Joshua C. Denny, M.D.

Professor

josh.denny@vanderbilt.edu

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Faculty Appointments
Professor of Biomedical Informatics Professor of Medicine
Education
M.S., Biomedical Informatics, Vanderbilt University, Nashville, TennesseeM.D., Medicine, Vanderbilt University, Nashville, TennesseeB.S., Molecular Biology, Vanderbilt University, Nashville, Tennessee
Office Address
2525 West End, Suite 1475
Nashville, TN 37203
Research Keywords
Precision and personalized medicine, clinical phenotyping and phenomics, phenome wide association studies (PheWAS), genomics and pharmacogenomics, natural language processing
Publications
Cronin RM, Fabbri D, Denny JC, Rosenbloom ST, Jackson GP. A comparison of rule-based and machine learning approaches for classifying patient portal messages. Int J Med Inform [print-electronic]. 2017 Sep; 105: 110-20. PMID: 28750904, PMCID: PMC5546247, PII: S1386-5056(17)30181-8, DOI: 10.1016/j.ijmedinf.2017.06.004, ISSN: 1872-8243.

Hellwege JN, Jeff JM, Wise LA, Gallagher CS, Wellons M, Hartmann KE, Jones SF, Torstenson ES, Dickinson S, Ruiz-Narváez EA, Rohland N, Allen A, Reich D, Tandon A, Pasaniuc B, Mancuso N, Im HK, Hinds DA, Palmer JR, Rosenberg L, Denny JC, Roden DM, Stewart EA, Morton CC, Kenny EE, Edwards TL, Velez Edwards DR. A multi-stage genome-wide association study of uterine fibroids in African Americans. Hum. Genet [print-electronic]. 2017 Aug 8/23/2017; PMID: 28836065, PII: 10.1007/s00439-017-1836-1, DOI: 10.1007/s00439-017-1836-1, ISSN: 1432-1203.

Karnes JH, Shaffer CM, Cronin R, Bastarache L, Gaudieri S, James I, Pavlos R, Steiner H, Mosley JD, Mallal S, Denny JC, Phillips EJ, Roden DM. Influence of human leukocyte antigen (HLA) alleles and killer cell immunoglobulin-like receptors (KIR) types on heparin-induced thrombocytopenia (HIT). Pharmacotherapy [print-electronic]. 2017 Jul 7/8/2017; PMID: 28688202, DOI: 10.1002/phar.1983, ISSN: 1875-9114.

Chen Y, Lask TA, Mei Q, Chen Q, Moon S, Wang J, Nguyen K, Dawodu T, Cohen T, Denny JC, Xu H. An active learning-enabled annotation system for clinical named entity recognition. BMC Med Inform Decis Mak. 2017 Jul 7/5/2017; 17(Suppl 2): 82. PMID: 28699546, PMCID: PMC5506567, PII: 10.1186/s12911-017-0466-9, DOI: 10.1186/s12911-017-0466-9, ISSN: 1472-6947.

Wells QS, Veatch OJ, Fessel JP, Joon AY, Levinson RT, Mosley JD, Held EP, Lindsay CS, Shaffer CM, Weeke PE, Glazer AM, Bersell KR, Van Driest SL, Karnes JH, Blair MA, Lagrone LW, Su YR, Bowton EA, Feng Z, Ky B, Lenihan DJ, Fisch MJ, Denny JC, Roden DM. Genome-wide association and pathway analysis of left ventricular function after anthracycline exposure in adults. Pharmacogenet. Genomics. 2017 Jul; 27(7): 247-54. PMID: 28542097, PMCID: PMC5502740, DOI: 10.1097/FPC.0000000000000284, ISSN: 1744-6880.

Zheng NS, Bastarache LA, Bastarache JA, Lu Y, Ware LB, Shu XO, Denny JC, Long J. A common deletion in the haptoglobin gene associated with blood cholesterol levels among Chinese women. J. Hum. Genet [print-electronic]. 2017 Jun 6/29/2017; PMID: 28659611, PII: jhg201766, DOI: 10.1038/jhg.2017.66, ISSN: 1435-232X.

Christophersen IE, Rienstra M, Roselli C, Yin X, Geelhoed B, Barnard J, Lin H, Arking DE, Smith AV, Albert CM, Chaffin M, Tucker NR, Li M, Klarin D, Bihlmeyer NA, Low SK, Weeke PE, Müller-Nurasyid M, Smith JG, Brody JA, Niemeijer MN, Dörr M, Trompet S, Huffman J, Gustafsson S, Schurmann C, Kleber ME, Lyytikäinen LP, Seppälä I, Malik R, Horimoto ARVR, Perez M, Sinisalo J, Aeschbacher S, Thériault S, Yao J, Radmanesh F, Weiss S, Teumer A, Choi SH, Weng LC, Clauss S, Deo R, Rader DJ, Shah SH, Sun A, Hopewell JC, Debette S, Chauhan G, Yang Q, Worrall BB, Paré G, Kamatani Y, Hagemeijer YP, Verweij N, Siland JE, Kubo M, Smith JD, Van Wagoner DR, Bis JC, Perz S, Psaty BM, Ridker PM, Magnani JW, Harris TB, Launer LJ, Shoemaker MB, Padmanabhan S, Haessler J, Bartz TM, Waldenberger M, Lichtner P, Arendt M, Krieger JE, Kähönen M, Risch L, Mansur AJ, Peters A, Smith BH, Lind L, Scott SA, Lu Y, Bottinger EB, Hernesniemi J, Lindgren CM, Wong JA, Huang J, Eskola M, Morris AP, Ford I, Reiner AP, Delgado G, Chen LY, Chen YI, Sandhu RK, Li M, Boerwinkle E, Eisele L, Lannfelt L, Rost N, Anderson CD, Taylor KD, Campbell A, Magnusson PK, Porteous D, Hocking LJ, Vlachopoulou E, Pedersen NL, Nikus K, Orho-Melander M, Hamsten A, Heeringa J, Denny JC, Kriebel J, Darbar D, Newton-Cheh C, Shaffer C, Macfarlane PW, Heilmann-Heimbach S, Almgren P, Huang PL, Sotoodehnia N, Soliman EZ, Uitterlinden AG, Hofman A, Franco OH, Völker U, Jöckel KH, Sinner MF, Lin HJ, Guo X, , , Dichgans M, Ingelsson E, Kooperberg C, Melander O, Loos RJF, Laurikka J, Conen D, Rosand J, van der Harst P, Lokki ML, Kathiresan S, Pereira A, Jukema JW, Hayward C, Rotter JI, März W, Lehtimäki T, Stricker BH, Chung MK, Felix SB, Gudnason V, Alonso A, Roden DM, Kääb S, Chasman DI, Heckbert SR, Benjamin EJ, Tanaka T, Lunetta KL, Lubitz SA, Ellinor PT, . Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation. Nat. Genet [print-electronic]. 2017 Jun; 49(6): 946-52. PMID: 28416818, PII: ng.3843, DOI: 10.1038/ng.3843, ISSN: 1546-1718.

Sperber NR, Carpenter JS, Cavallari LH, J Damschroder L, Cooper-DeHoff RM, Denny JC, Ginsburg GS, Guan Y, Horowitz CR, Levy KD, Levy MA, Madden EB, Matheny ME, Pollin TI, Pratt VM, Rosenman M, Voils CI, W Weitzel K, Wilke RA, Ryanne Wu R, Orlando LA. Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network. BMC Med Genomics. 2017 May 5/22/2017; 10(1): 35. PMID: 28532511, PMCID: PMC5441047, PII: 10.1186/s12920-017-0273-2, DOI: 10.1186/s12920-017-0273-2, ISSN: 1755-8794.

Karnes JH, Bastarache L, Shaffer CM, Gaudieri S, Xu Y, Glazer AM, Mosley JD, Zhao S, Raychaudhuri S, Mallal S, Ye Z, Mayer JG, Brilliant MH, Hebbring SJ, Roden DM, Phillips EJ, Denny JC. Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Sci Transl Med. 2017 May 5/10/2017; 9(389): PMID: 28490672, PMCID: PMC5563969, PII: 9/389/eaai8708, DOI: 10.1126/scitranslmed.aai8708, ISSN: 1946-6242.

Liang J, Le TH, Edwards DRV, Tayo BO, Gaulton KJ, Smith JA, Lu Y, Jensen RA, Chen G, Yanek LR, Schwander K, Tajuddin SM, Sofer T, Kim W, Kayima J, McKenzie CA, Fox E, Nalls MA, Young JH, Sun YV, Lane JM, Cechova S, Zhou J, Tang H, Fornage M, Musani SK, Wang H, Lee J, Adeyemo A, Dreisbach AW, Forrester T, Chu PL, Cappola A, Evans MK, Morrison AC, Martin LW, Wiggins KL, Hui Q, Zhao W, Jackson RD, Ware EB, Faul JD, Reiner AP, Bray M, Denny JC, Mosley TH, Palmas W, Guo X, Papanicolaou GJ, Penman AD, Polak JF, Rice K, Taylor KD, Boerwinkle E, Bottinger EP, Liu K, Risch N, Hunt SC, Kooperberg C, Zonderman AB, Laurie CC, Becker DM, Cai J, Loos RJF, Psaty BM, Weir DR, Kardia SLR, Arnett DK, Won S, Edwards TL, Redline S, Cooper RS, Rao DC, Rotter JI, Rotimi C, Levy D, Chakravarti A, Zhu X, Franceschini N. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. PLoS Genet. 2017 May; 13(5): e1006728. PMID: 28498854, PMCID: PMC5446189, PII: PGENETICS-D-16-02810, DOI: 10.1371/journal.pgen.1006728, ISSN: 1553-7404.

