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For: Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput Biol 2015;11:e1004573. [PMID: 26565399 PMCID: PMC4643905 DOI: 10.1371/journal.pcbi.1004573] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/29/2015] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Mi K, Xu R, Liu X. RFW captures species-level metagenomic functions by integrating genome annotation information. CELL REPORTS METHODS 2024;4:100932. [PMID: 39662474 DOI: 10.1016/j.crmeth.2024.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 09/01/2024] [Accepted: 11/14/2024] [Indexed: 12/13/2024]
2
Trecarten S, Fongang B, Liss M. Current Trends and Challenges of Microbiome Research in Prostate Cancer. Curr Oncol Rep 2024;26:477-487. [PMID: 38573440 DOI: 10.1007/s11912-024-01520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
3
Chetty A, Blekhman R. Multi-omic approaches for host-microbiome data integration. Gut Microbes 2024;16:2297860. [PMID: 38166610 PMCID: PMC10766395 DOI: 10.1080/19490976.2023.2297860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]  Open
4
Pavia MJ, Finn D, Macedo-Tafur F, Tello-Espinoza R, Penaccio C, Bouskill N, Cadillo-Quiroz H. Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients. Environ Microbiol 2023;25:2388-2403. [PMID: 37501535 DOI: 10.1111/1462-2920.16469] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
5
Sulit AK, Kolisnik T, Frizelle FA, Purcell R, Schmeier S. MetaFunc: taxonomic and functional analyses of high throughput sequencing for microbiomes. GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2023;4:e4. [PMID: 39295912 PMCID: PMC11406379 DOI: 10.1017/gmb.2022.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/06/2022] [Accepted: 12/13/2022] [Indexed: 09/21/2024]
6
Navgire GS, Goel N, Sawhney G, Sharma M, Kaushik P, Mohanta YK, Mohanta TK, Al-Harrasi A. Analysis and Interpretation of metagenomics data: an approach. Biol Proced Online 2022;24:18. [PMID: 36402995 PMCID: PMC9675974 DOI: 10.1186/s12575-022-00179-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/20/2022]  Open
7
Wang Y, Dong Q, Hu S, Zou H, Wu T, Shi J, Zhang H, Sheng Y, Sun W, Kong X, Chen L. Decoding microbial genomes to understand their functional roles in human complex diseases. IMETA 2022;1:e14. [PMID: 38868571 PMCID: PMC10989872 DOI: 10.1002/imt2.14] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/20/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2024]
8
Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient. mSystems 2022;7:e0099121. [PMID: 35166562 PMCID: PMC8845567 DOI: 10.1128/msystems.00991-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
9
Jovel J, Nimaga A, Jordan T, O’Keefe S, Patterson J, Thiesen A, Hotte N, Bording-Jorgensen M, Subedi S, Hamilton J, Carpenter EJ, Lauga B, Elahi S, Madsen KL, Wong GKS, Mason AL. Metagenomics Versus Metatranscriptomics of the Murine Gut Microbiome for Assessing Microbial Metabolism During Inflammation. Front Microbiol 2022;13:829378. [PMID: 35185850 PMCID: PMC8851394 DOI: 10.3389/fmicb.2022.829378] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/11/2022] [Indexed: 01/26/2023]  Open
10
Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. THE ISME JOURNAL 2021;15:2206-2232. [PMID: 33612832 PMCID: PMC8319197 DOI: 10.1038/s41396-021-00917-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
11
Fan TJ, Goeser L, Lu K, Faith JJ, Hansen JJ. Enterococcus faecalis Glucosamine Metabolism Exacerbates Experimental Colitis. Cell Mol Gastroenterol Hepatol 2021;12:1373-1389. [PMID: 34246809 PMCID: PMC8479252 DOI: 10.1016/j.jcmgh.2021.06.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]
12
Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 2021;10:65088. [PMID: 33944776 PMCID: PMC8096432 DOI: 10.7554/elife.65088] [Citation(s) in RCA: 924] [Impact Index Per Article: 308.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 04/21/2021] [Indexed: 02/06/2023]  Open
13
