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Joshua C. Denny, M.D., M.S. - Publications

Affiliations: 
Biomedical Informatics Vanderbilt University School of Medicine, Nashville, TN, United States 
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331 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Ritchie SC, Taylor HJ, Liang Y, Manikpurage HD, Pennells L, Foguet C, Abraham G, Gibson JT, Jiang X, Liu Y, Xu Y, Kim LG, Mahajan A, McCarthy MI, Kaptoge S, ... ... Denny JC, et al. Integrated clinical risk prediction of type 2 diabetes with a multifactorial polygenic risk score. Medrxiv : the Preprint Server For Health Sciences. PMID 39228710 DOI: 10.1101/2024.08.22.24312440  0.388
2024 Haddad A, Radhakrishnan A, McGee S, Smith JD, Karnes JH, Venner E, Wheeler MM, Patterson K, Walker K, Kalra D, Kalla SE, Wang Q, Gibbs RA, Jarvik GP, Sanchez J, ... ... Denny JC, et al. Frequency of pharmacogenomic variation and medication exposures among All of Us Participants. Medrxiv : the Preprint Server For Health Sciences. PMID 38946996 DOI: 10.1101/2024.06.12.24304664  0.59
2024 Lin YC, Zhang S, Vessels T, Bastarache L, Bejan CA, Hsie RS, Philips EJ, Ruderfer DM, Pulley JM, Edwards TL, Wells QS, Warner JL, Denny JC, Roden DM, Kang H, et al. Overcome the Limitation of Phenome-Wide Association Studies (PheWAS): Extension of PheWAS to Efficient and Robust Large-Scale ICD Codes Analysis. Medrxiv : the Preprint Server For Health Sciences. PMID 38699370 DOI: 10.1101/2024.04.15.24305098  0.646
2024 Tran TC, Schlueter DJ, Zeng C, Mo H, Carroll RJ, Denny JC. PheWAS analysis on large-scale biobank data with PheTK. Medrxiv : the Preprint Server For Health Sciences. PMID 38410487 DOI: 10.1101/2024.02.12.24302720  0.503
2024 Suzuki K, Hatzikotoulas K, Southam L, Taylor HJ, Yin X, Lorenz KM, Mandla R, Huerta-Chagoya A, Melloni GEM, Kanoni S, Rayner NW, Bocher O, Arruda AL, Sonehara K, Namba S, ... ... Denny JC, et al. Genetic drivers of heterogeneity in type 2 diabetes pathophysiology. Nature. PMID 38374256 DOI: 10.1038/s41586-024-07019-6  0.416
2024 Li R, Benz L, Duan R, Denny JC, Hakonarson H, Mosley JD, Smoller JW, Wei WQ, Ritchie MD, Moore JH, Chen Y. mixWAS: An efficient distributed algorithm for mixed-outcomes genome-wide association studies. Medrxiv : the Preprint Server For Health Sciences. PMID 38260403 DOI: 10.1101/2024.01.09.24301073  0.605
2023 Wei WQ, Guardo C, Gandireddy S, Yan C, Ong H, Kerchberger V, Dickson A, Pfaff E, Master H, Basford M, Tran N, Mancuso S, Syed T, Zhao Z, Feng Q, ... ... Denny J, et al. Genetic and Survey Data Improves Performance of Machine Learning Model for Long COVID. Research Square. PMID 38196610 DOI: 10.21203/rs.3.rs-3749510/v1  0.679
2023 Schlueter DJ, Sulieman L, Mo H, Keaton JM, Ferrara TM, Williams A, Qian J, Stubblefield O, Zeng C, Tran TC, Bastarache L, Dai J, Babbar A, Ramirez A, Goleva SB, ... Denny JC, et al. Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research Program. Journal of the American Medical Informatics Association : Jamia. PMID 37885303 DOI: 10.1093/jamia/ocad205  0.78
2023 Deflaux N, Selvaraj MS, Condon HR, Mayo K, Haidermota S, Basford MA, Lunt C, Philippakis AA, Roden DM, Denny JC, Musick A, Collins R, Allen N, Effingham M, Glazer D, et al. Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis. Nature Communications. 14: 5419. PMID 37669985 DOI: 10.1038/s41467-023-41185-x  0.416
2023 Schuler BA, Bastarache L, Wang J, He J, Van Driest SL, Denny JC. Population genetic testing and SERPINA1 sequencing identifies unidentified alpha-1 antitrypsin deficiency alleles and gene-environment interaction with hepatitis C infection. Plos One. 18: e0286469. PMID 37651384 DOI: 10.1371/journal.pone.0286469  0.516
2023 Cassini T, Bastarache L, Zeng C, Han ST, Wang J, He J, Denny JC. A Test of Automated Use of Electronic Health Records to Aid in Diagnosis of Genetic Disease. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 100966. PMID 37622442 DOI: 10.1016/j.gim.2023.100966  0.563
2023 Bastarache L, Delozier S, Pandit A, He J, Lewis A, Annis AC, LeFaive J, Denny JC, Carroll RJ, Altman RB, Hughey JJ, Zawistowski M, Peterson JF. The phenotype-genotype reference map: Improving biobank data science through replication. American Journal of Human Genetics. PMID 37607538 DOI: 10.1016/j.ajhg.2023.07.012  0.733
2023 Mayo KR, Basford MA, Carroll RJ, Dillon M, Fullen H, Leung J, Master H, Rura S, Sulieman L, Kennedy N, Banks E, Bernick D, Gauchan A, Lichtenstein L, Mapes BM, ... ... Denny JC, et al. The Data and Research Center: Creating a Secure, Scalable, and Sustainable Ecosystem for Biomedical Research. Annual Review of Biomedical Data Science. 6: 443-464. PMID 37561600 DOI: 10.1146/annurev-biodatasci-122120-104825  0.77
2023 Allaire P, He J, Mayer J, Moat L, Gerstenberger P, Wilhorn R, Strutz S, Kim DSL, Zeng C, Cox N, Shay JW, Denny J, Bastarache L, Hebbring S. Genetic and clinical determinants of telomere length. Hgg Advances. 4: 100201. PMID 37216007 DOI: 10.1016/j.xhgg.2023.100201  0.62
2023 Joo YY, Pacheco JA, Thompson WK, Rasmussen-Torvik LJ, Rasmussen LV, Lin FTJ, Andrade M, Borthwick KM, Bottinger E, Cagan A, Carrell DS, Denny JC, Ellis SB, Gottesman O, Linneman JG, et al. Multi-ancestry genome- and phenome-wide association studies of diverticular disease in electronic health records with natural language processing enriched phenotyping algorithm. Plos One. 18: e0283553. PMID 37196047 DOI: 10.1371/journal.pone.0283553  0.316
2023 Suzuki K, Hatzikotoulas K, Southam L, Taylor HJ, Yin X, Lorenz KM, Mandla R, Huerta-Chagoya A, Rayner NW, Bocher O, Ana Luiza de SVA, Sonehara K, Namba S, Lee SSK, Preuss MH, ... ... Denny JC, et al. Multi-ancestry genome-wide study in >2.5 million individuals reveals heterogeneity in mechanistic pathways of type 2 diabetes and complications. Medrxiv : the Preprint Server For Health Sciences. PMID 37034649 DOI: 10.1101/2023.03.31.23287839  0.418
2023 Schulkey CE, Litwin TR, Ellsworth G, Sansbury H, Ahmedani BK, Choi KW, Cronin R, Kloth Y, Ashbeck AW, Sutherland S, Mapes B, Begale M, Bhat G, King P, Marginean K, ... ... Denny J, et al. Design and Implementation of the All of Us Research Program COVID-19 Participant Experience (COPE) Survey. American Journal of Epidemiology. PMID 36799620 DOI: 10.1093/aje/kwad035  0.583
2022 Robinson JR, Carroll RJ, Bastarache L, Chen Q, Pirruccello J, Mou Z, Wei WQ, Connolly J, Mentch F, Crane PK, Hebbring SJ, Crosslin DR, Gordon AS, Rosenthal EA, Stanaway IB, ... ... Denny JC, et al. Quantifying the phenome-wide disease burden of obesity using electronic health records and genomics. Obesity (Silver Spring, Md.). PMID 36372681 DOI: 10.1002/oby.23561  0.793
2022 Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, ... ... Denny JC, et al. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nature Genetics. PMID 36333501 DOI: 10.1038/s41588-022-01213-w  0.467
2022 Ramirez AH, Sulieman L, Schlueter DJ, Halvorson A, Qian J, Ratsimbazafy F, Loperena R, Mayo K, Basford M, Deflaux N, Muthuraman KN, Natarajan K, Kho A, Xu H, Wilkins C, ... ... Denny JC, et al. The Research Program: Data quality, utility, and diversity. Patterns (New York, N.Y.). 3: 100570. PMID 36033590 DOI: 10.1016/j.patter.2022.100570  0.794
2022 Zhang X, Lucas AM, Veturi Y, Drivas TG, Bone WP, Verma A, Chung WK, Crosslin D, Denny JC, Hebbring S, Jarvik GP, Kullo I, Larson EB, Rasmussen-Torvik LJ, Schaid DJ, et al. Large-scale genomic analyses reveal insights into pleiotropy across circulatory system diseases and nervous system disorders. Nature Communications. 13: 3428. PMID 35701404 DOI: 10.1038/s41467-022-30678-w  0.553
2022 Feng YA, Stanaway IB, Connolly JJ, Denny JC, Luo Y, Weng C, Wei WQ, Weiss ST, Karlson EW, Smoller JW. Psychiatric manifestations of rare variation in medically actionable genes: a PheWAS approach. Bmc Genomics. 23: 385. PMID 35590255 DOI: 10.1186/s12864-022-08600-x  0.563
2022 Zeng C, Bastarache LA, Tao R, Venner E, Hebbring S, Andujar JD, Bland ST, Crosslin DR, Pratap S, Cooley A, Pacheco JA, Christensen KD, Perez E, Zawatsky CLB, Witkowski L, ... ... Denny JC, et al. Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases. Jama Oncology. PMID 35446370 DOI: 10.1001/jamaoncol.2022.0373  0.612
2022 Irlmeier R, Hughey JJ, Bastarache L, Denny JC, Chen Q. Cox Regression is Robust to Inaccurate EHR-extracted Event Time-an Application to EHR-based GWAS. Bioinformatics (Oxford, England). PMID 35157022 DOI: 10.1093/bioinformatics/btac086  0.563
2022 Wu P, Feng Q, Kerchberger VE, Nelson SD, Chen Q, Li B, Edwards TL, Cox NJ, Phillips EJ, Stein CM, Roden DM, Denny JC, Wei WQ. Integrating gene expression and clinical data to identify drug repurposing candidates for hyperlipidemia and hypertension. Nature Communications. 13: 46. PMID 35013250 DOI: 10.1038/s41467-021-27751-1  0.758
2022 Bastarache L, Denny JC, Roden DM. Phenome-Wide Association Studies. Jama. 327: 75-76. PMID 34982132 DOI: 10.1001/jama.2021.20356  0.625
2021 Glazer AM, Davogustto GE, Shaffer CM, Vanoye CG, Desai RR, Farber-Eger E, Dikilitas O, Shang N, Pacheco JA, Yang T, Muhammad A, Mosley JD, Van Driest SL, Wells QS, Shaffer LL, ... ... Denny J, et al. Arrhythmia Variant Associations and Reclassifications in the eMERGE-III Sequencing Study. Circulation. PMID 34930020 DOI: 10.1161/CIRCULATIONAHA.121.055562  0.801
2021 Althoff KN, Schlueter DJ, Anton-Culver H, Cherry J, Denny JC, Thomsen I, Karlson EW, Havers FP, Cicek MS, Thibodeau SN, Pinto LA, Lowy D, Malin BA, Ohno-Machado L, Williams C, et al. Antibodies to SARS-CoV-2 in All of Us Research Program Participants, January 2-March 18, 2020. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 34128970 DOI: 10.1093/cid/ciab519  0.514
2021 Liu G, Shi M, Mosley JD, Weng C, Zhang Y, Lee MTM, Jarvik GP, Hakonarson H, Namjou-Khales B, Sleiman P, Luo Y, Mentch F, Denny JC, Linton MF, Wei WQ, et al. A Mendelian Randomization Approach Using 3-HMG-Coenzyme-A Reductase Gene Variation to Evaluate the Association of Statin-Induced Low-Density Lipoprotein Cholesterol Lowering With Noncardiovascular Disease Phenotypes. Jama Network Open. 4: e2112820. PMID 34097045 DOI: 10.1001/jamanetworkopen.2021.12820  0.525
2021 Zheng NS, Stone CA, Jiang L, Shaffer CM, Kerchberger VE, Chung CP, Feng Q, Cox NJ, Stein CM, Roden DM, Denny JC, Phillips EJ, Wei WQ. High-throughput framework for genetic analyses of adverse drug reactions using electronic health records. Plos Genetics. 17: e1009593. PMID 34061827 DOI: 10.1371/journal.pgen.1009593  0.656
2021 Emdin CA, Haas ME, Khera AV, Aragam K, Chaffin M, Klarin D, Hindy G, Jiang L, Wei WQ, Feng Q, Karjalainen J, Havulinna A, Kiiskinen T, Bick A, Ardissino D, ... ... Denny J, et al. Correction: A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease. Plos Genetics. 17: e1009503. PMID 33822779 DOI: 10.1371/journal.pgen.1009503  0.481
2021 Denny JC, Collins FS. Precision medicine in 2030-seven ways to transform healthcare. Cell. 184: 1415-1419. PMID 33740447 DOI: 10.1016/j.cell.2021.01.015  0.401
2021 Wu P, Nelson SD, Zhao J, Stone CA, Feng Q, Chen Q, Larson EA, Li B, Cox NJ, Stein CM, Phillips EJ, Roden DM, Denny JC, Wei WQ. DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions. Journal of the American Medical Informatics Association : Jamia. PMID 33712848 DOI: 10.1093/jamia/ocab019  0.775
2021 Rosenthal EA, Crosslin DR, Gordon AS, Carrell DS, Stanaway IB, Larson EB, Grafton J, Wei WQ, Denny JC, Feng QP, Shah AS, Sturm AC, Ritchie MD, Pacheco JA, Hakonarson H, et al. Association between triglycerides, known risk SNVs and conserved rare variation in SLC25A40 in a multi-ancestry cohort. Bmc Medical Genomics. 14: 11. PMID 33407432 DOI: 10.1186/s12920-020-00854-2  0.536