Barnado A, Casey C, Carroll RJ, Wheless L, Denny JC, Crofford LJ. Developing Electronic Health Record Algorithms That Accurately Identify Patients With Systemic Lupus Erythematosus. Arthritis Care Res (Hoboken) [print-electronic]. 2017 May; 69(5): 687-93. PMID: 27390187, PMCID: PMC5219863, DOI: 10.1002/acr.22989, ISSN: 2151-4658.

Mosley JD, Shoemaker MB, Wells QS, Darbar D, Shaffer CM, Edwards TL, Bastarache L, McCarty CA, Thompson W, Chute CG, Jarvik GP, Crosslin DR, Larson EB, Kullo IJ, Pacheco JA, Peissig PL, Brilliant MH, Linneman JG, Witte JS, Denny JC, Roden DM. Investigating the Genetic Architecture of the PR Interval Using Clinical Phenotypes. Circ Cardiovasc Genet. 2017 Apr; 10(2): PMID: 28416512, PMCID: PMC5434456, PII: CIRCGENETICS.116.001482, DOI: 10.1161/CIRCGENETICS.116.001482, ISSN: 1942-3268.

Pulley JM, Shirey-Rice JK, Lavieri RR, Jerome RN, Zaleski NM, Aronoff DM, Bastarache L, Niu X, Holroyd KJ, Roden DM, Skaar EP, Niswender CM, Marnett LJ, Lindsley CW, Ekstrom LB, Bentley AR, Bernard GR, Hong CC, Denny JC. Accelerating Precision Drug Development and Drug Repurposing by Leveraging Human Genetics. Assay Drug Dev Technol [print-electronic]. 2017 Apr; 15(3): 113-9. PMID: 28379727, PMCID: PMC5399743, DOI: 10.1089/adt.2016.772, ISSN: 1557-8127.

Boortz KA, Syring KE, Pound LD, Mo H, Bastarache L, Oeser JK, McGuinness OP, Denny JC, O'Brien RM. Effects of G6pc2 deletion on body weight and cholesterol in mice. J. Mol. Endocrinol [print-electronic]. 2017 Apr; 58(3): 127-39. PMID: 28122818, PMCID: PMC5380368, PII: JME-16-0202, DOI: 10.1530/JME-16-0202, ISSN: 1479-6813.

Wu Y, Denny JC, Trent Rosenbloom S, Miller RA, Giuse DA, Wang L, Blanquicett C, Soysal E, Xu J, Xu H. A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). J Am Med Inform Assoc. 2017 Apr 4/1/2017; 24(e1): e79-e86. PMID: 27539197, PII: ocw109, DOI: 10.1093/jamia/ocw109, ISSN: 1527-974X.

Nadkarni GN, Galarneau G, Ellis SB, Nadukuru R, Zhang J, Scott SA, Schurmann C, Li R, Rasmussen-Torvik LJ, Kho AN, Hayes MG, Pacheco JA, Manolio TA, Chisholm RL, Roden DM, Denny JC, Kenny EE, Bottinger EP. Apolipoprotein L1 Variants and Blood Pressure Traits in African Americans. J. Am. Coll. Cardiol. 2017 Mar 3/28/2017; 69(12): 1564-74. PMID: 28335839, PMCID: PMC5479565, PII: S0735-1097(17)30436-9, DOI: 10.1016/j.jacc.2017.01.040, ISSN: 1558-3597.

Li M, Li Y, Weeks O, Mijatovic V, Teumer A, Huffman JE, Tromp G, Fuchsberger C, Gorski M, Lyytikäinen LP, Nutile T, Sedaghat S, Sorice R, Tin A, Yang Q, Ahluwalia TS, Arking DE, Bihlmeyer NA, Böger CA, Carroll RJ, Chasman DI, Cornelis MC, Dehghan A, Faul JD, Feitosa MF, Gambaro G, Gasparini P, Giulianini F, Heid I, Huang J, Imboden M, Jackson AU, Jeff J, Jhun MA, Katz R, Kifley A, Kilpeläinen TO, Kumar A, Laakso M, Li-Gao R, Lohman K, Lu Y, Mägi R, Malerba G, Mihailov E, Mohlke KL, Mook-Kanamori DO, Robino A, Ruderfer D, Salvi E, Schick UM, Schulz CA, Smith AV, Smith JA, Traglia M, Yerges-Armstrong LM, Zhao W, Goodarzi MO, Kraja AT, Liu C, Wessel J, , , Boerwinkle E, Borecki IB, Bork-Jensen J, Bottinger EP, Braga D, Brandslund I, Brody JA, Campbell A, Carey DJ, Christensen C, Coresh J, Crook E, Curhan GC, Cusi D, de Boer IH, de Vries AP, Denny JC, Devuyst O, Dreisbach AW, Endlich K, Esko T, Franco OH, Fulop T, Gerhard GS, Glümer C, Gottesman O, Grarup N, Gudnason V, Hansen T, Harris TB, Hayward C, Hocking L, Hofman A, Hu FB, Husemoen LL, Jackson RD, Jørgensen T, Jørgensen ME, Kähönen M, Kardia SL, König W, Kooperberg C, Kriebel J, Launer LJ, Lauritzen T, Lehtimäki T, Levy D, Linksted P, Linneberg A, Liu Y, Loos RJ, Lupo A, Meisinger C, Melander O, Metspalu A, Mitchell P, Nauck M, Nürnberg P, Orho-Melander M, Parsa A, Pedersen O, Peters A, Peters U, Polasek O, Porteous D, Probst-Hensch NM, Psaty BM, Qi L, Raitakari OT, Reiner AP, Rettig R, Ridker PM, Rivadeneira F, Rossouw JE, Schmidt F, Siscovick D, Soranzo N, Strauch K, Toniolo D, Turner ST, Uitterlinden AG, Ulivi S, Velayutham D, Völker U, Völzke H, Waldenberger M, Wang JJ, Weir DR, Witte D, Kuivaniemi H, Fox CS, Franceschini N, Goessling W, Köttgen A, Chu AY. SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function. J. Am. Soc. Nephrol [print-electronic]. 2017 Mar; 28(3): 981-94. PMID: 27920155, PMCID: PMC5328154, PII: ASN.2016020131, DOI: 10.1681/ASN.2016020131, ISSN: 1533-3450.

Doss J, Mo H, Carroll RJ, Crofford LJ, Denny JC. Reply [letter]. Arthritis & rheumatology (Hoboken, N.J.). 2017 Mar; 69(3): 680-1. PMID: 27860419, DOI: 10.1002/art.39997, ISSN: 2326-5205.

Feng Q, Wei WQ, Chung CP, Levinson RT, Bastarache L, Denny JC, Stein CM. The effect of genetic variation in PCSK9 on the LDL-cholesterol response to statin therapy. Pharmacogenomics J [print-electronic]. 2017 Mar; 17(2): 204-8. PMID: 26902539, PMCID: PMC4995153, PII: tpj20163, DOI: 10.1038/tpj.2016.3, ISSN: 1473-1150.

Webb TR, Erdmann J, Stirrups KE, Stitziel NO, Masca NG, Jansen H, Kanoni S, Nelson CP, Ferrario PG, König IR, Eicher JD, Johnson AD, Hamby SE, Betsholtz C, Ruusalepp A, Franzén O, Schadt EE, Björkegren JL, Weeke PE, Auer PL, Schick UM, Lu Y, Zhang H, Dube MP, Goel A, Farrall M, Peloso GM, Won HH, Do R, van Iperen E, Kruppa J, Mahajan A, Scott RA, Willenborg C, Braund PS, van Capelleveen JC, Doney AS, Donnelly LA, Asselta R, Merlini PA, Duga S, Marziliano N, Denny JC, Shaffer C, El-Mokhtari NE, Franke A, Heilmann S, Hengstenberg C, Hoffmann P, Holmen OL, Hveem K, Jansson JH, Jöckel KH, Kessler T, Kriebel J, Laugwitz KL, Marouli E, Martinelli N, McCarthy MI, Van Zuydam NR, Meisinger C, Esko T, Mihailov E, Escher SA, Alver M, Moebus S, Morris AD, Virtamo J, Nikpay M, Olivieri O, Provost S, AlQarawi A, Robertson NR, Akinsansya KO, Reilly DF, Vogt TF, Yin W, Asselbergs FW, Kooperberg C, Jackson RD, Stahl E, Müller-Nurasyid M, Strauch K, Varga TV, Waldenberger M, , Zeng L, Chowdhury R, Salomaa V, Ford I, Jukema JW, Amouyel P, Kontto J, , Nordestgaard BG, Ferrières J, Saleheen D, Sattar N, Surendran P, Wagner A, Young R, Howson JM, Butterworth AS, Danesh J, Ardissino D, Bottinger EP, Erbel R, Franks PW, Girelli D, Hall AS, Hovingh GK, Kastrati A, Lieb W, Meitinger T, Kraus WE, Shah SH, McPherson R, Orho-Melander M, Melander O, Metspalu A, Palmer CN, Peters A, Rader DJ, Reilly MP, Loos RJ, Reiner AP, Roden DM, Tardif JC, Thompson JR, Wareham NJ, Watkins H, Willer CJ, Samani NJ, Schunkert H, Deloukas P, Kathiresan S, . Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease. J. Am. Coll. Cardiol. 2017 Feb 2/21/2017; 69(7): 823-36. PMID: 28209224, PMCID: PMC5314135, PII: S0735-1097(16)37341-7, DOI: 10.1016/j.jacc.2016.11.056, ISSN: 1558-3597.

