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For: Hahn AS, Konwar KM, Louca S, Hanson NW, Hallam SJ. The information science of microbial ecology. Curr Opin Microbiol 2016;31:209-16. [PMID: 27183115 DOI: 10.1016/j.mib.2016.04.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/14/2016] [Accepted: 04/16/2016] [Indexed: 01/07/2023]
Number Cited by Other Article(s)
1
Sun E, König SG, Cirstea M, Hallam SJ, Graves ML, Oliver DC. Development of a data science CURE in microbiology using publicly available microbiome datasets. Front Microbiol 2022;13:1018237. [PMID: 36312919 PMCID: PMC9597637 DOI: 10.3389/fmicb.2022.1018237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/26/2022] [Indexed: 11/21/2022]  Open
2
Djemiel C, Maron PA, Terrat S, Dequiedt S, Cottin A, Ranjard L. Inferring microbiota functions from taxonomic genes: a review. Gigascience 2022;11:giab090. [PMID: 35022702 PMCID: PMC8756179 DOI: 10.1093/gigascience/giab090] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022]  Open
3
Basher ARMA, Mclaughlin RJ, Hallam SJ. Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision. J Comput Biol 2021;28:1075-1103. [PMID: 34520674 DOI: 10.1089/cmb.2021.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
4
Winkle JJ, Karamched BR, Bennett MR, Ott W, Josić K. Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia. PLoS Comput Biol 2021;17:e1009381. [PMID: 34550968 PMCID: PMC8489724 DOI: 10.1371/journal.pcbi.1009381] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/04/2021] [Accepted: 08/25/2021] [Indexed: 12/04/2022]  Open
5
Dill-McFarland KA, König SG, Mazel F, Oliver DC, McEwen LM, Hong KY, Hallam SJ. An integrated, modular approach to data science education in microbiology. PLoS Comput Biol 2021;17:e1008661. [PMID: 33630850 PMCID: PMC7906378 DOI: 10.1371/journal.pcbi.1008661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]  Open
6
M A Basher AR, McLaughlin RJ, Hallam SJ. Metabolic pathway inference using multi-label classification with rich pathway features. PLoS Comput Biol 2020;16:e1008174. [PMID: 33001968 PMCID: PMC7529316 DOI: 10.1371/journal.pcbi.1008174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022]  Open
7
Yu H, Xue D, Wang Y, Zheng W, Zhang G, Wang Z. Molecular ecological network analysis of the response of soil microbial communities to depth gradients in farmland soils. Microbiologyopen 2020;9:e983. [PMID: 31902141 PMCID: PMC7066466 DOI: 10.1002/mbo3.983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]  Open
8
Haruta S, Yamamoto K. Model Microbial Consortia as Tools for Understanding Complex Microbial Communities. Curr Genomics 2018;19:723-733. [PMID: 30532651 PMCID: PMC6225455 DOI: 10.2174/1389202919666180911131206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023]  Open
9
Farley SS, Dawson A, Goring SJ, Williams JW. Situating Ecology as a Big-Data Science: Current Advances, Challenges, and Solutions. Bioscience 2018. [DOI: 10.1093/biosci/biy068] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
10
Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium [corrected] Strains from a Freshwater Ecosystem. GENOME ANNOUNCEMENTS 2018;6:6/5/e00009-18. [PMID: 29437085 PMCID: PMC5794932 DOI: 10.1128/genomea.00009-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
11
Chen Z, Zheng Y, Ding C, Ren X, Yuan J, Sun F, Li Y. Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017;145:111-118. [PMID: 28711820 DOI: 10.1016/j.ecoenv.2017.07.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
12
Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, del Rio TG, Suttle CA, Tringe S, Hallam SJ. A compendium of multi-omic sequence information from the Saanich Inlet water column. Sci Data 2017;4:170160. [PMID: 29087368 PMCID: PMC5663217 DOI: 10.1038/sdata.2017.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/02/2017] [Indexed: 01/08/2023]  Open
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