2020 Emdin CA, Haas M, Ajmera V, Simon TG, Homburger J, Neben C, Jiang L, Wei WQ, Feng Q, Zhou A, Denny J, Corey K, Loomba R, Kathiresan S, Khera AV. Association of genetic variation with cirrhosis: a multi-trait genome-wide association and gene-environment interaction study. Gastroenterology. PMID 33310085 DOI: 10.1053/j.gastro.2020.12.011  0.562
2020 Goldstein JA, Weinstock JS, Bastarache LA, Larach DB, Fritsche LG, Schmidt EM, Brummett CM, Kheterpal S, Abecasis GR, Denny JC, Zawistowski M. LabWAS: Novel findings and study design recommendations from a meta-analysis of clinical labs in two independent biobanks. Plos Genetics. 16: e1009077. PMID 33175840 DOI: 10.1371/journal.pgen.1009077  0.779
2020 DeLozier S, Speltz P, Brito J, Tang LA, Wang J, Smith JC, Giuse D, Phillips E, Williams K, Strickland T, Davogustto G, Roden D, Denny JC. Real-time clinical note monitoring to detect conditions for rapid follow-up: A case study of clinical trial enrollment in drug-induced torsades de pointes and Stevens-Johnson syndrome. Journal of the American Medical Informatics Association : Jamia. PMID 33120413 DOI: 10.1093/jamia/ocaa213  0.644
2020 Zheng NS, Feng Q, Kerchberger VE, Zhao J, Edwards TL, Cox NJ, Stein CM, Roden DM, Denny JC, Wei WQ. PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. Journal of the American Medical Informatics Association : Jamia. PMID 32974638 DOI: 10.1093/jamia/ocaa104  0.679
2020 Namjou B, Stanaway IB, Lingren T, Mentch FD, Benoit B, Dikilitas O, Niu X, Shang N, Shoemaker AH, Carey DJ, Mirshahi T, Singh R, Nestor JG, Hakonarson H, Denny JC, et al. Evaluation of the MC4R gene across eMERGE network identifies many unreported obesity-associated variants. International Journal of Obesity (2005). PMID 32952152 DOI: 10.1038/S41366-020-00675-4  0.35
2020 Mapes BM, Foster CS, Kusnoor SV, Epelbaum MI, AuYoung M, Jenkins G, Lopez-Class M, Richardson-Heron D, Elmi A, Surkan K, Cronin RM, Wilkins CH, Pérez-Stable EJ, Dishman E, Denny JC, et al. Diversity and inclusion for the All of Us research program: A scoping review. Plos One. 15: e0234962. PMID 32609747 DOI: 10.1371/Journal.Pone.0234962  0.635
2020 Jia G, Lu Y, Wen W, Long J, Liu Y, Tao R, Li B, Denny JC, Shu XO, Zheng W. Evaluating the Utility of Polygenic Risk Scores in Identifying High-Risk Individuals for Eight Common Cancers. Jnci Cancer Spectrum. 4: pkaa021. PMID 32596635 DOI: 10.1093/Jncics/Pkaa021  0.318
2020 Mosley JD, Levinson RT, Farber-Eger E, Edwards TL, Hellwege JN, Hung AM, Giri A, Shuey MM, Shaffer CM, Shi M, Brittain EL, Chung WK, Kullo IJ, Arruda-Olson AM, Jarvik GP, ... ... Denny JC, et al. The polygenic architecture of left ventricular mass mirrors the clinical epidemiology. Scientific Reports. 10: 7561. PMID 32372017 DOI: 10.1038/S41598-020-64525-Z  0.485
2020 Emdin CA, Haas ME, Khera AV, Aragam K, Chaffin M, Klarin D, Hindy G, Jiang L, Wei WQ, Feng Q, Karjalainen J, Havulinna A, Kiiskinen T, Bick A, Ardissino D, ... ... Denny J, et al. A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease. Plos Genetics. 16: e1008629. PMID 32282858 DOI: 10.1371/Journal.Pgen.1008629  0.553
2020 Bajaj A, Ihegword A, Qiu C, Small AM, Wei WQ, Bastarache L, Feng Q, Kember RL, Risman M, Bloom RD, Birtwell DL, Williams H, Shaffer CM, Chen J, Center RG, ... Denny JC, et al. Phenome-wide association analysis suggests the APOL1 linked disease spectrum primarily drives kidney-specific pathways. Kidney International. PMID 32247630 DOI: 10.1016/J.Kint.2020.01.027  0.71
2020 Jerome RN, Joly MM, Kennedy N, Shirey-Rice JK, Roden DM, Bernard GR, Holroyd KJ, Denny JC, Pulley JM. Leveraging Human Genetics to Identify Safety Signals Prior to Drug Marketing Approval and Clinical Use. Drug Safety. PMID 32112228 DOI: 10.1007/S40264-020-00915-6  0.442
2020 Choi L, Beck C, McNeer E, Weeks HL, Williams ML, James NT, Niu X, Abou-Khalil BW, Birdwell KA, Roden DM, Stein CM, Bejan CA, Denny JC, Van Driest SL. Development of a System for Post-marketing Population Pharmacokinetic and Pharmacodynamic Studies using Real-World Data from Electronic Health Records. Clinical Pharmacology and Therapeutics. PMID 31957870 DOI: 10.1002/Cpt.1787  0.459
2020 Weeks HL, Beck C, McNeer E, Williams ML, Bejan CA, Denny JC, Choi L. medExtractR: A targeted, customizable approach to medication extraction from electronic health records. Journal of the American Medical Informatics Association : Jamia. PMID 31943012 DOI: 10.1093/Jamia/Ocz207  0.371
2020 Joo YY, Actkins K, Pacheco JA, Basile AO, Carroll R, Crosslin DR, Day F, Denny JC, Velez Edwards DR, Hakonarson H, Harley JB, Hebbring SJ, Ho K, Jarvik GP, Jones M, et al. A polygenic and phenotypic risk prediction for Polycystic Ovary Syndrome evaluated by Phenome-wide association studies. The Journal of Clinical Endocrinology and Metabolism. PMID 31917831 DOI: 10.1210/Clinem/Dgz326  0.504
2020 Emdin CA, Haas ME, Khera AV, Aragam K, Chaffin M, Klarin D, Hindy G, Jiang L, Wei W, Feng Q, Karjalainen J, Havulinna A, Kiiskinen T, Bick A, Ardissino D, ... ... Denny J, et al. Association of MARC1 A165T with metabolic traits. Plos Genetics. DOI: 10.1371/Journal.Pgen.1008629.S005  0.548
2020 Emdin CA, Haas ME, Khera AV, Aragam K, Chaffin M, Klarin D, Hindy G, Jiang L, Wei W, Feng Q, Karjalainen J, Havulinna A, Kiiskinen T, Bick A, Ardissino D, ... ... Denny J, et al. Distribution of ancestry in each cohort. Plos Genetics. DOI: 10.1371/Journal.Pgen.1008629.S003  0.512
2019 Hughey JJ, Rhoades SD, Fu DY, Bastarache L, Denny JC, Chen Q. Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record. Bmc Genomics. 20: 805. PMID 31684865 DOI: 10.1186/S12864-019-6192-1  0.616
2019 Zhang L, Zhang Y, Cai T, Ahuja Y, He Z, Ho YL, Beam A, Cho K, Carroll R, Denny J, Kohane I, Liao K, Cai T. Automated Grouping of Medical Codes via Multiview Banded Spectral Clustering. Journal of Biomedical Informatics. 103322. PMID 31672532 DOI: 10.1016/J.Jbi.2019.103322  0.554
2019 Schmidt AF, Holmes MV, Preiss D, Swerdlow DI, Denaxas S, Fatemifar G, Faraway R, Finan C, Valentine D, Fairhurst-Hunter Z, Hartwig FP, Horta BL, Hypponen E, Power C, Moldovan M, ... ... Denny JC, et al. Phenome-wide association analysis of LDL-cholesterol lowering genetic variants in PCSK9. Bmc Cardiovascular Disorders. 19: 240. PMID 31664920 DOI: 10.1186/S12872-019-1187-Z  0.478
2019 Li X, Meng X, He Y, Spiliopoulou A, Timofeeva M, Wei WQ, Gifford A, Yang T, Varley T, Tzoulaki I, Joshi P, Denny JC, Mckeigue P, Campbell H, Theodoratou E. Genetically determined serum urate levels and cardiovascular and other diseases in UK Biobank cohort: A phenome-wide mendelian randomization study. Plos Medicine. 16: e1002937. PMID 31626644 DOI: 10.1371/Journal.Pmed.1002937  0.589
2019 Bastarache L, Hughey JJ, Goldstein JA, Bastraache JA, Das S, Zaki NC, Zeng C, Tang LA, Roden DM, Denny JC. Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease. Journal of the American Medical Informatics Association : Jamia. PMID 31609419 DOI: 10.1093/Jamia/Ocz179  0.78
2019 Robinson JR, Carroll RJ, Bastarache L, Chen Q, Mou Z, Wei WQ, Connolly JJ, Mentch F, Sleiman P, Crane PK, Hebbring SJ, Stanaway IB, Crosslin DR, Gordon AS, Rosenthal EA, ... ... Denny JC, et al. Association of Genetic Risk of Obesity with Postoperative Complications Using Mendelian Randomization. World Journal of Surgery. PMID 31605180 DOI: 10.1007/S00268-019-05202-9  0.771
2019 Wu P, Gifford A, Meng X, Li X, Campbell H, Varley T, Zhao J, Carroll R, Bastarache L, Denny JC, Theodoratou E, Wei WQ. Developing and Evaluating Mappings of ICD-10 and ICD-10-CM Codes to PheCodes. Jmir Medical Informatics. PMID 31553307 DOI: 10.2196/14325  0.795
2019 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, ... ... Denny JC, et al. Making work visible for electronic phenotype implementation: lessons learned from the eMERGE network. Journal of Biomedical Informatics. 103293. PMID 31542521 DOI: 10.1016/J.Jbi.2019.103293  0.561
2019 Meng X, Li X, Timofeeva MN, He Y, Spiliopoulou A, Wei WQ, Gifford A, Wu H, Varley T, Joshi P, Denny JC, Farrington SM, Zgaga L, Dunlop MG, McKeigue P, et al. Phenome-wide Mendelian-randomization study of genetically determined vitamin D on multiple health outcomes using the UK Biobank study. International Journal of Epidemiology. PMID 31518429 DOI: 10.1093/Ije/Dyz182  0.525
2019 Shi Y, Graves JA, Garbett SP, Zhou Z, Marathi R, Wang X, Harrell FE, Lasko TA, Denny JC, Roden DM, Peterson JF, Schildcrout JS. A Decision-Theoretic Approach to Panel-Based, Preemptive Genotyping. Mdm Policy & Practice. 4: 2381468319864337. PMID 31453360 DOI: 10.1177/2381468319864337  0.446
2019 Zhao J, Zhang Y, Schlueter DJ, Wu P, Eric Kerchberger V, Trent Rosenbloom S, Wells QS, Feng Q, Denny JC, Wei WQ. Detecting Time-Evolving Phenotypic Topics via Tensor Factorization on Electronic Health Records: Cardiovascular Disease Case Study. Journal of Biomedical Informatics. 103270. PMID 31445983 DOI: 10.1016/J.Jbi.2019.103270  0.775
2019 Hripcsak G, Shang N, Peissig PL, Rasmussen LV, Liu C, Benoit B, Carroll RJ, Carrell DS, Denny JC, Dikilitas O, Gainer VS, Marie Howell K, Klann JG, Kullo IJ, Lingren T, et al. Facilitating phenotype transfer using a common data model. Journal of Biomedical Informatics. 103253. PMID 31325501 DOI: 10.1016/J.Jbi.2019.103253  0.656
2019 Wei Q, Chen Y, Salimi M, Denny JC, Mei Q, Lasko TA, Chen Q, Wu S, Franklin A, Cohen T, Xu H. Cost-aware active learning for named entity recognition in clinical text. Journal of the American Medical Informatics Association : Jamia. PMID 31294792 DOI: 10.1093/Jamia/Ocz102  0.521
2019 Taylor CO, Lemke KW, Richards TM, Roe KD, He T, Arruda-Olson A, Carrell D, Denny JC, Hripcsak G, Kiryluk K, Kullo I, Larson EB, Peissig P, Walton NA, Wei-Qi W, et al. Comorbidity Characterization Among eMERGE Institutions: A Pilot Evaluation with the Johns Hopkins Adjusted Clinical Groups® System. Amia Joint Summits On Translational Science Proceedings. Amia Joint Summits On Translational Science. 2019: 145-152. PMID 31258966  0.544
2019 Edwards TL, Giri A, Hellwege JN, Hartmann KE, Stewart EA, Jeff JM, Bray MJ, Pendergrass SA, Torstenson ES, Keaton JM, Jones SH, Gogoi RP, Kuivaniemi H, Jackson KL, Kho AN, ... ... Denny JC, et al. A -Ethnic Genome-Wide Association Study of Uterine Fibroids. Frontiers in Genetics. 10: 511. PMID 31249589 DOI: 10.3389/Fgene.2019.00511  0.499
2019 Gill D, Georgakis MK, Koskeridis F, Jiang L, Feng Q, Wei WQ, Theodoratou E, Elliott P, Denny JC, Malik R, Evangelou E, Dehghan A, Dichgans M, Tzoulaki I. Use of Genetic Variants Related to Antihypertensive Drugs to Inform on Efficacy and Side Effects. Circulation. PMID 31234639 DOI: 10.1161/Circulationaha.118.038814  0.585
2019 Cronin RM, Jerome RN, Mapes B, Andrade R, Johnston R, Ayala J, Schlundt D, Bonnet K, Kripalani S, Goggins K, Wallston KA, Couper MP, Elliott MR, Harris P, Begale M, ... ... Denny JC, et al. Development of the Initial Surveys for the All of Us Research Program. Epidemiology (Cambridge, Mass.). PMID 31045611 DOI: 10.1097/Ede.0000000000001028  0.627
2019 Bastarache L, Bastarache JA, Denny JC. Case 40-2018: A Woman with Recurrent Sinusitis, Cough, and Bronchiectasis. The New England Journal of Medicine. 380: 1382-1383. PMID 30943357 DOI: 10.1056/Nejmc1901268  0.515
2019 Scott MKD, Quinn K, Li Q, Carroll R, Warsinske H, Vallania F, Chen S, Carns MA, Aren K, Sun J, Koloms K, Lee J, Baral J, Kropski J, Zhao H, ... ... Denny J, et al. Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study. The Lancet. Respiratory Medicine. PMID 30935881 DOI: 10.1016/S2213-2600(18)30508-3  0.512