Schmidt AF, Swerdlow DI, Holmes MV, Patel RS, Fairhurst-Hunter Z, Lyall DM, Hartwig FP, Horta BL, Hyppönen E, Power C, Moldovan M, van Iperen E, Hovingh GK, Demuth I, Norman K, Steinhagen-Thiessen E, Demuth J, Bertram L, Liu T, Coassin S, Willeit J, Kiechl S, Willeit K, Mason D, Wright J, Morris R, Wanamethee G, Whincup P, Ben-Shlomo Y, McLachlan S, Price JF, Kivimaki M, Welch C, Sanchez-Galvez A, Marques-Vidal P, Nicolaides A, Panayiotou AG, Onland-Moret NC, van der Schouw YT, Matullo G, Fiorito G, Guarrera S, Sacerdote C, Wareham NJ, Langenberg C, Scott R, Luan J, Bobak M, Malyutina S, Pajak A, Kubinova R, Tamosiunas A, Pikhart H, Husemoen LL, Grarup N, Pedersen O, Hansen T, Linneberg A, Simonsen KS, Cooper J, Humphries SE, Brilliant M, Kitchner T, Hakonarson H, Carrell DS, McCarty CA, Kirchner HL, Larson EB, Crosslin DR, de Andrade M, Roden DM, Denny JC, Carty C, Hancock S, Attia J, Holliday E, O'Donnell M, Yusuf S, Chong M, Pare G, van der Harst P, Said MA, Eppinga RN, Verweij N, Snieder H, , Christen T, Mook-Kanamori DO, Gustafsson S, Lind L, Ingelsson E, Pazoki R, Franco O, Hofman A, Uitterlinden A, Dehghan A, Teumer A, Baumeister S, Dörr M, Lerch MM, Völker U, Völzke H, Ward J, Pell JP, Smith DJ, Meade T, Maitland-van der Zee AH, Baranova EV, Young R, Ford I, Campbell A, Padmanabhan S, Bots ML, Grobbee DE, Froguel P, Thuillier D, Balkau B, Bonnefond A, Cariou B, Smart M, Bao Y, Kumari M, Mahajan A, Ridker PM, Chasman DI, Reiner AP, Lange LA, Ritchie MD, Asselbergs FW, Casas JP, Keating BJ, Preiss D, Hingorani AD, , Sattar N. PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study. Lancet Diabetes Endocrinol [print-electronic]. 2017 Feb; 5(2): 97-105. PMID: 27908689, PMCID: PMC5266795, PII: S2213-8587(16)30396-5, DOI: 10.1016/S2213-8587(16)30396-5, ISSN: 2213-8595.

Doss J, Mo H, Carroll RJ, Crofford LJ, Denny JC. Phenome-Wide Association Study of Rheumatoid Arthritis Subgroups Identifies Association Between Seronegative Disease and Fibromyalgia. Arthritis & rheumatology (Hoboken, N.J.). 2017 Feb; 69(2): 291-300. PMID: 27589350, PMCID: PMC5274573, DOI: 10.1002/art.39851, ISSN: 2326-5205.

Soysal E, Warner JL, Denny JC, Xu H. Identifying Metastases-related Information from Pathology Reports of Lung Cancer Patients. AMIA Jt Summits Transl Sci Proc. 2017; 2017: 268-77. PMID: 28815141, PMCID: PMC5543353, ISSN: 2153-4063.

Lee HJ, Jiang M, Wu Y, Shaffer CM, Cleator JH, Friedman EA, Lewis JP, Roden DM, Denny J, Xu H. A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. AMIA Jt Summits Transl Sci Proc. 2017; 2017: 185-92. PMID: 28815128, PMCID: PMC5543340, ISSN: 2153-4063.

Wei WQ, Bastarache LA, Carroll RJ, Marlo JE, Osterman TJ, Gamazon ER, Cox NJ, Roden DM, Denny JC. Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record. PLoS ONE. 2017; 12(7): e0175508. PMID: 28686612, PMCID: PMC5501393, PII: PONE-D-16-36822, DOI: 10.1371/journal.pone.0175508, ISSN: 1932-6203.

Zhang X, Pérez-Stable EJ, Bourne PE, Peprah E, Duru OK, Breen N, Berrigan D, Wood F, Jackson JS, Wong DWS, Denny J. Big Data Science: Opportunities and Challenges to Address Minority Health and Health Disparities in the 21st Century. Ethn Dis. 2017; 27(2): 95-106. PMID: 28439179, PMCID: PMC5398183, PII: ed.27.2.95, DOI: 10.18865/ed.27.2.95, ISSN: 1049-510X.

Robinson JR, Kennedy VE, Doss Y, Bastarache L, Denny J, Warner JL. Defining the complex phenotype of severe systemic loxoscelism using a large electronic health record cohort. PLoS ONE. 2017; 12(4): e0174941. PMID: 28422977, PMCID: PMC5396866, PII: PONE-D-16-51072, DOI: 10.1371/journal.pone.0174941, ISSN: 1932-6203.

Dumitrescu L, Ritchie MD, Denny JC, El Rouby NM, McDonough CW, Bradford Y, Ramirez AH, Bielinski SJ, Basford MA, Chai HS, Peissig P, Carrell D, Pathak J, Rasmussen LV, Wang X, Pacheco JA, Kho AN, Hayes MG, Matsumoto M, Smith ME, Li R, Cooper-DeHoff RM, Kullo IJ, Chute CG, Chisholm RL, Jarvik GP, Larson EB, Carey D, McCarty CA, Williams MS, Roden DM, Bottinger E, Johnson JA, de Andrade M, Crawford DC. Genome-wide study of resistant hypertension identified from electronic health records. PLoS ONE. 2017; 12(2): e0171745. PMID: 28222112, PMCID: PMC5319785, PII: PONE-D-16-40169, DOI: 10.1371/journal.pone.0171745, ISSN: 1932-6203.

Karnes JH, Shaffer CM, Bastarache L, Gaudieri S, Glazer AM, Steiner HE, Mosley JD, Mallal S, Denny JC, Phillips EJ, Roden DM. Comparison of HLA allelic imputation programs. PLoS ONE. 2017; 12(2): e0172444. PMID: 28207879, PMCID: PMC5312875, PII: PONE-D-16-48785, DOI: 10.1371/journal.pone.0172444, ISSN: 1932-6203.

Schildcrout JS, Denny JC, Roden DM. On the Potential of Preemptive Genotyping Towards Preventing Medication-Related Adverse Events: Results from the South Korean National Health Insurance Database [letter]. Drug Saf. 2017 Jan; 40(1): 1-2. PMID: 27873192, PMCID: PMC5225656, PII: 10.1007/s40264-016-0476-z, DOI: 10.1007/s40264-016-0476-z, ISSN: 1179-1942.

Teixeira PL, Wei WQ, Cronin RM, Mo H, VanHouten JP, Carroll RJ, LaRose E, Bastarache LA, Rosenbloom ST, Edwards TL, Roden DM, Lasko TA, Dart RA, Nikolai AM, Peissig PL, Denny JC. Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. J Am Med Inform Assoc [print-electronic]. 2017 Jan; 24(1): 162-71. PMID: 27497800, PMCID: PMC5201185, PII: ocw071, DOI: 10.1093/jamia/ocw071, ISSN: 1527-974X.

Mosley JD, van Driest SL, Wells QS, Shaffer CM, Edwards TL, Bastarache L, McCarty CA, Thompson W, Chute CG, Jarvik GP, Crosslin DR, Larson EB, Kullo IJ, Pacheco JA, Peissig PL, Brilliant MH, Linneman JG, Denny JC, Roden DM. Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile Using Historical Data. Circ Cardiovasc Genet [print-electronic]. 2016 Dec; 9(6): 521-30. PMID: 27780847, PMCID: PMC5177499, PII: CIRCGENETICS.116.001530, DOI: 10.1161/CIRCGENETICS.116.001530, ISSN: 1942-3268.

Kolek MJ, Graves AJ, Xu M, Bian A, Teixeira PL, Shoemaker MB, Parvez B, Xu H, Heckbert SR, Ellinor PT, Benjamin EJ, Alonso A, Denny JC, Moons KG, Shintani AK, Harrell FE, Roden DM, Darbar D. Evaluation of a Prediction Model for the Development of Atrial Fibrillation in a Repository of Electronic Medical Records. JAMA Cardiol. 2016 Dec 12/1/2016; 1(9): 1007-13. PMID: 27732699, PMCID: PMC5293184, PII: 2566170, DOI: 10.1001/jamacardio.2016.3366, ISSN: 2380-6591.

Postmus I, Warren HR, Trompet S, Arsenault BJ, Avery CL, Bis JC, Chasman DI, de Keyser CE, Deshmukh HA, Evans DS, Feng Q, Li X, Smit RA, Smith AV, Sun F, Taylor KD, Arnold AM, Barnes MR, Barratt BJ, Betteridge J, Boekholdt SM, Boerwinkle E, Buckley BM, Chen YI, de Craen AJ, Cummings SR, Denny JC, Dubé MP, Durrington PN, Eiriksdottir G, Ford I, Guo X, Harris TB, Heckbert SR, Hofman A, Hovingh GK, Kastelein JJ, Launer LJ, Liu CT, Liu Y, Lumley T, McKeigue PM, Munroe PB, Neil A, Nickerson DA, Nyberg F, O'Brien E, O'Donnell CJ, Post W, Poulter N, Vasan RS, Rice K, Rich SS, Rivadeneira F, Sattar N, Sever P, Shaw-Hawkins S, Shields DC, Slagboom PE, Smith NL, Smith JD, Sotoodehnia N, Stanton A, Stott DJ, Stricker BH, Stürmer T, Uitterlinden AG, Wei WQ, Westendorp RG, Whitsel EA, Wiggins KL, Wilke RA, Ballantyne CM, Colhoun HM, Cupples LA, Franco OH, Gudnason V, Hitman G, Palmer CN, Psaty BM, Ridker PM, Stafford JM, Stein CM, Tardif JC, Caulfield MJ, Jukema JW, Rotter JI, Krauss RM. Meta-analysis of genome-wide association studies of HDL cholesterol response to statins. J. Med. Genet [print-electronic]. 2016 Dec; 53(12): 835-45. PMID: 27587472, PMCID: PMC5309131, PII: jmedgenet-2016-103966, DOI: 10.1136/jmedgenet-2016-103966, ISSN: 1468-6244.

