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Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.
Hu B, Canon S, Eloe-Fadrosh EA, Anubhav, Babinski M, Corilo Y, Davenport K, Duncan WD, Fagnan K, Flynn M, Foster B, Hays D, Huntemann M, Jackson EKP, Kelliher J, Li PE, Lo CC, Mans D, McCue LA, Mouncey N, Mungall CJ, Piehowski PD, Purvine SO, Smith M, Varghese NJ, Winston D, Xu Y, Chain PSG. Hu B, et al. Among authors: mungall cj. Front Bioinform. 2022 Jan 17;1:826370. doi: 10.3389/fbinf.2021.826370. eCollection 2021. Front Bioinform. 2022. PMID: 36303775 Free PMC article. Review.
An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.
Schadt C, Martin S, Carrell A, Fortner A, Hopp D, Jacobson D, Klingeman D, Kristy B, Phillips J, Piatkowski B, Miller MA, Smith M, Patil S, Flynn M, Canon S, Clum A, Mungall CJ, Pennacchio C, Bowen B, Louie K, Northen T, Eloe-Fadrosh EA, Mayes MA, Muchero W, Weston DJ, Mitchell J, Doktycz M. Schadt C, et al. Among authors: mungall cj. Sci Data. 2024 Apr 5;11(1):339. doi: 10.1038/s41597-024-03069-7. Sci Data. 2024. PMID: 38580669 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.
Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability.
Meyer R, Appeltans W, Duncan WD, Dimitrova M, Gan YM, Stjernegaard Jeppesen T, Mungall C, Paul DL, Provoost P, Robertson T, Schriml L, Suominen S, Walls R, Sweetlove M, Ung V, Van de Putte A, Wallis E, Wieczorek J, Buttigieg PL. Meyer R, et al. Biodivers Data J. 2023 Oct 3;11:e112420. doi: 10.3897/BDJ.11.e112420. eCollection 2023. Biodivers Data J. 2023. PMID: 37829294 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.
Brain Data Standards - A method for building data-driven cell-type ontologies.
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. Tan SZK, et al. Among authors: mungall cj. Sci Data. 2023 Jan 24;10(1):50. doi: 10.1038/s41597-022-01886-2. Sci Data. 2023. PMID: 36693887 Free PMC article.
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.
Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies.
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. Tan SZK, et al. Among authors: mungall cj. Sci Data. 2023 Apr 28;10(1):246. doi: 10.1038/s41597-023-02165-4. Sci Data. 2023. PMID: 37117232 Free PMC article. No abstract available.
165 results