2019 Brackman DJ, Yee SW, Enogieru OJ, Shaffer C, Ranatunga D, Denny JC, Wei WQ, Kamatani Y, Kubo M, Roden DM, Jorgenson E, Giacomini KM. Genome-wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol. Clinical Pharmacology and Therapeutics. PMID 30924126 DOI: 10.1002/Cpt.1439  0.659
2019 Zhang X, Veturi Y, Verma S, Bone W, Verma A, Lucas A, Hebbring S, Denny JC, Stanaway IB, Jarvik GP, Crosslin D, Larson EB, Rasmussen-Torvik L, Pendergrass SA, Smoller JW, et al. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 272-283. PMID 30864329  0.596
2019 Unlu G, Gamazon ER, Qi X, Levic DS, Bastarache L, Denny JC, Roden DM, Mayzus I, Breyer M, Zhong X, Konkashbaev AI, Rzhetsky A, Knapik EW, Cox NJ. GRIK5 Genetically Regulated Expression Associated with Eye and Vascular Phenomes: Discovery through Iteration among Biobanks, Electronic Health Records, and Zebrafish. American Journal of Human Genetics. PMID 30827500 DOI: 10.1016/J.Ajhg.2019.01.017  0.655
2019 Safarova MS, Satterfield BA, Fan X, Austin EE, Ye Z, Bastarache L, Zheng N, Ritchie MD, Borthwick KM, Williams MS, Larson EB, Scrol A, Jarvik GP, Crosslin DR, Leppig K, ... ... Denny JC, et al. A phenome-wide association study to discover pleiotropic effects of , , and . Npj Genomic Medicine. 4: 3. PMID 30774981 DOI: 10.1038/S41525-019-0078-7  0.798
2019 Zhao J, Feng Q, Wu P, Warner JL, Denny JC, Wei WQ. Using topic modeling via non-negative matrix factorization to identify relationships between genetic variants and disease phenotypes: A case study of Lipoprotein(a) (LPA). Plos One. 14: e0212112. PMID 30759150 DOI: 10.1371/Journal.Pone.0212112  0.799
2019 Zhao J, Feng Q, Wu P, Lupu RA, Wilke RA, Wells QS, Denny JC, Wei WQ. Learning from Longitudinal Data in Electronic Health Record and Genetic Data to Improve Cardiovascular Event Prediction. Scientific Reports. 9: 717. PMID 30679510 DOI: 10.1038/S41598-018-36745-X  0.773
2019 Salem JE, Shoemaker MB, Bastarache L, Shaffer CM, Glazer AM, Kroncke B, Wells QS, Shi M, Straub P, Jarvik GP, Larson EB, Velez Edwards DR, Edwards TL, Davis LK, Hakonarson H, ... ... Denny JC, et al. Association of Thyroid Function Genetic Predictors With Atrial Fibrillation: A Phenome-Wide Association Study and Inverse-Variance Weighted Average Meta-analysis. Jama Cardiology. PMID 30673079 DOI: 10.1001/Jamacardio.2018.4615  0.755
2019 Jorge A, Castro VM, Barnado A, Gainer V, Hong C, Cai T, Cai T, Carroll R, Denny JC, Crofford L, Costenbader KH, Liao KP, Karlson EW, Feldman CH. Identifying lupus patients in electronic health records: Development and validation of machine learning algorithms and application of rule-based algorithms. Seminars in Arthritis and Rheumatism. PMID 30665626 DOI: 10.1016/J.Semarthrit.2019.01.002  0.514
2019 Challen R, Denny J, Pitt M, Gompels L, Edwards T, Tsaneva-Atanasova K. Artificial intelligence, bias and clinical safety. Bmj Quality & Safety. PMID 30636200 DOI: 10.1136/Bmjqs-2018-008370  0.336
2019 Giri A, Hellwege JN, Keaton JM, Park J, Qiu C, Warren HR, Torstenson ES, Kovesdy CP, Sun YV, Wilson OD, Robinson-Cohen C, Roumie CL, Chung CP, Birdwell KA, Damrauer SM, ... ... Denny JC, et al. Trans-ethnic association study of blood pressure determinants in over 750,000 individuals. Nature Genetics. 51: 51-62. PMID 30578418 DOI: 10.1038/S41588-018-0303-9  0.673
2019 Barnado A, Carroll RJ, Casey C, Wheless L, Denny JC, Crofford LJ. Phenome-wide association study identifies dsDNA as a driver of major organ involvement in systemic lupus erythematosus. Lupus. 28: 66-76. PMID 30477398 DOI: 10.1177/0961203318815577  0.517
2018 Robinson JR, Wei WQ, Roden DM, Denny JC. Defining Phenotypes from Clinical Data to Drive Genomic Research. Annual Review of Biomedical Data Science. 1: 69-92. PMID 34109303 DOI: 10.1146/annurev-biodatasci-080917-013335  0.775
2018 Zebrowski AM, Ellis DE, Barg FK, Sperber NR, Bernhardt BA, Denny JC, Dexter PR, Ginsburg GS, Horowitz CR, Johnson JA, Levy MA, Orlando LA, Pollin TI, Skaar TC, Kimmel SE. Qualitative study of system-level factors related to genomic implementation. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 30467402 DOI: 10.1038/S41436-018-0378-9  0.312
2018 Hall TO, Stanaway IB, Carrell DS, Carroll RJ, Denny JC, Hakonarson H, Larson EB, Mentch FD, Peissig PL, Pendergrass SA, Rosenthal EA, Jarvik GP, Crosslin DR. Unfolding of hidden white blood cell count phenotypes for gene discovery using latent class mixed modeling. Genes and Immunity. PMID 30459343 DOI: 10.1038/S41435-018-0051-Y  0.556
2018 Stanaway IB, Hall TO, Rosenthal EA, Palmer M, Naranbhai V, Knevel R, Namjou-Khales B, Carroll RJ, Kiryluk K, Gordon AS, Linder J, Howell KM, Mapes BM, Lin FTJ, Joo YY, ... ... Denny JC, et al. The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype. Genetic Epidemiology. PMID 30298529 DOI: 10.1002/Gepi.22167  0.678
2018 Rhoades SD, Bastarache L, Denny JC, Hughey JJ. Pulling the covers in electronic health records for an association study with self-reported sleep behaviors. Chronobiology International. 1-11. PMID 30183400 DOI: 10.1080/07420528.2018.1508152  0.512
2018 Feng Q, Wei WQ, Chung CP, Levinson RT, Sundermann AC, Mosley JD, Bastarache L, Ferguson JF, Cox NJ, Roden DM, Denny JC, Linton MF, Edwards DRV, Stein CM. Relationship between very low low-density lipoprotein cholesterol concentrations not due to statin therapy and risk of type 2 diabetes: A US-based cross-sectional observational study using electronic health records. Plos Medicine. 15: e1002642. PMID 30153257 DOI: 10.1371/Journal.Pmed.1002642  0.72
2018 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, ... ... Denny JC, et al. A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. Journal of the American Medical Informatics Association : Jamia. PMID 30124903 DOI: 10.1093/Jamia/Ocy101  0.602
2018 Zhou W, Nielsen JB, Fritsche LG, Dey R, Gabrielsen ME, Wolford BN, LeFaive J, VandeHaar P, Gagliano SA, Gifford A, Bastarache LA, Wei WQ, Denny JC, Lin M, Hveem K, et al. Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. Nature Genetics. PMID 30104761 DOI: 10.1038/S41588-018-0184-Y  0.703
2018 Wang L, Pittman KJ, Barker JR, Salinas RE, Stanaway IB, Williams GD, Carroll RJ, Balmat T, Ingham A, Gopalakrishnan AM, Gibbs KD, Antonia AL, Heitman J, Lee SC, ... ... Denny JC, et al. An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host & Microbe. 24: 308-323.e6. PMID 30092202 DOI: 10.1016/J.Chom.2018.07.007  0.57
2018 Jerome RN, Pulley JM, Roden DM, Shirey-Rice JK, Bastarache LA, Bernard G, Ekstrom L, Lancaster WJ, Denny JC. Reply to Ward and Colleagues' Comment on "Using Human Experiments of Nature to Predict Drug Safety Issues: An Example with PCSK9 Inhibitors". Drug Safety. PMID 30066313 DOI: 10.1007/S40264-018-0701-Z  0.606
2018 Kowalec K, Wright GEB, Drögemöller BI, Aminkeng F, Bhavsar AP, Kingwell E, Yoshida EM, Traboulsee A, Marrie RA, Kremenchutzky M, Campbell TL, Duquette P, Chalasani N, Wadelius M, Hallberg P, ... ... Denny JC, et al. Common variation near IRF6 is associated with IFN-β-induced liver injury in multiple sclerosis. Nature Genetics. PMID 30013178 DOI: 10.1038/S41588-018-0168-Y  0.492
2018 Shuey MM, Gandelman JS, Chung CP, Nian H, Yu C, Denny JC, Brown NJ. Characteristics and treatment of African-American and European-American patients with resistant hypertension identified using the electronic health record in an academic health centre: a case-control study. Bmj Open. 8: e021640. PMID 29950471 DOI: 10.1136/Bmjopen-2018-021640  0.325
2018 Choi L, Carroll RJ, Beck C, Mosley JD, Roden DM, Denny JC, Van Driest SL. Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects. Bioinformatics (Oxford, England). PMID 29912272 DOI: 10.1093/Bioinformatics/Bty306  0.661
2018 Denny JC, Mosley JD. Disease Heritability Studies Harness the Healthcare System to Achieve Massive Scale. Cell. 173: 1568-1570. PMID 29906443 DOI: 10.1016/J.Cell.2018.05.053  0.364
2018 Roselli C, Chaffin MD, Weng LC, Aeschbacher S, Ahlberg G, Albert CM, Almgren P, Alonso A, Anderson CD, Aragam KG, Arking DE, Barnard J, Bartz TM, Benjamin EJ, Bihlmeyer NA, ... ... Denny JC, et al. Multi-ethnic genome-wide association study for atrial fibrillation. Nature Genetics. PMID 29892015 DOI: 10.1038/S41588-018-0133-9  0.473
2018 Bloodworth MH, Rusznak M, Bastarache L, Wang J, Denny JC, Peebles RS. Association of ST2 polymorphisms with atopy, asthma and leukemia. The Journal of Allergy and Clinical Immunology. PMID 29787780 DOI: 10.1016/J.Jaci.2018.03.020  0.554
2018 Liang J, Le TH, Velez Edwards DR, Tayo BO, Gaulton KJ, Smith JA, Lu Y, Jensen RA, Chen G, Yanek LR, Schwander K, Tajuddin SM, Sofer T, Kim W, Kayima J, ... ... Denny JC, et al. Correction: Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. Plos Genetics. 14: e1007345. PMID 29750786 DOI: 10.1371/Journal.Pgen.1007345  0.316
2018 Smith JC, Chen Q, Denny JC, Roden DM, Johnson KB, Miller RA. Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions. Applied Clinical Informatics. 9: 313-325. PMID 29742757 DOI: 10.1055/S-0038-1646963  0.727
2018 Goldstein JA, Bastarache LA, Denny JC, Pulley JM, Aronoff DM. PregOMICS-Leveraging systems biology and bioinformatics for drug repurposing in maternal-child health. American Journal of Reproductive Immunology (New York, N.Y. : 1989). e12971. PMID 29726581 DOI: 10.1111/Aji.12971  0.748
2018 Wei WQ, Li X, Feng Q, Kubo M, Kullo IJ, Peissig PL, Karlson EW, Jarvik GP, Lee MTM, Shang N, Larson EA, Edwards T, Shaffer C, Mosley JD, Maeda S, ... ... Denny JC, et al. Variants are Associated with Residual Cardiovascular Risk in Patients Receiving Statins. Circulation. PMID 29703846 DOI: 10.1161/Circulationaha.117.031356  0.659
2018 Roden DM, Van Driest SL, Wells QS, Mosley JD, Denny JC, Peterson JF. Opportunities and Challenges in Cardiovascular Pharmacogenomics: From Discovery to Implementation. Circulation Research. 122: 1176-1190. PMID 29700066 DOI: 10.1161/Circresaha.117.310965  0.48
2018 Emdin CA, Khera AV, Chaffin M, Klarin D, Natarajan P, Aragam K, Haas M, Bick A, Zekavat SM, Nomura A, Ardissino D, Wilson JG, Schunkert H, McPherson R, Watkins H, ... ... Denny J, et al. Analysis of predicted loss-of-function variants in UK Biobank identifies variants protective for disease. Nature Communications. 9: 1613. PMID 29691411 DOI: 10.1038/S41467-018-03911-8  0.608
2018 Barnado A, Carroll RJ, Casey C, Wheless L, Denny JC, Crofford LJ. Phenome-wide association study identifies marked increased in burden of comorbidities in African Americans with systemic lupus erythematosus. Arthritis Research & Therapy. 20: 69. PMID 29636090 DOI: 10.1186/S13075-018-1561-8  0.515
2018 Bastarache L, Hughey JJ, Hebbring S, Marlo J, Zhao W, Ho WT, Van Driest SL, McGregor TL, Mosley JD, Wells QS, Temple M, Ramirez AH, Carroll R, Osterman T, Edwards T, ... ... Denny JC, et al. Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. Science (New York, N.Y.). 359: 1233-1239. PMID 29590070 DOI: 10.1126/Science.Aal4043  0.805
2018 Barnado A, Carroll RJ, Casey C, Wheless L, Denny JC, Crofford LJ. Phenome-wide association studies uncover a novel association of increased atrial fibrillation in males with systemic lupus erythematosus. Arthritis Care & Research. PMID 29481723 DOI: 10.1002/Acr.23553  0.568
2018 Volpi S, Bult C, Chisholm RL, Deverka PA, Ginsburg GS, Jacob HJ, Kasapi M, McLeod HL, Roden DM, Williams MS, Green ED, Lyman Rodriguez L, Aronson S, Cavallari LH, Denny JC, et al. Research directions in the clinical implementation of pharmacogenomics - An Overview of US programs and projects. Clinical Pharmacology and Therapeutics. PMID 29460415 DOI: 10.1002/Cpt.1048  0.47