Bokulich NA, Ziemski M, Robeson MS, Kaehler BD. Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. Comput Struct Biotechnol J 2020;18:4048-4062. [PMID: 33363701 PMCID: PMC7744638 DOI: 10.1016/j.csbj.2020.11.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022]  Open
14
Xing Z, Zhang Y, Li M, Guo C, Mi S. RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing. Microorganisms 2020;8:E1563. [PMID: 33050530 PMCID: PMC7650719 DOI: 10.3390/microorganisms8101563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]  Open
15
Bradley R, Langley BO, Ryan JJ, Phipps J, Hanes DA, Stack E, Jansson JK, Metz TO, Stevens JF. Xanthohumol microbiome and signature in healthy adults (the XMaS trial): a phase I triple-masked, placebo-controlled clinical trial. Trials 2020;21:835. [PMID: 33028396 PMCID: PMC7542976 DOI: 10.1186/s13063-020-04769-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022]  Open
16
Yang J, Howe A, Lee J, Yoo K, Park J. An Improved Approach to Identify Bacterial Pathogens to Human in Environmental Metagenome. J Microbiol Biotechnol 2020;30:1335-1342. [PMID: 32627750 PMCID: PMC9728302 DOI: 10.4014/jmb.2005.05033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/08/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022]
17
Pérez-Cobas AE, Gomez-Valero L, Buchrieser C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 2020;6:mgen000409. [PMID: 32706331 PMCID: PMC7641418 DOI: 10.1099/mgen.0.000409] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/30/2020] [Indexed: 12/23/2022]  Open
18
Johnson DR, Pomati F. A brief guide for the measurement and interpretation of microbial functional diversity. Environ Microbiol 2020;22:3039-3048. [PMID: 32608092 DOI: 10.1111/1462-2920.15147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/23/2020] [Accepted: 06/28/2020] [Indexed: 11/29/2022]
19
Zhu C, Miller M, Zeng Z, Wang Y, Mahlich Y, Aptekmann A, Bromberg Y. Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-030320-041014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
20
Nalven SG, Ward CP, Payet JP, Cory RM, Kling GW, Sharpton TJ, Sullivan CM, Crump BC. Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo‐alteration for freshwater microbes. Environ Microbiol 2020;22:3505-3521. [DOI: 10.1111/1462-2920.15121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/03/2020] [Indexed: 12/25/2022]
21
Yang G, Shi C, Zhang S, Liu Y, Li Z, Gao F, Cui Y, Yan Y, Li M. Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus). PeerJ 2020;8:e9124. [PMID: 32518722 PMCID: PMC7258971 DOI: 10.7717/peerj.9124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 04/14/2020] [Indexed: 12/29/2022]  Open
22
Nazeen S, Yu YW, Berger B. Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. Genome Biol 2020;21:47. [PMID: 32093762 PMCID: PMC7038607 DOI: 10.1186/s13059-020-1933-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 01/10/2020] [Indexed: 01/09/2023]  Open
23
Treiber ML, Taft DH, Korf I, Mills DA, Lemay DG. Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. BMC Bioinformatics 2020;21:74. [PMID: 32093654 PMCID: PMC7041091 DOI: 10.1186/s12859-020-3416-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/17/2020] [Indexed: 01/04/2023]  Open
24
Jiang D, Armour CR, Hu C, Mei M, Tian C, Sharpton TJ, Jiang Y. Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Front Genet 2019;10:995. [PMID: 31781153 PMCID: PMC6857202 DOI: 10.3389/fgene.2019.00995] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022]  Open
25
Taxonomic and functional assessment using metatranscriptomics reveals the effect of Angus cattle on rumen microbial signatures. Animal 2019;14:731-744. [PMID: 31662129 DOI: 10.1017/s1751731119002453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
26
Douglas GM, Langille MGI. Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes. Genome Biol Evol 2019;11:2750-2766. [PMID: 31504488 PMCID: PMC6777429 DOI: 10.1093/gbe/evz184] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/16/2022]  Open
27
