Please note: this page is hand-curated and may be out of date. See our Paperpile folder of BBOP publications for a more complete list. **Last updated 2024-02-06

  1. O’Neil ST, Schaper K, Elsarboukh G, Reese JT, Moxon SAT, Harris NL, Munoz-Torres MC, Robinson PN, Haendel MA, Mungall CJ. Phenomics Assistant: An Interface for LLM-based Biomedical Knowledge Graph Exploration. bioRxiv. 2024. p. 2024.01.31.578275. https://www.biorxiv.org/content/biorxiv/early/2024/02/02/2024.01.31.578275
  2. Groza T, Caufield H, Gration D, Baynam G, Haendel MA, Robinson PN, Mungall CJ, Reese JT. An evaluation of GPT models for phenotype concept recognition. BMC Med Inform Decis Mak. BioMed Central; 2024 Jan 31;24(1):1–12. https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-024-02439-w
  3. Harris NL, 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. https://f1000research.com/articles/12-1568/pdf
  4. 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. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Res. 2023 Nov 24; http://dx.doi.org/10.1093/nar/gkad1082 PMID: 38000386
  5. 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 M-C, 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, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts AM, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2023 Nov 11; http://dx.doi.org/10.1093/nar/gkad1005 PMID: 37953324
  6. Matentzoglu N, Caufield JH, Hegde HB, Reese JT, Moxon S, Kim H, Harris NL, Haendel MA, Mungall CJ. MapperGPT: Large Language Models for Linking and Mapping Entities. arXiv [cs.CL]. 2023. http://arxiv.org/abs/2310.03666
  7. Antony B, Blau H, Casiraghi E, Loomba JJ, Callahan TJ, Laraway BJ, Wilkins KJ, Antonescu CC, Valentini G, Williams AE, Robinson PN, Reese JT, Murali TM, N3C consortium. Predictive models of long COVID. EBioMedicine. 2023 Sep 4;96:104777. http://dx.doi.org/10.1016/j.ebiom.2023.104777 PMID: 37672869
  8. Reese J, Danis D, Caufield JH, Casiraghi E, Valentini G, Mungall CJ, Robinson PN. On the limitations of large language models in clinical diagnosis. medRxiv. 2023. p. 2023.07.13.23292613. https://www.medrxiv.org/content/10.1101/2023.07.13.23292613v1
  9. 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, Mungall CJ, Haendel MA, Robinson PN. The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease. medRxiv. 2023. https://www.medrxiv.org/content/10.1101/2023.07.13.23292612v1
  10. 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. KG-Hub-building and exchanging biological knowledge graphs. Bioinformatics. 2023 Jul 1;39(7). http://dx.doi.org/10.1093/bioinformatics/btad418 PMCID: PMC10336030
  11. Joachimiak MP, Harry Caufield J, Harris N, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv [q-bio.GN]. 2023. http://arxiv.org/abs/2305.13338
  12. Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, 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; https://link.springer.com/10.1007/s00335-023-09992-1 PMID: 37076585
  13. Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, Kim H, Moxon SAT, Reese JT, Haendel MA, Robinson PN, Mungall CJ. Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. arXiv [cs.AI]. 2023. http://arxiv.org/abs/2304.02711
  14. Karlebach G, Carmody L, Sundaramurthi JC, Casiraghi E, Hansen P, Reese J, Mungall CJ, Valentini G, Robinson PN. An expectation-maximization framework for comprehensive prediction of isoform-specific functions. Bioinformatics. 2023 Apr 3;39(4). https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad132/7079798 PMCID: PMC10079350
  15. Chan LE, Thessen AE, Duncan WD, Matentzoglu N, Schmitt C, Grondin CJ, Vasilevsky N, McMurry JA, Robinson PN, Mungall CJ, 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. http://dx.doi.org/10.1186/s13326-023-00283-x PMCID: PMC9951428
  16. Cappelletti L, Taverni S, Fontana T, Joachimiak MP, Reese J, 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. http://dx.doi.org/10.1007/978-3-031-34960-7_26
  17. 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. Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes. EBioMedicine. 2022 Dec 21;87:104413. http://dx.doi.org/10.1016/j.ebiom.2022.104413 PMCID: PMC9769411
  18. Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 Mar 3; https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyad031/7068118 PMID: 36866529