Jackson KL, Mbagwu M, Pacheco JA, Baldridge AS, Viox DJ, Linneman JG, Shukla SK, Peissig PL, Borthwick KM, Carrell DA, Bielinski SJ, Kirby JC, Denny JC, Mentch FD, Vazquez LM, Rasmussen-Torvik LJ, Kho AN. Performance of an electronic health record-based phenotype algorithm to identify community associated methicillin-resistant Staphylococcus aureus cases and controls for genetic association studies. BMC Infect. Dis. 2016 Nov 11/17/2016; 16(1): 684. PMID: 27855652, PMCID: PMC5114817, PII: 10.1186/s12879-016-2020-2, DOI: 10.1186/s12879-016-2020-2, ISSN: 1471-2334.

Iwuchukwu OF, Ramirez AH, Shi Y, Bowton EA, Kawai VK, Schildcrout JS, Roden DM, Denny JC, Stein CM. Genetic determinants of variability in warfarin response after the dose-titration phase. Pharmacogenet. Genomics. 2016 Nov; 26(11): 510-6. PMID: 27632229, PMCID: PMC5300764, DOI: 10.1097/FPC.0000000000000244, ISSN: 1744-6880.

Kirby JC, Speltz P, Rasmussen LV, Basford M, Gottesman O, Peissig PL, Pacheco JA, Tromp G, Pathak J, Carrell DS, Ellis SB, Lingren T, Thompson WK, Savova G, Haines J, Roden DM, Harris PA, Denny JC. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J Am Med Inform Assoc [print-electronic]. 2016 Nov; 23(6): 1046-52. PMID: 27026615, PMCID: PMC5070514, PII: ocv202, DOI: 10.1093/jamia/ocv202, ISSN: 1527-974X.

Roden DM, Mosley JD, Denny JC. Finding a Needle in a QT Interval Big Data Haystack: The Role for Orthogonal Datasets [editorial]. J. Am. Coll. Cardiol. 2016 Oct 10/18/2016; 68(16): 1765-8. PMID: 27737743, PII: S0735-1097(16)34938-5, DOI: 10.1016/j.jacc.2016.08.012, ISSN: 1558-3597.

Daneshjou R, Cavallari LH, Weeke PE, Karczewski KJ, Drozda K, Perera MA, Johnson JA, Klein TE, Bustamante CD, Roden DM, Shaffer C, Denny JC, Zehnder JL, Altman RB. Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans. Mol Genet Genomic Med. 2016 Sep; 4(5): 513-20. PMID: 27652279, PMCID: PMC5023936, PII: MGG3226, DOI: 10.1002/mgg3.226, ISSN: 2324-9269.

Denny JC, Bastarache L, Roden DM. Phenome-Wide Association Studies as a Tool to Advance Precision Medicine. Annu Rev Genomics Hum Genet [print-electronic]. 2016 Aug 8/31/2016; 17: 353-73. PMID: 27147087, PMCID: PMC5480096, DOI: 10.1146/annurev-genom-090314-024956, ISSN: 1545-293X.

Verma A, Verma SS, Pendergrass SA, Crawford DC, Crosslin DR, Kuivaniemi H, Bush WS, Bradford Y, Kullo I, Bielinski SJ, Li R, Denny JC, Peissig P, Hebbring S, De Andrade M, Ritchie MD, Tromp G. EMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants. BMC Med Genomics. 2016 Aug 8/12/2016; 9 Suppl 1: 32. PMID: 27535653, PMCID: PMC4989894, PII: 10.1186/s12920-016-0191-8, DOI: 10.1186/s12920-016-0191-8, ISSN: 1755-8794.

Jiang G, Kiefer RC, Rasmussen LV, Solbrig HR, Mo H, Pacheco JA, Xu J, Montague E, Thompson WK, Denny JC, Chute CG, Pathak J. Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. J Biomed Inform [print-electronic]. 2016 Aug; 62: 232-42. PMID: 27392645, PMCID: PMC5490836, PII: S1532-0464(16)30062-4, DOI: 10.1016/j.jbi.2016.07.008, ISSN: 1532-0480.

Joshi AD, Andersson C, Buch S, Stender S, Noordam R, Weng LC, Weeke PE, Auer PL, Boehm B, Chen C, Choi H, Curhan G, Denny JC, De Vivo I, Eicher JD, Ellinghaus D, Folsom AR, Fuchs C, Gala M, Haessler J, Hofman A, Hu F, Hunter DJ, Janssen HL, Kang JH, Kooperberg C, Kraft P, Kratzer W, Lieb W, Lutsey PL, Darwish Murad S, Nordestgaard BG, Pasquale LR, Reiner AP, Ridker PM, Rimm E, Rose LM, Shaffer CM, Schafmayer C, Tamimi RM, Uitterlinden AG, Völker U, Völzke H, Wakabayashi Y, Wiggs JL, Zhu J, Roden DM, Stricker BH, Tang W, Teumer A, Hampe J, Tybjærg-Hansen A, Chasman DI, Chan AT, Johnson AD. Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-Wide Association Studies. Gastroenterology [print-electronic]. 2016 Aug; 151(2): 351-363.e28. PMID: 27094239, PMCID: PMC4959966, PII: S0016-5085(16)30110-X, DOI: 10.1053/j.gastro.2016.04.007, ISSN: 1528-0012.

Bush WS, Crosslin DR, Owusu-Obeng A, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D, Doheny KF, Gallego CJ, Gordon AS, Keating B, Kirby J, Kitchner T, Manzi S, Mejia AR, Pan V, Perry CL, Peterson JF, Prows CA, Ralston J, Scott SA, Scrol A, Smith M, Stallings SC, Veldhuizen T, Wolf W, Volpi S, Wiley K, Li R, Manolio T, Bottinger E, Brilliant MH, Carey D, Chisholm RL, Chute CG, Haines JL, Hakonarson H, Harley JB, Holm IA, Kullo IJ, Jarvik GP, Larson EB, McCarty CA, Williams MS, Denny JC, Rasmussen-Torvik LJ, Roden DM, Ritchie MD. Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network. Clin. Pharmacol. Ther [print-electronic]. 2016 Aug; 100(2): 160-9. PMID: 26857349, PMCID: PMC5010878, DOI: 10.1002/cpt.350, ISSN: 1532-6535.

Tajuddin SM, Schick UM, Eicher JD, Chami N, Giri A, Brody JA, Hill WD, Kacprowski T, Li J, Lyytikäinen LP, Manichaikul A, Mihailov E, O'Donoghue ML, Pankratz N, Pazoki R, Polfus LM, Smith AV, Schurmann C, Vacchi-Suzzi C, Waterworth DM, Evangelou E, Yanek LR, Burt A, Chen MH, van Rooij FJ, Floyd JS, Greinacher A, Harris TB, Highland HM, Lange LA, Liu Y, Mägi R, Nalls MA, Mathias RA, Nickerson DA, Nikus K, Starr JM, Tardif JC, Tzoulaki I, Velez Edwards DR, Wallentin L, Bartz TM, Becker LC, Denny JC, Raffield LM, Rioux JD, Friedrich N, Fornage M, Gao H, Hirschhorn JN, Liewald DC, Rich SS, Uitterlinden A, Bastarache L, Becker DM, Boerwinkle E, de Denus S, Bottinger EP, Hayward C, Hofman A, Homuth G, Lange E, Launer LJ, Lehtimäki T, Lu Y, Metspalu A, O'Donnell CJ, Quarells RC, Richard M, Torstenson ES, Taylor KD, Vergnaud AC, Zonderman AB, Crosslin DR, Deary IJ, Dörr M, Elliott P, Evans MK, Gudnason V, Kähönen M, Psaty BM, Rotter JI, Slater AJ, Dehghan A, White HD, Ganesh SK, Loos RJ, Esko T, Faraday N, Wilson JG, Cushman M, Johnson AD, Edwards TL, Zakai NA, Lettre G, Reiner AP, Auer PL. Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases. Am. J. Hum. Genet [print-electronic]. 2016 Jul 7/7/2016; 99(1): 22-39. PMID: 27346689, PMCID: PMC5005433, PII: S0002-9297(16)30137-9, DOI: 10.1016/j.ajhg.2016.05.003, ISSN: 1537-6605.

Richesson RL, Sun J, Pathak J, Kho AN, Denny JC. Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods. Artif Intell Med [print-electronic]. 2016 Jul; 71: 57-61. PMID: 27506131, PMCID: PMC5480212, PII: S0933-3657(16)30064-1, DOI: 10.1016/j.artmed.2016.05.005, ISSN: 1873-2860.

Frey LJ, Bernstam EV, Denny JC. Precision medicine informatics [editorial]. J Am Med Inform Assoc [print-electronic]. 2016 Jul; 23(4): 668-70. PMID: 27274018, PMCID: PMC4926751, PII: ocw053, DOI: 10.1093/jamia/ocw053, ISSN: 1527-974X.

Peterson JF, Field JR, Unertl KM, Schildcrout JS, Johnson DC, Shi Y, Danciu I, Cleator JH, Pulley JM, McPherson JA, Denny JC, Laposata M, Roden DM, Johnson KB. Physician response to implementation of genotype-tailored antiplatelet therapy. Clin. Pharmacol. Ther [print-electronic]. 2016 Jul; 100(1): 67-74. PMID: 26693963, PMCID: PMC4899238, DOI: 10.1002/cpt.331, ISSN: 1532-6535.

Oetjens MT, Bush WS, Denny JC, Birdwell K, Kodaman N, Verma A, Dilks HH, Pendergrass SA, Ritchie MD, Crawford DC. Evidence for extensive pleiotropy among pharmacogenes. Pharmacogenomics [print-electronic]. 2016 Jun; 17(8): 853-66. PMID: 27249515, PMCID: PMC5352965, DOI: 10.2217/pgs-2015-0007, ISSN: 1744-8042.

