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‎publications_selected.md‎

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Niyonkuru E, <b>Caufield JH</b>, Carmody LC, Gargano MA, Toro S, Whetzel PL, Blau H, Gomez MS, Casiraghi E, Chimirri L, <b>Reese JT</b>, Valentini G, Haendel MA, <b>Mungall CJ</b>, Robinson PN. Leveraging generative AI to accelerate biocuration of medical actions for rare disease. medRxiv. 2024 Aug 22; http://dx.doi.org/10.1101/2024.08.22.24310814 PMCID: PMC11370550
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Chan LE, Casiraghi E, Reese J, Harmon QE, Schaper K, Hegde H, Valentini G, Schmitt C, Motsinger-Reif A, Hall JE, <b>Mungall CJ</b>, Robinson PN, Haendel MA. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. Int J Med Inform. 2024 Jul;187:105461. http://dx.doi.org/10.1016/j.ijmedinf.2024.105461 PMCID: PMC11188727
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Chan LE, Casiraghi E, <b>Reese J</b>, Harmon QE, Schaper K, Hegde H, Valentini G, Schmitt C, Motsinger-Reif A, Hall JE, <b>Mungall CJ</b>, Robinson PN, Haendel MA. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. Int J Med Inform. 2024 Jul;187:105461. http://dx.doi.org/10.1016/j.ijmedinf.2024.105461 PMCID: PMC11188727
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Bridges YS, de Souza V, Cortes KG, Haendel M, <b>Harris NL</b>, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, <b>Mungall CJ</b>, Osumi-Sutherland DJ, Robinson PN, Smedley D, Jacobsen JOB. Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. bioRxiv. 2024. p. 2024.06.13.598672. https://www.biorxiv.org/content/10.1101/2024.06.13.598672v1
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Mullen KR, Tammen I, Matentzoglu NA, Mather M, <b>Mungall CJ</b>, Haendel MA, Nicholas FW, Toro S, Vertebrate Breed Ontology Consortium, the. The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization. arXiv e-prints. 2024 Jun 1;arXiv:2406.02623. https://ui.adsabs.harvard.edu/abs/2024arXiv240602623M
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Avaylon M, Ly R, Tritt A, Dichter B, Bouchard KE, <b>Mungall CJ</b>, Ruebel O. Methods for linking data to online resources and ontologies with applications to neurophysiology. ArXiv. 2024 May 30;abs/2406.00063. http://dx.doi.org/10.48550/arXiv.2406.00063
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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, <b>Mungall CJ</b>, 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. An open source knowledge graph ecosystem for the life sciences. Sci Data. 2024 Apr 11;11(1):363. http://dx.doi.org/10.1038/s41597-024-03171-w PMCID: PMC11009265
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Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, <b></b>Reese J</b>, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, <b>Mungall CJ</b>, 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. An open source knowledge graph ecosystem for the life sciences. Sci Data. 2024 Apr 11;11(1):363. http://dx.doi.org/10.1038/s41597-024-03171-w PMCID: PMC11009265
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Joachimiak MP, Miller MA, Harry Caufield J, Ly R, <b>Harris NL</b>, Tritt A, <b>Mungall CJ</b>, Bouchard KE. The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies. arXiv [cs.LG]. 2024. http://arxiv.org/abs/2404.03044
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<b>Joachimiak MP, Miller MA, Harry Caufield J</b>, Ly R, <b>Harris NL</b>, Tritt A, <b>Mungall CJ</b>, Bouchard KE. The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies. arXiv [cs.LG]. 2024. http://arxiv.org/abs/2404.03044
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Wright A, Wilkinson MD, <b>Mungall CJ</b>, Cain S, Richards S, Sternberg P, Provin E, Jacobs JL, Geib S, Raciti D, Yook K, Stein L, Molik DC. FAIR Header Reference genome: a TRUSTworthy standard. Brief Bioinform. 2024 Mar 27;25(3). http://dx.doi.org/10.1093/bib/bbae122 PMCID: PMC10981671
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Cappelletti L, Rekerle L, Fontana T, Hansen P, Casiraghi E, Ravanmehr V, <b>Mungall CJ</b>, Yang J, Spranger L, Karlebach G, <b>Caufield JH</b>, Carmody L, Coleman B, Oprea T, <b>Reese J</b>b>, Valentini G, Robinson PN. Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning. Bioinform Adv. 2024 Mar 4; https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae036/7619101