  19. Thessen A, Cooper L, Swetnam T, Hegde H, Reese J, Elser J, Jaiswal P. Using knowledge graphs to infer gene expression in plants. Frontiers Artificial Intelligence Appl. 2023;6. https://www.frontiersin.org/articles/10.3389/frai.2023.1201002
  20. 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. Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 2023 May 17;18(5):e0285433. http://dx.doi.org/10.1371/journal.pone.0285433 PMCID: PMC10191354
  21. Karlebach G, Carmody L, Sundaramurthi JC, Casiraghi E, Hansen P, Reese J, Mungall CJ, Valentini G, Robinson PN. An expectation-maximization framework for comprehensive prediction of isoform-specific functions. Bioinformatics. 2023 Apr 3;39(4). https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad132/7079798 PMCID: PMC10079350
  22. Cappelletti L, Fontana T, Casiraghi E, Ravanmehr V, Callahan TJ, Cano C, Joachimiak MP, Mungall CJ, Robinson PN, Reese J, Valentini G. GRAPE for fast and scalable graph processing and random-walk-based embedding. Nature Computational Science. Nature Publishing Group; 2023 Jun 26;3(6):552–568. https://www.nature.com/articles/s43588-023-00465-8
  23. Cappelletti L, Taverni S, Fontana T, Joachimiak MP, Reese J, 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. http://dx.doi.org/10.1007/978-3-031-34960-7_26
  24. Tan SZK, Kir H, Aevermann BD, Gillespie T, Harris N, Hawrylycz MJ, Jorstad NL, Lein ES, Matentzoglu N, Miller JA, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Staats B, Vermillion J, Yadav A, Zhang Y, Scheuermann RH, Osumi-Sutherland D. Brain Data Standards - A method for building data-driven cell-type ontologies. Sci Data. 2023 Jan 24;10(1):50. http://dx.doi.org/10.1038/s41597-022-01886-2 PMCID: PMC9873614
  25. 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. Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes. EBioMedicine. 2022 Dec 21;87:104413. http://dx.doi.org/10.1016/j.ebiom.2022.104413 PMCID: PMC9769411
  26. Chan LE, Casiraghi E, Laraway B, Coleman B, Blau H, Zaman A, Harris NL, Wilkins K, Antony B, Gargano M, Valentini G, Sahner D, Haendel M, Robinson PN, Bramante C, Reese J, N3C consortium. Metformin is associated with reduced COVID-19 severity in patients with prediabetes. Diabetes Res Clin Pract. 2022 Nov 15;194:110157. http://dx.doi.org/10.1016/j.diabres.2022.110157 PMCID: PMC9663381
  27. Vasilevsky N, Matentzoglu N, Toro S, Flack J, Hamosh A, Robinson P, Haendel M, Mungall C. 129. Standardization of cancer terminology in the Mondo Disease Ontology. Cancer Genet. Elsevier; 2022 Nov 1;268:41. https://doi.org/10.1016/j.cancergen.2022.10.132
  28. Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database. 2022 Oct 8;2022. http://dx.doi.org/10.1093/database/baac087 PMID: 36208225
  29. Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. Nature Publishing Group; 2022 Jun 15;40(6):817–820. https://www.nature.com/articles/s41587-022-01357-4
  30. 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, The Biomedical Data Translator Consortium. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. Wiley; 2022 Jun 6; https://onlinelibrary.wiley.com/doi/10.1111/cts.13302
  31. Fecho K, Thessen AT, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Dančík V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, Hyde G, Johs A, Su A, Qin G, Zhu Q, Biomedical Data Translator Consortium. Progress Toward a Universal Biomedical Data Translator. Clin Transl Sci. Wiley Online Library; 2022 May 25; http://dx.doi.org/10.1111/cts.13301 PMID: 35611543
  32. Danis D, Jacobsen JOB, Balachandran P, Zhu Q, Yilmaz F, Reese J, Haimel M, Lyon GJ, Helbig I, Mungall CJ, Beck CR, Lee C, Smedley D, Robinson PN. SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing. Genome Med. 2022 Apr 28;14(1):44. http://dx.doi.org/10.1186/s13073-022-01046-6 PMID: 35484572
  33. Jacobsen JO, Kelly C, Cipriani V, Consortium GER, Mungall CJ, Reese J, Danis D, Robinson PN, Smedley D. Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease. Hum Mutat. Wiley; 2022 Apr 7; https://onlinelibrary.wiley.com/doi/10.1002/humu.2438 PMID: 35391505
  34. Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde H, Hoyt AL, Hoyt CT, Jiao D, Jiménez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ. A Simple Standard for Sharing Ontological Mappings (SSSOM). Database. 2022 May 25;2022. http://dx.doi.org/10.1093/database/baac035 PMID: 35616100.
