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Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context.
Darnell SS, Overall RW, Guarracino A, Colonna V, Villani F, Garrison E, Isaac A, Muli P, Muriithi FM, Kabui A, Kilyungi M, Lisso F, Kibet A, Muhia B, Nijveen H, Yousefi S, Ashbrook D, Huang P, Suh GE, Umar M, Batten C, Chen H, Sen Ś, Williams RW, Prins P. Darnell SS, et al. Among authors: prins p. bioRxiv [Preprint]. 2024 Oct 21:2024.10.16.618663. doi: 10.1101/2024.10.16.618663. bioRxiv. 2024. PMID: 39463999 Free PMC article. Preprint.
Building pangenome graphs.
Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Nahnsen S, Yang Z, Mwaniki MN, Nobrega FL, Wu Y, Chen H, de Ligt J, Sudmant PH, Soranzo N, Colonna V, Williams RW, Prins P. Garrison E, et al. Among authors: prins p. bioRxiv [Preprint]. 2024 Oct 2:2023.04.05.535718. doi: 10.1101/2023.04.05.535718. bioRxiv. 2024. Update in: Nat Methods. 2024 Nov;21(11):2008-2012. doi: 10.1038/s41592-024-02430-3. PMID: 37066137 Free PMC article. Updated. Preprint.
ODGI: understanding pangenome graphs.
Guarracino A, Heumos S, Nahnsen S, Prins P, Garrison E. Guarracino A, et al. Among authors: prins p. Bioinformatics. 2022 Jun 27;38(13):3319-3326. doi: 10.1093/bioinformatics/btac308. Bioinformatics. 2022. PMID: 35552372 Free PMC article.
Pangenome graph layout by Path-Guided Stochastic Gradient Descent.
Heumos S, Guarracino A, Schmelzle JM, Li J, Zhang Z, Hagmann J, Nahnsen S, Prins P, Garrison E. Heumos S, et al. Among authors: prins p. Bioinformatics. 2024 Jul 1;40(7):btae363. doi: 10.1093/bioinformatics/btae363. Bioinformatics. 2024. PMID: 38960860 Free PMC article.
GeneNetwork: A Toolbox for Systems Genetics.
Mulligan MK, Mozhui K, Prins P, Williams RW. Mulligan MK, et al. Among authors: prins p. Methods Mol Biol. 2017;1488:75-120. doi: 10.1007/978-1-4939-6427-7_4. Methods Mol Biol. 2017. PMID: 27933521 Free PMC article.
Speeding up eQTL scans in the BXD population using GPUs.
Trotter C, Kim H, Farage G, Prins P, Williams RW, Broman KW, Sen Ś. Trotter C, et al. Among authors: prins p. G3 (Bethesda). 2021 Dec 8;11(12):jkab254. doi: 10.1093/g3journal/jkab254. G3 (Bethesda). 2021. PMID: 34499130 Free PMC article.
GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships.
Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P, Chen H. Gunturkun MH, et al. Among authors: prins p. G3 (Bethesda). 2022 May 6;12(5):jkac059. doi: 10.1093/g3journal/jkac059. G3 (Bethesda). 2022. PMID: 35285473 Free PMC article.
226 results