2018 Goldstein JA, Bastarache LA, Denny JC, Roden DM, Pulley JM, Aronoff DM. Calcium Channel Blockers as Drug Repurposing Candidates for Gestational Diabetes: Mining large scale genomic and electronic health records data to repurpose medications. Pharmacological Research. PMID 29448118 DOI: 10.1016/J.Phrs.2018.02.013  0.776
2018 Li X, Meng X, Spiliopoulou A, Timofeeva M, Wei WQ, Gifford A, Shen X, He Y, Varley T, McKeigue P, Tzoulaki I, Wright AF, Joshi P, Denny JC, Campbell H, et al. MR-PheWAS: exploring the causal effect of SUA level on multiple disease outcomes by using genetic instruments in UK Biobank. Annals of the Rheumatic Diseases. PMID 29437585 DOI: 10.1136/Annrheumdis-2017-212534  0.56
2018 Zhao J, Cheng F, Jia P, Cox N, Denny JC, Zhao Z. An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies. Genome Medicine. 10: 7. PMID 29378629 DOI: 10.1186/S13073-018-0513-X  0.368
2018 Roden DM, Van Driest SL, Mosley JD, Wells QS, Robinson JR, Denny JC, Peterson JF. Benefit of pre-emptive pharmacogenetic information on clinical outcome. Clinical Pharmacology and Therapeutics. PMID 29377064 DOI: 10.1002/Cpt.1035  0.697
2018 White KD, Abe R, Ardern-Jones M, Beachkofsky T, Bouchard C, Carleton B, Chodosh J, Cibotti R, Davis R, Denny JC, Dodiuk-Gad RP, Ergen EN, Goldman JL, Holmes JH, Hung SI, et al. SJS/TEN 2017: Building Multidisciplinary Networks to Drive Science and Translation. The Journal of Allergy and Clinical Immunology. in Practice. 6: 38-69. PMID 29310768 DOI: 10.1016/J.Jaip.2017.11.023  0.324
2018 Barnado A, Carroll RJ, Casey C, Denny JC, Crofford LJ. AA-01 Phenome-wide association studies uncover hierarchy of autoantibodies in systemic lupus erythematosus Lupus Science & Medicine. 5. DOI: 10.1136/Lupus-2018-Lsm.20  0.522
2018 Robinson JR, Carroll RJ, Bastarache L, Mou Z, Jackson GP, Roden DM, Denny JC. Association of Obesity with Postoperative Complications Using Phenome-Wide Association Studies and Mendelian Randomization Journal of the American College of Surgeons. 227. DOI: 10.1016/J.Jamcollsurg.2018.07.192  0.692
2018 Phillips EJ, Wei W, Shaffer CM, Feng Q, Stone CA, Stein CM, Roden DM, Denny JC. A High-Throughput Genetic Analysis of Common Drug Allergy Labels Using Data from a Large Biobank Journal of Allergy and Clinical Immunology. 141: AB399. DOI: 10.1016/J.Jaci.2017.12.937  0.643
2017 Jerome RN, Pulley JM, Roden DM, Shirey-Rice JK, Bastarache LA, R Bernard G, B Ekstrom L, Lancaster WJ, Denny JC. Using Human 'Experiments of Nature' to Predict Drug Safety Issues: An Example with PCSK9 Inhibitors. Drug Safety. PMID 29185237 DOI: 10.1007/S40264-017-0616-0  0.621
2017 Denny JC, Van Driest SL, Wei WQ, Roden DM. The influence of big (clinical) data and genomics on precision medicine and drug development. Clinical Pharmacology and Therapeutics. PMID 29171014 DOI: 10.1002/Cpt.951  0.687
2017 Robinson JR, Denny JC, Roden DM, Van Driest SL. Genome-wide and Phenome-wide Approaches to Understand Variable Drug Actions in Electronic Health Records. Clinical and Translational Science. PMID 29148204 DOI: 10.1111/Cts.12522  0.718
2017 Manolio TA, Hutter CM, Avigan M, Cibotti R, Davis RL, Denny JC, Grenade L, Wheatley LM, Carrington MN, Chantratita W, Chung WH, Dalton AD, Hung SI, Lee MTM, Leeder JS, et al. Research Directions in Genetic Predispositions to Stevens-Johnson Syndrome / Toxic Epidermal Necrolysis. Clinical Pharmacology and Therapeutics. PMID 29105735 DOI: 10.1002/Cpt.890  0.301
2017 Liu DJ, Peloso GM, Yu H, Butterworth AS, Wang X, Mahajan A, Saleheen D, Emdin C, Alam D, Alves AC, Amouyel P, Di Angelantonio E, Arveiler D, Assimes TL, Auer PL, ... ... Denny JC, et al. Exome-wide association study of plasma lipids in >300,000 individuals. Nature Genetics. PMID 29083408 DOI: 10.1038/Ng.3977  0.441
2017 Rosenbloom ST, Carroll RJ, Warner JL, Matheny ME, Denny JC. Representing Knowledge Consistently Across Health Systems. Yearbook of Medical Informatics. 26: 139-147. PMID 29063555 DOI: 10.15265/Iy-2017-018  0.693
2017 Dohn MR, Kooker CG, Bastarache L, Jessen T, Rinaldi C, Varney S, Mazalouskas MD, Pan H, Oliver KH, Velez Edwards DR, Sutcliffe JS, Denny JC, Carneiro AMD. The Gain-of-Function Integrin β3 Pro33 Variant Alters the Serotonin System in the Mouse Brain. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 29038237 DOI: 10.1523/Jneurosci.1482-17.2017  0.54
2017 Bejan CA, Angiolillo J, Conway D, Nash R, Shirey-Rice JK, Lipworth L, Cronin RM, Pulley J, Kripalani S, Barkin S, Johnson KB, Denny JC. Mining 100 million notes to find homelessness and adverse childhood experiences: 2 case studies of rare and severe social determinants of health in electronic health records. Journal of the American Medical Informatics Association : Jamia. PMID 29016793 DOI: 10.1093/Jamia/Ocx059  0.637
2017 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, ... ... Denny JC, et al. Erratum to: A multi-stage genome-wide association study of uterine fibroids in African Americans. Human Genetics. PMID 28975356 DOI: 10.1007/S00439-017-1846-Z  0.441
2017 Peissig P, Schwei KM, Kadolph C, Finamore J, Cancel E, McCarty CA, Okorie A, Thomas KL, Allen Pacheco J, Pathak J, Ellis SB, Denny JC, Rasmussen LV, Tromp G, Williams MS, et al. Prototype Development: Context-Driven Dynamic XML Ophthalmologic Data Capture Application. Jmir Medical Informatics. 5: e27. PMID 28903894 DOI: 10.2196/Medinform.7465  0.32
2017 Weng LC, Lunetta KL, Müller-Nurasyid M, Smith AV, Thériault S, Weeke PE, Barnard J, Bis JC, Lyytikäinen LP, Kleber ME, Martinsson A, Lin HJ, Rienstra M, Trompet S, Krijthe BP, ... ... Denny JC, et al. Genetic Interactions with Age, Sex, Body Mass Index, and Hypertension in Relation to Atrial Fibrillation: The AFGen Consortium. Scientific Reports. 7: 11303. PMID 28900195 DOI: 10.1038/S41598-017-09396-7  0.591
2017 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, ... ... Denny JC, et al. A multi-stage genome-wide association study of uterine fibroids in African Americans. Human Genetics. PMID 28836065 DOI: 10.1007/S00439-017-1836-1  0.476
2017 Cronin RM, Fabbri D, Denny JC, Rosenbloom ST, Jackson GP. A comparison of rule-based and machine learning approaches for classifying patient portal messages. International Journal of Medical Informatics. 105: 110-120. PMID 28750904 DOI: 10.1016/J.Ijmedinf.2017.06.004  0.708
2017 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, ... ... Denny JC, et al. Erratum: Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation. Nature Genetics. 49: 1286. PMID 28747752 DOI: 10.1038/ng0817-1286c  0.379
2017 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 Medical Informatics and Decision Making. 17: 82. PMID 28699546 DOI: 10.1186/S12911-017-0466-9  0.548
2017 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. PMID 28688202 DOI: 10.1002/Phar.1983  0.738
2017 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. 12: e0175508. PMID 28686612 DOI: 10.1371/Journal.Pone.0175508  0.8
2017 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. Journal of Human Genetics. PMID 28659611 DOI: 10.1038/Jhg.2017.66  0.571
2017 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, ... ... Denny JC, et al. Genome-wide association and pathway analysis of left ventricular function after anthracycline exposure in adults. Pharmacogenetics and Genomics. PMID 28542097 DOI: 10.1097/Fpc.0000000000000284  0.709
2017 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, et al. Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network. Bmc Medical Genomics. 10: 35. PMID 28532511 DOI: 10.1186/S12920-017-0273-2  0.336
2017 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, ... ... Denny JC, et al. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. Plos Genetics. 13: e1006728. PMID 28498854 DOI: 10.1371/Journal.Pgen.1006728  0.345
2017 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, ... ... Denny JC, et al. Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Science Translational Medicine. 9. PMID 28490672 DOI: 10.1126/Scitranslmed.Aai8708  0.786
2017 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. Ethnicity & Disease. 27: 95-106. PMID 28439179 DOI: 10.18865/Ed.27.2.95  0.313
2017 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. 12: e0174941. PMID 28422977 DOI: 10.1371/Journal.Pone.0174941  0.738
2017 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, ... ... Denny JC, et al. Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation. Nature Genetics. PMID 28416818 DOI: 10.1038/Ng.3843  0.497
2017 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, ... ... Denny JC, et al. Accelerating Precision Drug Development and Drug Repurposing by Leveraging Human Genetics. Assay and Drug Development Technologies. PMID 28379727 DOI: 10.1089/Adt.2016.772  0.669
2017 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, et al. Apolipoprotein L1 Variants and Blood Pressure Traits in African Americans. Journal of the American College of Cardiology. 69: 1564-1574. PMID 28335839 DOI: 10.1016/J.Jacc.2017.01.040  0.444
2017 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, et al. Genome-wide study of resistant hypertension identified from electronic health records. Plos One. 12: e0171745. PMID 28222112 DOI: 10.1371/Journal.Pone.0171745  0.718
2017 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. 12: e0172444. PMID 28207879 DOI: 10.1371/Journal.Pone.0172444  0.765
2017 Heit JA, Armasu SM, McCauley BM, Kullo IJ, Sicotte H, Pathak J, Chute CG, Gottesman O, Bottinger EP, Denny JC, Roden DM, Li R, Ritchie MD, de Andrade M. Identification of unique venous thromboembolism-susceptibility variants in African-Americans. Thrombosis and Haemostasis. PMID 28203683 DOI: 10.1160/Th16-08-0652  0.623
2017 Boortz KA, Syring KE, Pound LD, Mo H, Bastarache L, Oeser JK, McGuinness OP, Denny JC, O'Brien R. Effects of G6pc2 deletion on body weight and cholesterol in mice. Journal of Molecular Endocrinology. PMID 28122818 DOI: 10.1530/Jme-16-0202  0.562
2016 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, ... ... Denny JC, et al. SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function. Journal of the American Society of Nephrology : Jasn. PMID 27920155 DOI: 10.1681/Asn.2016020131  0.55
2016 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, ... ... Denny JC, et al. PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study. The Lancet. Diabetes & Endocrinology. PMID 27908689 DOI: 10.1016/S2213-8587(16)30396-5  0.435
2016 Wiley LK, Vanhouten JP, Samuels DC, Aldrich MC, Roden DM, Peterson JF, Denny JC. STRATEGIES FOR EQUITABLE PHARMACOGENOMIC-GUIDED WARFARIN DOSING AMONG EUROPEAN AND AFRICAN AMERICAN INDIVIDUALS IN A CLINICAL POPULATION. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 545-556. PMID 27897005  0.752
2016 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. Drug Safety. PMID 27873192 DOI: 10.1007/S40264-016-0476-Z  0.481
2016 Doss J, Mo H, Carroll RJ, Crofford LJ, Denny JC. Response to Letter from Drs. Wolfe and Walitt. Arthritis & Rheumatology (Hoboken, N.J.). PMID 27860419 DOI: 10.1002/art.39997  0.639
2016 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, et al. 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 Infectious Diseases. 16: 684. PMID 27855652 DOI: 10.1186/S12879-016-2020-2  0.326
2016 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, ... ... Denny JC, et al. Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile using Historical Data. Circulation. Cardiovascular Genetics. PMID 27780847 DOI: 10.1161/Circgenetics.116.001530  0.709
2016 Shekhar A, Lin X, Liu FY, Zhang J, Mo H, Bastarache L, Denny JC, Cox NJ, Delmar M, Roden DM, Fishman GI, Park DS. Transcription factor ETV1 is essential for rapid conduction in the heart. The Journal of Clinical Investigation. PMID 27775552 DOI: 10.1172/Jci87968  0.622
