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For: Niu SY, Yang J, McDermaid A, Zhao J, Kang Y, Ma Q. Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes. Brief Bioinform 2019;19:1415-1429. [PMID: 28481971 DOI: 10.1093/bib/bbx051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 12/12/2022]  Open
Number Cited by Other Article(s)
1
Alanzi AR. Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods. J Microbiol Biotechnol 2024;35:e2407064. [PMID: 39639495 PMCID: PMC11813339 DOI: 10.4014/jmb.2407.07064] [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] [Received: 08/14/2024] [Revised: 10/22/2024] [Accepted: 10/30/2024] [Indexed: 12/07/2024]
2
Wang J, Ou Y, Li R, Tao C, Liu H, Li R, Shen Z, Shen Q. The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024;283:116982. [PMID: 39217893 DOI: 10.1016/j.ecoenv.2024.116982] [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: 05/30/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
3
Wen L, Yang L, Chen C, Li J, Fu J, Liu G, Kan Q, Ho CT, Huang Q, Lan Y, Cao Y. Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods. Crit Rev Food Sci Nutr 2023;64:8367-8383. [PMID: 37068005 DOI: 10.1080/10408398.2023.2199425] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
4
Kuraji R, Shiba T, Dong TS, Numabe Y, Kapila YL. Periodontal treatment and microbiome-targeted therapy in management of periodontitis-related nonalcoholic fatty liver disease with oral and gut dysbiosis. World J Gastroenterol 2023;29:967-996. [PMID: 36844143 PMCID: PMC9950865 DOI: 10.3748/wjg.v29.i6.967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023]  Open
5
Chaudhari HG, Prajapati S, Wardah ZH, Raol G, Prajapati V, Patel R, Shati AA, Alfaifi MY, Elbehairi SEI, Sayyed RZ. Decoding the microbial universe with metagenomics: a brief insight. Front Genet 2023;14:1119740. [PMID: 37197021 PMCID: PMC10183756 DOI: 10.3389/fgene.2023.1119740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023]  Open
6
Zhao B, van Bodegom PM, Trimbos KB. Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA. Mol Ecol Resour 2023;23:81-91. [PMID: 35899418 PMCID: PMC10087510 DOI: 10.1111/1755-0998.13691] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
7
Ko KKK, Chng KR, Nagarajan N. Metagenomics-enabled microbial surveillance. Nat Microbiol 2022;7:486-496. [PMID: 35365786 DOI: 10.1038/s41564-022-01089-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
8
Biotechnological approaches in agriculture and environmental management - bacterium Kocuria rhizophila 14ASP as heavy metal and salt- tolerant plant growth- promoting strain. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00826-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
9
Liu Z, Ma A, Mathé E, Merling M, Ma Q, Liu B. Network analyses in microbiome based on high-throughput multi-omics data. Brief Bioinform 2021;22:1639-1655. [PMID: 32047891 PMCID: PMC7986608 DOI: 10.1093/bib/bbaa005] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/06/2023]  Open
10
Mehta S, Kumar P, Crane M, Johnson JE, Sajulga R, Nguyen DDA, McGowan T, Arntzen MØ, Griffin TJ, Jagtap PD. Updates on metaQuantome Software for Quantitative Metaproteomics. J Proteome Res 2021;20:2130-2137. [PMID: 33683127 DOI: 10.1021/acs.jproteome.0c00960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
11
Imchen M, Moopantakath J, Kumavath R, Barh D, Tiwari S, Ghosh P, Azevedo V. Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. Front Genet 2020;11:563975. [PMID: 33240317 PMCID: PMC7677515 DOI: 10.3389/fgene.2020.563975] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022]  Open
12
Prayogo FA, Budiharjo A, Kusumaningrum HP, Wijanarka W, Suprihadi A, Nurhayati N. Metagenomic applications in exploration and development of novel enzymes from nature: a review. J Genet Eng Biotechnol 2020;18:39. [PMID: 32749574 PMCID: PMC7403272 DOI: 10.1186/s43141-020-00043-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
13
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: 1.2] [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
14
Jo J, Oh J, Park C. Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists. J Microbiol 2020;58:176-192. [PMID: 32108314 DOI: 10.1007/s12275-020-9525-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
15
Breitwieser FP, Lu J, Salzberg SL. A review of methods and databases for metagenomic classification and assembly. Brief Bioinform 2019;20:1125-1136. [PMID: 29028872 PMCID: PMC6781581 DOI: 10.1093/bib/bbx120] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/22/2017] [Indexed: 12/13/2022]  Open
16
Niu SY, Liu B, Ma Q, Chou WC. rSeqTU-A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units. Front Genet 2019;10:374. [PMID: 31156694 PMCID: PMC6529933 DOI: 10.3389/fgene.2019.00374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/09/2019] [Indexed: 11/13/2022]  Open
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