Hoh BL, Gong Y, McDonough CW, Waters MF, Royster AJ, Sheehan TO, Burkley B, Langaee TY, Mocco J, Zuckerman SL, Mummareddy N, Stephens ML, Ingram C, Shaffer CM, Denny JC, Brilliant MH, Kitchner TE, Linneman JG, Roden DM, Johnson JA. CYP2C19 and CES1 polymorphisms and efficacy of clopidogrel and aspirin dual antiplatelet therapy in patients with symptomatic intracranial atherosclerotic disease. J. Neurosurg [print-electronic]. 2016 Jun; 124(6): 1746-51. PMID: 26587656, PMCID: PMC4915569, DOI: 10.3171/2015.6.JNS15795, ISSN: 1933-0693.

Friedman EA, Texeira L, Delaney J, Weeke PE, Lynch DR, Kasasbeh E, Song Y, Harrell FE, Denny JC, Hamm HE, Roden DM, Cleator JH. Evaluation of the F2R IVS-14A/T PAR1 polymorphism with subsequent cardiovascular events and bleeding in patients who have undergone percutaneous coronary intervention. J. Thromb. Thrombolysis. 2016 May; 41(4): 656-62. PMID: 26446588, PII: 10.1007/s11239-015-1285-4, DOI: 10.1007/s11239-015-1285-4, ISSN: 1573-742X.

Mosley JD, Witte JS, Larkin EK, Bastarache L, Shaffer CM, Karnes JH, Stein CM, Phillips E, Hebbring SJ, Brilliant MH, Mayer J, Ye Z, Roden DM, Denny JC. Identifying genetically driven clinical phenotypes using linear mixed models. Nat Commun. 2016 Apr 4/25/2016; 7: 11433. PMID: 27109359, PMCID: PMC4848547, PII: ncomms11433, DOI: 10.1038/ncomms11433, ISSN: 2041-1723.

Heatherly R, Rasmussen LV, Peissig PL, Pacheco JA, Harris P, Denny JC, Malin BA. A multi-institution evaluation of clinical profile anonymization. J Am Med Inform Assoc [print-electronic]. 2016 Apr; 23(e1): e131-7. PMID: 26567325, PMCID: PMC4954623, PII: ocv154, DOI: 10.1093/jamia/ocv154, ISSN: 1527-974X.

Wiley LK, Tarczy-Hornoch P, Denny JC, Freimuth RR, Overby CL, Shah N, Martin RD, Sarkar IN. Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. J Am Med Inform Assoc [print-electronic]. 2016 Mar; 23(2): 413-9. PMID: 26911808, PII: ocv111, DOI: 10.1093/jamia/ocv111, ISSN: 1527-974X.

Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA. The phenotypic legacy of admixture between modern humans and Neandertals. Science. 2016 Feb 2/12/2016; 351(6274): 737-41. PMID: 26912863, PMCID: PMC4849557, PII: 351/6274/737, DOI: 10.1126/science.aad2149, ISSN: 1095-9203.

Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW. Joint mouse-human phenome-wide association to test gene function and disease risk. Nat Commun. 2016 Feb 2/2/2016; 7: 10464. PMID: 26833085, PMCID: PMC4740880, PII: ncomms10464, DOI: 10.1038/ncomms10464, ISSN: 2041-1723.

Pattaro C, Teumer A, Gorski M, Chu AY, Li M, Mijatovic V, Garnaas M, Tin A, Sorice R, Li Y, Taliun D, Olden M, Foster M, Yang Q, Chen MH, Pers TH, Johnson AD, Ko YA, Fuchsberger C, Tayo B, Nalls M, Feitosa MF, Isaacs A, Dehghan A, d'Adamo P, Adeyemo A, Dieffenbach AK, Zonderman AB, Nolte IM, van der Most PJ, Wright AF, Shuldiner AR, Morrison AC, Hofman A, Smith AV, Dreisbach AW, Franke A, Uitterlinden AG, Metspalu A, Tonjes A, Lupo A, Robino A, Johansson Å, Demirkan A, Kollerits B, Freedman BI, Ponte B, Oostra BA, Paulweber B, Krämer BK, Mitchell BD, Buckley BM, Peralta CA, Hayward C, Helmer C, Rotimi CN, Shaffer CM, Müller C, Sala C, van Duijn CM, Saint-Pierre A, Ackermann D, Shriner D, Ruggiero D, Toniolo D, Lu Y, Cusi D, Czamara D, Ellinghaus D, Siscovick DS, Ruderfer D, Gieger C, Grallert H, Rochtchina E, Atkinson EJ, Holliday EG, Boerwinkle E, Salvi E, Bottinger EP, Murgia F, Rivadeneira F, Ernst F, Kronenberg F, Hu FB, Navis GJ, Curhan GC, Ehret GB, Homuth G, Coassin S, Thun GA, Pistis G, Gambaro G, Malerba G, Montgomery GW, Eiriksdottir G, Jacobs G, Li G, Wichmann HE, Campbell H, Schmidt H, Wallaschofski H, Völzke H, Brenner H, Kroemer HK, Kramer H, Lin H, Leach IM, Ford I, Guessous I, Rudan I, Prokopenko I, Borecki I, Heid IM, Kolcic I, Persico I, Jukema JW, Wilson JF, Felix JF, Divers J, Lambert JC, Stafford JM, Gaspoz JM, Smith JA, Faul JD, Wang JJ, Ding J, Hirschhorn JN, Attia J, Whitfield JB, Chalmers J, Viikari J, Coresh J, Denny JC, Karjalainen J, Fernandes JK, Endlich K, Butterbach K, Keene KL, Lohman K, Portas L, Launer LJ, Lyytikäinen LP, Yengo L, Franke L, Ferrucci L, Rose LM, Kedenko L, Rao M, Struchalin M, Kleber ME, Cavalieri M, Haun M, Cornelis MC, Ciullo M, Pirastu M, de Andrade M, McEvoy MA, Woodward M, Adam M, Cocca M, Nauck M, Imboden M, Waldenberger M, Pruijm M, Metzger M, Stumvoll M, Evans MK, Sale MM, Kähönen M, Boban M, Bochud M, Rheinberger M, Verweij N, Bouatia-Naji N, Martin NG, Hastie N, Probst-Hensch N, Soranzo N, Devuyst O, Raitakari O, Gottesman O, Franco OH, Polasek O, Gasparini P, Munroe PB, Ridker PM, Mitchell P, Muntner P, Meisinger C, Smit JH, , , , , , Kovacs P, Wild PS, Froguel P, Rettig R, Mägi R, Biffar R, Schmidt R, Middelberg RP, Carroll RJ, Penninx BW, Scott RJ, Katz R, Sedaghat S, Wild SH, Kardia SL, Ulivi S, Hwang SJ, Enroth S, Kloiber S, Trompet S, Stengel B, Hancock SJ, Turner ST, Rosas SE, Stracke S, Harris TB, Zeller T, Zemunik T, Lehtimäki T, Illig T, Aspelund T, Nikopensius T, Esko T, Tanaka T, Gyllensten U, Völker U, Emilsson V, Vitart V, Aalto V, Gudnason V, Chouraki V, Chen WM, Igl W, März W, Koenig W, Lieb W, Loos RJ, Liu Y, Snieder H, Pramstaller PP, Parsa A, O'Connell JR, Susztak K, Hamet P, Tremblay J, de Boer IH, Böger CA, Goessling W, Chasman DI, Köttgen A, Kao WH, Fox CS. Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. Nat Commun. 2016 Jan 1/21/2016; 7: 10023. PMID: 26831199, PMCID: PMC4735748, PII: ncomms10023, DOI: 10.1038/ncomms10023, ISSN: 2041-1723.

Van Driest SL, Wells QS, Stallings S, Bush WS, Gordon A, Nickerson DA, Kim JH, Crosslin DR, Jarvik GP, Carrell DS, Ralston JD, Larson EB, Bielinski SJ, Olson JE, Ye Z, Kullo IJ, Abul-Husn NS, Scott SA, Bottinger E, Almoguera B, Connolly J, Chiavacci R, Hakonarson H, Rasmussen-Torvik LJ, Pan V, Persell SD, Smith M, Chisholm RL, Kitchner TE, He MM, Brilliant MH, Wallace JR, Doheny KF, Shoemaker MB, Li R, Manolio TA, Callis TE, Macaya D, Williams MS, Carey D, Kapplinger JD, Ackerman MJ, Ritchie MD, Denny JC, Roden DM. Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records. JAMA. 2016 Jan 1/5/2016; 315(1): 47-57. PMID: 26746457, PMCID: PMC4758131, PII: 2480485, DOI: 10.1001/jama.2015.17701, ISSN: 1538-3598.

Weitzel KW, Alexander M, Bernhardt BA, Calman N, Carey DJ, Cavallari LH, Field JR, Hauser D, Junkins HA, Levin PA, Levy K, Madden EB, Manolio TA, Odgis J, Orlando LA, Pyeritz R, Wu RR, Shuldiner AR, Bottinger EP, Denny JC, Dexter PR, Flockhart DA, Horowitz CR, Johnson JA, Kimmel SE, Levy MA, Pollin TI, Ginsburg GS, . The IGNITE network: a model for genomic medicine implementation and research. BMC Med Genomics. 2016 Jan 1/5/2016; 9: 1. PMID: 26729011, PMCID: PMC4700677, PII: 10.1186/s12920-015-0162-5, DOI: 10.1186/s12920-015-0162-5, ISSN: 1755-8794.

Duan R, Cao M, Wu Y, Huang J, Denny JC, Xu H, Chen Y. An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. AMIA Annu Symp Proc. 2016; 2016: 1764-73. PMID: 28269935, PMCID: PMC5333313, ISSN: 1942-597X.