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Cappelletti L, Rekerle L, Fontana T, Hansen P, Casiraghi E, Ravanmehr V, <b>Mungall CJ</b>, Yang J, Spranger L, Karlebach G, <b>Caufield JH</b>, Carmody L, Coleman B, Oprea T, Reese J, Valentini G, Robinson PN. Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning. Bioinform Adv. 2024 Mar 4; https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae036/7619101
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<b>Caufield JH</b>, Hegde H, Emonet V, <b>Harris NL</b>, Joachimiak MP, Matentzoglu N, Kim H, Moxon S, <b>Reese JT</b>, Haendel MA, Robinson PN, <b>Mungall CJ</b>. Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinformatics. 2024 Mar 4;40(3). http://dx.doi.org/10.1093/bioinformatics/btae104 PMCID: PMC10924283
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<b>Caufield JH</b>, Hegde H, Emonet V, <b>Harris NL</b>, <b>Joachimiak MP</b>, Matentzoglu N, Kim H, <b>Moxon S</b>, <b>Reese JT</b>, Haendel MA, Robinson PN, <b>Mungall CJ</b>. Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinformatics. 2024 Mar 4;40(3). http://dx.doi.org/10.1093/bioinformatics/btae104 PMCID: PMC10924283
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<b>Reese JT</b>, Danis D, <b>Caufield JH</b>, Groza T, Casiraghi E, Valentini G, <b>Mungall CJ</b>, Robinson PN. On the limitations of large language models in clinical diagnosis. medRxiv. 2024 Feb 26; http://dx.doi.org/10.1101/2023.07.13.23292613 PMCID: PMC10370243
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Eloe-Fadrosh EA, <b>Mungall CJ</b>, Miller MA, Smith M, Patil SS, Kelliher JM, Johnson LYD, Rodriguez FE, Chain PSG, Hu B, Thornton MB, McCue LA, McHardy AC, <b>Harris NL</b>, Reddy TBK, Mukherjee S, Hunter CI, Walls R, Schriml LM. A practical approach to using the Genomic Standards Consortium MIxS reporting standard for comparative genomics and metagenomics. Methods Mol Biol. 2024;2802:587–609. https://link.springer.com/protocol/10.1007/978-1-0716-3838-5_20 PMID: 38819573
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Eloe-Fadrosh EA, <b>Mungall CJ</b>, <b>Miller MA</b>, Smith M, Patil SS, Kelliher JM, Johnson LYD, Rodriguez FE, Chain PSG, Hu B, Thornton MB, McCue LA, McHardy AC, <b>Harris NL</b>, Reddy TBK, Mukherjee S, Hunter CI, Walls R, Schriml LM. A practical approach to using the Genomic Standards Consortium MIxS reporting standard for comparative genomics and metagenomics. Methods Mol Biol. 2024;2802:587–609. https://link.springer.com/protocol/10.1007/978-1-0716-3838-5_20 PMID: 38819573
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O’Neil ST, Schaper K, Elsarboukh G, <b>Reese JT, Moxon SAT, Harris NL</b>, Munoz-Torres MC, Robinson PN, Haendel MA, <b>Mungall CJ</b>. Phenomics Assistant: An Interface for LLM-based Biomedical Knowledge Graph Exploration. bioRxiv. 2024. p. 2024.01.31.578275. <a target="_new" href="https://www.biorxiv.org/content/biorxiv/early/2024/02/02/2024.01.31.578275">https://www.biorxiv.org/content/biorxiv/early/2024/02/02/2024.01.31.578275</a></li><li>
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Groza T, <b>Caufield H</b>, Gration D, Baynam G, Haendel MA, Robinson PN, <b>Mungall CJ, Reese JT</b>. An evaluation of GPT models for phenotype concept recognition. BMC Med Inform Decis Mak. BioMed Central; 2024 Jan 31;24(1):1–12. <a target="_new" href="https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-024-02439-w">https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-024-02439-w</a></li><li>
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<b>Harris NL</b>, Fields CJ, Hokamp K, Just J, Khetani R, Maia J, Ménager H, Munoz-Torres MC, Unni D, Williams J. BOSC 2023, the 24th annual Bioinformatics Open Source Conference. F1000Res. F1000 Research Ltd; 2023 Dec 7;12:1568. <a target="_new" href="https://f1000research.com/articles/12-1568/pdf">https://f1000research.com/articles/12-1568/pdf</a></li><li>

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