2016 Roden DM, Mosley JD, Denny JC. Finding a Needle in a QT Interval Big Data Haystack: The Role for Orthogonal Datasets. Journal of the American College of Cardiology. 68: 1765-1768. PMID 27737743 DOI: 10.1016/J.Jacc.2016.08.012  0.44
2016 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, et al. Evaluation of a Prediction Model for the Development of Atrial Fibrillation in a Repository of Electronic Medical Records. Jama Cardiology. PMID 27732699 DOI: 10.1001/Jamacardio.2016.3366  0.571
2016 Rasmussen LV, Overby CL, Connolly J, Chute CG, Denny JC, Freimuth R, Hartzler AL, Holm IA, Manzi S, Pathak J, Peissig PL, Smith M, Williams MS, Shirts BH, Stoffel EM, et al. Practical considerations for implementing genomic information resources. Experiences from eMERGE and CSER. Applied Clinical Informatics. 7: 870-882. PMID 27652374 DOI: 10.4338/Aci-2016-04-Ra-0060  0.495
2016 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. Molecular Genetics & Genomic Medicine. 4: 513-520. PMID 27652279 DOI: 10.1002/Mgg3.226  0.554
2016 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. Pharmacogenetics and Genomics. PMID 27632229 DOI: 10.1097/Fpc.0000000000000244  0.623
2016 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.). PMID 27589350 DOI: 10.1002/Art.39851  0.715
2016 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, ... ... Denny JC, et al. Meta-analysis of genome-wide association studies of HDL cholesterol response to statins. Journal of Medical Genetics. PMID 27587472 DOI: 10.1136/Jmedgenet-2016-103966  0.543
2016 Wu Y, Denny JC, Rosenbloom ST, 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). Journal of the American Medical Informatics Association : Jamia. PMID 27539197 DOI: 10.1093/Jamia/Ocw109  0.694
2016 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, et al. eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants. Bmc Medical Genomics. 9: 32. PMID 27535653 DOI: 10.1186/S12920-016-0191-8  0.369
2016 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. Artificial Intelligence in Medicine. 71: 57-61. PMID 27506131 DOI: 10.1016/J.Artmed.2016.05.005  0.389
2016 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, et al. Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. Journal of the American Medical Informatics Association : Jamia. PMID 27497800 DOI: 10.1093/Jamia/Ocw071  0.797
2016 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 Genomic Medicine. 1. PMID 27482468 DOI: 10.1038/Npjgenmed.2016.6  0.616
2016 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, et al. Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder. Plos One. 11: e0159621. PMID 27472449 DOI: 10.1371/Journal.Pone.0159621  0.343
2016 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. Journal of Biomedical Informatics. PMID 27392645 DOI: 10.1016/J.Jbi.2016.07.008  0.523
2016 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 & Research. PMID 27390187 DOI: 10.1002/Acr.22989  0.557
2016 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, ... ... Denny JC, et al. Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases. American Journal of Human Genetics. PMID 27346689 DOI: 10.1016/J.Ajhg.2016.05.003  0.608
2016 Frey LJ, Bernstam EV, Denny JC. Precision medicine informatics. Journal of the American Medical Informatics Association : Jamia. 23: 668-70. PMID 27274018 DOI: 10.1093/Jamia/Ocw053  0.324
2016 Denny JC, Bastarache L, Roden DM. Phenome-Wide Association Studies as a Tool to Advance Precision Medicine. Annual Review of Genomics and Human Genetics. PMID 27147087 DOI: 10.1146/Annurev-Genom-090314-024956  0.71
2016 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. Nature Communications. 7: 11433. PMID 27109359 DOI: 10.1038/Ncomms11433  0.683
2016 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, et al. Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-wide Association Studies. Gastroenterology. PMID 27094239 DOI: 10.1053/J.Gastro.2016.04.007  0.49
2016 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, ... ... Denny JC, et al. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. Journal of the American Medical Informatics Association : Jamia. PMID 27026615 DOI: 10.1093/Jamia/Ocv202  0.483
2016 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, ... ... Denny JC, et al. The phenotypic legacy of admixture between modern humans and Neandertals. Science (New York, N.Y.). 351: 737-41. PMID 26912863 DOI: 10.1126/Science.Aad2149  0.676
2016 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. Journal of the American Medical Informatics Association : Jamia. PMID 26911808 DOI: 10.1093/Jamia/Ocv111  0.734
2016 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. The Pharmacogenomics Journal. PMID 26902539 DOI: 10.1038/Tpj.2016.3  0.58
2016 Bush WS, Crosslin DR, Obeng AO, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D, Doheny KF, Gallego CJ, Gordon AS, Keating B, Kirby J, ... ... Denny JC, et al. Genetic Variation among 82 Pharmacogenes: the PGRN-Seq data from the eMERGE Network. Clinical Pharmacology and Therapeutics. PMID 26857349 DOI: 10.1002/Cpt.350  0.643
2016 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, ... ... Denny JC, et al. Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications. 7: 10464. PMID 26833085 DOI: 10.1038/Ncomms10464  0.622
2016 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, ... ... Denny JC, et al. Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. Nature Communications. 7: 10023. PMID 26831199 DOI: 10.1038/Ncomms10023  0.526
2016 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, ... ... Denny JC, et al. Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records. Jama. 315: 47-57. PMID 26746457 DOI: 10.1001/Jama.2015.17701  0.549
2016 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, ... ... Denny JC, et al. The IGNITE network: a model for genomic medicine implementation and research. Bmc Medical Genomics. 9: 1. PMID 26729011 DOI: 10.1186/S12920-015-0162-5  0.337
2016 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. American Journal of Respiratory and Critical Care Medicine. 193: 98-100. PMID 26720789 DOI: 10.1164/Rccm.201507-1267Le  0.573
2016 Roden DM, Denny JC. Integrating electronic health record genotype and phenotype datasets to transform patient care. Clinical Pharmacology & Therapeutics. 99: 298-305. PMID 26667791 DOI: 10.1002/Cpt.321  0.491
2015 Cronin RM, Fabbri D, Denny JC, Jackson GP. Automated Classification of Consumer Health Information Needs in Patient Portal Messages. Amia ... Annual Symposium Proceedings. Amia Symposium. 2015: 1861-70. PMID 26958285  0.599
2015 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, et al. CMTR1 is associated with increased asthma exacerbations in patients taking inhaled corticosteroids. Immunity, Inflammation and Disease. 3: 350-9. PMID 26734457 DOI: 10.1002/Iid3.73  0.466
2015 Teumer A, Tin A, Sorice R, Gorski M, Yeo NC, Chu AY, Li M, Li Y, Mijatovic V, Ko YA, Taliun D, Luciani A, Chen MH, Yang Q, Foster MC, ... ... Denny JC, et al. Genome-wide Association Studies Identify Genetic Loci Associated with Albuminuria in Diabetes. Diabetes. PMID 26631737 DOI: 10.2337/Db15-1313  0.523
2015 Schildcrout JS, Shi Y, Danciu I, Bowton E, Field JR, Pulley JM, Basford M, Gregg W, Cowan J, Harrell FE, Roden DM, Peterson JF, Denny JC. A prognostic model based on readily available clinical data enriched a preemptive pharmacogenetic testing program. Journal of Clinical Epidemiology. PMID 26628336 DOI: 10.1016/J.Jclinepi.2015.08.028  0.464
2015 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, et al. Practical considerations in genomic decision support: The eMERGE experience. Journal of Pathology Informatics. 6: 50. PMID 26605115 DOI: 10.4103/2153-3539.165999  0.574
2015 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, et al. CYP2C19 and CES1 polymorphisms and efficacy of clopidogrel and aspirin dual antiplatelet therapy in patients with symptomatic intracranial atherosclerotic disease. Journal of Neurosurgery. 1-6. PMID 26587656 DOI: 10.3171/2015.6.Jns15795  0.495
2015 Heatherly R, Rasmussen LV, Peissig PL, Pacheco JA, Harris P, Denny JC, Malin BA. A multi-institution evaluation of clinical profile anonymization. Journal of the American Medical Informatics Association : Jamia. PMID 26567325 DOI: 10.1093/Jamia/Ocv154  0.381
2015 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, et al. A conceptual model for translating omic data into clinical action. Journal of Pathology Informatics. 6: 46. PMID 26430534 DOI: 10.4103/2153-3539.163985  0.598
2015 Chen Y, Lasko TA, Mei Q, Denny JC, Xu H. A study of active learning methods for named entity recognition in clinical text. Journal of Biomedical Informatics. PMID 26385377 DOI: 10.1016/J.Jbi.2015.09.010  0.555
2015 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, ... ... Denny JC, et al. Penetrance of Hemochromatosis in HFE Genotypes Resulting in p.Cys282Tyr and p.[Cys282Tyr];[His63Asp] in the eMERGE Network. American Journal of Human Genetics. PMID 26365338 DOI: 10.1016/J.Ajhg.2015.08.008  0.462
2015 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, ... ... Denny JC, et al. Desiderata for computable representations of electronic health records-driven phenotype algorithms. Journal of the American Medical Informatics Association : Jamia. PMID 26342218 DOI: 10.1093/Jamia/Ocv112  0.617
2015 Wei WQ, Teixeira PL, Mo H, Cronin RM, Warner JL, Denny JC. Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. Journal of the American Medical Informatics Association : Jamia. PMID 26338219 DOI: 10.1093/Jamia/Ocv130  0.781
2015 Mosley JD, Brittain EL, Loyd JE, Denny JC, Austin ED, Larkin EK. Letter by Mosley Regarding Article, "Iron Homeostasis and Pulmonary Hypertension: Iron Deficiency Leads to Pulmonary Vascular Remodeling in the Rat". Circulation Research. 117: e56-7. PMID 26316607 DOI: 10.1161/Circresaha.115.306867  0.3
2015 Wiley LK, Moretz JD, Denny JC, Peterson JF, Bush WS. Phenotyping Adverse Drug Reactions: Statin-Related Myotoxicity. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2015: 466-70. PMID 26306287  0.733
2015 Karol SE, Yang W, Van Driest SL, Chang TY, Kaste S, Bowton E, Basford M, Bastarache L, Roden DM, Denny JC, Larsen E, Winick N, Carroll WL, Cheng C, Pei D, et al. Genetics of glucocorticoid-associated osteonecrosis in children with acute lymphoblastic leukemia. Blood. PMID 26265699 DOI: 10.1182/Blood-2015-05-643601  0.654
2015 Jiang G, Solbrig HR, Kiefer R, Rasmussen LV, Mo H, Speltz P, Thompson WK, Denny JC, Chute CG, Pathak J. A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution. Studies in Health Technology and Informatics. 216: 1098. PMID 26262397 DOI: 10.3233/978-1-61499-564-7-1098  0.483
2015 Peterson JF, Field JR, Shi Y, Schildcrout JS, Denny JC, McGregor TL, Van Driest SL, Pulley JM, Lubin IM, Laposata M, Roden DM, Clayton EW. Attitudes of clinicians following large-scale pharmacogenomics implementation. The Pharmacogenomics Journal. PMID 26261062 DOI: 10.1038/Tpj.2015.57  0.332
2015 Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC, Nicolae DL, Cox NJ, Im HK. A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics. 47: 1091-8. PMID 26258848 DOI: 10.1038/Ng.3367  0.552
2015 Xu J, Rasmussen LV, Shaw PL, Jiang G, Kiefer RC, Mo H, Pacheco JA, Speltz P, Zhu Q, Denny JC, Pathak J, Thompson WK, Montague E. Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research. Journal of the American Medical Informatics Association : Jamia. PMID 26224336 DOI: 10.1093/Jamia/Ocv070  0.355