Mo H, Jiang G, Pacheco JA, Kiefer R, Rasmussen LV, Pathak J, Denny JC, Thompson WK. A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. AMIA Jt Summits Transl Sci Proc. 2016; 2016: 167-75. PMID: 27570665, PMCID: PMC5001760, ISSN: 2153-4063.

Li H, Achour I, Bastarache L, Berghout J, Gardeux V, Li J, Lee Y, Pesce L, Yang X, Ramos KS, Foster I, Denny JC, Moore JH, Lussier YA. Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. NPJ Genom Med [print-electronic]. 2016; 1: PMID: 27482468, PMCID: PMC4966659, DOI: 10.1038/npjgenmed.2016.6, ISSN: 2056-7944.

Lingren T, Chen P, Bochenek J, Doshi-Velez F, Manning-Courtney P, Bickel J, Wildenger Welchons L, Reinhold J, Bing N, Ni Y, Barbaresi W, Mentch F, Basford M, Denny J, Vazquez L, Perry C, Namjou B, Qiu H, Connolly J, Abrams D, Holm IA, Cobb BA, Lingren N, Solti I, Hakonarson H, Kohane IS, Harley J, Savova G. Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder. PLoS ONE. 2016; 11(7): e0159621. PMID: 27472449, PMCID: PMC4966969, PII: PONE-D-15-53303, DOI: 10.1371/journal.pone.0159621, ISSN: 1932-6203.

Claar DD, Larkin EK, Bastarache L, Blackwell TS, Loyd JE, Hartert TV, Denny JC, Kropski JA. A Phenome-Wide Association Study Identifies a Novel Asthma Risk Locus Near TERC [letter]. Am. J. Respir. Crit. Care Med. 2016 Jan 1/1/2016; 193(1): 98-100. PMID: 26720789, PMCID: PMC4731616, DOI: 10.1164/rccm.201507-1267LE, ISSN: 1535-4970.

Borthwick KM, Smelser DT, Bock JA, Elmore JR, Ryer EJ, Ye Z, Pacheco JA, Carrell DS, Michalkiewicz M, Thompson WK, Pathak J, Bielinski SJ, Denny JC, Linneman JG, Peissig PL, Kho AN, Gottesman O, Parmar H, Kullo IJ, McCarty CA, Böttinger EP, Larson EB, Jarvik GP, Harley JB, Bajwa T, Franklin DP, Carey DJ, Kuivaniemi H, Tromp G. EPhenotyping for Abdominal Aortic Aneurysm in the Electronic Medical Records and Genomics (eMERGE) Network: Algorithm Development and Konstanz Information Miner Workflow. Int J Biomed Data Min [print-electronic]. 2015 Dec; 4(1): PMID: 27054044, PMCID: PMC4820287, ISSN: 2090-4916.

Chen Y, Lasko TA, Mei Q, Denny JC, Xu H. A study of active learning methods for named entity recognition in clinical text. J Biomed Inform [print-electronic]. 2015 Dec; 58: 11-8. PMID: 26385377, PMCID: PMC4934373, PII: S1532-0464(15)00203-8, DOI: 10.1016/j.jbi.2015.09.010, ISSN: 1532-0480.

Dahlin A, Denny J, Roden DM, Brilliant MH, Ingram C, Kitchner TE, Linneman JG, Shaffer CM, Weeke P, Xu H, Kubo M, Tamari M, Clemmer GL, Ziniti J, McGeachie MJ, Tantisira KG, Weiss ST, Wu AC. CMTR1 is associated with increased asthma exacerbations in patients taking inhaled corticosteroids. Immun Inflamm Dis. 2015 Dec; 3(4): 350-9. PMID: 26734457, PMCID: PMC4693729, PII: IID373, DOI: 10.1002/iid3.73, ISSN: 2050-4527.

Mo H, Thompson WK, Rasmussen LV, Pacheco JA, Jiang G, Kiefer R, Zhu Q, Xu J, Montague E, Carrell DS, Lingren T, Mentch FD, Ni Y, Wehbe FH, Peissig PL, Tromp G, Larson EB, Chute CG, Pathak J, Denny JC, Speltz P, Kho AN, Jarvik GP, Bejan CA, Williams MS, Borthwick K, Kitchner TE, Roden DM, Harris PA. Desiderata for computable representations of electronic health records-driven phenotype algorithms. J Am Med Inform Assoc [print-electronic]. 2015 Nov; 22(6): 1220-30. PMID: 26342218, PMCID: PMC4639716, PII: ocv112, DOI: 10.1093/jamia/ocv112, ISSN: 1527-974X.

Gallego CJ, Burt A, Sundaresan AS, Ye Z, Shaw C, Crosslin DR, Crane PK, Fullerton SM, Hansen K, Carrell D, Kuivaniemi H, Derr K, de Andrade M, McCarty CA, Kitchner TE, Ragon BK, Stallings SC, Papa G, Bochenek J, Smith ME, Aufox SA, Pacheco JA, Patel V, Friesema EM, Erwin AL, Gottesman O, Gerhard GS, Ritchie M, Motulsky AG, Kullo IJ, Larson EB, Tromp G, Brilliant MH, Bottinger E, Denny JC, Roden DM, Williams MS, Jarvik GP. Penetrance of Hemochromatosis in HFE Genotypes Resulting in p.Cys282Tyr and p.[Cys282Tyr];[His63Asp] in the eMERGE Network. Am. J. Hum. Genet [print-electronic]. 2015 Oct 10/1/2015; 97(4): 512-20. PMID: 26365338, PMCID: PMC4596892, PII: S0002-9297(15)00330-4, DOI: 10.1016/j.ajhg.2015.08.008, ISSN: 1537-6605.

Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Cobb BL, Denny JC, Hakonarson H, Hartzler AL, Hripcsak G, Kannry J, Kohane IS, Kullo IJ, Lin S, Manzi S, Marsolo K, Overby CL, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden DM, Tromp G, Uphoff T, Weng C, Wolf W, Williams MS, Starren J. Practical considerations in genomic decision support: The eMERGE experience. J Pathol Inform. 2015; 6: 50. PMID: 26605115, PMCID: PMC4629307, PII: JPI-6-50, DOI: 10.4103/2153-3539.165999, ISSN: 2229-5089.

Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Denny J, Freimuth RR, Hartzler A, Kannry J, Kohane IS, Kullo IJ, Lin S, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden D, Tromp G, Williams MS, Starren J. A conceptual model for translating omic data into clinical action. J Pathol Inform. 2015; 6: 46. PMID: 26430534, PMCID: PMC4584438, PII: JPI-6-46, DOI: 10.4103/2153-3539.163985, ISSN: 2229-5089.

Wei WQ, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC. Development and evaluation of an ensemble resource linking medications to their indications. J Am Med Inform Assoc [print-electronic]. 2013 Sep; 20(5): 954-61. PMID: 23576672, PMCID: PMC3756263, PII: amiajnl-2012-001431, DOI: 10.1136/amiajnl-2012-001431, ISSN: 1527-974X.

Jeff JM, Ritchie MD, Denny JC, Kho AN, Ramirez AH, Crosslin D, Armstrong L, Basford MA, Wolf WA, Pacheco JA, Chisholm RL, Roden DM, Hayes MG, Crawford DC. Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans. Ann. Hum. Genet [print-electronic]. 2013 Jul; 77(4): 321-32. PMID: 23534349, PMCID: PMC3743946, DOI: 10.1111/ahg.12023, ISSN: 1469-1809.

Oetjens MT, Denny JC, Ritchie MD, Gillani NB, Richardson DM, Restrepo NA, Pulley JM, Dilks HH, Basford MA, Bowton E, Masys DR, Wilke RA, Roden DM, Crawford DC. Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records. Pharmacogenomics. 2013 May; 14(7): 735-44. PMID: 23651022, PMCID: PMC3725600, DOI: 10.2217/pgs.13.64, ISSN: 1744-8042.

Westbrook MJ, Wright MF, Van Driest SL, McGregor TL, Denny JC, Zuvich RL, Clayton EW, Brothers KB. Mapping the incidentalome: estimating incidental findings generated through clinical pharmacogenomics testing. Genet. Med [print-electronic]. 2013 May; 15(5): 325-31. PMID: 23196672, PMCID: PMC3648626, PII: gim2012147, DOI: 10.1038/gim.2012.147, ISSN: 1530-0366.

Theobald CN, Stover DG, Choma NN, Hathaway J, Green JK, Peterson NB, Sponsler KC, Vasilevskis EE, Kripalani S, Sergent J, Brown NJ, Denny JC. The effect of reducing maximum shift lengths to 16 hours on internal medicine interns' educational opportunities. Acad Med. 2013 Apr; 88(4): 512-8. PMID: 23425987, PMCID: PMC3638874, DOI: 10.1097/ACM.0b013e318285800f, ISSN: 1938-808X.

Heatherly RD, Loukides G, Denny JC, Haines JL, Roden DM, Malin BA. Enabling genomic-phenomic association discovery without sacrificing anonymity. PLoS ONE [print-electronic]. 2013; 8(2): e53875. PMID: 23405076, PMCID: PMC3566194, PII: PONE-D-12-36146, DOI: 10.1371/journal.pone.0053875, ISSN: 1932-6203.

Schildcrout JS, Denny JC, Bowton E, Gregg W, Pulley JM, Basford MA, Cowan JD, Xu H, Ramirez AH, Crawford DC, Ritchie MD, Peterson JF, Masys DR, Wilke RA, Roden DM. Optimizing drug outcomes through pharmacogenetics: a case for preemptive genotyping. Clin. Pharmacol. Ther [print-electronic]. 2012 Aug; 92(2): 235-42. PMID: 22739144, PMCID: PMC3785311, PII: clpt201266, DOI: 10.1038/clpt.2012.66, ISSN: 1532-6535.

