Publications

2020

• Neil S. Zheng; Jeremy L. Warner; Travis J. Osterman; Quinn S. Wells; Xiao-Ou Shu; Stephen A. Deppen; Seth J. Karp; Shon Dwyer; QiPing Feng; Nancy J. Cox; Josh F. Peterson; C. Michael Stein; Dan M. Roden; Kevin B. Johnson; Wei-Qi Wei. A retrospective approach to evaluating potential adverse outcomes associated with delay of procedures for cardiovascular and cancer-related diagnoses in the context of COVID-19. Journal of Biomedical Informatics. 2020
• Zheng NS, Feng QP, Kerchberger VE, Zhao J, Edwards TL, Cox NJ, Stein CM, Roden DM, Denny JC, Wei WQ. PheMap: a Multi-resource Knowledgebase for High-throughput Phenotyping within Electronic Health Records. Journal of American Medical Informatics Associations (2020). https://doi.org/10.1093/jamia/ocaa104
• Minta Thomas, Lori C Sakoda, Michael Hoffmeister, Elisabeth A Rosenthal, Jeffrey K Lee, Franzel JB van Duijnhoven, Elizabeth A Platz, Anna H Wu, Christopher H Dampier, Albert de la Chapelle, Alicja Wolk, Amit D Joshi, Andrea Burnett-Hartman, Andrea Gsur, Annika Lindblom, Antoni Castells, Aung Ko Win, Bahram Namjou, Bethany Van Guelpen, Catherine M Tangen, Qianchuan He, Christopher I Li, Clemens Schafmayer, Corinne E Joshu, Cornelia M Ulrich, D Timothy Bishop, Daniel D Buchanan, Daniel Schaid, David A Drew, David C Muller, David Duggan, David R Crosslin, Demetrius Albanes, Edward L Giovannucci, Eric Larson, Flora Qu, Frank Mentch, Graham G Giles, Hakon Hakonarson, Heather Hampel, Ian B Stanaway, Jane C Figueiredo, Jeroen R Huyghe, Jessica Minnier, Jenny Chang-Claude, Jochen Hampe, John B Harley, Kala Visvanathan, Keith R Curtis, Kenneth Offit, Li Li, Loic Le Marchand, Ludmila Vodickova, Marc J Gunter, Mark A Jenkins, Martha L Slattery, Mathieu Lemire, Michael O Woods, Mingyang Song, Neil Murphy, Noralane M Lindor, Ozan Dikilitas, Paul DP Pharoah, Peter T Campbell, Polly A Newcomb, Roger L Milne, Robert J MacInnis, Sergi Castellví-Bel, Shuji Ogino, Sonja I Berndt, Stéphane Bézieau, Stephen N Thibodeau, Steven J Gallinger, Syed H Zaidi, Tabitha A Harrison, Temitope O Keku, Thomas J Hudson, Veronika Vymetalkova, Victor Moreno, Vicente Martín, Volker Arndt, Wei-Qi Wei, Wendy Chung, Yu-Ru Su, Richard B Hayes, Emily White, Pavel Vodicka, Graham Casey, Stephen B Gruber, Robert E Schoen, Andrew T Chan, John D Potter, Hermann Brenner, Gail P Jarvik, Douglas A Corley, Ulrike Peters, Li Hsu. Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk. The American Journal of Human Genetics. 2020. https://doi.org/10.1016/j.ajhg.2020.07.006
• Kristi Krebs, Jonas Bovijn, Neil Zheng, Maarja Lepamets, Jenny C Censin, Tuuli Jürgenson, Dage Särg, Erik Abner, Triin Laisk, Yang Luo, Line Skotte, Frank Geller, Bjarke Feenstra, Wei Wang, Adam Auton, Michelle Agee, Stella Aslibekyan, Robert K Bell, Katarzyna Bryc, Sarah K Clark, Sarah L Elson, Kipper Fletez-Brant, Pierre Fontanillas, Nicholas A Furlotte, Pooja M Gandhi, Karl Heilbron, Barry Hicks, David A Hinds, Karen E Huber, Ethan M Jewett, Yunxuan Jiang, Aaron Kleinman, Keng-Han Lin, Nadia K Litterman, Marie K Luff, Jennifer C McCreight, Matthew H McIntyre, Kimberly F McManus, Joanna L Mountain, Sahar V Mozaffari, Priyanka Nandakumar, Elizabeth S Noblin, Carrie AM Northover, Jared O’Connell, Aaron A Petrakovitz, Steven J Pitts, G David Poznik, J Fah Sathirapongsasuti, Anjali J Shastri, Janie F Shelton, Suyash Shringarpure, Chao Tian, Joyce Y Tung, Robert J Tunney, Vladimir Vacic, Xin Wang, Amir S Zare, Soumya Raychaudhuri, Tõnu Esko, Andres Metspalu, Sven Laur, Dan M Roden, Wei-Qi Wei, Michael V Holmes, Cecilia M Lindgren, Elizabeth J Phillips, Reedik Mägi, Lili Milani, João Fadista. Genome-wide study identifies association between HLA-B∗ 55: 01 and Self-Reported Penicillin Allergy. The American Journal of Human Genetics 107 (4), 612-621
• Kevin B Johnson, Wei‐Qi Wei, Dilhan Weeraratne, Mark E Frisse, Karl Misulis, Kyu Rhee, Juan Zhao, Jane L Snowdon. Precision medicine, AI, and the future of personalized health care. Clinical and translational science. 2020