Zhu C, Miller M, Marpaka S, Vaysberg P, Rühlemann MC, Wu G, Heinsen FA, Tempel M, Zhao L, Lieb W, Franke A, Bromberg Y. Functional sequencing read annotation for high precision microbiome analysis. Nucleic Acids Res 2019;46:e23. [PMID: 29194524 PMCID: PMC5829635 DOI: 10.1093/nar/gkx1209] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/27/2017] [Indexed: 01/16/2023]  Open
28
Klasek SA, Torres ME, Loher M, Bohrmann G, Pape T, Colwell FS. Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion. Front Microbiol 2019;10:1436. [PMID: 31281306 PMCID: PMC6596357 DOI: 10.3389/fmicb.2019.01436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022]  Open
29
Kwak J, Park J. What we can see from very small size sample of metagenomic sequences. BMC Bioinformatics 2018;19:399. [PMID: 30390617 PMCID: PMC6215618 DOI: 10.1186/s12859-018-2431-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023]  Open
30
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 2018. [PMID: 30377376 DOI: 10.1038/s41592-018-0176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
31
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 2018;15:962-968. [PMID: 30377376 PMCID: PMC6235447 DOI: 10.1038/s41592-018-0176-y] [Citation(s) in RCA: 953] [Impact Index Per Article: 158.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/17/2018] [Indexed: 01/06/2023]
32
Role of the Gut Microbiome in Vertebrate Evolution. mSystems 2018;3:mSystems00174-17. [PMID: 29629413 PMCID: PMC5881020 DOI: 10.1128/msystems.00174-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 12/18/2022]  Open
33
Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol 2017;18:228. [PMID: 29187204 PMCID: PMC5708111 DOI: 10.1186/s13059-017-1359-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
34
Cheng Y, Wang Y, Li Y, Zhang Y, Liu T, Wang Y, Sharpton TJ, Zhu W. Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing. Front Microbiol 2017;8:2165. [PMID: 29163444 PMCID: PMC5681530 DOI: 10.3389/fmicb.2017.02165] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/23/2017] [Indexed: 11/13/2022]  Open
35
Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS. Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice. mSystems 2017;2:e00036-17. [PMID: 28904997 PMCID: PMC5585689 DOI: 10.1128/msystems.00036-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/08/2017] [Indexed: 02/08/2023]  Open
36
Bradley PH, Pollard KS. Proteobacteria explain significant functional variability in the human gut microbiome. MICROBIOME 2017;5:36. [PMID: 28330508 PMCID: PMC5363007 DOI: 10.1186/s40168-017-0244-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/13/2017] [Indexed: 05/06/2023]
37
Ferretti P, Farina S, Cristofolini M, Girolomoni G, Tett A, Segata N. Experimental metagenomics and ribosomal profiling of the human skin microbiome. Exp Dermatol 2017;26:211-219. [DOI: 10.1111/exd.13210] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
38
Moller AG, Liang C. Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics. PeerJ 2017;5:e2844. [PMID: 28097058 PMCID: PMC5228507 DOI: 10.7717/peerj.2844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 11/29/2016] [Indexed: 01/12/2023]  Open
39
Nayfach S, Pollard KS. Toward Accurate and Quantitative Comparative Metagenomics. Cell 2016;166:1103-1116. [PMID: 27565341 DOI: 10.1016/j.cell.2016.08.007] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/11/2016] [Accepted: 08/03/2016] [Indexed: 01/08/2023]
40
Nguyen NP, Nute M, Mirarab S, Warnow T. HIPPI: highly accurate protein family classification with ensembles of HMMs. BMC Genomics 2016;17:765. [PMID: 28185571 PMCID: PMC5123343 DOI: 10.1186/s12864-016-3097-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
41
Tangherlini M, Dell'Anno A, Zeigler Allen L, Riccioni G, Corinaldesi C. Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses. Sci Rep 2016;6:28428. [PMID: 27329207 PMCID: PMC4916513 DOI: 10.1038/srep28428] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]  Open
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