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2020 – today
- 2024
[j26]Chao Yan
, Henry H. Ong, Monika E. Grabowska, Matthew S. Krantz, Wu-Chen Su, Alyson L. Dickson, Josh F. Peterson, QiPing Feng, Dan M. Roden, C. Michael Stein, Vern Eric Kerchberger, Bradley A. Malin, Wei-Qi Wei:
Large language models facilitate the generation of electronic health record phenotyping algorithms. J. Am. Medical Informatics Assoc. 31(9): 1994-2001 (2024)- [j25]Chao Yan, Monika E. Grabowska, Alyson L. Dickson, Bingshan Li, Zhexing Wen, Dan M. Roden, C. Michael Stein, Peter J. Embí, Josh F. Peterson, QiPing Feng, Bradley A. Malin, Wei-Qi Wei:
Leveraging generative AI to prioritize drug repurposing candidates for Alzheimer's disease with real-world clinical validation. npj Digit. Medicine 7(1) (2024) - 2023
- [j24]Nick Strayer, Siwei Zhang, Lydia Yao, Tess Vessels, Cosmin Adrian Bejan, Ryan S. Hsi, Jana K. Shirey-Rice, Justin M. Balko, Douglas B. Johnson, Elizabeth J. Phillips, Alex Bick, Todd L. Edwards, Digna R. Velez Edwards, Jill M. Pulley, Quinn Stanton Wells, Michael R. Savona, Nancy J. Cox, Dan M. Roden, Douglas M. Ruderfer, Yaomin Xu:
Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs. Bioinform. 39(1) (2023) - [j23]Megan M. Shuey, William W. Stead, Ida Aka, April L. Barnado, Lisa Bastarache, Elly Brokamp, Meredith Campbell, Robert J. Carroll, Jeffrey A. Goldstein, Adam Lewis, Beth A. Malow, Jonathan D. Mosley, Travis Osterman, Dolly A Padovani-Claudio, Andrea Ramirez, Dan M. Roden, Bryce A Schuler, Edward Siew, Jennifer Sucre, Isaac Thomsen, Rory J. Tinker, Sara Van Driest, Colin Walsh, Jeremy L. Warner, Quinn Stanton Wells, Lee E. Wheless:
Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics. Bioinform. 39(10) (2023) - 2022
- [j22]Lina M. Sulieman, Robert M. Cronin, Robert J. Carroll, Karthik Natarajan, Kayla Marginean, Brandy Mapes, Dan M. Roden, Paul A. Harris, Andrea H. Ramirez:
Comparing medical history data derived from electronic health records and survey answers in the All of Us Research Program. J. Am. Medical Informatics Assoc. 29(7): 1131-1141 (2022) - [j21]Ken Wiley, Laura Findley, Madison Goldrich, Tejinder K. Rakhra-Burris, Ana Stevens, Pamela Williams, Carol J. Bult, Rex L. Chisholm, Patricia Deverka, Geoffrey S. Ginsburg, Eric D. Green, Gail P. Jarvik, George A. Mensah, Erin Ramos, Mary V. Relling, Dan M. Roden, Robb Rowley, Gil Alterovitz, Samuel J. Aronson, Lisa Bastarache, James J. Cimino, Erin L. Crowgey, Guilherme Del Fiol, Robert R. Freimuth, Mark A. Hoffman, Janina M. Jeff, Kevin B. Johnson, Kensaku Kawamoto, Subha Madhavan, Eneida A. Mendonça, Lucila Ohno-Machado, Siddharth Pratap, Casey Overby Taylor, Marylyn D. Ritchie, Nephi Walton, Chunhua Weng, Teresa Zayas-Cabán, Teri A. Manolio, Marc S. Williams:
A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. J. Am. Medical Informatics Assoc. 29(8): 1342-1349 (2022) - [j20]Andrea H. Ramirez, Lina M. Sulieman, David J. Schlueter, Alese E. Halvorson, Jun Qian, Francis Ratsimbazafy, Roxana Loperena-Cortes, Kelsey R. Mayo, Melissa A. Basford, Nicole Deflaux, Karthik Muthuraman, Karthik Natarajan, Abel N. Kho, Hua Xu, Consuelo H. Wilkins, Hoda Anton-Culver, Eric Boerwinkle, Mine Cicek, Cheryl R. Clark, Elizabeth Cohn, Lucila Ohno-Machado, Sheri D. Schully, Brian K. Ahmedani, Maria Argos, Robert M. Cronin, Christopher J. O'Donnell, Mona Fouad, David B. Goldstein, Philip Greenland, Scott J. Hebbring, Elizabeth W. Karlson, Parinda Khatri, Bruce Korf, Jordan W. Smoller, Stephen Sodeke, John Wilbanks, Justin Hentges, Stephen Mockrin, Christopher Lunt, Stephanie A. Devaney, Kelly Gebo, Joshua C. Denny, Robert J. Carroll, David Glazer, Paul A. Harris, George Hripcsak, Anthony A. Philippakis, Dan M. Roden:
The All of Us Research Program: Data quality, utility, and diversity. Patterns 3(8): 100570 (2022) - 2021
- [j19]Sarah DeLozier, Peter Speltz, Jason Brito, Leigh Anne Tang, Janey Wang, Joshua C. Smith, Dario A. Giuse, Elizabeth Phillips, Kristina Williams, T. Stephen Strickland, Giovanni Davogustto, Dan M. Roden, Joshua C. Denny:
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. J. Am. Medical Informatics Assoc. 28(1): 126-131 (2021) - [j18]Patrick Wu, Scott D. Nelson, Juan Zhao, Cosby A. Stone Jr., QiPing Feng, Qingxia Chen, Eric A. Larson, Bingshan Li, Nancy J. Cox, C. Michael Stein, Elizabeth Phillips, Dan M. Roden, Joshua C. Denny, Wei-Qi Wei:
DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions. J. Am. Medical Informatics Assoc. 28(7): 1421-1430 (2021) - [j17]Neil S. Zheng, Jeremy L. Warner, Travis J. Osterman, Quinn Stanton 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. J. Biomed. Informatics 113: 103657 (2021) - [j16]Sarah DeLozier, Sarah Bland, Melissa McPheeters, Quinn Stanton Wells, Eric Farber-Eger, Cosmin Adrian Bejan, Daniel Fabbri, S. Trent Rosenbloom, Dan M. Roden, Kevin B. Johnson, Wei-Qi Wei, Josh F. Peterson, Lisa Bastarache:
Phenotyping coronavirus disease 2019 during a global health pandemic: Lessons learned from the characterization of an early cohort. J. Biomed. Informatics 117: 103777 (2021) - 2020
- [j15]Neil S. Zheng, QiPing Feng, Vern Eric Kerchberger, Juan Zhao, Todd L. Edwards, Nancy J. Cox, C. Michael Stein, Dan M. Roden, Joshua C. Denny, Wei-Qi Wei:
PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. J. Am. Medical Informatics Assoc. 27(11): 1675-1687 (2020) - [j14]Ryan L. Collins, Harrison Brand, Konrad J. Karczewski, Xuefang Zhao, Jessica Alföldi, Laurent C. Francioli, Amit V. Khera, Chelsea Lowther, Laura D. Gauthier, Harold Wang, Nicholas A. Watts, Matthew Solomonson, Alexander Baumann, Ruchi Munshi, Mark Walker, Christopher W. Whelan, Yongqing Huang, Ted Brookings, Ted Sharpe, Matthew R. Stone, Elise Valkanas, Jack Fu, Grace Tiao, Kristen M. Laricchia, Valentín Ruano-Rubio, Christine Stevens, Namrata Gupta, Caroline Cusick, Lauren Margolin, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Kristen M. Connolly, Miguel Covarrubias, Beryl B. Cummings, Mark J. Daly, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Stacey Gabriel, Jeff Gentry, Thibault Jeandet, Diane Kaplan, Christopher Llanwarne, Eric V. Minikel, Benjamin M. Neale, Sam Novod, Anne H. O'Donnell-Luria, Nikelle Petrillo, Timothy Poterba, David Roazen, Andrea Saltzman, Kaitlin E. Samocha, Molly Schleicher, Cotton