353-6. Epub 2014 Sep 12.

20.

Evaluation of matched control algorithms in EHR-based phenotyping studies: a case study of inflammatory bowel disease comorbidities.

Castro VM, Apperson WK, Gainer VS, Ananthakrishnan AN, Goodson AP, Wang TD, Herrick CD, Murphy SN.

J Biomed Inform. 2014 Dec;52:105-11. doi: 10.1016/j.jbi.2014.08.012. Epub 2014 Sep 6.

21.

Improving the power of genetic association tests with imperfect phenotype derived from electronic medical records.

Sinnott JA, Dai W, Liao KP, Shaw SY, Ananthakrishnan AN, Gainer VS, Karlson EW, Churchill S, Szolovits P, Murphy S, Kohane I, Plenge R, Cai T.

Hum Genet. 2014 Nov;133(11):1369-82. doi: 10.1007/s00439-014-1466-9. Epub 2014 Jul 26.

22.

Colonoscopy is associated with a reduced risk for colon cancer and mortality in patients with inflammatory bowel diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

Clin Gastroenterol Hepatol. 2015 Feb;13(2):322-329.e1. doi: 10.1016/j.cgh.2014.07.018. Epub 2014 Jul 17.

23.

Higher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases.

Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

Aliment Pharmacol Ther. 2014 May;39(10):1136-42. doi: 10.1111/apt.12706. Epub 2014 Mar 18.

24.

Thromboprophylaxis is associated with reduced post-hospitalization venous thromboembolic events in patients with inflammatory bowel diseases.

Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Scoville E, Konijeti GG, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

Clin Gastroenterol Hepatol. 2014 Nov;12(11):1905-10. doi: 10.1016/j.cgh.2014.02.034. Epub 2014 Mar 12.

25.

Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease.

Ananthakrishnan AN, Cagan A, Gainer VS, Cheng SC, Cai T, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

J Crohns Colitis. 2014 Sep;8(9):956-63. doi: 10.1016/j.crohns.2014.01.019. Epub 2014 Feb 19.

26.

Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases.

Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

Clin Gastroenterol Hepatol. 2014 Aug;12(8):1342-8.e1. doi: 10.1016/j.cgh.2013.12.030. Epub 2014 Jan 7.

27.

Modeling disease severity in multiple sclerosis using electronic health records.

Xia Z, Secor E, Chibnik LB, Bove RM, Cheng S, Chitnis T, Cagan A, Gainer VS, Chen PJ, Liao KP, Shaw SY, Ananthakrishnan AN, Szolovits P, Weiner HL, Karlson EW, Murphy SN, Savova GK, Cai T, Churchill SE, Plenge RM, Kohane IS, De Jager PL.

PLoS One. 2013 Nov 11;8(11):e78927. doi: 10.1371/journal.pone.0078927. eCollection 2013.

28.

Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases.

Ananthakrishnan AN, Cheng SC, Cai T, Cagan A, Gainer VS, Szolovits P, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP.

Clin Gastroenterol Hepatol. 2014 May;12(5):821-7. doi: 10.1016/j.cgh.2013.10.011. Epub 2013 Oct 23.

29.

Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population.

Liao KP, Cai T, Gainer VS, Cagan A, Murphy SN, Liu C, Churchill S, Shaw SY, Kohane I, Solomon DH, Plenge RM, Karlson EW.

Arthritis Care Res (Hoboken). 2013 Dec;65(12):2046-50. doi: 10.1002/acr.22091.

30.

Normalization of plasma 25-hydroxy vitamin D is associated with reduced risk of surgery in Crohn's disease.

Ananthakrishnan AN, Cagan A, Gainer VS, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Plenge RM, Murphy SN, Liao KP.

Inflamm Bowel Dis. 2013 Aug;19(9):1921-7. doi: 10.1097/MIB.0b013e3182902ad9.

31.

Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls.

Liao KP, Diogo D, Cui J, Cai T, Okada Y, Gainer VS, Murphy SN, Gupta N, Mirel D, Ananthakrishnan AN, Szolovits P, Shaw SY, Raychaudhuri S, Churchill S, Kohane I, Karlson EW, Plenge RM.

Ann Rheum Dis. 2014 Jun;73(6):1170-5. doi: 10.1136/annrheumdis-2012-203202. Epub 2013 May 28.

32.

Improving case definition of Crohn's disease and ulcerative colitis in electronic medical records using natural language processing: a novel informatics approach.

Ananthakrishnan AN, Cai T, Savova G, Cheng SC, Chen P, Perez RG, Gainer VS, Murphy SN, Szolovits P, Xia Z, Shaw S, Churchill S, Karlson EW, Kohane I, Plenge RM, Liao KP.

Inflamm Bowel Dis. 2013 Jun;19(7):1411-20. doi: 10.1097/MIB.0b013e31828133fd.

33.

QT interval and antidepressant use: a cross sectional study of electronic health records.

Castro VM, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Erb JL, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH.

BMJ. 2013 Jan 29;346:f288. doi: 10.1136/bmj.f288.

34.

Similar risk of depression and anxiety following surgery or hospitalization for Crohn's disease and ulcerative colitis.

