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fix minor formatting issue and remove some duplicate publications
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* **Mungall CJ**, Malik A, Korn DR, **Reese JT**, O’Boyle NM, Hastings J. Chemical classification program synthesis using generative artificial intelligence. Journal of Cheminformatics, 2025 Oct 1;17(1). http://dx.doi.org/10.1186/s13321-025-01092-3
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* Sierk M, Danis D, **Patil S,** Kishor N, Mondal R, Jha A, Chen Q, Yan C, Munoz-Torres M, Meerzaman D, Robinson PN, **Reese JT**. Oncopacket: Integration of cancer research data using GA4GH phenopackets. Bioinformatics. Oxford University Press (OUP); 2025 Sept 29;(btaf546). [http://dx.doi.org/10.1093/bioinformatics/btaf546](http://dx.doi.org/10.1093/bioinformatics/btaf546) PMID: 41017641
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* Vasilevsky NA, Toro S, Matentzoglu N, Flack JE, Mullen KR, Hegde H, Gehrke S, Whetzel PL, Shwetar Y, **Harris NL**, Ngu MS, Alyea GL, Kane MS, Roncaglia P, Sid E, Thaxton CL, Wood V, Abraham RS, Achatz MI, Ajuyah P, Amberger JS, Babb L, Baker J, Balhoff JP, Berg JS, Bhalla A, Bofill-De Ros X, Braun IR, Broeren EC, Byer BK, Byrne AB, Callahan TJ, Carmody LC, Chan LE, Clause AR, Cohen JS, DeLuca M, Deuitch NT, Flowers M, Fraser J, Fujiwara T, Gitau V, Goldstein JL, Gration D, Groza T, Gyori BM, Hankey W, Hilton JA, Himmelstein DS, Hong SS, Hoyt CT, Huether R, Hurwitz E, Jacobsen JOB, Kikuchi A, Köhler S, Korn DR, Lagorce D, Laraway BJ, Li JY, Malheiro AJ, McLaughlin J, Meldal BHM, Mohan S, **Moxon SAT**, Munoz-Torres MC, Nelson TH, Nicholas FW, Ochoa D, Olson D, Oprea TI, Oskotsky TT, Osumi-Sutherland D, Paris K, Parkinson HE, Pendlington ZM, Peng XP, Pizzino A, Plon SE, Powell BC, Ratliff JC, Rehm HL, Remennik L, Riggs ER, Roberts S, Robinson PN, Ross JE, Schaper K, Schilder BM, Schmidt JL, Sharp EW, Similuk MN, Smedley D, Sneddon TP, Sparks R, Stefancsik R, Stupp GS, Sundar S, Takatsuki T, Tammen I, Tshering KC, Unni DR, Valasek E, Vanderver A, Wagner AH, Webb RF, Welter D, Yaya-Stupp D, Zankl A, Zhang XA, McMurry JA, Chute CG, Hamosh A, **Mungall CJ**, Haendel MA. Mondo: Integrating disease terminology across communities. Genetics. Oxford University Press (OUP); 2025 Oct 6;(iyaf215). http://dx.doi.org/10.1093/genetics/iyaf215
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* Alamenciak T, Arnillas CA, **Caufield H**, Compton K, Drew K, Frühstückl R, Heger T, König-Ries B, **Mungall C, Moxon S, Reese J,** Tardif J, Vogt L. Ecolink: Towards a knowledge graph schema for complex environmental systems. Communications in Computer and Information Science. Cham: Springer Nature Switzerland; 2026\. p. 353–366. http://dx.doi.org/10.1007/978-3-032-06136-2\_33
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* Alamenciak T, Arnillas CA, **Caufield H**, Compton K, Drew K, Frühstückl R, Heger T, König-Ries B, **Mungall C, Moxon S, Reese J,** Tardif J, Vogt L. Ecolink: Towards a knowledge graph schema for complex environmental systems. Communications in Computer and Information Science. Cham: Springer Nature Switzerland; 2026\. p. 353–366. http://dx.doi.org/10.1007/978-3-032-06136-2_33
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* Cortes KG, Sundar S, Gehrke S, Manpearl K, Lin J, Korn DR, **Caufield H**, Schaper K, **Reese J**, Koirala K, Hunter LE, Carter EK, DeLuca M, Krishnan A, **Mungall C**, Haendel M. Improving biomedical knowledge graph quality: A community approach. arXiv \[q-bio.OT\]. 2025\. [http://arxiv.org/abs/2508.21774](http://arxiv.org/abs/2508.21774) \[Preprint\]
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* **Harris NL**, Hokamp K, Maia J, Ménager H, Munoz-Torres MC, Ohta T, Unni D, Williams J. BOSC 2025, the 26th Bioinformatics Open Source Conference. F1000Research 2025 Sep 9\. [https://f1000research.com/articles/14-887/pdf](https://f1000research.com/articles/14-887/pdf) \[Not peer-reviewed\]
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* Korn DR, Golden P, Odell A, Cortes K, Sundar S, Schaper K, Gehrke S, Cox C, **Caufield H, Reese J,** Morris E, **Mungall CJ**, Haendel M. Koza and Koza-Hub for born-interoperable knowledge graph generation using KGX. arXiv \[cs.DB\]. 2025\. http://arxiv.org/abs/2509.09096 \[Preprint\]
