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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: smith ml. Nat Microbiol. 2023 May;8(5):751-753. doi: 10.1038/s41564-023-01361-7. Nat Microbiol. 2023. PMID: 37069400 No abstract available.
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. Front Bioinform. 2022 Jan 17;1:826370. doi: 10.3389/fbinf.2021.826370. eCollection 2021. Front Bioinform. 2022. PMID: 36303775 Free PMC article. Review.
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. 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. Sci Rep. 2025 Mar 22;15(1):9887. doi: 10.1038/s41598-025-89991-1. Sci Rep. 2025. PMID: 40121238 Free PMC article.
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. Sci Data. 2024 Apr 5;11(1):339. doi: 10.1038/s41597-024-03069-7. Sci Data. 2024. PMID: 38580669 Free PMC article.
Hi-C metagenome sequencing reveals soil phage-host interactions.
Wu R, Davison MR, Nelson WC, Smith ML, Lipton MS, Jansson JK, McClure RS, McDermott JE, Hofmockel KS. Wu R, et al. Among authors: smith ml. Nat Commun. 2023 Nov 23;14(1):7666. doi: 10.1038/s41467-023-42967-z. Nat Commun. 2023. PMID: 37996432 Free PMC article.
2,089 results