• Sabrina L. Mitchell, Daniel A. Carranza Leon, Sandip Chaugai, Vivian K. Kawai, Rebecca T. Levinson, Wei-Qi Wei, C. Michael Stein. Pharmacogenetics of hypoglycemia associated with sulfonylurea therapy in usual clinical care. Pharmacogenomics J (2020). https://doi.org/10.1038/s41397-020-0171-4
• Ozan Dikilitas, Daniel J Schaid, Matthew L Kosel, Robert J Carroll, Christopher G Chute, Joshua A Denny, Alex Fedotov, QiPing Feng, Hakon Hakonarson, Gail P Jarvik, Ming Ta Michael Lee, Jennifer A Pacheco, Robb Rowley, Patrick M Sleiman, C Michael Stein, Amy C Sturm, Wei-Qi Wei, Georgia L Wiesner, Marc S Williams, Yanfei Zhang, Teri A Manolio, Iftikhar J Kullo. Predictive Utility of Polygenic Risk Scores for Coronary Heart Disease in Three Major Racial and Ethnic Groups. The American Journal of Human Genetics (2020). https://doi.org/10.1016/j.ajhg.2020.04.002
• Yao Hu, Mariaelisa Graff, Jeffrey Haessler, Steven Buyske, Stephanie A Bien, Ran Tao, Heather M Highland, Katherine K Nishimura, Niha Zubair, Yingchang Lu, Marie Verbanck, Austin T Hilliard, Derek Klarin, Scott M Damrauer, Yuk-Lam Ho, Peter WF Wilson, Kyong-Mi Chang, Philip S Tsao, Kelly Cho, Christopher J O’Donnell, Themistocles L Assimes, Lauren E Petty, Jennifer E Below, Ozan Dikilitas, Daniel J Schaid, Matthew L Kosel, Iftikhar J Kullo, Laura J Rasmussen-Torvik, Gail P Jarvik, Qiping Feng, Wei-Qi Wei, Eric B Larson, Frank D Mentch, Berta Almoguera, Patrick M Sleiman, Laura M Raffield, Adolfo Correa, Lisa W Martin, Martha Daviglus, Tara C Matise, Jose Luis Ambite, Christopher S Carlson, Ron Do, Ruth JF Loos, Lynne R Wilkens, Loic Le Marchand, Chris Haiman, Daniel O Stram, Lucia A Hindorff, Kari E North, Charles Kooperberg, Iona Cheng, Ulrike Peters. Minority-centric meta-analyses of blood lipid levels identify novel loci in the Population Architecture using Genomics and Epidemiology (PAGE) study. PLoS genetics 16 (3), e1008684. 2020
• Connor A Emdin, Mary E Haas, Amit V Khera, Krishna Aragam, Mark Chaffin, Derek Klarin, George Hindy, Lan Jiang, Wei-Qi Wei, Qiping Feng, Juha Karjalainen, Aki Havulinna, Tuomo Kiiskinen, Alexander Bick, Diego Ardissino, James G Wilson, Heribert Schunkert, Ruth McPherson, Hugh Watkins, Roberto Elosua, Matthew J Bown, Nilesh J Samani, Usman Baber, Jeanette Erdmann, Namrata Gupta, John Danesh, Danish Saleheen, Kyong-Mi Chang, Marijana Vujkovic, Ben Voight, Scott Damrauer, Julie Lynch, David Kaplan, Marina Serper, Philip Tsao, Million Veteran Program, Josep Mercader, Craig Hanis, Mark Daly, Joshua Denny, Stacey Gabriel, Sekar Kathiresan. A missense variant in mitochondrial amidoxime reducing component 1 gene and protection against liver disease. PLoS genetics 16 (4), e1008629. 2020
• Prathima Anandi, Alyson L Dickson, QiPing Feng, Wei-Qi Wei, William D Dupont, Dale Plummer, Ge Liu, Rany Octaria, Katherine A Barker, Vivian K Kawai, Kelly Birdwell, Nancy J Cox, Adriana Hung, C Michael Stein, Cecilia P Chung. Combining clinical and candidate gene data into a risk score for azathioprine-associated leukopenia in routine clinical practice. The Pharmacogenomics Journal, 1-10, 2020
• Archna Bajaj, Andrea Ihegword, Chengxiang Qiu, Aeron M Small, Wei-Qi Wei, Lisa Bastarache, QiPing Feng, Rachel L Kember, Marjorie Risman, Roy D Bloom, David L Birtwell, Heather Williams, Christian M Shaffer, Jinbo Chen, Regeneron Genetics Center, Joshua C Denny, Daniel J Rader, C Michael Stein, Scott M Damrauer, Katalin Susztak. Phenome-wide association analysis suggests the APOL1 linked disease spectrum primarily drives kidney-specific pathways. Kidney International, 2020
• Jamie R Robinson, Robert J Carroll, Lisa Bastarache, Qingxia Chen, Zongyang Mou, Wei-Qi Wei, John J Connolly, Frank Mentch, Patrick Sleiman, Paul K Crane, Scott J Hebbring, Ian B Stanaway, David R Crosslin, Adam S Gordon, Elisabeth A Rosenthal, David Carrell, M Geoffrey Hayes, Wei Wei, Lynn Petukhova, Bahram Namjou, Ge Zhang, Maya S Safarova, Nephi A Walton, Christopher Still, Erwin P Bottinger, Ruth JF Loos, Shawn N Murphy, Gretchen P Jackson, Iftikhar J Kullo, Hakon Hakonarson, Gail P Jarvik, Eric B Larson, Chunhua Weng, Dan M Roden, Joshua C Denny. Association of Genetic Risk of Obesity with Postoperative Complications Using Mendelian Randomization. World journal of surgery. 44, pages84–94(2020).

