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For: 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] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/27/2017] [Indexed: 01/16/2023]  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
Contreras-Peruyero H, Nuñez I, Vazquez-Rosas-Landa M, Santana-Quinteros D, Pashkov A, Carranza-Barragán ME, Perez-Estrada R, Guerrero-Flores S, Balanzario E, Muñiz Sánchez V, Nakamura M, Ramírez-Ramírez LL, Sélem-Mojica N. CAMDA 2023: Finding patterns in urban microbiomes. Front Genet 2024;15:1449461. [PMID: 39655221 PMCID: PMC11625776 DOI: 10.3389/fgene.2024.1449461] [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: 06/15/2024] [Accepted: 11/07/2024] [Indexed: 12/12/2024]  Open
3
Yan L, Xu J, Lou F, Dong Y, Lv S, Kang N, Luo Z, Liu Y, Pu J, Zhong X, Ji P, Xie P, Jin X. Alterations of oral microbiome and metabolic signatures and their interaction in oral lichen planus. J Oral Microbiol 2024;16:2422164. [PMID: 39498115 PMCID: PMC11533246 DOI: 10.1080/20002297.2024.2422164] [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: 05/29/2024] [Revised: 08/03/2024] [Accepted: 09/03/2024] [Indexed: 11/07/2024]  Open
4
Chung HC, Friedberg I, Bromberg Y. Assembling bacterial puzzles: piecing together functions into microbial pathways. NAR Genom Bioinform 2024;6:lqae109. [PMID: 39184378 PMCID: PMC11344244 DOI: 10.1093/nargab/lqae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/24/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]  Open
5
Mahlich Y, Zhu C, Chung H, Velaga PK, De Paolis Kaluza M, Radivojac P, Friedberg I, Bromberg Y. Learning from the unknown: exploring the range of bacterial functionality. Nucleic Acids Res 2023;51:10162-10175. [PMID: 37739408 PMCID: PMC10602916 DOI: 10.1093/nar/gkad757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]  Open
6
Hoarfrost A, Aptekmann A, Farfañuk G, Bromberg Y. Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. Nat Commun 2022;13:2606. [PMID: 35545619 PMCID: PMC9095714 DOI: 10.1038/s41467-022-30070-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/30/2022] [Indexed: 12/22/2022]  Open
7
Bağcı C, Patz S, Huson DH. DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences. Curr Protoc 2021;1:e59. [PMID: 33656283 DOI: 10.1002/cpz1.59] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
8
Honarbakhsh M, Ericsson A, Zhong G, Isoherranen N, Zhu C, Bromberg Y, Van Buiten C, Malta K, Joseph L, Sampath H, Lackey AI, Storch J, Vetriani C, Chikindas ML, Breslin P, Quadro L. Impact of vitamin A transport and storage on intestinal retinoid homeostasis and functions. J Lipid Res 2021;62:100046. [PMID: 33587919 PMCID: PMC8020483 DOI: 10.1016/j.jlr.2021.100046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/15/2021] [Accepted: 01/29/2021] [Indexed: 12/15/2022]  Open
9
Wu G, Zhao N, Zhang C, Lam YY, Zhao L. Guild-based analysis for understanding gut microbiome in human health and diseases. Genome Med 2021;13:22. [PMID: 33563315 PMCID: PMC7874449 DOI: 10.1186/s13073-021-00840-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/26/2021] [Indexed: 12/14/2022]  Open
10
Van Damme R, Hölzer M, Viehweger A, Müller B, Bongcam-Rudloff E, Brandt C. Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PLoS Comput Biol 2021;17:e1008716. [PMID: 33561126 PMCID: PMC7899367 DOI: 10.1371/journal.pcbi.1008716] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 02/22/2021] [Accepted: 01/17/2021] [Indexed: 01/12/2023]  Open
11
Gaeta NC, Bean E, Miles AM, de Carvalho DUOG, Alemán MAR, Carvalho JS, Gregory L, Ganda E. A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated Environment. Front Microbiol 2020;11:590325. [PMID: 33304338 PMCID: PMC7701293 DOI: 10.3389/fmicb.2020.590325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/16/2020] [Indexed: 12/17/2022]  Open
12
Zhu C, Miller M, Lusskin N, Bergk Pinto B, Maccario L, Häggblom M, Vogel T, Larose C, Bromberg Y. Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds. Microbiologyopen 2020;9:e1100. [PMID: 32762019 PMCID: PMC7520998 DOI: 10.1002/mbo3.1100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022]  Open
13
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]
14
Utro F, Haiminen N, Siragusa E, Gardiner LJ, Seabolt E, Krishna R, Kaufman JH, Parida L. Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes. iScience 2020;23:100988. [PMID: 32248063 PMCID: PMC7125348 DOI: 10.1016/j.isci.2020.100988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 12/14/2022]  Open
15
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
16
Metagenomic insights into the changes in microbial community and antimicrobial resistance genes associated with different salt content of red pepper (Capsicum annuum L.) sauce. Food Microbiol 2020;85:103295. [DOI: 10.1016/j.fm.2019.103295] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/03/2019] [Accepted: 08/07/2019] [Indexed: 01/06/2023]
17
Zhu C, Miller M, Lusskin N, Mahlich Y, Wang Y, Zeng Z, Bromberg Y. Fingerprinting cities: differentiating subway microbiome functionality. Biol Direct 2019;14:19. [PMID: 31666099 PMCID: PMC6822482 DOI: 10.1186/s13062-019-0252-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 10/02/2019] [Indexed: 12/21/2022]  Open
18
Elolimy A, Alharthi A, Zeineldin M, Parys C, Helmbrecht A, Loor JJ. Supply of Methionine During Late-Pregnancy Alters Fecal Microbiota and Metabolome in Neonatal Dairy Calves Without Changes in Daily Feed Intake. Front Microbiol 2019;10:2159. [PMID: 31608024 PMCID: PMC6761860 DOI: 10.3389/fmicb.2019.02159] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 09/02/2019] [Indexed: 12/12/2022]  Open
19
Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population. mSphere 2019;4:4/2/e00152-19. [PMID: 30894435 PMCID: PMC6429046 DOI: 10.1128/mspheredirect.00152-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
20
Miller M, Zhu C, Bromberg Y. clubber: removing the bioinformatics bottleneck in big data analyses. J Integr Bioinform 2017;14:/j/jib.ahead-of-print/jib-2017-0020/jib-2017-0020.xml. [PMID: 28609295 PMCID: PMC5929469 DOI: 10.1515/jib-2017-0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/27/2017] [Indexed: 11/17/2022]  Open
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