2015 Bielinski SJ, Pathak J, Carrell DS, Takahashi PY, Olson JE, Larson NB, Liu H, Sohn S, Wells QS, Denny JC, Rasmussen-Torvik LJ, Pacheco JA, Jackson KL, Lesnick TG, Gullerud RE, et al. A Robust e-Epidemiology Tool in Phenotyping Heart Failure with Differentiation for Preserved and Reduced Ejection Fraction: the Electronic Medical Records and Genomics (eMERGE) Network. Journal of Cardiovascular Translational Research. PMID 26195183 DOI: 10.1007/S12265-015-9644-2  0.36
2015 Wu Y, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Song M, Xu H. A Preliminary Study of Clinical Abbreviation Disambiguation in Real Time. Applied Clinical Informatics. 6: 364-74. PMID 26171081 DOI: 10.4338/Aci-2014-10-Ra-0088  0.708
2015 Mosley JD, Shaffer CM, Van Driest SL, Weeke PE, Wells QS, Karnes JH, Velez Edwards DR, Wei WQ, Teixeira PL, Bastarache L, Crawford DC, Li R, Manolio TA, Bottinger EP, McCarty CA, ... ... Denny JC, et al. A genome-wide association study identifies variants in KCNIP4 associated with ACE inhibitor-induced cough. The Pharmacogenomics Journal. PMID 26169577 DOI: 10.1038/Tpj.2015.51  0.803
2015 Owens AP, Edwards TL, Antoniak S, Geddings JE, Jahangir E, Wei WQ, Denny JC, Boulaftali Y, Bergmeier W, Daugherty A, Sampson UK, Mackman N. Platelet Inhibitors Reduce Rupture in a Mouse Model of Established Abdominal Aortic Aneurysm. Arteriosclerosis, Thrombosis, and Vascular Biology. 35: 2032-41. PMID 26139462 DOI: 10.1161/Atvbaha.115.305537  0.513
2015 Sun J, Zhao M, Jia P, Wang L, Wu Y, Iverson C, Zhou Y, Bowton E, Roden DM, Denny JC, Aldrich MC, Xu H, Zhao Z. Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. Plos Computational Biology. 11: e1004202. PMID 26083494 DOI: 10.1371/Journal.Pcbi.1004202  0.452
2015 Denny JC, Spickard A, Speltz PJ, Poirier R, Rosenstiel D, Powers JS. Using natural language processing to provide personalized learning opportunities from trainee clinical notes. Journal of Biomedical Informatics. PMID 26070431 DOI: 10.1016/J.Jbi.2015.06.004  0.331
2015 Wei WQ, Denny JC. Extracting research-quality phenotypes from electronic health records to support precision medicine. Genome Medicine. 7: 41. PMID 25937834 DOI: 10.1186/S13073-015-0166-Y  0.655
2015 Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, Pappas DA, Kremer JM, Barton A, Coenen MJ, Franke B, ... ... Denny JC, et al. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. Plos One. 10: e0122271. PMID 25849893 DOI: 10.1371/Journal.Pone.0122271  0.609
2015 Chen Y, Ghosh J, Bejan CA, Gunter CA, Gupta S, Kho A, Liebovitz D, Sun J, Denny J, Malin B. Building bridges across electronic health record systems through inferred phenotypic topics. Journal of Biomedical Informatics. 55: 82-93. PMID 25841328 DOI: 10.1016/J.Jbi.2015.03.011  0.363
2015 Carroll RJ, Eyler AE, Denny JC. Intelligent use and clinical benefits of electronic health records in rheumatoid arthritis. Expert Review of Clinical Immunology. 11: 329-37. PMID 25660652 DOI: 10.1586/1744666X.2015.1009895  0.525
2015 Karnes JH, Cronin RM, Rollin J, Teumer A, Pouplard C, Shaffer CM, Blanquicett C, Bowton EA, Cowan JD, Mosley JD, Van Driest SL, Weeke PE, Wells QS, Bakchoul T, Denny JC, et al. A genome-wide association study of heparin-induced thrombocytopenia using an electronic medical record. Thrombosis and Haemostasis. 113: 772-81. PMID 25503805 DOI: 10.1160/Th14-08-0670  0.715
2015 Weeke P, Denny JC, Basterache L, Shaffer C, Bowton E, Ingram C, Darbar D, Roden DM. Examining rare and low-frequency genetic variants previously associated with lone or familial forms of atrial fibrillation in an electronic medical record system: a cautionary note. Circulation. Cardiovascular Genetics. 8: 58-63. PMID 25410959 DOI: 10.1161/Circgenetics.114.000718  0.503
2015 Lin C, Karlson EW, Dligach D, Ramirez MP, Miller TA, Mo H, Braggs NS, Cagan A, Gainer V, Denny JC, Savova GK. Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. Journal of the American Medical Informatics Association : Jamia. 22: e151-61. PMID 25344930 DOI: 10.1136/Amiajnl-2014-002642  0.305
2015 Bejan CA, Wei WQ, Denny JC. Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. Journal of the American Medical Informatics Association : Jamia. 22: e162-76. PMID 25336593 DOI: 10.1136/Amiajnl-2014-002954  0.576
2015 Crosslin DR, Carrell DS, Burt A, Kim DS, Underwood JG, Hanna DS, Comstock BA, Baldwin E, de Andrade M, Kullo IJ, Tromp G, Kuivaniemi H, Borthwick KM, McCarty CA, Peissig PL, ... ... Denny JC, et al. Genetic variation in the HLA region is associated with susceptibility to herpes zoster. Genes and Immunity. 16: 1-7. PMID 25297839 DOI: 10.1038/Gene.2014.51  0.563
2015 Naidoo D, Wu AC, Brilliant MH, Denny J, Ingram C, Kitchner TE, Linneman JG, McGeachie MJ, Roden DM, Shaffer CM, Shah A, Weeke P, Weiss ST, Xu H, Medina MW. A polymorphism in HLA-G modifies statin benefit in asthma. The Pharmacogenomics Journal. 15: 272-7. PMID 25266681 DOI: 10.1038/Tpj.2014.55  0.428
2015 Xu H, Aldrich MC, Chen Q, Liu H, Peterson NB, Dai Q, Levy M, Shah A, Han X, Ruan X, Jiang M, Li Y, Julien JS, Warner J, Friedman C, ... ... Denny JC, et al. Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. Journal of the American Medical Informatics Association : Jamia. 22: 179-91. PMID 25053577 DOI: 10.1136/Amiajnl-2014-002649  0.461
2014 Overby CL, Rasmussen LV, Hartzler A, Connolly JJ, Peterson JF, Hedberg RE, Freimuth RR, Shirts BH, Denny JC, Larson EB, Chute CG, Jarvik GP, Ralston JD, Shuldiner AR, Starren J, et al. A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2014: 944-53. PMID 25954402  0.485
2014 Chen Y, Wrenn J, Xu H, Spickard A, Habermann R, Powers J, Denny JC. Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2014: 375-84. PMID 25954341  0.512
2014 Wei WQ, Feng Q, Weeke P, Bush W, Waitara MS, Iwuchukwu OF, Roden DM, Wilke RA, Stein CM, Denny JC. Creation and Validation of an EMR-based Algorithm for Identifying Major Adverse Cardiac Events while on Statins. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2014: 112-9. PMID 25717410  0.633
2014 Jeff JM, Brown-Gentry K, Goodloe R, Ritchie MD, Denny JC, Kho AN, Armstrong LL, McClellan B, Mayo P, Allen M, Jin H, Gillani NB, Schnetz-Boutaud N, Dilks HH, Basford MA, et al. Replication of SCN5A Associations with Electrocardio-graphic Traits in African Americans from Clinical and Epidemiologic Studies. Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. Evobio (Conference), Author. 2014: 939-951. PMID 25590050 DOI: 10.1007/978-3-662-45523-4_76  0.462
2014 Kawai VK, Cunningham A, Vear SI, Van Driest SL, Oginni A, Xu H, Jiang M, Li C, Denny JC, Shaffer C, Bowton E, Gage BF, Ray WA, Roden DM, Stein CM. Genotype and risk of major bleeding during warfarin treatment. Pharmacogenomics. 15: 1973-83. PMID 25521356 DOI: 10.2217/Pgs.14.153  0.464
2014 Iwuchukwu OF, Feng Q, Wei WQ, Jiang L, Jiang M, Xu H, Denny JC, Wilke RA, Krauss RM, Roden DM, Stein CM. Genetic variation in the UGT1A locus is associated with simvastatin efficacy in a clinical practice setting. Pharmacogenomics. 15: 1739-1747. PMID 25493567 DOI: 10.2217/Pgs.14.128  0.661
2014 Namjou B, Marsolo K, Caroll RJ, Denny JC, Ritchie MD, Verma SS, Lingren T, Porollo A, Cobb BL, Perry C, Kottyan LC, Rothenberg ME, Thompson SD, Holm IA, Kohane IS, et al. Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis. Frontiers in Genetics. 5: 401. PMID 25477900 DOI: 10.3389/Fgene.2014.00401  0.386
2014 Malinowski JR, Denny JC, Bielinski SJ, Basford MA, Bradford Y, Peissig PL, Carrell D, Crosslin DR, Pathak J, Rasmussen L, Pacheco J, Kho A, Newton KM, Li R, Kullo IJ, et al. Genetic variants associated with serum thyroid stimulating hormone (TSH) levels in European Americans and African Americans from the eMERGE Network. Plos One. 9: e111301. PMID 25436638 DOI: 10.1371/Journal.Pone.0111301  0.619
2014 Stitziel NO, Won HH, Morrison AC, Peloso GM, Do R, Lange LA, Fontanillas P, Gupta N, Duga S, Goel A, Farrall M, Saleheen D, Ferrario P, König I, ... ... Denny JC, et al. Inactivating mutations in NPC1L1 and protection from coronary heart disease. The New England Journal of Medicine. 371: 2072-82. PMID 25390462 DOI: 10.1056/Nejmoa1405386  0.621
2014 Ritchie MD, Verma SS, Hall MA, Goodloe RJ, Berg RL, Carrell DS, Carlson CS, Chen L, Crosslin DR, Denny JC, Jarvik G, Li R, Linneman JG, Pathak J, Peissig P, et al. Electronic medical records and genomics (eMERGE) network exploration in cataract: several new potential susceptibility loci. Molecular Vision. 20: 1281-95. PMID 25352737  0.603
2014 Postmus I, Trompet S, Deshmukh HA, Barnes MR, Li X, Warren HR, Chasman DI, Zhou K, Arsenault BJ, Donnelly LA, Wiggins KL, Avery CL, Griffin P, Feng Q, Taylor KD, ... ... Denny JC, et al. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins. Nature Communications. 5: 5068. PMID 25350695 DOI: 10.1038/ncomms6068  0.547
2014 Cronin RM, Field JR, Bradford Y, Shaffer CM, Carroll RJ, Mosley JD, Bastarache L, Edwards TL, Hebbring SJ, Lin S, Hindorff LA, Crane PK, Pendergrass SA, Ritchie MD, Crawford DC, ... ... Denny JC, et al. Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index. Frontiers in Genetics. 5: 250. PMID 25177340 DOI: 10.3389/Fgene.2014.00250  0.806
2014 Xie W, Kantarcioglu M, Bush WS, Crawford D, Denny JC, Heatherly R, Malin BA. SecureMA: protecting participant privacy in genetic association meta-analysis. Bioinformatics (Oxford, England). 30: 3334-41. PMID 25147357 DOI: 10.1093/Bioinformatics/Btu561  0.374
2014 Denny JC. Surveying Recent Themes in Translational Bioinformatics: Big Data in EHRs, Omics for Drugs, and Personal Genomics Yearb Med Inform. 9: 199-205. PMID 25123743 DOI: 10.15265/Iy-2014-0015  0.371
2014 Ho JC, Ghosh J, Steinhubl SR, Stewart WF, Denny JC, Malin BA, Sun J. Limestone: high-throughput candidate phenotype generation via tensor factorization. Journal of Biomedical Informatics. 52: 199-211. PMID 25038555 DOI: 10.1016/J.Jbi.2014.07.001  0.401
2014 Heatherly R, Denny JC, Haines JL, Roden DM, Malin BA. Size matters: how population size influences genotype-phenotype association studies in anonymized data. Journal of Biomedical Informatics. 52: 243-50. PMID 25038554 DOI: 10.1016/J.Jbi.2014.07.005  0.523
2014 Crawford DC, Crosslin DR, Tromp G, Kullo IJ, Kuivaniemi H, Hayes MG, Denny JC, Bush WS, Haines JL, Roden DM, McCarty CA, Jarvik GP, Ritchie MD. eMERGEing progress in genomics-the first seven years. Frontiers in Genetics. 5: 184. PMID 24987407 DOI: 10.3389/Fgene.2014.00184  0.515
2014 Rasmussen-Torvik LJ, Stallings SC, Gordon AS, Almoguera B, Basford MA, Bielinski SJ, Brautbar A, Brilliant MH, Carrell DS, Connolly JJ, Crosslin DR, Doheny KF, Gallego CJ, Gottesman O, Kim DS, ... ... Denny JC, et al. Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems. Clinical Pharmacology and Therapeutics. 96: 482-9. PMID 24960519 DOI: 10.1038/Clpt.2014.137  0.643
2014 Arking DE, Pulit SL, Crotti L, van der Harst P, Munroe PB, Koopmann TT, Sotoodehnia N, Rossin EJ, Morley M, Wang X, Johnson AD, Lundby A, Gudbjartsson DF, Noseworthy PA, Eijgelsheim M, ... ... Denny JC, et al. Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nature Genetics. 46: 826-36. PMID 24952745 DOI: 10.1038/Ng.3014  0.483
2014 Bowton E, Field JR, Wang S, Schildcrout JS, Van Driest SL, Delaney JT, Cowan J, Weeke P, Mosley JD, Wells QS, Karnes JH, Shaffer C, Peterson JF, Denny JC, Roden DM, et al. Biobanks and electronic medical records: enabling cost-effective research. Science Translational Medicine. 6: 234cm3. PMID 24786321 DOI: 10.1126/Scitranslmed.3008604  0.508
2014 Carroll RJ, Bastarache L, Denny JC. R PheWAS: Data analysis and plotting tools for phenome-wide association studies in the R environment Bioinformatics. 30: 2375-2376. PMID 24733291 DOI: 10.1093/Bioinformatics/Btu197  0.704