2019

•  Joshua L. Bonkowsky, Jacob Wilkes, Jian Ying,  Wei-Qi Wei. Novel and known morbidities of leukodystrophies identified using a phenome-wide association study. Neurology: Clinical Practice. Dec 2019, 10.1212/CPJ.0000000000000783;
• Feng Q, Wei WQ, Chaugai S, Carranza Leon BG, Kawai V, Carranza Leon DA, Jiang L, Zhong X, Liu G, Ihegword A, Shaffer CM, Linton MF, Chung CP, Stein CM. A Genetic Approach to the Association Between PCSK9 and Sepsis. JAMA Netw Open. 2019 Sep 4;2(9):e1911130. doi: 10.1001/jamanetworkopen.2019.11130.
• Patrick Wu, Aliya Gifford, Xiangrui Meng, Xue Li, Harry Campbell, Tim Varley, Juan Zhao, Robert Carroll, Lisa Bastarache, Joshua C Denny, Evropi Theodoratou, Wei-Qi Wei. Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation. JMIR Med Inform. 2019 Nov 29;7(4):e14325. doi: 10.2196/14325. 
• 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, Campbell H, Theodoratou E. Phenome-wide Mendelian-randomiz ation study of genetically determined vitamin D on multiple health outcomes using the UK Biobank study. Int J Epidemiol. 2019 Sep 13. pii: dyz182. doi: 10.1093/ije/dyz182. [Epub ahead of print]
• Shang N, Liu C, Rasmussen LV, Ta CN, Caroll RJ, Benoit B, Lingren T, Dikilitas O, Mentch FD, Carrell DS, Wei WQ, Luo Y, Gainer VS, Kullo IJ, Pacheco JA, Hakonarson H, Walunas TL, Denny JC, Wiley K, Murphy SN, Hripcsak G, Weng C. Making work visible for electronic phenotype implementation: lessons learned from the eMERGE network. J Biomed Inform. 2019 Sep 19:103293. doi: 10.1016/j.jbi.2019.103293. [Epub ahead of print]
• Hripcsak G, Shang N, Peissig PL, Rasmussen LV, Liu C, Benoit B, Carroll RJ, Carrell DS, Denny JC, Dikilitas O, Gainer VS, Howell KM, Klann JG, Kullo IJ, Lingren T, Mentch FD, Murphy SN, Natarajan K, Pacheco JA, Wei WQ, Wiley K, Weng C. Facilitating phenotype transfer using a common data model. J Biomed Inform. 2019 Aug;96:103253. doi: 10.1016/j.jbi.2019.103253. Epub 2019 Jul 17. PMID: 31325501 PMCID: PMC6697565
• Zhao J, Zhang Y, Schlueter DJ, Wu P, Kerchberger VE, Rosenbloom TS, Wells QS, Feng Q, Denny JC, Wei WQ. Detecting Time-Evolving Phenotypic Topics via Tensor Factorization on Electronic Health Records: Cardiovascular Disease Case Study. J Biomed Inform. 2019 Aug 22:103270. doi: 10.1016/j.jbi.2019.103270. PMID: 31445983
• Namjou B, Lingren T, Huang Y, Parameswaran S, Cobb BL5 Stanaway IB, Connolly JJ, Mentch FD, Benoit B, Niu X, Wei WQ, Carroll RJ, Pacheco JA, Harley ITW, Divanovic S, Carrell DS, Larson EB, Carey DJ, Verma S, Ritchie MD, Gharavi AG, Murphy S, Williams MS, Crosslin DR, Jarvik GP, Kullo IJ, Hakonarson H, Li R; eMERGE Network, Xanthakos SA, Harley JB. GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network. BMC Med. 2019 Jul 17;17(1):135. doi: 10.1186/s12916-019-1364-z.
• Gill D, Georgakis MK, Koskeridis F, Jiang , 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. 2019 Jun. doi: 10.1161/CIRCULATIONAHA.118.038814.
• 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 WQ, Ye Z, Chute CG, Weiner JP. Comorbidity Characterization Among eMERGE Institutions: A Pilot Evaluation with the Johns Hopkins Adjusted Clinical Groups® System. AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:145-152. eCollection 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. Clin Pharmacol Ther. 2019 Mar 28. doi: 10.1002/cpt.1439. PMID: 30924126
• 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, Hakonarson H, Sleiman P, Weng C, Fasel D, Wei WQ, Kullo I, Schaid D, Chung WK, Ritchie MD. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pac Symp Biocomput. 2019;24:272-283. PMID: 30864329
• 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. 2019 Feb 13;14(2):e0212112. doi: 10.1371/journal.pone.0212112. eCollection 2019. PMID: 30759150 PMCID: PMC6374022
• 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, Rasmussen-Torvik LJ, Pendergrass SA5, Sturm AC, Namjou B, Shah AS, Carroll RJ, Chung WK, Wei WQ, Feng Q, Stein CM, Roden DM, Manolio TA, Schaid DJ, Denny JC, Hebbring SJ, de Andrade M, Kullo IJ. A phenome-wide association study to discover pleiotropic effects of PCSK9, APOB, and LDLR. NPJ Genom Med. 2019 Feb 11;4:3. doi: 10.1038/s41525-019-0078-7. eCollection 2019. PMID: 30774981 PMCID: PMC6370860
• 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, Hakonarson H, Sleiman P, Weng C, Fasel D, Wei WQ, Kullo I, Schaid D, Chung WK, Ritchie MD. Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network. Pac Symp Biocomput. 2019;24:272-283. PMID: 30864329
• Juan Zhao, QiPing Feng, Patrick Wu, Roxana A. Lupu, Russell A. Wilke, Quinn S. Wells, Joshua C. Denny, and Wei-Qi Wei, Learning from Longitudinal Data in Electronic Health Record and Genetic Data to Improve Cardiovascular Event Prediction, Scientific Reports volume 9, Article number: 717 (2019) PMID: 30679510

