메뉴 건너뛰기




Volumn 30, Issue 23, 2014, Pages 3421-3423

READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 84920732990     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu533     Document Type: Article
Times cited : (123)

References (23)
  • 1
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R10.
    • (2010) Genome Biol. , vol.11
    • Anders, S.1    Huber, W.2
  • 2
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: Freely available Python tools for computational molecular biology and bioinformatics
    • Cock, P.J. et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.1
  • 3
    • 84867318866 scopus 로고    scopus 로고
    • EasyRNASeq: A bioconductor package for processing RNA-Seq data
    • Delhomme, N. et al. (2012) easyRNASeq: a bioconductor package for processing RNA-Seq data. Bioinformatics, 28, 2532-2533.
    • (2012) Bioinformatics , vol.28 , pp. 2532-2533
    • Delhomme, N.1
  • 4
    • 84878482772 scopus 로고    scopus 로고
    • High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates
    • Dugar, G. et al. (2013) High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet., 9, e1003495.
    • (2013) PLoS Genet. , vol.9
    • Dugar, G.1
  • 5
    • 80053929391 scopus 로고    scopus 로고
    • Progress in prokaryotic transcriptomics
    • Filiatrault, M.J. (2011) Progress in prokaryotic transcriptomics. Curr. Opin. Microbiol., 14, 579-586.
    • (2011) Curr. Opin. Microbiol. , vol.14 , pp. 579-586
    • Filiatrault, M.J.1
  • 6
    • 84889664774 scopus 로고    scopus 로고
    • Evaluation of read count based RNAseq analysis methods
    • Guo, Y. et al. (2013) Evaluation of read count based RNAseq analysis methods. BMC Genomics, 14 (Suppl. 8), S2.
    • (2013) BMC Genomics , vol.14
    • Guo, Y.1
  • 7
    • 70349667200 scopus 로고    scopus 로고
    • Fast mapping of short sequences with mismatches, insertions and deletions using index structures
    • Hoffmann, S. et al. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput. Biol., 5, e1000502.
    • (2009) PLoS Comput. Biol. , vol.5
    • Hoffmann, S.1
  • 8
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: A 2D graphics environment
    • Hunter, J.D. (2007)Matplotlib: a 2D graphics environment. Comput. Sci. Eng., 9, 90.
    • (2007) Comput. Sci. Eng. , vol.9
    • Hunter, J.D.1
  • 9
    • 84855916545 scopus 로고    scopus 로고
    • Protein-RNA interactions: New genomic technologies and perspectives
    • König, J. et al. (2012) Protein-RNA interactions: new genomic technologies and perspectives. Nat. Rev. Genet., 13, 77-83.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 77-83
    • König, J.1
  • 10
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 12
    • 84881504578 scopus 로고    scopus 로고
    • Computational analysis of bacterial RNA-Seq data
    • McClure, R. et al. (2013) Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res., 41, e140.
    • (2013) Nucleic Acids Res. , vol.41
    • McClure, R.1
  • 13
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • Mortazavi, A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
    • (2008) Nat. Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1
  • 14
    • 34247500374 scopus 로고    scopus 로고
    • Python for scientific computing
    • Oliphant, T.E. (2007) Python for scientific computing. Comput. Sci. Eng., 9, 90.
    • (2007) Comput. Sci. Eng. , vol.9
    • Oliphant, T.E.1
  • 15
    • 84903692193 scopus 로고    scopus 로고
    • Lacking alignments? the next generation sequencing mapper segemehl revisited
    • Otto, C. et al. (2014) Lacking alignments? The next generation sequencing mapper segemehl revisited. Bioinformatics, 30, 1837-1843.
    • (2014) Bioinformatics , vol.30 , pp. 1837-1843
    • Otto, C.1
  • 16
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • Ozsolak, F. and Milos, P.M. (2011) RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet., 12, 87-98.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 17
    • 84883644707 scopus 로고    scopus 로고
    • Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
    • Rapaport, F. et al. (2013) Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol., 14, R95.
    • (2013) Genome Biol. , vol.14
    • Rapaport, F.1
  • 18
    • 84885962211 scopus 로고    scopus 로고
    • Evaluating statistical analysis models for RNA sequencing experiments
    • Reeb, P.D. and Steibel, J.P. (2013) Evaluating statistical analysis models for RNA sequencing experiments. Front Genet., 4, 178.
    • (2013) Front Genet. , vol.4
    • Reeb, P.D.1    Steibel, J.P.2
  • 19
    • 77949425194 scopus 로고    scopus 로고
    • The primary transcriptome of the major human pathogen Helicobacter pylori
    • Sharma, C.M. et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature, 2, 14.
    • (2010) Nature , vol.2
    • Sharma, C.M.1
  • 20
    • 84904265834 scopus 로고    scopus 로고
    • Differential RNA-seq: The approach behind and the biological insight gained
    • Sharma, C.M. and Vogel, J. (2014) Differential RNA-seq: the approach behind and the biological insight gained. Curr. Opin. Microbiol., 19, 97-105.
    • (2014) Curr. Opin. Microbiol. , vol.19 , pp. 97-105
    • Sharma, C.M.1    Vogel, J.2
  • 21
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z. et al. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1
  • 22
    • 84898618335 scopus 로고    scopus 로고
    • Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells
    • Zhao, S. et al. (2014) Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One, 9, e78644.
    • (2014) PLoS One , vol.9
    • Zhao, S.1
  • 23
    • 84857757047 scopus 로고    scopus 로고
    • The primary transcriptome of barley chloroplasts: Numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase
    • Zhelyazkova, P. et al. (2012) The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. Plant Cell, 24, 123-136.
    • (2012) Plant Cell , vol.24 , pp. 123-136
    • Zhelyazkova, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.