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Volumn 17, Issue 1, 2016, Pages

COMAN: A web server for comprehensive metatranscriptomics analysis

Author keywords

Computational biology; Metatranscriptomics; Microbial community; Microbial RNA Seq; Web servers

Indexed keywords

UNTRANSLATED RNA; TRANSCRIPTOME;

EID: 84981308664     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2964-z     Document Type: Article
Times cited : (33)

References (31)
  • 2
    • 84906330280 scopus 로고    scopus 로고
    • Metatranscriptomic analysis of arctic peat soil microbiota
    • Tveit AT, Urich T, Svenning MM. Metatranscriptomic analysis of arctic peat soil microbiota. Appl Environ Microbiol. 2014;80(18):5761-72.
    • (2014) Appl Environ Microbiol , vol.80 , Issue.18 , pp. 5761-5772
    • Tveit, A.T.1    Urich, T.2    Svenning, M.M.3
  • 3
    • 77955963505 scopus 로고    scopus 로고
    • Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed
    • Booijink CC, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M, de Vos WM. Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol. 2010;76(16):5533-40.
    • (2010) Appl Environ Microbiol , vol.76 , Issue.16 , pp. 5533-5540
    • Booijink, C.C.1    Boekhorst, J.2    Zoetendal, E.G.3    Smidt, H.4    Kleerebezem, M.5    Vos, W.M.6
  • 6
    • 84872535919 scopus 로고    scopus 로고
    • Xenobiotics shape the physiology and gene expression of the active human gut microbiome
    • Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell. 2013;152(1-2):39-50.
    • (2013) Cell , vol.152 , Issue.1-2 , pp. 39-50
    • Maurice, C.F.1    Haiser, H.J.2    Turnbaugh, P.J.3
  • 7
    • 84899761579 scopus 로고    scopus 로고
    • Metatranscriptomics of the human oral microbiome during health and disease
    • Jorth P, Turner KH, Gumus P, Nizam N, Buduneli N, Whiteley M. Metatranscriptomics of the human oral microbiome during health and disease. MBio. 2014;5(2):e01012-01014.
    • (2014) MBio , vol.5 , Issue.2 , pp. e01012-01014
    • Jorth, P.1    Turner, K.H.2    Gumus, P.3    Nizam, N.4    Buduneli, N.5    Whiteley, M.6
  • 8
    • 79952314593 scopus 로고    scopus 로고
    • A pipeline for RNA-seq data processing and quality assessment
    • Goncalves A, Tikhonov A, Brazma A, Kapushesky M. A pipeline for RNA-seq data processing and quality assessment. Bioinformatics. 2011;27(6):867-9.
    • (2011) Bioinformatics , vol.27 , Issue.6 , pp. 867-869
    • Goncalves, A.1    Tikhonov, A.2    Brazma, A.3    Kapushesky, M.4
  • 10
    • 79960656161 scopus 로고    scopus 로고
    • ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
    • Friedman BA, Maniatis T. ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data. Genome Biol. 2011;12(7):R69.
    • (2011) Genome Biol , vol.12 , Issue.7 , pp. R69
    • Friedman, B.A.1    Maniatis, T.2
  • 16
    • 84925021592 scopus 로고    scopus 로고
    • Fast and sensitive protein alignment using DIAMOND
    • Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59-60.
    • (2015) Nat Methods , vol.12 , Issue.1 , pp. 59-60
    • Buchfink, B.1    Xie, C.2    Huson, D.H.3
  • 17
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997;278(5338):631-7.
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 18
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 19
    • 79959986975 scopus 로고    scopus 로고
    • KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
    • Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L: KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 2011, 39(Web Server issue):W316-322.
    • (2011) Nucleic Acids Res , vol.39 , Issue.WEB SERVER ISSUE , pp. W316-W322
    • Xie, C.1    Mao, X.2    Huang, J.3    Ding, Y.4    Wu, J.5    Dong, S.6    Kong, L.7    Gao, G.8    Li, C.Y.9    Wei, L.10
  • 23
    • 70049085269 scopus 로고    scopus 로고
    • A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
    • Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol. 2009;5(8):e1000465.
    • (2009) PLoS Comput Biol , vol.5 , Issue.8
    • Ye, Y.1    Doak, T.G.2
  • 25
    • 84952837525 scopus 로고    scopus 로고
    • A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes
    • e01263-15
    • Ni Y, Li J, Panagiotou G. A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes. MBio. 2015;6(6):e01263-15.
    • (2015) MBio , vol.6 , Issue.6
    • Ni, Y.1    Li, J.2    Panagiotou, G.3
  • 26
    • 77649168721 scopus 로고    scopus 로고
    • A general co-expression network-based approach to gene expression analysis: comparison and applications
    • Ruan J, Dean AK, Zhang W. A general co-expression network-based approach to gene expression analysis: comparison and applications. BMC Syst Biol. 2010;4:8.
    • (2010) BMC Syst Biol , vol.4 , pp. 8
    • Ruan, J.1    Dean, A.K.2    Zhang, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.