2018

• Feng Q, Wei WQ, Chaugai S, Leon BGC, Mosley JD, Leon DAC, Jiang L, Ihegword A, Shaffer CM, Linton MF, Chung CP, Stein CM.. Association Between Low-Density Lipoprotein Cholesterol Levels and Risk for Sepsis Among Patients Admitted to the Hospital With Infection. JAMA Netw Open. 2019 Jan 4;2(1):e187223. doi: 10.1001/jamanetworkopen.2018.7223. PMID: 30657536
• 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, DuVall SL, Klarin D, Cho K, Wang Y, Evangelou E, Cabrera CP, Wain LV, Shrestha R, Mautz BS, Akwo EA, Sargurupremraj M, Debette S, Boehnke M, Scott LJ, Luan J, Zhao JH, Willems SM, Thériault S, Shah N, Oldmeadow C, Almgren P, Li-Gao R, Verweij N, Boutin TS, Mangino M, Ntalla I, Feofanova E, Surendran P, Cook JP, Karthikeyan S, Lahrouchi N, Liu C, Sepúlveda N, Richardson TG, Kraja A, Amouyel P, Farrall M, Poulter NR; Understanding Society Scientific Group; International Consortium for Blood Pressure; Blood Pressure-International Consortium of Exome Chip Studies, Laakso M, Zeggini E, Sever P, Scott RA, Langenberg C, Wareham NJ, Conen D, Palmer CNA, Attia J, Chasman DI, Ridker PM, Melander O, Mook-Kanamori DO, Harst PV, Cucca F, Schlessinger D, Hayward C, Spector TD, Jarvelin MR, Hennig BJ, Timpson NJ, Wei WQ, Smith JC, Xu Y, Matheny ME, Siew EE, Lindgren C, Herzig KH, Dedoussis G, Denny JC, Psaty BM, Howson JMM, Munroe PB, Newton-Cheh C, Caulfield MJ, Elliott P, Gaziano JM, Concato J, Wilson PWF, Tsao PS, Velez Edwards DR, Susztak K; Million Veteran Program, O'Donnell CJ, Hung AM, Edwards TL.. Trans-ethnic association study of blood pressure determinants in over 750,000 individuals. Nat Genet. 2019 Jan;51(1):51-62. doi: 10.1038/s41588-018-0303-9. Epub 2018 Dec 21. PMID: 30578418
• Chaugai S, Dickson AL, Shuey MM, Feng Q, Barker KA, Wei WQ, Luther JM, Stein CM, Chung CP.. Co-Prescription of Strong CYP1A2 Inhibitors and the Risk of Tizanidine-Associated Hypotension: A Retrospective Cohort Study. Clin Pharmacol Ther. 2018 Sep 17. doi: 10.1002/cpt.1233. PMID: 30223305
• 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, Horikoshi M, Ritchie M, Williams MS, Larson EB, Crosslin DR, Bland ST, Pacheco JA, Rasmussen-Torvik LJ, Cronkite D, Hripcsak G, Cox NJ, Wilke RA, Stein CM, Rotter JI, Momozawa Y, Roden DM, Krauss RM, Denny JC.. LPA Variants are Associated with Residual Cardiovascular Risk in Patients Receiving Statins. Circulation. 2018;CIRCULATIONAHA.117.031356
• 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 Med. 2018 Aug 28;15(8):e1002642. doi: 10.1371/journal.pmed.1002642. eCollection 2018 Aug. PMID: 30153257
• 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, Kang HM, Abecasis GR, Willer CJ, Lee S. Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. Nat Genet. 2018 Sep;50(9):1335-1341. doi: 10.1038/s41588-018-0184-y. Epub 2018 Aug 13. PMID: 30104761
