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KG-Hub-building and exchanging biological knowledge graphs.
Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. Caufield JH, et al. Bioinformatics. 2023 Jul 1;39(7):btad418. doi: 10.1093/bioinformatics/btad418. Bioinformatics. 2023. PMID: 37389415 Free PMC article.
Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes.
Reese JT, Blau H, Casiraghi E, Bergquist T, Loomba JJ, Callahan TJ, Laraway B, Antonescu C, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Caufield JH, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN; N3C Consortium; RECOVER Consortium. Reese JT, et al. Among authors: caufield jh. EBioMedicine. 2023 Jan;87:104413. doi: 10.1016/j.ebiom.2022.104413. Epub 2022 Dec 21. EBioMedicine. 2023. PMID: 36563487 Free PMC article.
Gene Set Summarization using Large Language Models.
Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Joachimiak MP, et al. Among authors: caufield jh. ArXiv [Preprint]. 2023 May 25:arXiv:2305.13338v2. ArXiv. 2023. PMID: 37292480 Free PMC article. Preprint.
Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning.
Cappelletti L, Rekerle L, Fontana T, Hansen P, Casiraghi E, Ravanmehr V, Mungall CJ, Yang JJ, Spranger L, Karlebach G, Caufield JH, Carmody L, Coleman B, Oprea TI, Reese J, Valentini G, Robinson PN. Cappelletti L, et al. Among authors: caufield jh. Bioinform Adv. 2024 Mar 4;4(1):vbae036. doi: 10.1093/bioadv/vbae036. eCollection 2024. Bioinform Adv. 2024. PMID: 38577542 Free PMC article.
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.
Putman TE, Schaper K, Matentzoglu N, Rubinetti VP, Alquaddoomi FS, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese JT, Braun I, Bruskiewich RM, Cappelletti L, Carbon S, Caron AR, Chan LE, Chute CG, Cortes KG, De Souza V, Fontana T, Harris NL, Hartley EL, Hurwitz E, Jacobsen JOB, Krishnamurthy M, Laraway BJ, McLaughlin JA, McMurry JA, Moxon SAT, Mullen KR, O'Neil ST, Shefchek KA, Stefancsik R, Toro S, Vasilevsky NA, Walls RL, Whetzel PL, Osumi-Sutherland D, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC. Putman TE, et al. Among authors: caufield jh. Nucleic Acids Res. 2024 Jan 5;52(D1):D938-D949. doi: 10.1093/nar/gkad1082. Nucleic Acids Res. 2024. PMID: 38000386 Free PMC article.
The Human Phenotype Ontology in 2024: phenotypes around the world.
Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Čady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He YO, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Čajbiková NN, Nurnberger JI Jr, Og… See abstract for full author list ➔ Gargano MA, et al. Among authors: caufield jh. Nucleic Acids Res. 2024 Jan 5;52(D1):D1333-D1346. doi: 10.1093/nar/gkad1005. Nucleic Acids Res. 2024. PMID: 37953324 Free PMC article.
On the limitations of large language models in clinical diagnosis.
Reese JT, Danis D, Caufield JH, Groza T, Casiraghi E, Valentini G, Mungall CJ, Robinson PN. Reese JT, et al. Among authors: caufield jh. medRxiv [Preprint]. 2024 Feb 26:2023.07.13.23292613. doi: 10.1101/2023.07.13.23292613. medRxiv. 2024. PMID: 37503093 Free PMC article. Preprint.
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. Among authors: caufield jh. 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.
31 results