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* Niyonkuru E, **Caufield JH**, Carmody L, Gargano M, Toro S, Whetzel PL, Blau H, Gomez MS, Casiraghi E, Chimirri L, **Reese JT,** Valentini G, Haendel MA, **Mungall CJ**, Robinson PN. Leveraging generative AI to assist biocuration of medical actions for rare disease. Bioinform Adv. Oxford University Press; 2025 Jun 12;vbaf141. http://dx.doi.org/10.1093/bioadv/vbaf141/63477910/vbaf141
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* Karamarie Fecho, Gwênlyn Glusman, Sergio E. Baranzini, Chris Bizon, Matthew Brush, William Byrd, Lawrence Chung, Andrew Crouse, Eric Deutsch, Michel Dumontier, Aleksandra Foksinska, Jennifer Hadlock, Kaiwen He, Sui Huang, Robert Hubal, Gregory M. Hyde, Sharat Israni, Kelyne Kenmogne, David Koslicki, Jana Dorfman Marcette, Ewy A. Mathe, Abrar Mesbah, **Sierra A. T. Moxon, Christopher J. Mungall**, John Osborne, Carrie Pasfield, Guangrong Qin, Stephen A. Ramsey, **Justin Reese**, Jared C. Roach, Reese Rose, Karthik Soman, Andrew I. Su, Casey Ta, Gaurav Vaidya, Rosina Weber, Qi Wei, Mark Williams, Chunlei Wu, Colleen Xu, Chase Yakaboski, The Biomedical Data Translator Consortium. Announcing the biomedical data Translator: Initial public release. *Clin Transl Sci*. Wiley; 2025; doi: 10.1111/cts.70284.
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* Karamarie Fecho, Gwênlyn Glusman, Sergio E. Baranzini, Chris Bizon, Matthew Brush, William Byrd, Lawrence Chung, Andrew Crouse, Eric Deutsch, Michel Dumontier, Aleksandra Foksinska, Jennifer Hadlock, Kaiwen He, Sui Huang, Robert Hubal, Gregory M. Hyde, Sharat Israni, Kelyne Kenmogne, David Koslicki, Jana Dorfman Marcette, Ewy A. Mathe, Abrar Mesbah, **Sierra A. T. Moxon, Christopher J. Mungall**, John Osborne, Carrie Pasfield, Guangrong Qin, Stephen A. Ramsey, **Justin Reese**, Jared C. Roach, Reese Rose, Karthik Soman, Andrew I. Su, Casey Ta, Gaurav Vaidya, Rosina Weber, Qi Wei, Mark Williams, Chunlei Wu, Colleen Xu, Chase Yakaboski, The Biomedical Data Translator Consortium. Announcing the biomedical data Translator: Initial public release. *Clin Transl Sci*. Wiley; 2025; http://dx.doi.org/10.1111/cts.70284.
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* Mullen KR, Tammen I, Matentzoglu NA, Mather M, Balhoff JP, Esdaile E, Leroy G, Park CA, Rando HM, Saklou NT, Webb TL, Vasilevsky NA, **Mungall CJ**, Haendel MA, Nicholas FW, Toro S. The Vertebrate Breed Ontology: Toward effective breed data standardization. J Vet Intern Med. Wiley; 2025 Jul;39(4):e70133. http://dx.doi.org/10.1111/jvim.70133 PMCID: PMC12103836
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* Preprint: **Mungall CJ**, Malik A, Korn DR, **Reese JT,** O’Boyle NM, Noel, Hastings J. Chemical classification program synthesis using generative artificial intelligence. arXiv \[cs.AI\]. 2025\. http://arxiv.org/abs/2505.18470
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* Preprint: Krishnamurthy M, Korn D, Haendel MA, **Mungall CJ**, Thessen AE. A dynamic framework for semantic grouping of Common Data Elements (CDE) using embeddings and clustering. arXiv \[cs.IR\]. 2025\. http://arxiv.org/abs/2506.02160
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* Bridges Y, Souza V de, Cortes KG, Haendel M, **Harris NL**, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, **Mungall CJ**, Odell A, Osumi-Sutherland D, Robinson PN, Smedley D, Jacobsen JOB. Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval \- Phenotypic inference Evaluation framework. BMC Bioinformatics. England; 2025 Mar 22;26(1):87. http://dx.doi.org/10.1186/s12859-025-06105-4 PMID: 40121479
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* Matentzoglu N, Bello S, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff J, Balk MA, Bradford YM, Bridges Y, Callahan TJ, **Caufield H,** Cuzick A, Carmody L, Caron AR, De Souza V, Engel S, Fey P, Fisher M, Gehrke S, Grove C, Hansen P, **Harris NL**, Harris M, Harris L, Ibrahim A, Jacobsen JOB, Köhler S, McMurry J, Munoz-Fuentes V, Munoz-Torres M, Parkinson H, Pendlington Z, Pilgrim C, Robb SMC, Robinson PN, Seager J, Segerdell E, Smedley D, Sollis E, Toro S, Vasilevsky N, Wood V, Haendel MA, **Mungall CJ**, McLaughlin JA, Osumi-Sutherland D. The Unified Phenotype Ontology : a framework for cross-species integrative phenomics. Genetics. Oxford University Press; 2025 Mar 1;229(3):iyaf027. https://doi.org/10.1186/s12859-025-06105-4 PMID: 40048704