• Mosley JD, Feng Q, Wells QS, Van Driest SL, Shaffer CM, Edwards TL, Bastarache L, Wei WQ, Davis LK, McCarty CA, Thompson W, Chute CG, Jarvik GP, Gordon AS, Palmer MR, Crosslin DR, Larson EB, Carrell DS, Kullo IJ, Pacheco JA, Peissig PL, Brilliant MH, Linneman JG, Namjou B, Williams MS, Ritchie MD, Borthwick KM, Verma SS, Karnes JH, Weiss ST, Wang TJ, Stein CM, Denny JC, Roden DM. A study paradigm integrating prospective epidemiologic cohorts and electronic health records to identify disease biomarkers. Nat Commun. 2018 Aug 30;9(1):3522. doi: 10.1038/s41467-018-05624-4. PMID: 30166544
• JR Robinson, WQ Wei, DM Roden, JC Denny. Defining Phenotypes from Clinical Data to Drive Genomic Research. Annual Reviews, 2018; 4139 El Camino Way, PO Box 10139, Palo Alto, California 94303-0139, USA
• Ji X, Bossé Y, Landi MT, Gui J, Xiao X, Qian D, Joubert P, Lamontagne M, Li Y, Gorlov I, de Biasi M, Han Y, Gorlova O, Hung RJ, Wu X, McKay J, Zong X, Carreras-Torres R, Christiani DC, Caporaso N, Johansson M, Liu G, Bojesen SE, Le Marchand L, Albanes D, Bickeböller H, Aldrich MC, Bush WS, Tardon A, Rennert G, Chen C, Teare MD, Field JK, Kiemeney LA, Lazarus P, Haugen A, Lam S, Schabath MB, Andrew AS, Shen H, Hong YC, Yuan JM, Bertazzi PA, Pesatori AC, Ye Y, Diao N, Su L, Zhang R, Brhane Y, Leighl N, Johansen JS, Mellemgaard A, Saliba W, Haiman C, Wilkens L, Fernandez-Somoano A, Fernandez-Tardon G, van der Heijden EHFM, Kim JH, Dai J, Hu Z, Davies MPA, Marcus MW, Brunnström H, Manjer J, Melander O, Muller DC, Overvad K, Trichopoulou A, Tumino R, Doherty J, Goodman GE, Cox A, Taylor F, Woll P, Brüske I, Manz J, Muley T, Risch A, Rosenberger A, Grankvist K, Johansson M, Shepherd F, Tsao MS, Arnold SM, Haura EB, Bolca C, Holcatova I, Janout V, Kontic M, Lissowska J, Mukeria A, Ognjanovic S, Orlowski TM, Scelo G, Swiatkowska B, Zaridze D, Bakke P, Skaug V, Zienolddiny S, Duell EJ, Butler LM, Koh WP, Gao YT, Houlston R, McLaughlin J, Stevens V, Nickle DC, Obeidat M, Timens W, Zhu B, Song L, Artigas MS, Tobin MD, Wain LV, Gu F, Byun J, Kamal A, Zhu D, Tyndale RF, Wei WQ, Chanock S, Brennan P, Amos CI. Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk. Nat Commun. 2018 Aug 13;9(1):3221. doi: 10.1038/s41467-018-05074-y. PMID: 30104567
• Bastarache L, Hughey JJ, Hebbring S, Marlo J, Zhao W, Ho WT, Driest SLV, McGregor TL, Mosley JD, Wells QS, Temple M, Ramirez AH, Carroll R, Osterman T, Edwards T, Ruderfer D, Edwards DRV, Hamid R, Cogan J, Glazer A, Wei W-Q, Feng Q, Brilliant M, Zhao ZJ, Cox NJ, Roden DM, Denny JC. Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. Science 2018; 359: 1233–1239.