Pulley JM, Denny JC, Peterson JF, Bernard GR, Vnencak-Jones CL, Ramirez AH, Delaney JT, Bowton E, Brothers K, Johnson K, Crawford DC, Schildcrout J, Masys DR, Dilks HH, Wilke RA, Clayton EW, Shultz E, Laposata M, McPherson J, Jirjis JN, Roden DM. Operational implementation of prospective genotyping for personalized medicine: the design of the Vanderbilt PREDICT project. Clin. Pharmacol. Ther [print-electronic]. 2012 Jul; 92(1): 87-95. PMID: 22588608, PMCID: PMC3581305, PII: clpt2011371, DOI: 10.1038/clpt.2011.371, ISSN: 1532-6535.

Roden DM, Xu H, Denny JC, Wilke RA. Electronic medical records as a tool in clinical pharmacology: opportunities and challenges. Clin. Pharmacol. Ther. 2012 Jun; 91(6): 1083-86. PMID: 22534870, PMCID: PMC3819803, PII: clpt201242, DOI: 10.1038/clpt.2012.42, ISSN: 1532-6535.

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. Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J Am Med Inform Assoc [print-electronic]. 2012 Jun; 19(e1): e162-9. PMID: 22374935, PMCID: PMC3392871, PII: amiajnl-2011-000583, DOI: 10.1136/amiajnl-2011-000583, ISSN: 1527-974X.

Stenner SP, Johnson KB, Denny JC. PASTE: patient-centered SMS text tagging in a medication management system. J Am Med Inform Assoc [print-electronic]. 2012 May; 19(3): 368-74. PMID: 21984605, PMCID: PMC3341792, PII: amiajnl-2011-000484, DOI: 10.1136/amiajnl-2011-000484, ISSN: 1527-974X.

Ramirez AH, Shi Y, Schildcrout JS, Delaney JT, Xu H, Oetjens MT, Zuvich RL, Basford MA, Bowton E, Jiang M, Speltz P, Zink R, Cowan J, Pulley JM, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health record. Pharmacogenomics [print-electronic]. 2012 Mar; 13(4): 407-18. PMID: 22329724, PMCID: PMC3361510, DOI: 10.2217/pgs.11.164, ISSN: 1744-8042.

Delaney JT, Ramirez AH, Bowton E, Pulley JM, Basford MA, Schildcrout JS, Shi Y, Zink R, Oetjens M, Xu H, Cleator JH, Jahangir E, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Predicting clopidogrel response using DNA samples linked to an electronic health record. Clin. Pharmacol. Ther [print-electronic]. 2012 Feb; 91(2): 257-63. PMID: 22190063, PMCID: PMC3621954, PII: clpt2011221, DOI: 10.1038/clpt.2011.221, ISSN: 1532-6535.

Birdwell KA, Grady B, Choi L, Xu H, Bian A, Denny JC, Jiang M, Vranic G, Basford M, Cowan JD, Richardson DM, Robinson MP, Ikizler TA, Ritchie MD, Stein CM, Haas DW. The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients. Pharmacogenet. Genomics. 2012 Jan; 22(1): 32-42. PMID: 22108237, PMCID: PMC3237759, DOI: 10.1097/FPC.0b013e32834e1641, ISSN: 1744-6880.

Denny JC, Choma NN, Peterson JF, Miller RA, Bastarache L, Li M, Peterson NB. Natural language processing improves identification of colorectal cancer testing in the electronic medical record. Med Decis Making [print-electronic]. 2012 Jan; 32(1): 188-97. PMID: 21393557, PII: 0272989X11400418, DOI: 10.1177/0272989X11400418, ISSN: 1552-681X.

Wu Y, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Xu H. A comparative study of current Clinical Natural Language Processing systems on handling abbreviations in discharge summaries. AMIA Annu Symp Proc [print-electronic]. 2012; 2012: 997-1003. PMID: 23304375, PMCID: PMC3540461, ISSN: 1942-597X.

Liu M, Shah A, Jiang M, Peterson NB, Dai Q, Aldrich MC, Chen Q, Bowton EA, Liu H, Denny JC, Xu H. A study of transportability of an existing smoking status detection module across institutions. AMIA Annu Symp Proc [print-electronic]. 2012; 2012: 577-86. PMID: 23304330, PMCID: PMC3540509, ISSN: 1942-597X.

Jiang M, Denny JC, Tang B, Cao H, Xu H. Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method. AMIA Annu Symp Proc [print-electronic]. 2012; 2012: 409-16. PMID: 23304311, PMCID: PMC3540581, ISSN: 1942-597X.

Denny JC. Chapter 13: Mining electronic health records in the genomics era. PLoS Comput. Biol [print-electronic]. 2012; 8(12): e1002823. PMID: 23300414, PMCID: PMC3531280, PII: PCOMPBIOL-D-12-01458, DOI: 10.1371/journal.pcbi.1002823, ISSN: 1553-7358.

Xu H, AbdelRahman S, Lu Y, Denny JC, Doan S. Applying semantic-based probabilistic context-free grammar to medical language processing--a preliminary study on parsing medication sentences. J Biomed Inform [print-electronic]. 2011 Dec; 44(6): 1068-75. PMID: 21856440, PMCID: PMC3226929, PII: S1532-0464(11)00136-5, DOI: 10.1016/j.jbi.2011.08.009, ISSN: 1532-0480.

Schildcrout JS, Haneuse S, Peterson JF, Denny JC, Matheny ME, Waitman LR, Miller RA. Analyses of longitudinal, hospital clinical laboratory data with application to blood glucose concentrations. Stat Med [print-electronic]. 2011 Nov 11/30/2011; 30(27): 3208-20. PMID: 21948391, PMCID: PMC3339442, DOI: 10.1002/sim.4352, ISSN: 1097-0258.

Denny JC, Crawford DC, Ritchie MD, Bielinski SJ, Basford MA, Bradford Y, Chai HS, Bastarache L, Zuvich R, Peissig P, Carrell D, Ramirez AH, Pathak J, Wilke RA, Rasmussen L, Wang X, Pacheco JA, Kho AN, Hayes MG, Weston N, Matsumoto M, Kopp PA, Newton KM, Jarvik GP, Li R, Manolio TA, Kullo IJ, Chute CG, Chisholm RL, Larson EB, McCarty CA, Masys DR, Roden DM, de Andrade M. Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. Am. J. Hum. Genet. 2011 Oct 10/7/2011; 89(4): 529-42. PMID: 21981779, PMCID: PMC3188836, PII: S0002-9297(11)00398-3, DOI: 10.1016/j.ajhg.2011.09.008, ISSN: 1537-6605.

Jiang M, Chen Y, Liu M, Rosenbloom ST, Mani S, Denny JC, Xu H. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc [print-electronic]. 2011 Sep; 18(5): 601-6. PMID: 21508414, PMCID: PMC3168315, PII: amiajnl-2011-000163, DOI: 10.1136/amiajnl-2011-000163, ISSN: 1527-974X.

Xu H, Jiang M, Oetjens M, Bowton EA, Ramirez AH, Jeff JM, Basford MA, Pulley JM, Cowan JD, Wang X, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. J Am Med Inform Assoc. 2011 Jul; 18(4): 387-91. PMID: 21672908, PMCID: PMC3128409, PII: amiajnl-2011-000208, DOI: 10.1136/amiajnl-2011-000208, ISSN: 1527-974X.

Wilke RA, Xu H, Denny JC, Roden DM, Krauss RM, McCarty CA, Davis RL, Skaar T, Lamba J, Savova G. The emerging role of electronic medical records in pharmacogenomics. Clin. Pharmacol. Ther [print-electronic]. 2011 Mar; 89(3): 379-86. PMID: 21248726, PMCID: PMC3204342, PII: clpt2010260, DOI: 10.1038/clpt.2010.260, ISSN: 1532-6535.

Xu H, Fu Z, Shah A, Chen Y, Peterson NB, Chen Q, Mani S, Levy MA, Dai Q, Denny JC. Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases. AMIA Annu Symp Proc [print-electronic]. 2011; 2011: 1564-72. PMID: 22195222, PMCID: PMC3243156, ISSN: 1942-597X.

Wu Y, Rosenbloom ST, Denny JC, Miller RA, Mani S, Giuse DA, Xu H. Detecting abbreviations in discharge summaries using machine learning methods. AMIA Annu Symp Proc [print-electronic]. 2011; 2011: 1541-9. PMID: 22195219, PMCID: PMC3243185, ISSN: 1942-597X.

Liu M, Jiang M, Kawai VK, Stein CM, Roden DM, Denny JC, Xu H. Modeling drug exposure data in electronic medical records: an application to warfarin. AMIA Annu Symp Proc [print-electronic]. 2011; 2011: 815-23. PMID: 22195139, PMCID: PMC3243123, ISSN: 1942-597X.

Carroll RJ, Eyler AE, Denny JC. Naïve Electronic Health Record phenotype identification for Rheumatoid arthritis. AMIA Annu Symp Proc [print-electronic]. 2011; 2011: 189-96. PMID: 22195070, PMCID: PMC3243261, ISSN: 1942-597X.

Sastre EA, Denny JC, McCoy JA, McCoy AB, Spickard A. Teaching evidence-based medicine: Impact on students' literature use and inpatient clinical documentation. Med Teach. 2011; 33(6): e306-12. PMID: 21609166, DOI: 10.3109/0142159X.2011.565827, ISSN: 1466-187X.

Turner SD, Berg RL, Linneman JG, Peissig PL, Crawford DC, Denny JC, Roden DM, McCarty CA, Ritchie MD, Wilke RA. Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PLoS ONE. 2011; 6(5): e19586. PMID: 21589926, PMCID: PMC3092760, PII: PONE-D-11-00174, DOI: 10.1371/journal.pone.0019586, ISSN: 1932-6203.

Denny JC, Speltz P, Maddox R, Stein G, Xu H, Spickard A. Comparing content coverage in medical curriculum to trainee-authored clinical notes. AMIA Annu Symp Proc. 2010 Nov 11/13/2010; 2010: 157-61. PMID: 21346960, PMCID: PMC3041398, ISSN: 1942-597X.

