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Cohort-based learning for microbiome research community standards.
Kelliher JM, Rudolph M, Vangay P, Abbas A, Borton MA, Davenport ER, Davenport KW, Erazo NG, Herman C, Karstens L, Kocurek B, Lutz HL, Myers KS, Ockert I, Rodriguez FE, Santistevan C, Saunders JK, Smith ML, Vogtmann E, Windsor A, Wood-Charlson EM, Woodley L, Eloe-Fadrosh EA. Kelliher JM, et al. Among authors: rodriguez fe. Nat Microbiol. 2023 May;8(5):751-753. doi: 10.1038/s41564-023-01361-7. Nat Microbiol. 2023. PMID: 37069400 No abstract available.
A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics.
Eloe-Fadrosh EA, Mungall CJ, Miller MA, Smith M, Patil SS, Kelliher JM, Johnson LYD, Rodriguez FE, Chain PSG, Hu B, Thornton MB, McCue LA, McHardy AC, Harris NL, Reddy TBK, Mukherjee S, Hunter CI, Walls R, Schriml LM. Eloe-Fadrosh EA, et al. Among authors: rodriguez fe. Methods Mol Biol. 2024;2802:587-609. doi: 10.1007/978-1-0716-3838-5_20. Methods Mol Biol. 2024. PMID: 38819573
Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.
Kelliher JM, Xu Y, Flynn MC, Babinski M, Canon S, Cavanna E, Clum A, Corilo YE, Fujimoto G, Giberson C, Johnson LYD, Li KJ, Li PE, Li V, Lo CC, Lynch W, Piehowski P, Prime K, Purvine S, Rodriguez F, Roux S, Shakya M, Smith M, Sarrafan S, Cholia S, McCue LA, Mungall C, Hu B, Eloe-Fadrosh EA, Chain PSG. Kelliher JM, et al. Comput Struct Biotechnol J. 2024 Sep 27;23:3575-3583. doi: 10.1016/j.csbj.2024.09.018. eCollection 2024 Dec. Comput Struct Biotechnol J. 2024. PMID: 39963423 Free PMC article.
Quantifying the impact of workshops promoting microbiome data standards and data stewardship.
Kelliher JM, Rodriguez FE, Johnson LYD, Roux S, Smith M, Clum A, Lynch W, Bias CH, Finks SS, Keenum I, Kiledal EA, Lin HA, Longley R, McDonald R, Pitot TM, Rodríguez-Ramos J, Shen J, Sprockett DD, Swift J, Yadav A, Eloe-Fadrosh EA. Kelliher JM, et al. Among authors: rodriguez fe. Sci Rep. 2025 Mar 22;15(1):9887. doi: 10.1038/s41598-025-89991-1. Sci Rep. 2025. PMID: 40121238 Free PMC article.
A cost and community perspective on the barriers to microbiome data reuse.
Kelliher JM, Johnson LYD, Rodriguez FE, Saunders JK, Kroeger ME, Hanson B, Robinson AJ, Anthony WE, Van Goethem MW, Kiledal A, Shibl AA, de Andrade AAS, Ettinger CL, Gupta CL, Robinson CRP, Zuniga C, Sprockett D, Machado DT, Skoog EJ, Oduwole I, Rothman JA, Prime K, Lane KR, Lemos LN, Karstens L, McCauley M, Seyoum MM, Elmassry MM, Guzel M, Longley R, Roux S, Pitot TM, Eloe-Fadrosh EA. Kelliher JM, et al. Among authors: rodriguez fe. Front Bioinform. 2025 Apr 9;5:1585717. doi: 10.3389/fbinf.2025.1585717. eCollection 2025. Front Bioinform. 2025. PMID: 40270679 Free PMC article.
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