2014 Jeff JM, Armstrong LL, Ritchie MD, Denny JC, Kho AN, Basford MA, Wolf WA, Pacheco JA, Li R, Chisholm RL, Roden DM, Hayes MG, Crawford DC. Admixture mapping and subsequent fine-mapping suggests a biologically relevant and novel association on chromosome 11 for type 2 diabetes in African Americans. Plos One. 9: e86931. PMID 24595071 DOI: 10.1371/Journal.Pone.0086931  0.489
2014 Okada Y, Diogo D, Greenberg JD, Mouassess F, Achkar WA, Fulton RS, Denny JC, Gupta N, Mirel D, Gabriel S, Li G, Kremer JM, Pappas DA, Carroll RJ, Eyler AE, et al. Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene. Plos One. 9: e87645. PMID 24520335 DOI: 10.1371/Journal.Pone.0087645  0.523
2014 Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S, Graham RR, Manoharan A, Ortmann W, Bhangale T, Denny JC, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 506: 376-81. PMID 24390342 DOI: 10.1038/Nature12873  0.547
2014 Karnes JH, Van Driest S, Bowton EA, Weeke PE, Mosley JD, Peterson JF, Denny JC, Roden DM. Using systems approaches to address challenges for clinical implementation of pharmacogenomics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 6: 125-35. PMID 24319008 DOI: 10.1002/Wsbm.1255  0.497
2014 Oetjens M, Bush WS, Birdwell KA, Dilks HH, Bowton EA, Denny JC, Wilke RA, Roden DM, Crawford DC. Utilization of an EMR-biorepository to identify the genetic predictors of calcineurin-inhibitor toxicity in heart transplant recipients. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 253-264. PMID 24297552  0.382
2014 Van Driest SL, Shi Y, Bowton EA, Schildcrout JS, Peterson JF, Pulley J, Denny JC, Roden DM. Clinically actionable genotypes among 10,000 patients with preemptive pharmacogenomic testing. Clinical Pharmacology and Therapeutics. 95: 423-31. PMID 24253661 DOI: 10.1038/Clpt.2013.229  0.507
2014 Kolek MJ, Parvez B, Muhammad R, Shoemaker MB, Blair MA, Stubblefield T, Kucera GA, Denny JC, Roden DM, Darbar D. A common variant on chromosome 4q25 is associated with prolonged PR interval in subjects with and without atrial fibrillation. The American Journal of Cardiology. 113: 309-13. PMID 24161141 DOI: 10.1016/J.Amjcard.2013.08.045  0.442
2014 Wei WQ, Feng Q, Jiang L, Waitara MS, Iwuchukwu OF, Roden DM, Jiang M, Xu H, Krauss RM, Rotter JI, Nickerson DA, Davis RL, Berg RL, Peissig PL, McCarty CA, ... ... Denny JC, et al. Characterization of statin dose response in electronic medical records. Clinical Pharmacology and Therapeutics. 95: 331-8. PMID 24096969 DOI: 10.1038/Clpt.2013.202  0.665
2014 Shameer K, Denny JC, Ding K, Jouni H, Crosslin DR, de Andrade M, Chute CG, Peissig P, Pacheco JA, Li R, Bastarache L, Kho AN, Ritchie MD, Masys DR, Chisholm RL, et al. A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. Human Genetics. 133: 95-109. PMID 24026423 DOI: 10.1007/S00439-013-1355-7  0.737
2014 Chang T, Yang W, Sara VDL, Kaste SC, Bowten EA, Basford M, Bastarache L, Roden DM, Denny JC, Mattano LA, Larsen EC, Winick NJ, Carroll WL, Cheng C, Pei D, et al. Glutamate Receptor Polymorphisms Contribute to Glucocorticoid-Associated Osteonecrosis Blood. 124: 367-367. DOI: 10.1182/Blood.V124.21.367.367  0.66
2013 Wei WQ, Mosley JD, Bastarache L, Denny JC. Validation and enhancement of a computable medication indication resource (MEDI) using a large practice-based dataset Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2013: 1448-1456. PMID 24551419  0.684
2013 McPeek Hinz ER, Bastarache L, Denny JC. A natural language processing algorithm to define a venous thromboembolism phenotype. Amia ... Annual Symposium Proceedings. Amia Symposium. 2013: 975-83. PMID 24551388  0.557
2013 Smith JC, Denny JC, Chen Q, Nian H, Spickard A, Rosenbloom ST, Miller RA. Lessons learned from developing a drug evidence base to support pharmacovigilance. Applied Clinical Informatics. 4: 596-617. PMID 24454585 DOI: 10.4338/Aci-2013-08-Ra-0062  0.784
2013 Wei WQ, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC. Development of an ensemble resource linking MEDications to their Indications (MEDI). Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2013: 172. PMID 24303333  0.773
2013 Pathak J, Kho AN, Denny JC. Electronic health records-driven phenotyping: Challenges, recent advances, and perspectives Journal of the American Medical Informatics Association. 20. PMID 24302669 DOI: 10.1136/Amiajnl-2013-002428  0.419
2013 Denny JC, Bastarache L, Ritchie MD, Carroll RJ, Zink R, Mosley JD, Field JR, Pulley JM, Ramirez AH, Bowton E, Basford MA, Carrell DS, Peissig PL, Kho AN, Pacheco JA, et al. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nature Biotechnology. 31: 1102-10. PMID 24270849 DOI: 10.1038/Nbt.2749  0.826
2013 Davis MF, Sriram S, Bush WS, Denny JC, Haines JL. Automated extraction of clinical traits of multiple sclerosis in electronic medical records. Journal of the American Medical Informatics Association : Jamia. 20: e334-40. PMID 24148554 DOI: 10.1136/Amiajnl-2013-001999  0.536
2013 Overby CL, Kohane I, Kannry JL, Williams MS, Starren J, Bottinger E, Gottesman O, Denny JC, Weng C, Tarczy-Hornoch P, Hripcsak G. Opportunities for genomic clinical decision support interventions. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 15: 817-23. PMID 24051479 DOI: 10.1038/Gim.2013.128  0.353
2013 Wu Y, Lei J, Wei WQ, Tang B, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Zheng K, Xu H. Analyzing differences between chinese and english clinical text: a cross-institution comparison of discharge summaries in two languages. Studies in Health Technology and Informatics. 192: 662-6. PMID 23920639 DOI: 10.3233/978-1-61499-289-9-662  0.772
2013 Tatonetti NP, Denny JC, Altman RB. Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al. Journal of the American Medical Informatics Association : Jamia. 20: 591. PMID 23876381 DOI: 10.1136/Amiajnl-2012-001603  0.481
2013 Chen Y, Carroll RJ, Hinz ERM, Shah A, Eyler AE, Denny JC, Xu H. Applying active learning to high-throughput phenotyping algorithms for electronic health records data Journal of the American Medical Informatics Association. 20: e253-e259. PMID 23851443 DOI: 10.1136/Amiajnl-2013-001945  0.67
2013 Lasko TA, Denny JC, Levy MA. Computational phenotype discovery using unsupervised feature learning over noisy, sparse, and irregular clinical data. Plos One. 8: e66341. PMID 23826094 DOI: 10.1371/Journal.Pone.0066341  0.325
2013 Heatherly RD, Loukides G, Denny JC, Haines JL, Roden DM, Malin BA. Correction: Enabling Genomic-Phenomic Association Discovery without Sacrificing Anonymity. Plos One. 8. PMID 23825513 DOI: 10.1371/Annotation/Db45627A-50Ec-4C52-8B5F-95Dec75B1C80  0.44
2013 McDavid A, Crane PK, Newton KM, Crosslin DR, McCormick W, Weston N, Ehrlich K, Hart E, Harrison R, Kukull WA, Rottscheit C, Peissig P, Stefanski E, McCarty CA, Zuvich RL, ... ... Denny JC, et al. Enhancing the power of genetic association studies through the use of silver standard cases derived from electronic medical records. Plos One. 8: e63481. PMID 23762230 DOI: 10.1371/Journal.Pone.0063481  0.362
2013 Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, Sanderson SC, Kannry J, Zinberg R, Basford MA, Brilliant M, Carey DJ, Chisholm RL, Chute CG, Connolly JJ, ... ... Denny JC, et al. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 15: 761-71. PMID 23743551 DOI: 10.1038/Gim.2013.72  0.626
2013 Ding K, de Andrade M, Manolio TA, Crawford DC, Rasmussen-Torvik LJ, Ritchie MD, Denny JC, Masys DR, Jouni H, Pachecho JA, Kho AN, Roden DM, Chisholm R, Kullo IJ. Genetic variants that confer resistance to malaria are associated with red blood cell traits in African-Americans: an electronic medical record-based genome-wide association study. G3 (Bethesda, Md.). 3: 1061-8. PMID 23696099 DOI: 10.1534/G3.113.006452  0.531
2013 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. 14: 735-44. PMID 23651022 DOI: 10.2217/Pgs.13.64  0.491
2013 Wei WQ, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC. Development and evaluation of an ensemble resource linking medications to their indications. Journal of the American Medical Informatics Association : Jamia. 20: 954-61. PMID 23576672 DOI: 10.1136/Amiajnl-2012-001431  0.78
2013 Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H. A hybrid system for temporal information extraction from clinical text Journal of the American Medical Informatics Association. 20: 828-835. PMID 23571849 DOI: 10.1136/Amiajnl-2013-001635  0.544
2013 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. Annals of Human Genetics. 77: 321-32. PMID 23534349 DOI: 10.1111/Ahg.12023  0.694
2013 Newton KM, Peissig PL, Kho AN, Bielinski SJ, Berg RL, Choudhary V, Basford M, Chute CG, Kullo IJ, Li R, Pacheco JA, Rasmussen LV, Spangler L, Denny JC. Validation of electronic medical record-based phenotyping algorithms: results and lessons learned from the eMERGE network. Journal of the American Medical Informatics Association : Jamia. 20: e147-54. PMID 23531748 DOI: 10.1136/Amiajnl-2012-000896  0.561
2013 Ritchie MD, Denny JC, Zuvich RL, Crawford DC, Schildcrout JS, Bastarache L, Ramirez AH, Mosley JD, Pulley JM, Basford MA, Bradford Y, Rasmussen LV, Pathak J, Chute CG, Kullo IJ, et al. Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk. Circulation. 127: 1377-85. PMID 23463857 DOI: 10.1161/Circulationaha.112.000604  0.758
2013 Heatherly RD, Loukides G, Denny JC, Haines JL, Roden DM, Malin BA. Enabling genomic-phenomic association discovery without sacrificing anonymity. Plos One. 8: e53875. PMID 23405076 DOI: 10.1371/Journal.Pone.0053875  0.528
2013 Denny JC, Schildcrout JS, Pulley JM, Roden DM. Response to "doubt about the feasibility of preemptive genotyping" Clinical Pharmacology and Therapeutics. 93: 234. PMID 23249779 DOI: 10.1038/Clpt.2012.223  0.401
2013 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. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 15: 325-31. PMID 23196672 DOI: 10.1038/Gim.2012.147  0.306
2013 Liu M, McPeek Hinz ER, Matheny ME, Denny JC, Schildcrout JS, Miller RA, Xu H. Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records. Journal of the American Medical Informatics Association : Jamia. 20: 420-6. PMID 23161894 DOI: 10.1136/Amiajnl-2012-001119  0.604
2013 Reeves RM, Ong FR, Matheny ME, Denny JC, Aronsky D, Gobbel GT, Montella D, Speroff T, Brown SH. Detecting temporal expressions in medical narratives. International Journal of Medical Informatics. 82: 118-27. PMID 22595284 DOI: 10.1016/J.Ijmedinf.2012.04.006  0.463
2013 Heit JA, de Andrade M, Armasu SM, Kullo IJ, Pathak J, Chute CG, Gottesman O, Bottinger EP, Denny JC, Roden DM, Li R, Ritchie MD. Genome-Wide Association Study (GWAS) Of Venous Thromboembolism (VTE) In African-Americans From The Electronic Medical Records & Genomics (eMERGE) Networkm Blood. 122: 458-458. DOI: 10.1182/Blood.V122.21.458.458  0.621
2012 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 ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2012: 997-1003. PMID 23304375  0.678
2012 Mani S, Chen Y, Elasy T, Clayton W, Denny J. Type 2 diabetes risk forecasting from EMR data using machine learning. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2012: 606-15. PMID 23304333  0.506
2012 Denny JC. Chapter 13: Mining electronic health records in the genomics era. Plos Computational Biology. 8. PMID 23300414 DOI: 10.1371/Journal.Pcbi.1002823  0.415
2012 Rasmussen-Torvik LJ, Pacheco JA, Wilke RA, Thompson WK, Ritchie MD, Kho AN, Muthalagu A, Hayes MG, Armstrong LL, Scheftner DA, Wilkins JT, Zuvich RL, Crosslin D, Roden DM, Denny JC, et al. High density GWAS for LDL cholesterol in African Americans using electronic medical records reveals a strong protective variant in APOE. Clinical and Translational Science. 5: 394-9. PMID 23067351 DOI: 10.1111/J.1752-8062.2012.00446.X  0.495