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* **Joachimiak MP, Miller MA, Caufield JH,** Ly R, **Harris NL**, Tritt A, **Mungall CJ**, Bouchard KE. The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies. **Applied Ontology** (2025). [https://journals.sagepub.com/doi/abs/10.1177/15705838241304103](https://journals.sagepub.com/doi/abs/10.1177/15705838241304103)
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* Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ, **Caufield H**, Cuzick A, Carmody LC, Caron AR, de Souza V, Engel SR, Fey P, Fisher M, Gehrke S, Grove C, Hansen P, **Harris NL**, Harris MA, Harris L, Ibrahim A, Jacobsen JOB, Köhler S, McMurry JA, Munoz-Fuentes V, Munoz-Torres MC, Parkinson H, Pendlington ZM, Pilgrim C, Robb SMC, Robinson PN, Seager J, Segerdell E, Smedley D, Sollis E, Toro S, Vasilevsky N, Wood V, Haendel MA, **Mungall CJ**, McLaughlin JA, Osumi-Sutherland D. The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics. bioRxiv. 2024\. http://dx.doi.org/10.1101/2024.09.18.613276
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* **Joachimiak MP, Miller MA, Caufield JH,** Ly R, **Harris NL**, Tritt A, **Mungall CJ**, Bouchard KE. The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies. **Applied Ontology** (2025). [https://journals.sagepub.com/doi/abs/10.1177/15705838241304103](https://journals.sagepub.com/doi/abs/10.1177/15705838241304103)
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* Preprint: Chimirri L, **Caufield JH**, Matentzoglu N, Gargano MA, Bridges Y, Cazalla M, Chen S, Danis D, Dingemanns AJM, Gehle PJ, Graefe ASL, Gu W, Ladewig MS, Lapunzina P, Nevado J, Ogishima S, Seelow D, Tenorio Castano JA, Turnovec M, de Vries BBA, Wang K, Wissink K, Yuksel Z, Zucca G, **Mungall CJ**, Haendel MA, **Reese J**, Robinson PN. Consistent performance of GPT-4o in rare disease diagnosis across nine languages and 4967 cases. medRxiv. 2025\. p. 2025.02.26.25322769.
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* Preprint: Santangelo BE, Hegde H, **Caufield JH, Reese J**, Kliegr T, Hunter LE, Lozupone CA, **Mungall CJ**, **Joachimiak MP**. KG-microbe \- building modular and scalable knowledge graphs for microbiome and microbial sciences. bioRxiv. 2025\. p. 2025.02.24.639989. [http://biorxiv.org/content/early/2025/02/28/2025.02.24.639989.abstract](http://biorxiv.org/content/early/2025/02/28/2025.02.24.639989.abstract)
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* Preprint: Rekerle L, Danis D, Rehburg F, Graefe ASL, Bily V, Caballero-Oteyza A, Cacheiro P, Chimirri L, Chong JX, Connelly E, de Vries BBA, Dingemans AJM, Duyzend MH, Freiberger T, Gehle P, Groza T, Hansen P, Jacobsen JOB, Klocperk A, Ladewig MS, Love MI, Marcello AJ, Mordhorst A, Munoz-Torres MC, Reese J, Schütz C, Smedley D, Strauss T, Vladyka O, Zocche D, Thun S, **Mungall CJ**, Haendel MA, Robinson PN. GA4GH phenopacket-driven characterization of genotype-phenotype correlations in Mendelian disorders. medRxiv. 2025\. https://www.medrxiv.org/content/medrxiv/early/2025/03/06/2025.03.05.25323315.full.pdf
@@ -56,10 +55,7 @@ title: Selected BBOP publications
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- Preprint: Carmody LC, Gargano MA, Toro S, Vasilevsky NA, Adam MP, Blau H, Chan LE, Gomez-Andres D, Horvath R, Ladewig MS, Lewis-Smith D, Lochmueller H, Matentzoglu NA, Munoz-Torres MC, Schuetz C, Kraus ML, Seitz B, Similuk MN, Sparks T, Strauss T, Swietlik EM, Thompson R, Zhang XA, <b>Mungall CJ</b>, Haendel MA, Robinson PN. The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease. medRxiv. 2023. <a target="_new" href="https://www.medrxiv.org/content/10.1101/2023.07.13.23292612v1">https://www.medrxiv.org/content/10.1101/2023.07.13.23292612v1</a>
