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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: smith m. Front Bioinform. 2022 Jan 17;1:826370. doi: 10.3389/fbinf.2021.826370. eCollection 2021. Front Bioinform. 2022. PMID: 36303775 Free PMC article. Review.
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.
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: smith m. Sci Data. 2024 Apr 5;11(1):339. doi: 10.1038/s41597-024-03069-7. Sci Data. 2024. PMID: 38580669 Free PMC article.
Rapid remodeling of the soil lipidome in response to a drying-rewetting event.
Couvillion SP, Danczak RE, Naylor D, Smith ML, Stratton KG, Paurus VL, Bloodsworth KJ, Farris Y, Schmidt DJ, Richardson RE, Bramer LM, Fansler SJ, Nakayasu ES, McDermott JE, Metz TO, Lipton MS, Jansson JK, Hofmockel KS. Couvillion SP, et al. Among authors: smith ml. Microbiome. 2023 Feb 27;11(1):34. doi: 10.1186/s40168-022-01427-4. Microbiome. 2023. PMID: 36849975 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. Nat Commun. 2023 Nov 23;14(1):7666. doi: 10.1038/s41467-023-42967-z. Nat Commun. 2023. PMID: 37996432 Free PMC article.
Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil.
Peterson MJ, Handakumbura PP, Thompson AM, Russell ZR, Kim YM, Fansler SJ, Smith ML, Toyoda JG, Chu RK, Stanfill BA, Fransen SC, Bailey VL, Jansson C, Hixson KK, Callister SJ. Peterson MJ, et al. Among authors: smith ml. PLoS One. 2021 Dec 8;16(12):e0259937. doi: 10.1371/journal.pone.0259937. eCollection 2021. PLoS One. 2021. PMID: 34879068 Free PMC article.
Toolbox of individual-level interventions against online misinformation.
Kozyreva A, Lorenz-Spreen P, Herzog SM, Ecker UKH, Lewandowsky S, Hertwig R, Ali A, Bak-Coleman J, Barzilai S, Basol M, Berinsky AJ, Betsch C, Cook J, Fazio LK, Geers M, Guess AM, Huang H, Larreguy H, Maertens R, Panizza F, Pennycook G, Rand DG, Rathje S, Reifler J, Schmid P, Smith M, Swire-Thompson B, Szewach P, van der Linden S, Wineburg S. Kozyreva A, et al. Among authors: smith m. Nat Hum Behav. 2024 May 13. doi: 10.1038/s41562-024-01881-0. Online ahead of print. Nat Hum Behav. 2024. PMID: 38740990 Review.
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