2017

• Joshua C. Denny, Sarah V. Driest, Wei-Qi Wei, Dan M. Roden. The influence of big (clinical) data and genomics on precision medicine and drug development. Clin Pharmacol Ther. 2017 Nov 24. doi: 10.1002/cpt.951. PMID: 29171014
• 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, Theodoratou E. MR-PheWAS: exploring the causal effect of SUA level on multiple disease outcomes by using genetic instruments in UK Biobank. Ann Rheum Dis. 2018 Feb 6. pii: annrheumdis-2017-212534. doi: 10.1136/annrheumdis-2017-212534.
• Wei-Qi Wei, Lisa Bastarache, Robert J Carroll, Joy E Marlo, Travis Osterman, Eric R. Gamazon, Nancy J. Cox, Dan Roden, Joshua C. Denny. Evaluating of Phecodes, Clinical Classification Software, and ICD-9-CM codes for Phenome-wide Association Studies in the Electronic Health Record. Plos ONE, 2017
• Qiping Feng, Wei-Qi Wei, Cecilia Chung, Rebecca Levinson, Lisa Bastarache, Joshua Denny, and Michael Stein. The effect of genetic variation in PCSK9 on the LDL-cholesterol response to statin therapy. The Pharmacogenomics Journal, 2017 Mar;17(2):204-208.
• QiPing Feng, Wei-Qi Wei, Rebecca T Levinson, Jonathan D Mosley, and C Michael Stein. Replication and fine-mapping of genetic predictors of lipid traits in African–Americans. Journal of Human Genetics 62, 895–901 (2017).

2016

• Iris Postmus, Helen R Warren, Stella Trompet, Benoit J Arsenault, Christy L Avery, Joshua C Bis, Daniel I Chasman, Catherine E de Keyser, Harshal A Deshmukh, Daniel S Evans, QiPing Feng, Xiaohui Li, Roelof A J Smit, Albert V Smith, Fangui Sun, Kent D Taylor, Alice M Arnold, Michael R Barnes, Bryan J Barratt, John Betteridge, S Matthijs Boekholdt, Eric Boerwinkle, Brendan M Buckley, Y-D Ida Chen, Anton J M de Craen, Steven R Cummings, Joshua C Denny, Marie Pierre Dubé, Paul N Durrington, Gudny Eiriksdottir, Ian Ford, Xiuqing Guo, Tamara B Harris, Susan R Heckbert, Albert Hofman, G Kees Hovingh, John J P Kastelein, Leonore J Launer, Ching-Ti Liu, Yongmei Liu, Thomas Lumley, Paul M McKeigue, Patricia B Munroe, Andrew Neil, Deborah A Nickerson, Fredrik Nyberg, Eoin O'Brien, Christopher J O'Donnell, Wendy Post, Neil Poulter, Ramachandran S Vasan, Kenneth Rice, Stephen S Rich, Fernando Rivadeneira, Naveed Sattar, Peter Sever, Sue Shaw-Hawkins, Denis C Shields, P Eline Slagboom, Nicholas L Smith, Joshua D Smith, Nona Sotoodehnia, Alice Stanton, David J Stott, Bruno H Stricker, Til Stürmer, André G Uitterlinden, Wei-Qi Wei, Rudi G J Westendorp, Eric A Whitsel, Kerri L Wiggins, Russell A Wilke, Christie M Ballantyne, Helen M Colhoun, L Adrienne Cupples, Oscar H Franco, Vilmundur Gudnason, Graham Hitman, Colin N A Palmer, Bruce M Psaty, Paul M Ridker, Jeanette M Stafford, Charles M Stein, Jean-Claude Tardif, Mark J Caulfield, J Wouter Jukema, Jerome I Rotter, Ronald M Krauss. Meta-analysis of genome-wide association studies of HDL cholesterol response to statins. J Med Genet 2016;53:12 835-845 Published Online First: 1 September 2016 doi:10.1136/jmedgenet-2016-103966, PMID: 27587472
• Abiodun Adefurin, Leon Darghosian, Chimalum Okafor, Vivian Kawai, Chun Li, Anushi Shah, Wei-Qi Wei, Daniel Kurnik, C. Michael Stein. Alpha2A adrenergic receptor genetic variation contributes to hyperglycemia after myocardial infarction. International Journal of Cardiology, Volume 215, 15 July 2016, 482–486, PMID: 27131769
• Teixeira PL, Wei WQ, Cronin RM, Mo H, VanHouten JP, Carroll RJ, LaRose E, Bastarache LA, Rosenbloom ST, Edwards TL, Roden DM, Lasko TA, Dart RA, Nikolai AM, Peissig PL, Denny JC. Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. J Am Med Inform Assoc. 2016 Aug 7. pii: ocw071. doi: 10.1093/jamia/ocw071. PMID: 27497800
• Wei-Qi Wei, Pedro L. Teixeira, Huan Mo, Robert M. Cronin, Jeremy Warner, Joshua C. Denny. Combining Billing Codes, Clinical Notes, and Medications from Electronic Health Records Provides Superior Phenotyping Performance. J Am Med Inform Assoc. 2016 Apr;23(e1):e20-7. doi: 10.1093/jamia/ocv130.  PMID: 26338219