  35. Sternberg PW, Agapite J, …, Mungall CJ, …, Zhou P, Zytkovicz M, The Alliance of Genome Resources Consortium. Harmonizing model organism data in the Alliance of Genome Resources. Genetics. Oxford University Press (OUP); 2022 Feb 25; https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac022/6537086
  36. Hu, B., Canon, S., Eloe-Fadrosh, E. A., Anubhav, Babinski, M., Corilo, Y., Davenport, K., Duncan, W. D., Fagnan, K., Flynn, M., Foster, B., Hays, D., …, Mouncey, N., Mungall, C.J., … Chain, P. S. G. (2022). Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. Frontiers in Bioinformatics, 1. https://doi.org/10.3389/fbinf.2021.826370
  37. Nadendla S, Jackson R, Munro J, Quaglia F, Mészáros B, Olley D, Hobbs ET, Goralski SM, Chibucos M, Mungall CJ, Tosatto SCE, Erill I, Giglio MG. ECO: the Evidence and Conclusion Ontology, an update for 2022. Nucleic Acids Res. Oxford University Press; 2021 Nov 19; https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkab1025/6431816
  38. Eloe-Fadrosh, E.A., Ahmed, F., Anubhav, Babinski, M., Baumes, J., Borkum, M., Bramer, L., Canon, S., Christianson, D.S., Corilo, Y.E. Davenport, K.W., Davis, B., Drake, M., Duncan, W.D., … Chain, P.S.G., McCue, L.A., Mans, D., Mungall, C.J., Mouncey, N.J., Fagnan, K.T. (2022). The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D828–D836, https://doi.org/10.1093/nar/gkab990
  39. Coleman B, Casiraghi E, Blau H, Chan L, Haendel MA, Laraway B, Callahan TJ, Deer RR, Wilkins KJ, Reese J, Robinson PN. Risk of new-onset psychiatric sequelae of COVID-19 in the early and late post-acute phase. World Psychiatry. Wiley; 2022 Jun;21(2):319–320. https://onlinelibrary.wiley.com/doi/10.1002/wps.20992 PMID: 35524622
  40. Ravanmehr V, Blau H, Cappelletti L, Fontana T, Carmody L, Coleman B, George J, Reese J, Joachimiak M, Bocci G, Hansen P, Bult C, Rueter J, Casiraghi E, Valentini G, Mungall C, Oprea TI, Robinson PN. Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer. NAR Genom Bioinform. 2021 Dec;3(4):lqab113. http://dx.doi.org/10.1093/nargab/lqab113 PMCID: PMC8652379
  41. Good BM, Van Auken K, Hill DP, Mi H, Carbon S, Balhoff JP, Albou L-P, Thomas PD, Mungall CJ, Blake JA, D’Eustachio P. Reactome and the Gene Ontology: Digital convergence of data resources. Bioinformatics. 2021 May 8; http://dx.doi.org/10.1093/bioinformatics/btab325 PMID: 33964129
  42. Reese J, Coleman B, Chan L, Callahan TJ, Cappelletti L, Fontana T, Bradwell KR, Harris NL, Casiraghi E, Valentini G, Karlebach G, Deer R, McMurry JA, Haendel MA, Chute CG, Pfaff E, Moffitt R, Spratt H, Singh J, Mungall CJ, Williams AE, Robinson PN. Cyclooxygenase inhibitor use is associated with increased COVID-19 severity. medRxiv, 2021. http://dx.doi.org/10.1101/2021.04.13.21255438
  43. Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia J-M, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities. mSystems. American Society for Microbiology Journals; 2021 Feb 23;6(1). https://msystems.asm.org/content/6/1/e01194-20
  44. Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, ..., Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207–D1217. http://dx.doi.org/10.1093/nar/gkaa1043 PMCID: PMC7778952
  45. Joachimiak MP. Zinc against COVID-19? Symptom surveillance and deficiency risk groups. PLoS Negl Trop Dis. 2021 Jan;15(1):e0008895. http://dx.doi.org/10.1371/journal.pntd.0008895 PMCID: PMC7781367
  46. Gene Ontology Consortium. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2020 Dec 8; http://dx.doi.org/10.1093/nar/gkaa1113 PMID: 33290552
  47. Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ. KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. Patterns (N Y). 2020 Nov 9;100155. http://dx.doi.org/10.1016/j.patter.2020.100155 PMCID: PMC7649624
  48. Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput Biol. 2020 Nov;16(11):e1008376. http://dx.doi.org/10.1371/journal.pcbi.1008376 PMID: 33232313
  49. Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. Jamia Open. Oxford University Press; 2020 Sep 11; https://academic.oup.com/jamiaopen/advance-article-abstract/doi/10.1093/jamiaopen/ooaa030/5904414
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