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- <b>Caufield JH</b>, Putman T, Schaper K, Unni DR, <b>Hegde H</b>, Callahan TJ, Cappelletti L, <b>Moxon SAT</b>, Ravanmehr V, <b>Carbon S</b>, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, <b>Harris NL</b>, Munoz-Torres MC, Haendel MA, Robinson PN, <b>Joachimiak MP, Mungall CJ, Reese JT</b>. KG-Hub-building and exchanging biological knowledge graphs. Bioinformatics. 2023 Jul 1;39(7). <a target="_new" href="http://dx.doi.org/10.1093/bioinformatics/btad418">http://dx.doi.org/10.1093/bioinformatics/btad418</a> PMCID: PMC10336030
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- <b>Joachimiak MP, Harry Caufield J, Harris N, Mungall CJ</b>. Gene Set Summarization using Large Language Models. arXiv [q-bio.GN]. 2023. <a target="_new" href="http://arxiv.org/abs/2305.13338">http://arxiv.org/abs/2305.13338</a>- Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, <b>Harris NL</b>, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, <b>Mungall CJ</b>, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Mamm Genome. 2023 Apr 19; <a target="_new" href="https://link.springer.com/10.1007/s00335-023-09992-1">https://link.springer.com/10.1007/s00335-023-09992-1</a> PMID: 37076585
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- Karlebach G, Carmody L, Sundaramurthi JC, Casiraghi E, Hansen P, <b>Reese J, Mungall CJ</b>, Valentini G, Robinson PN. An expectation-maximization framework for comprehensive prediction of isoform-specific functions. Bioinformatics. 2023 Apr 3;39(4). <a target="_new" href="https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad132/7079798">https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad132/7079798</a> PMCID: PMC10079350
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- Chan LE, Thessen AE, Duncan WD, Matentzoglu N, Schmitt C, Grondin CJ, Vasilevsky N, McMurry JA, Robinson PN, <b>Mungall CJ</b>, Haendel MA. The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. J Biomed Semantics. 2023 Feb 24;14(1):3. <a target="_new" href="http://dx.doi.org/10.1186/s13326-023-00283-x">http://dx.doi.org/10.1186/s13326-023-00283-x</a> PMCID: PMC9951428
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- Cappelletti L, Taverni S, Fontana T, <b>Joachimiak MP, Reese J</b>, Robinson P, Casiraghi E, Valentini G. Degree-Normalization Improves Random-Walk-Based Embedding Accuracy in PPI Graphs. Bioinformatics and Biomedical Engineering. Springer Nature Switzerland; 2023. p. 372–383. <a target="_new" href="http://dx.doi.org/10.1007/978-3-031-34960-7_26">http://dx.doi.org/10.1007/978-3-031-34960-7_26</a>
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- <b>Reese JT</b>, 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. Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes. EBioMedicine. 2022 Dec 21;87:104413. <a target="_new" href="http://dx.doi.org/10.1016/j.ebiom.2022.104413">http://dx.doi.org/10.1016/j.ebiom.2022.104413</a> PMCID: PMC9769411
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- Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 Mar 3; <a target="_new" href="https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyad031/7068118">https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyad031/7068118</a> PMID: 36866529
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- Thessen A, Cooper L, Swetnam T, <b>Hegde H</b>, <b>Reese J</b>, Elser J, Jaiswal P. Using knowledge graphs to infer gene expression in plants. Frontiers Artificial Intelligence Appl. 2023;6. <a target="_new" href="https://www.frontiersin.org/articles/10.3389/frai.2023.1201002">https://www.frontiersin.org/articles/10.3389/frai.2023.1201002</a>
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- Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, <b>Reese J</b>, <b>Hegde H</b>, Ladewig MS, Seitz B, Munoz-Torres M, <b>Harris NL</b>, Rambla J, Baudis M, <b>Mungall CJ</b>, Haendel MA, Robinson PN. Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 2023 May 17;18(5):e0285433. <a target="_new" href="http://dx.doi.org/10.1371/journal.pone.0285433">http://dx.doi.org/10.1371/journal.pone.0285433</a> PMCID: PMC10191354

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