2015

• Owens AP 3rd, 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. Arterioscler Thromb Vasc Biol. 2015 Sep;35(9):2032-41. doi: 10.1161/ATVBAHA.115.305537. Erratum in: Arterioscler Thromb Vasc Biol. 2016 Feb;36(2):e18. PMID: 26139462
• Jonathan Mosley, Christian Shaffer, Sara Van Driest, Peter Weeke, Quinn Wells, Jason Karnes, Digna Velez Edwards, Wei-Qi Wei, Pedro Teixeira, Lisa Bastarache, Dana Crawford, Rongling Li, Teri Manolio, Erwin Bottinger, Catherine McCarty, James Linneman, Murray Brilliant, Jennifer Pacheco, Will Thompson, Rex Chisholm, Gail Jarvik, David Crosslin, David Carrell, Eric Baldwin, James Ralston, Eric Larson, Jane Grafton, Aaron Scrol, Hayan Jouni, Iftikhar Kullo, Gerard Tromp, Kenneth Borthwick, Helena Kuivaniemi, David Carey, Marylyn Ritchie, Yuki Bradford, Shefali Verma, Christopher Chute, Abirami Veluchamy, Moneeza Siddiqui, Colin Palmer, Andrew Morris, Alexander Doney, Seyed MahmoudPour, Anke-Hilse Maitland-van der Zee, Joshua Denny, and Dan Roden. A Genome-Wide Association Study Identifies Variants in KCNIP4 Associated with ACE Inhibitor Induced Cough. The Pharmacogenomics Journal, 2016 Jul 14. doi: 10.1038/tpj.2015.51. PMID: 26169577, PMCID: PMC4713364
• Wei WQ, Denny JC.  Extracting research-quality phenotypes from electronic health records to support precision medicine. Genome Medicine, 2015 7:41  doi:10.1186/s13073-015-0166-y PMCID: PMC4416392