2012 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. Clinical Pharmacology and Therapeutics. 92: 235-42. PMID 22739144 DOI: 10.1038/Clpt.2012.66  0.507
2012 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, et al. Operational implementation of prospective genotyping for personalized medicine: the design of the Vanderbilt PREDICT project. Clinical Pharmacology and Therapeutics. 92: 87-95. PMID 22588608 DOI: 10.1038/Clpt.2011.371  0.377
2012 Roden DM, Xu H, Denny JC, Wilke RA. Electronic medical records as a tool in clinical pharmacology: Opportunities and challenges Clinical Pharmacology and Therapeutics. 91: 1083-1086. PMID 22534870 DOI: 10.1038/Clpt.2012.42  0.511
2012 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, ... ... Denny JC, et al. Portability of an algorithm to identify rheumatoid arthritis in electronic health records. Journal of the American Medical Informatics Association : Jamia. 19: e162-9. PMID 22374935 DOI: 10.1136/Amiajnl-2011-000583  0.56
2012 Fullerton SM, Wolf WA, Brothers KB, Clayton EW, Crawford DC, Denny JC, Greenland P, Koenig BA, Leppig KA, Lindor NM, McCarty CA, McGuire AL, McPeek Hinz ER, Mirel DB, Ramos EM, et al. Return of individual research results from genome-wide association studies: experience of the Electronic Medical Records and Genomics (eMERGE) Network. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 14: 424-31. PMID 22361898 DOI: 10.1038/Gim.2012.15  0.364
2012 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, ... ... Denny JC, et al. Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health record. Pharmacogenomics. 13: 407-18. PMID 22329724 DOI: 10.2217/Pgs.11.164  0.663
2012 Peissig PL, Rasmussen LV, Berg RL, Linneman JG, McCarty CA, Waudby C, Chen L, Denny JC, Wilke RA, Pathak J, Carrell D, Kho AN, Starren JB. Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. Journal of the American Medical Informatics Association : Jamia. 19: 225-34. PMID 22319176 DOI: 10.1136/Amiajnl-2011-000456  0.368
2012 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, ... ... Denny JC, et al. Predicting clopidogrel response using DNA samples linked to an electronic health record. Clinical Pharmacology and Therapeutics. 91: 257-63. PMID 22190063 DOI: 10.1038/Clpt.2011.221  0.472
2012 Kho AN, Hayes MG, Rasmussen-Torvik L, Pacheco JA, Thompson WK, Armstrong LL, Denny JC, Peissig PL, Miller AW, Wei WQ, Bielinski SJ, Chute CG, Leibson CL, Jarvik GP, Crosslin DR, et al. Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study. Journal of the American Medical Informatics Association : Jamia. 19: 212-8. PMID 22101970 DOI: 10.1136/Amiajnl-2011-000439  0.706
2012 Stenner SP, Johnson KB, Denny JC. PASTE: Patient-centered SMS text tagging in a medication management system Journal of the American Medical Informatics Association. 19: 368-374. PMID 21984605 DOI: 10.1136/Amiajnl-2011-000484  0.788
2012 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. Medical Decision Making : An International Journal of the Society For Medical Decision Making. 32: 188-97. PMID 21393557 DOI: 10.1177/0272989X11400418  0.689
2011 Wu Y, Rosenbloom ST, Denny JC, Miller RA, Mani S, Giuse DA, Xu H. Detecting abbreviations in discharge summaries using machine learning methods. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2011: 1541-9. PMID 22195219  0.668
2011 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 ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2011: 815-823. PMID 22195139  0.384
2011 Conway M, Berg RL, Carrell D, Denny JC, Kho AN, Kullo IJ, Linneman JG, Pacheco JA, Peissig P, Rasmussen L, Weston N, Chute CG, Pathak J. Analyzing the heterogeneity and complexity of Electronic Health Record oriented phenotyping algorithms. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2011: 274-83. PMID 22195079  0.474
2011 Carroll RJ, Eyler AE, Denny JC. Naïve Electronic Health Record phenotype identification for Rheumatoid arthritis. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2011: 189-196. PMID 22195070  0.535
2011 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, et al. Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. American Journal of Human Genetics. 89: 529-42. PMID 21981779 DOI: 10.1016/J.Ajhg.2011.09.008  0.801
2011 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. Statistics in Medicine. 30: 3208-20. PMID 21948391 DOI: 10.1002/Sim.4352  0.581
2011 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 Journal of Biomedical Informatics. 44: 1068-1075. PMID 21856440 DOI: 10.1016/J.Jbi.2011.08.009  0.304
2011 Kullo IJ, Ding K, Shameer K, McCarty CA, Jarvik GP, Denny JC, Ritchie MD, Ye Z, Crosslin DR, Chisholm RL, Manolio TA, Chute CG. Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate. American Journal of Human Genetics. 89: 131-8. PMID 21700265 DOI: 10.1016/J.Ajhg.2011.05.019  0.543
2011 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. Journal of the American Medical Informatics Association : Jamia. 18: 387-91. PMID 21672908 DOI: 10.1136/Amiajnl-2011-000208  0.778
2011 Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsao PS, Tsau PS, Kohane I, Roden DM, Altman RB. Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels. Clinical Pharmacology and Therapeutics. 90: 133-42. PMID 21613990 DOI: 10.1038/Clpt.2011.83  0.547
2011 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. 6. PMID 21589926 DOI: 10.1371/Journal.Pone.0019586  0.496
2011 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. Journal of the American Medical Informatics Association : Jamia. 18: 601-6. PMID 21508414 DOI: 10.1136/Amiajnl-2011-000163  0.687
2011 Kho AN, Pacheco JA, Peissig PL, Rasmussen L, Newton KM, Weston N, Crane PK, Pathak J, Chute CG, Bielinski SJ, Kullo IJ, Li R, Manolio TA, Chisholm RL, Denny JC. Electronic medical records for genetic research: results of the eMERGE consortium. Science Translational Medicine. 3: 79re1. PMID 21508311 DOI: 10.1126/Scitranslmed.3001807  0.588
2011 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. Clinical Pharmacology and Therapeutics. 89: 379-86. PMID 21248726 DOI: 10.1038/Clpt.2010.260  0.517
2011 Rosenbloom ST, Denny JC, Xu H, Lorenzi N, Stead WW, Johnson KB. Data from clinical notes: A perspective on the tension between structure and flexible documentation Journal of the American Medical Informatics Association. 18: 181-186. PMID 21233086 DOI: 10.1136/Jamia.2010.007237  0.598
2011 Ramirez AH, Schildcrout JS, Blakemore DL, Masys DR, Pulley JM, Basford MA, Roden DM, Denny JC. Modulators of normal electrocardiographic intervals identified in a large electronic medical record. Heart Rhythm : the Official Journal of the Heart Rhythm Society. 8: 271-7. PMID 21044898 DOI: 10.1016/J.Hrthm.2010.10.034  0.656
2010 Denny JC, Ritchie MD, Crawford DC, Schildcrout JS, Ramirez AH, Pulley JM, Basford MA, Masys DR, Haines JL, Roden DM. Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science. Circulation. 122: 2016-21. PMID 21041692 DOI: 10.1161/Circulationaha.110.948828  0.682
2010 Rosenbloom ST, Stead WW, Denny JC, Giuse D, Lorenzi NM, Brown SH, Johnson KB. Generating Clinical Notes for Electronic Health Record Systems. Applied Clinical Informatics. 1: 232-243. PMID 21031148 DOI: 10.4338/Aci-2010-03-Ra-0019  0.658
2010 Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H. Integrating existing natural language processing tools for medication extraction from discharge summaries. Journal of the American Medical Informatics Association : Jamia. 17: 528-31. PMID 20819857 DOI: 10.1136/Jamia.2010.003855  0.583
2010 Dumitrescu L, Ritchie MD, Brown-Gentry K, Pulley JM, Basford M, Denny JC, Oksenberg JR, Roden DM, Haines JL, Crawford DC. Assessing the accuracy of observer-reported ancestry in a biorepository linked to electronic medical records. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 12: 648-50. PMID 20733501 DOI: 10.1097/Gim.0B013E3181Efe2Df  0.497
2010 Schildcrout JS, Basford MA, Pulley JM, Masys DR, Roden DM, Wang D, Chute CG, Kullo IJ, Carrell D, Peissig P, Kho A, Denny JC. An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records. Journal of Biomedical Informatics. 43: 914-23. PMID 20688191 DOI: 10.1016/J.Jbi.2010.07.011  0.62
2010 Denny JC, Peterson JF, Choma NN, Xu H, Miller RA, Bastarache L, Peterson NB. Extracting timing and status descriptors for colonoscopy testing from electronic medical records. Journal of the American Medical Informatics Association : Jamia. 17: 383-8. PMID 20595304 DOI: 10.1136/Jamia.2010.004804  0.713
2010 Loukides G, Denny JC, Malin B. The disclosure of diagnosis codes can breach research participants' privacy. Journal of the American Medical Informatics Association : Jamia. 17: 322-7. PMID 20442151 DOI: 10.1136/Jamia.2009.002725  0.349
2010 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. American Journal of Human Genetics. 86: 560-72. PMID 20362271 DOI: 10.1016/J.Ajhg.2010.03.003  0.718
2010 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. Medical Decision Making : An International Journal of the Society For Medical Decision Making. 30: 639-50. PMID 20354229 DOI: 10.1177/0272989X10364246  0.594
2010 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 (Oxford, England). 26: 1205-10. PMID 20335276 DOI: 10.1093/Bioinformatics/Btq126  0.681
2010 Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC. MedEx: A medication information extraction system for clinical narratives Journal of the American Medical Informatics Association. 17: 19-24. PMID 20064797 DOI: 10.1197/Jamia.M3378  0.8
2010 Liu M, Denny JC, Mani S, Chen Y, Hu Y, Xu H. Identifying potential drugs that induce QT prolongation using electronic medical records Bmc Bioinformatics. 11. DOI: 10.1186/1471-2105-11-S4-P2  0.575
2010 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. Erratum: Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record (American Journal of Human Genetics (2010) 86 (560-572)) American Journal of Human Genetics. 87. DOI: 10.1016/J.Ajhg.2010.06.018  0.532
2009 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 ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2009: 141. PMID 20351837  0.693
2009 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. Journal of the American Medical Informatics Association : Jamia. 16: 806-15. PMID 19717800 DOI: 10.1197/Jamia.M3037  0.584
2009 Denny JC, Bastarache L, Sastre EA, Spickard A. Tracking medical students' clinical experiences using natural language processing. Journal of Biomedical Informatics. 42: 781-9. PMID 19236956 DOI: 10.1016/J.Jbi.2009.02.004  0.601
2009 Denny JC, Miller RA, Waitman LR, Arrieta MA, Peterson JF. Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor. International Journal of Medical Informatics. 78: S34-42. PMID 18938105 DOI: 10.1016/J.Ijmedinf.2008.09.001  0.588
2008 Denny JC, Miller RA, Johnson KB, Spickard A. Development and evaluation of a clinical note section header terminology. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 156-60. PMID 18999303  0.521
2005 Denny JC, Spickard A, Miller RA, Schildcrout J, Darbar D, Rosenbloom ST, Peterson JF. Identifying UMLS concepts from ECG Impressions using KnowledgeMap. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 196-200. PMID 16779029  0.685
2005 Denny JC, Giuse DA, Jirjis JN. The Vanderbilt Experience with Electronic Health Records Seminars in Colon and Rectal Surgery. 16: 59-68. DOI: 10.1053/J.Scrs.2005.08.003  0.323
2003 Denny JC, Smithers JD, Miller RA, Spickard A. "Understanding" medical school curriculum content using KnowledgeMap. Journal of the American Medical Informatics Association : Jamia. 10: 351-62. PMID 12668688 DOI: 10.1197/Jamia.M1176  0.58
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