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GRAPE for fast and scalable graph processing and random-walk-based embedding.
Cappelletti L, Fontana T, Casiraghi E, Ravanmehr V, Callahan TJ, Cano C, Joachimiak MP, Mungall CJ, Robinson PN, Reese J, Valentini G. Cappelletti L, et al. Among authors: mungall cj. Nat Comput Sci. 2023 Jun;3(6):552-568. doi: 10.1038/s43588-023-00465-8. Epub 2023 Jun 26. Nat Comput Sci. 2023. PMID: 38177435 Free PMC article.
Unifying the identification of biomedical entities with the Bioregistry.
Hoyt CT, Balk M, Callahan TJ, Domingo-Fernández D, Haendel MA, Hegde HB, Himmelstein DS, Karis K, Kunze J, Lubiana T, Matentzoglu N, McMurry J, Moxon S, Mungall CJ, Rutz A, Unni DR, Willighagen E, Winston D, Gyori BM. Hoyt CT, et al. Among authors: mungall cj. Sci Data. 2022 Nov 19;9(1):714. doi: 10.1038/s41597-022-01807-3. Sci Data. 2022. PMID: 36402838 Free PMC article.
Phenopacket-tools: Building and validating GA4GH Phenopackets.
Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. Danis D, et al. Among authors: mungall cj. PLoS One. 2023 May 17;18(5):e0285433. doi: 10.1371/journal.pone.0285433. eCollection 2023. PLoS One. 2023. PMID: 37196000 Free PMC article.
An evaluation of GPT models for phenotype concept recognition.
Groza T, Caufield H, Gration D, Baynam G, Haendel MA, Robinson PN, Mungall CJ, Reese JT. Groza T, et al. Among authors: mungall cj. BMC Med Inform Decis Mak. 2024 Jan 31;24(1):30. doi: 10.1186/s12911-024-02439-w. BMC Med Inform Decis Mak. 2024. PMID: 38297371 Free PMC article.
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.
Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, Kim H, Moxon S, Reese JT, Haendel MA, Robinson PN, Mungall CJ. Caufield JH, et al. Among authors: mungall cj. Bioinformatics. 2024 Mar 4;40(3):btae104. doi: 10.1093/bioinformatics/btae104. Bioinformatics. 2024. PMID: 38383067 Free PMC article.
An open source knowledge graph ecosystem for the life sciences.
Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA Jr, Hunter LE. Callahan TJ, et al. Among authors: mungall cj. Sci Data. 2024 Apr 11;11(1):363. doi: 10.1038/s41597-024-03171-w. Sci Data. 2024. PMID: 38605048 Free PMC article.
Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests.
Chan LE, Casiraghi E, Reese J, Harmon QE, Schaper K, Hegde H, Valentini G, Schmitt C, Motsinger-Reif A, Hall JE, Mungall CJ, Robinson PN, Haendel MA. Chan LE, et al. Among authors: mungall cj. Int J Med Inform. 2024 Jul;187:105461. doi: 10.1016/j.ijmedinf.2024.105461. Epub 2024 Apr 17. Int J Med Inform. 2024. PMID: 38643701 Free PMC article.
A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery.
Danis D, Bamshad MJ, Bridges Y, Caballero-Oteyza A, Cacheiro P, Carmody LC, Chimirri L, Chong JX, Coleman B, Dalgleish R, Freeman PJ, Graefe ASL, Groza T, Hansen P, Jacobsen JOB, Klocperk A, Kusters M, Ladewig MS, Marcello AJ, Mattina T, Mungall CJ, Munoz-Torres MC, Reese JT, Rehburg F, Reis BCS, Schuetz C, Smedley D, Strauss T, Sundaramurthi JC, Thun S, Wissink K, Wagstaff JF, Zocche D, Haendel MA, Robinson PN. Danis D, et al. Among authors: mungall cj. HGG Adv. 2025 Jan 9;6(1):100371. doi: 10.1016/j.xhgg.2024.100371. Epub 2024 Oct 10. HGG Adv. 2025. PMID: 39394689 Free PMC article.
Efficient reinterpretation of rare disease cases using Exomiser.
Vestito L, Jacobsen JOB, Walker S, Cipriani V, Harris NL, Haendel MA, Mungall CJ, Robinson P, Smedley D. Vestito L, et al. Among authors: mungall cj. NPJ Genom Med. 2024 Dec 18;9(1):65. doi: 10.1038/s41525-024-00456-2. NPJ Genom Med. 2024. PMID: 39695184 Free PMC article.
175 results