Ananthakrishnan AN, Gainer VS, Cai T, Perez RG, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw S, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP.

Am J Gastroenterol. 2013 Apr;108(4):594-601. doi: 10.1038/ajg.2012.471. Epub 2013 Jan 22.

35.

Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease.

Ananthakrishnan AN, Gainer VS, Perez RG, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP.

Aliment Pharmacol Ther. 2013 Feb;37(4):445-54. doi: 10.1111/apt.12195. Epub 2013 Jan 7.

36.

Feasibility of studying brain morphology in major depressive disorder with structural magnetic resonance imaging and clinical data from the electronic medical record: a pilot study.

Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV.

Psychiatry Res. 2013 Mar 30;211(3):202-13. doi: 10.1016/j.pscychresns.2012.07.007. Epub 2012 Nov 11.

37.

Antidepressant response in patients with major depression exposed to NSAIDs: a pharmacovigilance study.

Gallagher PJ, Castro V, Fava M, Weilburg JB, Murphy SN, Gainer VS, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH.

Am J Psychiatry. 2012 Oct;169(10):1065-72. doi: 10.1176/appi.ajp.2012.11091325.

38.

Limbic system white matter microstructure and long-term treatment outcome in major depressive disorder: a diffusion tensor imaging study using legacy data.

Hoogenboom WS, Perlis RH, Smoller JW, Zeng-Treitler Q, Gainer VS, Murphy SN, Churchill SE, Kohane IS, Shenton ME, Iosifescu DV.

World J Biol Psychiatry. 2014 Feb;15(2):122-34. doi: 10.3109/15622975.2012.669499. Epub 2012 Apr 30.

39.

A mega-analysis of genome-wide association studies for major depressive disorder.

Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium, Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, Breen G, Byrne EM, Blackwood DH, Boomsma DI, Cichon S, Heath AC, Holsboer F, Lucae S, Madden PA, Martin NG, McGuffin P, Muglia P, Noethen MM, Penninx BP, Pergadia ML, Potash JB, Rietschel M, Lin D, Müller-Myhsok B, Shi J, Steinberg S, Grabe HJ, Lichtenstein P, Magnusson P, Perlis RH, Preisig M, Smoller JW, Stefansson K, Uher R, Kutalik Z, Tansey KE, Teumer A, Viktorin A, Barnes MR, Bettecken T, Binder EB, Breuer R, Castro VM, Churchill SE, Coryell WH, Craddock N, Craig IW, Czamara D, De Geus EJ, Degenhardt F, Farmer AE, Fava M, Frank J, Gainer VS, Gallagher PJ, Gordon SD, Goryachev S, Gross M, Guipponi M, Henders AK, Herms S, Hickie IB, Hoefels S, Hoogendijk W, Hottenga JJ, Iosifescu DV, Ising M, Jones I, Jones L, Jung-Ying T, Knowles JA, Kohane IS, Kohli MA, Korszun A, Landen M, Lawson WB, Lewis G, Macintyre D, Maier W, Mattheisen M, McGrath PJ, McIntosh A, McLean A, Middeldorp CM, Middleton L, Montgomery GM, Murphy SN, Nauck M, Nolen WA, Nyholt DR, O'Donovan M, Oskarsson H, Pedersen N, Scheftner WA, Schulz A, Schulze TG, Shyn SI, Sigurdsson E, Slager SL, Smit JH, Stefansson H, Steffens M, Thorgeirsson T, Tozzi F, Treutlein J, Uhr M, van den Oord EJ, Van Grootheest G, Völzke H, Weilburg JB, Willemsen G, Zitman FG, Neale B, Daly M, Levinson DF, Sullivan PF.

Mol Psychiatry. 2013 Apr;18(4):497-511. doi: 10.1038/mp.2012.21. Epub 2012 Apr 3.

40.

Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with major depressive disorder treated with antidepressants.

Castro VM, Gallagher PJ, Clements CC, Murphy SN, Gainer VS, Fava M, Weilburg JB, Churchill SE, Kohane IS, Iosifescu DV, Smoller JW, Perlis RH.

BMJ Open. 2012 Mar 30;2(2):e000544. doi: 10.1136/bmjopen-2011-000544. Print 2012.

41.

Portability of an algorithm to identify rheumatoid arthritis in electronic health records.

Carroll RJ, Thompson WK, Eyler AE, Mandelin AM, Cai T, Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H, Karlson EW, Perez RG, Gainer VS, Murphy SN, Ruderman EM, Pope RM, Plenge RM, Kho AN, Liao KP, Denny JC.

J Am Med Inform Assoc. 2012 Jun;19(e1):e162-9. Epub 2012 Feb 28.

42.

Using electronic medical records to enable large-scale studies in psychiatry: treatment resistant depression as a model.

Perlis RH, Iosifescu DV, Castro VM, Murphy SN, Gainer VS, Minnier J, Cai T, Goryachev S, Zeng Q, Gallagher PJ, Fava M, Weilburg JB, Churchill SE, Kohane IS, Smoller JW.

Psychol Med. 2012 Jan;42(1):41-50. doi: 10.1017/S0033291711000997. Epub 2011 Jun 20.

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