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An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges.
Fecho K, Bizon C, Issabekova T, Moxon S, Thessen AE, Abdollahi S, Baranzini SE, Belhu B, Byrd WE, Chung L, Crouse A, Duby MP, Ferguson S, Foksinska A, Forero L, Friedman J, Gardner V, Glusman G, Hadlock J, Hanspers K, Hinderer E, Hobbs C, Hyde G, Huang S, Koslicki D, Mease P, Muller S, Mungall CJ, Ramsey SA, Roach J, Rubin I, Schurman SH, Shalev A, Smith B, Soman K, Stemann S, Su AI, Ta C, Watkins PB, Williams MD, Wu C, Xu CH; Biomedical Data Translator Consortium. Fecho K, et al. Among authors: smith b. J Clin Transl Sci. 2023 Sep 14;7(1):e214. doi: 10.1017/cts.2023.619. eCollection 2023. J Clin Transl Sci. 2023. PMID: 37900350 Free PMC article.
Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity.
Dai CL, Kornilov SA, Roper RT, Cohen-Cline H, Jade K, Smith B, Heath JR, Diaz G, Goldman JD, Magis AT, Hadlock JJ. Dai CL, et al. Among authors: smith b. medRxiv [Preprint]. 2021 Feb 12:2020.10.14.20212803. doi: 10.1101/2020.10.14.20212803. medRxiv. 2021. Update in: Clin Infect Dis. 2021 Dec 16;73(12):2193-2204. doi: 10.1093/cid/ciab154 PMID: 33594379 Free PMC article. Updated. Preprint.
Progress toward a universal biomedical data translator.
Fecho K, Thessen AE, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Dančík V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, Hyde G, Johs A, Su AI, Qin G, Zhu Q; Biomedical Data Translator Consortium. Fecho K, et al. Clin Transl Sci. 2022 Aug;15(8):1838-1847. doi: 10.1111/cts.13301. Epub 2022 Jun 6. Clin Transl Sci. 2022. PMID: 35611543 Free PMC article. Review.
A biomedical open knowledge network harnesses the power of AI to understand deep human biology.
Baranzini SE, Börner K, Morris J, Nelson CA, Soman K, Schleimer E, Keiser M, Musen M, Pearce R, Reza T, Smith B, Herr BW 2nd, Oskotsky B, Rizk-Jackson A, Rankin KP, Sanders SJ, Bove R, Rose PW, Israni S, Huang S. Baranzini SE, et al. Among authors: smith b. AI Mag. 2022 Spring;43(1):46-58. doi: 10.1002/aaai.12037. Epub 2022 Mar 31. AI Mag. 2022. PMID: 36093122 Free PMC article.
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.
Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ; Biomedical Data Translator Consortium. Unni DR, et al. Clin Transl Sci. 2022 Aug;15(8):1848-1855. doi: 10.1111/cts.13302. Epub 2022 Jun 6. Clin Transl Sci. 2022. PMID: 36125173 Free PMC article. Review.
Biomedical knowledge graph-optimized prompt generation for large language models.
Soman K, Rose PW, Morris JH, Akbas RE, Smith B, Peetoom B, Villouta-Reyes C, Cerono G, Shi Y, Rizk-Jackson A, Israni S, Nelson CA, Huang S, Baranzini SE. Soman K, et al. Among authors: smith b. Bioinformatics. 2024 Sep 2;40(9):btae560. doi: 10.1093/bioinformatics/btae560. Bioinformatics. 2024. PMID: 39288310 Free PMC article.
Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19.
Lee JW, Su Y, Baloni P, Chen D, Pavlovitch-Bedzyk AJ, Yuan D, Duvvuri VR, Ng RH, Choi J, Xie J, Zhang R, Murray K, Kornilov S, Smith B, Magis AT, Hoon DSB, Hadlock JJ, Goldman JD, Price ND, Gottardo R, Davis MM, Hood L, Greenberg PD, Heath JR. Lee JW, et al. Among authors: smith b. Nat Biotechnol. 2022 Jan;40(1):110-120. doi: 10.1038/s41587-021-01020-4. Epub 2021 Sep 6. Nat Biotechnol. 2022. PMID: 34489601 Free PMC article.
Multiple early factors anticipate post-acute COVID-19 sequelae.
Su Y, Yuan D, Chen DG, Ng RH, Wang K, Choi J, Li S, Hong S, Zhang R, Xie J, Kornilov SA, Scherler K, Pavlovitch-Bedzyk AJ, Dong S, Lausted C, Lee I, Fallen S, Dai CL, Baloni P, Smith B, Duvvuri VR, Anderson KG, Li J, Yang F, Duncombe CJ, McCulloch DJ, Rostomily C, Troisch P, Zhou J, Mackay S, DeGottardi Q, May DH, Taniguchi R, Gittelman RM, Klinger M, Snyder TM, Roper R, Wojciechowska G, Murray K, Edmark R, Evans S, Jones L, Zhou Y, Rowen L, Liu R, Chour W, Algren HA, Berrington WR, Wallick JA, Cochran RA, Micikas ME; ISB-Swedish COVID-19 Biobanking Unit; Wrin T, Petropoulos CJ, Cole HR, Fischer TD, Wei W, Hoon DSB, Price ND, Subramanian N, Hill JA, Hadlock J, Magis AT, Ribas A, Lanier LL, Boyd SD, Bluestone JA, Chu H, Hood L, Gottardo R, Greenberg PD, Davis MM, Goldman JD, Heath JR. Su Y, et al. Among authors: smith b. Cell. 2022 Mar 3;185(5):881-895.e20. doi: 10.1016/j.cell.2022.01.014. Epub 2022 Jan 25. Cell. 2022. PMID: 35216672 Free PMC article.
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