Seed, José Soto, Kathleen Tibbetts, Charlotte Tolonen, Christopher Vittal, Gordon Wade, Arcturus Wang, Qingbo Wang, James S. Ware, Ben Weisburd, Nicola Whiffin, Carlos A. Aguilar Salinas, Tariq Ahmad, Christine M. Albert, Diego Ardissino, Gil Atzmon, John Barnard, Laurent Beaugerie, Emelia J. Benjamin, Michael Boehnke, Lori L. Bonnycastle, Erwin P. Bottinger, Donald W. Bowden, Matthew J. Bown, John C. Chambers, Juliana C. Chan, Daniel Chasman, Judy Cho, Mina K. Chung, Bruce Cohen, Adolfo Correa, Dana Dabelea, Dawood Darbar, Ravindranath Duggirala, Josée Dupuis, Patrick T. Ellinor, Roberto Elosua, Jeanette Erdmann, Tõnu Esko, Martti Färkkilä, Jose Florez, Andre Franke, Gad Getz, Benjamin Glaser, Stephen J. Glatt, David Goldstein, Clicerio Gonzalez, Leif Groop, Christopher A. Haiman, Craig Hanis, Matthew Harms, Mikko Hiltunen, Matti M. Holi, Christina M. Hultman, Mikko Kallela, Jaakko Kaprio, Sekar Kathiresan, Bong-Jo Kim, Young Jin Kim, George Kirov, Jaspal Kooner, Seppo Koskinen, Harlan M. Krumholz, Subra Kugathasan, Soo Heon Kwak, Markku Laakso, Terho Lehtimäki, Ruth J. F. Loos, Steven A. Lubitz, Ronald C. W. Ma, Daniel G. MacArthur, Jaume Marrugat, Kari M. Mattila, Steven A. McCarroll, Mark I. McCarthy, Dermot McGovern, Ruth McPherson, James B. Meigs, Olle Melander, Andres Metspalu, Peter M. Nilsson, Michael C. O'Donovan, Dost Öngür, Lorena Orozco, Michael J. Owen, Colin N. A. Palmer, Aarno Palotie, Kyong Soo Park, Carlos Pato, Ann E. Pulver, Nazneen Rahman, Anne M. Remes, John D. Rioux, Samuli Ripatti, Dan M. Roden, Danish Saleheen, Veikko Salomaa, Nilesh J. Samani, Jeremiah Scharf, Heribert Schunkert, Moore B. Shoemaker, Pamela Sklar, Hilkka Soininen, Harry Sokol, Tim Spector, Patrick F. Sullivan, Jaana Suvisaari, E. Shyong Tai, Yik Ying Teo, Tuomi Tiinamaija, Ming Tsuang, Dan Turner, Teresa Tusie-Luna, Erkki Vartiainen, Hugh Watkins, Rinse K. Weersma, Maija Wessman, James G. Wilson, Ramnik J. Xavier, Kent D. Taylor, Henry J. Lin, Stephen S. Rich, Wendy S. Post, Yii-Der Ida Chen, Jerome I. Rotter, Chad Nusbaum, Anthony A. Philippakis, Eric S. Lander, Michael E. Talkowski:
A structural variation reference for medical and population genetics. Nat. 581(7809): 444-451 (2020) - [c9]Sarah DeLozier, Peter Speltz, Jason Brito, Leigh Anne Tang, Janey Wang, Joshua C. Smith, Dario A. Giuse, Elizabeth Phillips, Kristina Williams, Teresa Strickland, Giovanni Davogustto, Dan M. Roden, Joshua C. Denny:
Real-time Clinical Note Monitoring to Detect Conditions for Follow-up: a Case Study of Clinical Trial Enrollment in Drug-induced Torsades de Pointes and Stevens-Johnson Syndrome. AMIA 2020 - [c8]Izabelle P. Humes, Roxana Loperena-Cortes, Melissa A. Basford, Kelsey R. Mayo, Joseph DiPaolo, David J. Schlueter, Jun Qian, Wei-Qi Wei, Robert J. Carroll, David Glazer, Paul A. Harris, Anthony A. Philippakis, Dan M. Roden, Andrea H. Ramirez:
The All of Us Research Program Researcher Workbench Phenotype Library: Five Disease Implementations. AMIA 2020 - [c7]Andrea H. Ramirez, Kelsey R. Mayo, Robert J. Carroll, Karthik Muthuraman, Melissa A. Basford, David Glazer, Paul A. Harris, Anthony A. Philippakis, Dan M. Roden:
The All of Us Research Program Researcher Workbench: Cloud based access and analytics to advance precision medicine. AMIA 2020
2010 – 2019
- 2019
- [j13]Lisa Bastarache, Jacob J. Hughey, Jeffery A. Goldstein, Julie A. Bastraache, Satya Das, Neil Charles Zaki, Chenjie Zeng, Leigh Anne Tang, Dan M. Roden, Joshua C. Denny:
Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease. J. Am. Medical Informatics Assoc. 26(12): 1437-1447 (2019) - 2018
- [j12]Joshua C. Smith, Qingxia Chen, Joshua C. Denny, Dan M. Roden, Kevin B. Johnson, Randolph A. Miller:
Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions. Appl. Clin. Inform. 09(02): 313-325 (2018) - [j11]Leena Choi, Robert J. Carroll, Cole Beck, Jonathan D. Mosley, Dan M. Roden, Joshua C. Denny, Sara L. Van Driest:
Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects. Bioinform. 34(17): 2988-2996 (2018) - [j10]Jennifer A. Pacheco, Luke V. Rasmussen, Richard C. Kiefer, Thomas R. Campion Jr., Peter Speltz, Robert J. Carroll, Sarah C. Stallings, Huan Mo, Monika Ahuja, Guoqian Jiang, Eric R. LaRose, Peggy L. Peissig, Ning Shang, Barbara Benoit, Vivian S. Gainer, Kenneth Borthwick, Kathryn L. Jackson, Ambrish Sharma, Andy Yizhou Wu, Abel N. Kho, Dan M. Roden, Jyotishman Pathak, Joshua C. Denny, William K. Thompson:
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments. J. Am. Medical Informatics Assoc. 25(11): 1540-1546 (2018) - 2017
- [j9]Pedro L. Teixeira, Wei-Qi Wei, Robert M. Cronin, Huan Mo, Jacob P. VanHouten, Robert J. Carroll, Eric LaRose, Lisa Bastarache, S. Trent Rosenbloom, Todd L. Edwards, Dan M. Roden, Thomas A. Lasko, Richard A. Dart, Anne M. Nikolai, Peggy L. Peissig, Joshua C. Denny:
Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals. J. Am. Medical Informatics Assoc. 24(1): 162-171 (2017) - [c6]Hee-Jin Lee, Min Jiang, Yonghui Wu, Christian Shaffer, John H. Cleator, Eitan Friedman, Joshua P. Lewis, Dan M. Roden, Joshua C. Denny, Hua Xu:
A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. CRI 2017 - [c5]Laura K. Wiley, Jacob P. VanHouten, David Samuels, Melinda Aldrich, Dan M. Roden, Josh F. Peterson, Joshua C. Denny:
Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population. PSB 2017: 545-556 - 2016
- [j8]Jacqueline Kirby, Peter Speltz, Luke V. Rasmussen, Melissa A. Basford, Omri Gottesman, Peggy L. Peissig, Jennifer A. Pacheco, Gerard Tromp, Jyotishman Pathak, David S. Carrell, Stephen B. Ellis, Todd Lingren, William K. Thompson, Guergana Savova, Jonathan L. Haines, Dan M. Roden, Paul A. Harris, Joshua C. Denny:
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J. Am. Medical Informatics Assoc. 23(6): 1046-1052 (2016) - 2015
- [j7]Hua Xu, Melinda C. Aldrich, Qingxia Chen, Hongfang Liu, Neeraja B. Peterson, Qi Dai, Mia A. Levy, Anushi Shah, Han Xue, Xiaoyang Ruan, Min Jiang, Ying Li, Jamii St Julien, Jeremy L. Warner, Carol Friedman, Dan M. Roden, Joshua C. Denny:
Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J. Am. Medical Informatics Assoc. 22(1): 179-191 (2015) - [j6]Huan Mo, William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Guoqian Jiang, Richard C. Kiefer, Qian Zhu, Jie Xu, Enid N. H. Montague, David S. Carrell, Todd Lingren, Frank D. Mentch, Yizhao Ni, Firas H. Wehbe, Peggy L. Peissig, Gerard Tromp, Eric B. Larson, Christopher G. Chute, Jyotishman Pathak, Joshua C. Denny, Peter Speltz, Abel N. Kho, Gail P. Jarvik, Cosmin Adrian Bejan, Marc S. Williams, Kenneth Borthwick, Terrie E. Kitchner, Dan M. Roden, Paul A. Harris:
Desiderata for computable representations of electronic health records-driven phenotype algorithms. J. Am. Medical Informatics Assoc. 22(6): 1220-1230 (2015) - [j5]Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu, Zhongming Zhao:
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput. Biol. 11(6) (2015) - 2014
- [j4]Raymond Heatherly, Joshua C. Denny, Jonathan L. Haines, Dan M. Roden, Bradley A. Malin:
Size matters: How population size influences genotype-phenotype association studies in anonymized data. J. Biomed. Informatics 52: 243-250 (2014) - [c4]Janina M. Jeff, Kristin Brown-Gentry, Robert J. Goodloe, Marylyn D. Ritchie, Joshua C. Denny, Abel N. Kho, Loren L. Armstrong, Bob McClellan Jr., Ping Mayo, Melissa Allen, Hailing Jin, Niloufar B. Gillani, Nathalie Schnetz-Boutaud, Holli H. Dilks, Melissa A. Basford, Jennifer A. Pacheco, Gail P. Jarvik, Rex L. Chisholm, Dan M. Roden, M. Geoffrey Hayes, Dana C. Crawford:
Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies. EvoApplications 2014: 939-951 - [c3]Matthew Oetjens, William S. Bush, Kelly A. Birdwell, Holli H. Dilks, Erica A. Bowton, Joshua C. Denny, Russell A. Wilke, Dan M. Roden, Dana C. Crawford:
Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients. Pacific Symposium on Biocomputing 2014: 253-264 - 2011
- [j3]Hua Xu, Min Jiang, Matthew Oetjens, Erica A. Bowton, Andrea H. Ramirez, Janina M. Jeff, Melissa A. Basford, Jill M. Pulley, James D. Cowan, Xiaoming Wang, Marylyn D. Ritchie, Daniel R. Masys, Dan M. Roden, Dana C. Crawford, Joshua C. Denny:
Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. J. Am. Medical Informatics Assoc. 18(4): 387-391 (2011) - [c2]Sarah A. Pendergrass, Scott M. Dudek, Dan M. Roden, Dana C. Crawford, Marylyn D. Ritchie:
Visual Integration of Results from a Large Dna Biobank (Biovu) Using Synthesis-View. Pacific Symposium on Biocomputing 2011: 265-275 - 2010
- [j2]Joshua C. Denny, Marylyn D. Ritchie, Melissa A. Basford, Jill M. Pulley, Lisa Bastarache, Kristin Brown-Gentry, Deede Wang, Daniel R. Masys, Dan M. Roden, Dana C. Crawford:
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinform. 26(9): 1205-1210 (2010) - [j1]Jonathan S. Schildcrout, Melissa A. Basford, Jill M. Pulley, Daniel R. Masys, Dan M. Roden, Deede Wang, Christopher G. Chute, Iftikhar J. Kullo, David Carrell, Peggy L. Peissig, Abel N. Kho, Joshua C. Denny:
An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records. J. Biomed. Informatics 43(6): 914-923 (2010)
2000 – 2009
- 2006
- [c1]Alison A. Motsinger, Brian S. Donahue, Nancy J. Brown, Dan M. Roden, Marylyn D. Ritchie:
Risk Factor Interactions and Genetic Effects Associated with Post-Operative Atrial Fibrillation. Pacific Symposium on Biocomputing 2006: 584-595
Coauthor Index
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