Matheny ME, Miller RA, Ikizler TA, Waitman LR, Denny JC, Schildcrout JS, Dittus RS, Peterson JF. Development of inpatient risk stratification models of acute kidney injury for use in electronic health records. Med Decis Making [print-electronic]. 2010 Nov; 30(6): 639-50. PMID: 20354229, PII: 0272989X10364246, DOI: 10.1177/0272989X10364246, ISSN: 1552-681X.

Loukides G, Denny JC, Malin B. The disclosure of diagnosis codes can breach research participants' privacy. J Am Med Inform Assoc. 2010 May; 17(3): 322-7. PMID: 20442151, PMCID: PMC2995712, PII: 17/3/322, DOI: 10.1136/jamia.2009.002725, ISSN: 1527-974X.

Denny JC, Ritchie MD, Basford MA, Pulley JM, Bastarache L, Brown-Gentry K, Wang D, Masys DR, Roden DM, Crawford DC. PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics [print-electronic]. 2010 May 5/1/2010; 26(9): 1205-10. PMID: 20335276, PMCID: PMC2859132, PII: btq126, DOI: 10.1093/bioinformatics/btq126, ISSN: 1367-4811.

Ritchie MD, Denny JC, Crawford DC, Ramirez AH, Weiner JB, Pulley JM, Basford MA, Brown-Gentry K, Balser JR, Masys DR, Haines JL, Roden DM. Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. Am. J. Hum. Genet [print-electronic]. 2010 Apr 4/9/2010; 86(4): 560-72. PMID: 20362271, PMCID: PMC2850440, PII: S0002-9297(10)00146-1, DOI: 10.1016/j.ajhg.2010.03.003, ISSN: 1537-6605.

Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC. MedEx: a medication information extraction system for clinical narratives. J Am Med Inform Assoc. 2010 Jan; 17(1): 19-24. PMID: 20064797, PMCID: PMC2995636, PII: 17/1/19, DOI: 10.1197/jamia.M3378, ISSN: 1527-974X.

Tamersoy A, Loukides G, Denny JC, Malin B. Anonymization of administrative billing codes with repeated diagnoses through censoring. AMIA Annu Symp Proc. 2010; 2010: 782-6. PMID: 21347085, PMCID: PMC3041421, ISSN: 1942-597X.

Peterson JF, Shi Y, Denny JC, Matheny ME, Schildcrout JS, Waitman LR, Miller RA. Prevalence and Clinical Significance of Discrepancies within Three Computerized Pre-Admission Medication Lists. AMIA Annu Symp Proc. 2010; 2010: 642-6. PMID: 21347057, PMCID: PMC3041392, ISSN: 1942-597X.

Denny JC, Spickard A, Johnson KB, Peterson NB, Peterson JF, Miller RA. Evaluation of a method to identify and categorize section headers in clinical documents. J Am Med Inform Assoc [print-electronic]. 2009 Nov; 16(6): 806-15. PMID: 19717800, PMCID: PMC3002123, PII: M3037, DOI: 10.1197/jamia.M3037, ISSN: 1527-974X.

Denny JC, Bastarache L, Sastre EA, Spickard A. Tracking medical students' clinical experiences using natural language processing. J Biomed Inform [print-electronic]. 2009 Oct; 42(5): 781-9. PMID: 19236956, PII: S1532-0464(09)00024-0, DOI: 10.1016/j.jbi.2009.02.004, ISSN: 1532-0480.

Denny JC, Miller RA, Waitman LR, Arrieta MA, Peterson JF. Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor. Int J Med Inform [print-electronic]. 2009 Apr; 78 Suppl 1: S34-42. PMID: 18938105, PMCID: PMC2728459, PII: S1386-5056(08)00162-7, DOI: 10.1016/j.ijmedinf.2008.09.001, ISSN: 1872-8243.

Denny JC, Peterson JF, Choma NN, Xu H, Miller RA, Bastarache L, Peterson NB. Development of a natural language processing system to identify timing and status of colonoscopy testing in electronic medical records. AMIA Annu Symp Proc. 2009; 2009: 141. PMID: 20351837, PMCID: PMC2815478, ISSN: 1942-597X.

Spickard A, Gigante J, Stein G, Denny JC. Automatic capture of student notes to augment mentor feedback and student performance on patient write-ups. J Gen Intern Med. 2008 Jul; 23(7): 979-84. PMID: 18612728, PMCID: PMC2517906, DOI: 10.1007/s11606-008-0608-y, ISSN: 1525-1497.

Denny JC, Arndt FV, Dupont WD, Neilson EG. Increased hospital mortality in patients with bedside hippus. Am. J. Med. 2008 Mar; 121(3): 239-45. PMID: 18328309, PII: S0002-9343(07)00939-4, DOI: 10.1016/j.amjmed.2007.09.014, ISSN: 1555-7162.

Denny JC, Miller RA, Johnson KB, Spickard A. Development and evaluation of a clinical note section header terminology. AMIA Annu Symp Proc. 2008; 156-60. PMID: 18999303, PMCID: PMC2656032, ISSN: 1942-597X.

Denny JC, Spickard A. Automated capture and assessment of medical student clinical experience. AMIA Annu Symp Proc. 2008; 926. PMID: 18999239, ISSN: 1942-597X.

Campion TR, Denny JC, Weinberg ST, Lorenzi NM, Waitman LR. Analysis of a computerized sign-out tool: identification of unanticipated uses and contradictory content. AMIA Annu Symp Proc. 2007; 99-104. PMID: 18693806, PMCID: PMC2655840, ISSN: 1942-597X.

Denny JC, Peterson JF. Identifying QT prolongation from ECG impressions using natural language processing and negation detection. Stud Health Technol Inform. 2007; 129(Pt 2): 1283-8. PMID: 17911921, ISSN: 0926-9630.

Spickard A, Denny J, Gigante J. A randomized study of feedback on student write-ups using an electronic portfolio. AMIA Annu Symp Proc. 2007; 1120. PMID: 18694217, ISSN: 1942-597X.

Denny J, Powers J, Spickard A, Miller R. A comparison of three methods for automatic text categorization for geriatrics. AMIA Annu Symp Proc. 2007; 931. PMID: 18694031, ISSN: 1942-597X.

Rosenbaum BP, Denny JC, Spickard A. Analysis of medical student content searches that resulted in unidentified UMLS concepts. AMIA Annu Symp Proc. 2006; 1079. PMID: 17238698, PMCID: PMC1839579, PII: 85820, ISSN: 1942-597X.

Denny JC, Smithers JD, Armstrong B, Spickard A. "Where do we teach what?" Finding broad concepts in the medical school curriculum. J Gen Intern Med. 2005 Oct; 20(10): 943-6. PMID: 16191143, PMCID: PMC1490241, PII: JGI203, DOI: 10.1111/j.1525-1497.2005.0203.x, ISSN: 1525-1497.

Wehbe FH, Denny JC, Spickard A. Can users estimate their usage of a web-based application? Validating a self-report usage questionnaire. AMIA Annu Symp Proc. 2005; 1151. PMID: 16779437, PMCID: PMC1560442, PII: 58951, ISSN: 1942-597X.

Denny JC, Spickard A, Miller RA, Schildcrout J, Darbar D, Rosenbloom ST, Peterson JF. Identifying UMLS concepts from ECG Impressions using KnowledgeMap. AMIA Annu Symp Proc. 2005; 196-200. PMID: 16779029, PMCID: PMC1479847, PII: 58024, ISSN: 1942-597X.

Camacho RC, Denny JC, Pencek RR, Koyama Y, Lacy DB, James FD, Wasserman DH. Portal venous hyperinsulinemia does not stimulate gut glucose absorption in the conscious dog. Metab. Clin. Exp. 2004 Oct; 53(10): 1290-5. PMID: 15375784, PII: S0026049504002343, ISSN: 0026-0495.

Denny JC, Smithers JD, Miller RA, Spickard A. "Understanding" medical school curriculum content using KnowledgeMap. J Am Med Inform Assoc [print-electronic]. 2003 Jul; 10(4): 351-62. PMID: 12668688, PMCID: PMC181986, PII: M1176, DOI: 10.1197/jamia.M1176, ISSN: 1067-5027.

Wehbe FH, Armstrong BK, Peachey MR, Denny JC, Spickard A. Formative evaluation to guide early deployment of an online content management tool for medical curriculum. AMIA Annu Symp Proc. 2003; 1049. PMID: 14728552, PMCID: PMC1479992, PII: D030003680, ISSN: 1942-597X.

Denny JC, Irani PR, Wehbe FH, Smithers JD, Spickard A. The KnowledgeMap project: development of a concept-based medical school curriculum database. AMIA Annu Symp Proc. 2003; 195-9. PMID: 14728161, PMCID: PMC1480333, PII: D030003640, ISSN: 1942-597X.

Coker RH, Koyama Y, Denny JC, Camacho RC, Lacy DB, Wasserman DH. Prevention of overt hypoglycemia during exercise: stimulation of endogenous glucose production independent of hepatic catecholamine action and changes in pancreatic hormone concentration. Diabetes. 2002 May; 51(5): 1310-8. PMID: 11978626, ISSN: 0012-1797.

Koyama Y, Coker RH, Denny JC, Lacy DB, Jabbour K, Williams PE, Wasserman DH. Role of carotid bodies in control of the neuroendocrine response to exercise. Am. J. Physiol. Endocrinol. Metab. 2001 Oct; 281(4): E742-8. PMID: 11551850, ISSN: 0193-1849.

Fasciotto BH, Denny JC, Greeley GH, Cohn DV. Processing of chromogranin A in the parathyroid: generation of parastatin-related peptides. Peptides. 2000 Sep; 21(9): 1389-401. PMID: 11072127, PII: S0196978100002837, ISSN: 0196-9781.