2014

• 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, 2015 Apr;22(e1):e162-76. doi: 10.1136/amiajnl-2014-002954. PMID: 25336593
• 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, 2014 Nov;15(14):1739-1747. PMID: 25493567  PMCID: PMC4292894
• Iris Postmus, Stella Trompet, Harshal Deshmukh, Michael Barnes, Xiaohui Li, Helen Warren, Daniel Chasman, Kaixin Zhou, Benoit Arsenault, Louise Donnelly, Kerri Wiggins, Christy Avery, Paula Griffin, QiPing Feng, Kent Taylor, Guo Li, Daniel Evans, Albert Smith, Catherine de Keyser, Andrew Johnson, Anton de Craen, David Stott, Brendan Buckley, Ian Ford, Rudi Westendorp, Eline Slagboom, Naveed Sattar, Patricia Munroe, Peter Sever, Neil Poulter, Alice Stanton, Denis Shields, Eoin O'Brien, Sue Shaw-Hawkins, Y.-D. Ida Chen, Deborah Nickerson, Joshua Smith, Marie-Pierre Dubé, Matthijs Boekholdt, Gerard Hovingh, John Kastelein, Paul McKeigue, John Betteridge, Andrew Neil, Paul Durrington, Alex Doney, Fiona Carr, Andrew Morris, Mark McCarthy, Leif Groop, Emma Ahlqvist, Joshua Bis, Kenneth Rice, Nicholas Smith, Thomas Lumley, Eric Whitsel, Til Stürmer, Eric Boerwinkle, Julius Ngwa, Christopher O'Donnell, Ramachandran Vasan, Wei-Qi Wei, Russell Wilke, Ching-Ti Liu, Fangui Sun, Xiuqing Guo, Susan Heckbert, Wendy Post, Nona Sotoodehnia, Alice Arnold, Jeanette Stafford, Jingzhong Ding, David Herrington, Stephen Kritchevsky, Gudny Eiriksdottir, Lenore Launer, Tamara Harris, Audrey Chu, Franco Giulianini, Jean MacFadyen, Bryan Barratt, Fredrik Nyberg, Bruno Stricker, André Uitterlinden, Albert Hofman, Fernando Rivadeneira, Valur Emilsson, Oscar Franco, Paul Ridker, Vilmundur Gudnason, Yongmei Liu, Joshua Denny, Christie Ballantyne, Jerome Rotter, L. Cupples, Bruce Psaty, Colin Palmer, Jean-Claude Tardif, Helen Colhoun, Graham Hitman, Ronald Krauss, J. Wouter Jukema, and Mark Caulfield. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins, Nature Communications, 2014 Oct 28;5:5068. doi: 10.1038/ncomms6068.. PMID: 25350695  PMCID: PMC4220464
• Wei WQ, Feng Q, Weeke P, Bush WS, 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, Joint Summits on Translational Science, 112-119,  San Francisco, CA, 2014.

2013

• DeGorter MK, Tirona  RG, Schwarz U, Yun-Hee Choi YH, Dresser GK, Suskin N, Myers K, Zou G, Iwuchukwu OF, Wei WQ, Wilke RA, Hegele RA and Kim RB. Clinical and pharmacogenetic predictors of circulating atorvastatin and rosuvastatin concentration in routine clinical care. Circulation: Cardiovascular Genetics, DOI: 10.1161/CIRCGENETICS.113.000099, 2013 PMCID:PMC3922121
• 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, Wilke RA, Denny JC.  Characterization of Statin Dose-response within Electronic Medical Records. Clinical Pharmacology andTherapeutics. 2014 Mar;95(3):331-8. doi: 10.1038/clpt.2013.202.  PMCID:PMC3944214
• 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. Stud Health Technol Inform. 2013;192:662-6.
• 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, 2013. 1448-1456. PMCID:PMC3900157
• 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 America Medical Informatics Association, 2013, doi:10.1136/amiajnl-2012-001431.  PMCID:PMC3756263
• Wei WQ, Leibson CL, Kho AN, Caraballo JP, Yawn BP, Jen A. Pacheco JA, Ransom JE, Chute CG.  The Absent Longitudinal Data Affects the Accuracy of an EMR-based Algorithm for Identifying Type 2 Diabetes Mellitus: a Population Based vs. Single Medical Center and Retrospective Study. International Journal of Medical Informatics. 2013 Apr;82(4):239-47. PMID:22762862 PMCID:PMC3478423
• Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG. Terminology representation guidelines for biomedical ontologies in the semantic web notations. Journal of Biomedical Informatics. 2013 Feb;46(1):128-38.PMID:23026232. PMCID: PMC3563768

2012

• Wei WQ, Leibson CL, Kho AN, Caraballo JP, Yawn BP, Jen A. Pacheco JA, Ransom JE, Chai HS, and Chute CG.  Data Fragmentation across Healthcare providers affects the Accuracy of an EMR-based Algorithm for Identifying Type 2 Diabetes Mellitus Subjects. Journal of America Medical Informatics Association. 2012. 2012 Mar-Apr;19(2):219-24.  PMCID: PMC3277630
• Kho AN, Hayes MG, Rasmussen-Torvik L, Pacheco AJ, Armstrong LL, Denny J, Peissig LP, Miller A, Wei WQ, Chute CG, Leibson CL,  Jarvik PG, Crosslin RD, Carlson SC, Newton MK  Wolf AW, Chisholm LR, Lowe LW. Use of Diverse Electronic Medical Record Systems to Identify Genetic Risk for Type 2 Diabetes within a Genome Wide Association Study. Journal of America Medical Informatics Association. 2011. 2012 Mar-Apr;19(2):212-8. PMCID: PMC3277617