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Current Limitations of Electronic Health Record Systems in Supporting Pragmatic Clinical Trials: Insights from the eMERGE Consortium.
Wagholikar KB, Pacheco JA, Gordon AS, Khan A, Khales BN, Benoit B, Kerman BJ, Weng C, Ta C, Prows CA, Johnson R, Roden DM, Crosslin D, McNally EM, Karlson EW, Mentch F, Jarvik GP, Wiesner GL, Hakonarson H, Cimino JJ, Thayer JG, Smoller JW, Linder JE, Connolly J, Peterson JF, Cortopassi J, Kiryluk K, Hamed M, Maradik M, Puckelwartz MJ, Naderian M, Walton N, Limdi N, Maripuri DP, Walunas T, Gainer V, Luo Y, Liu C, Kenny EE, Espinoza A, Rowley R, Wei WQ, Murphy SN. Wagholikar KB, et al. Among authors: benoit b. medRxiv [Preprint]. 2025 Apr 3:2025.04.01.25325049. doi: 10.1101/2025.04.01.25325049. medRxiv. 2025. PMID: 40236425 Free PMC article. Preprint.
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments.
Pacheco JA, Rasmussen LV, Kiefer RC, Campion TR, Speltz P, Carroll RJ, Stallings SC, Mo H, Ahuja M, Jiang G, LaRose ER, Peissig PL, Shang N, Benoit B, Gainer VS, Borthwick K, Jackson KL, Sharma A, Wu AY, Kho AN, Roden DM, Pathak J, Denny JC, Thompson WK. Pacheco JA, et al. Among authors: benoit b. J Am Med Inform Assoc. 2018 Nov 1;25(11):1540-1546. doi: 10.1093/jamia/ocy101. J Am Med Inform Assoc. 2018. PMID: 30124903 Free PMC article.
GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network.
Namjou B, Lingren T, Huang Y, Parameswaran S, Cobb BL, 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. Namjou B, et al. Among authors: benoit b. BMC Med. 2019 Jul 17;17(1):135. doi: 10.1186/s12916-019-1364-z. BMC Med. 2019. PMID: 31311600 Free PMC article.
Facilitating phenotype transfer using a common data model.
Hripcsak G, Shang N, Peissig PL, Rasmussen LV, Liu C, Benoit B, Carroll RJ, Carrell DS, Denny JC, Dikilitas O, Gainer VS, Howell KM, Klann JG, Kullo IJ, Lingren T, Mentch FD, Murphy SN, Natarajan K, Pacheco JA, Wei WQ, Wiley K, Weng C. Hripcsak G, et al. Among authors: benoit b. J Biomed Inform. 2019 Aug;96:103253. doi: 10.1016/j.jbi.2019.103253. Epub 2019 Jul 17. J Biomed Inform. 2019. PMID: 31325501 Free PMC article.
Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network.
Shang N, Liu C, Rasmussen LV, Ta CN, Caroll RJ, Benoit B, Lingren T, Dikilitas O, Mentch FD, Carrell DS, Wei WQ, Luo Y, Gainer VS, Kullo IJ, Pacheco JA, Hakonarson H, Walunas TL, Denny JC, Wiley K, Murphy SN, Hripcsak G, Weng C. Shang N, et al. Among authors: benoit b. J Biomed Inform. 2019 Nov;99:103293. doi: 10.1016/j.jbi.2019.103293. Epub 2019 Sep 19. J Biomed Inform. 2019. PMID: 31542521 Free PMC article.
Development of a COVID-19 Application Ontology for the ACT Network.
Visweswaran S, Samayamuthu MJ, Morris M, Weber GM, MacFadden D, Trevvett P, Klann JG, Gainer V, Benoit B, Murphy SN, Patel L, Mirkovic N, Borovskiy Y, Johnson RD, Wyatt MC, Wang AY, Follett RW, Chau N, Zhu W, Abajian M, Chuang A, Bahroos N, Reeder P, Xie D, Cai J, Sendro ER, Toto RD, Firestein GS, Nadler LM, Reis SE. Visweswaran S, et al. Among authors: benoit b. medRxiv [Preprint]. 2021 Apr 14:2021.03.15.21253596. doi: 10.1101/2021.03.15.21253596. medRxiv. 2021. Update in: JAMIA Open. 2021 Apr 19;4(2):ooab036. doi: 10.1093/jamiaopen/ooab036. PMID: 33791734 Free PMC article. Updated. Preprint.
Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies.
Shang N, Khan A, Polubriaginof F, Zanoni F, Mehl K, Fasel D, Drawz PE, Carrol RJ, Denny JC, Hathcock MA, Arruda-Olson AM, Peissig PL, Dart RA, Brilliant MH, Larson EB, Carrell DS, Pendergrass S, Verma SS, Ritchie MD, Benoit B, Gainer VS, Karlson EW, Gordon AS, Jarvik GP, Stanaway IB, Crosslin DR, Mohan S, Ionita-Laza I, Tatonetti NP, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Shang N, et al. Among authors: benoit b. NPJ Digit Med. 2021 Apr 13;4(1):70. doi: 10.1038/s41746-021-00428-1. NPJ Digit Med. 2021. PMID: 33850243 Free PMC article.
Neptune: an environment for the delivery of genomic medicine.
Eric V, Yi V, Murdock D, Kalla SE, Wu TJ, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei WQ, Chung WK, Weng C, Wiesner GL, Jarvik GP, Muzny D, Gibbs RA; eMERGE Consortium. Eric V, et al. Genet Med. 2021 Oct;23(10):1838-1846. doi: 10.1038/s41436-021-01230-w. Epub 2021 Jul 13. Genet Med. 2021. PMID: 34257418 Free PMC article.
Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions.
Yu J, Pacheco JA, Ghosh AS, Luo Y, Weng C, Shang N, Benoit B, Carrell DS, Carroll RJ, Dikilitas O, Freimuth RR, Gainer VS, Hakonarson H, Hripcsak G, Kullo IJ, Mentch F, Murphy SN, Peissig PL, Ramirez AH, Walton N, Wei WQ, Rasmussen LV. Yu J, et al. Among authors: benoit b. BMC Med Inform Decis Mak. 2022 Jan 28;22(1):23. doi: 10.1186/s12911-022-01759-z. BMC Med Inform Decis Mak. 2022. PMID: 35090449 Free PMC article.
316 results