메뉴 건너뛰기




Volumn 42, Issue D1, 2014, Pages

GWIPS-viz: Development of a ribo-seq genome browser

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC DATABASE; GENOMIC FRAGMENT; PRIORITY JOURNAL; PROTEIN SYNTHESIS; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; WEB BROWSER; ANIMAL; CHEMISTRY; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; INTERNET; METABOLISM; MOUSE; RIBOSOME; SEQUENCE ALIGNMENT; BACTERIAL GENOME; EXON; GENOME ANALYSIS; INFORMATION PROCESSING; INFORMATION RETRIEVAL; NONHUMAN; RNA SEQUENCE; SEQUENCE HOMOLOGY; VIRUS GENOME;

EID: 84891791498     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1035     Document Type: Article
Times cited : (183)

References (41)
  • 1
    • 83755163021 scopus 로고    scopus 로고
    • Molecular biology. Translation goes global
    • Weiss, R.B. and Atkins, J.F. (2011) Molecular biology. Translation goes global. Science, 334, 1509-1510.
    • (2011) Science , vol.334 , pp. 1509-1510
    • Weiss, R.B.1    Atkins, J.F.2
  • 2
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. and Weissman, J.S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.3    Weissman, J.S.4
  • 3
    • 77955644289 scopus 로고    scopus 로고
    • Mammalian microRNAs predominantly act to decrease target mRNA levels
    • Guo, H., Ingolia, N.T., Weissman, J.S. and Bartel, D.P. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466, 835-840.
    • (2010) Nature , vol.466 , pp. 835-840
    • Guo, H.1    Ingolia, N.T.2    Weissman, J.S.3    Bartel, D.P.4
  • 4
    • 81755184408 scopus 로고    scopus 로고
    • Wobble base-pairing slows in vivo translation elongation in metazoans
    • Stadler, M. and Fire, A. (2011) Wobble base-pairing slows in vivo translation elongation in metazoans. RNA, 17, 2063-2073.
    • (2011) RNA , vol.17 , pp. 2063-2073
    • Stadler, M.1    Fire, A.2
  • 5
    • 84857253794 scopus 로고    scopus 로고
    • Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling
    • Reid, D.W. and Nicchitta, C.V. (2012) Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling. J. Biol. Chem., 287, 5518-5527.
    • (2012) J. Biol. Chem. , vol.287 , pp. 5518-5527
    • Reid, D.W.1    Nicchitta, C.V.2
  • 7
    • 84866267681 scopus 로고    scopus 로고
    • Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
    • Lee, S., Liu, B., Huang, S.X., Shen, B. and Qian, S.B. (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl Acad. Sci. USA, 109, E2424-E2432.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109
    • Lee, S.1    Liu, B.2    Huang, S.X.3    Shen, B.4    Qian, S.B.5
  • 9
  • 10
    • 84873467908 scopus 로고    scopus 로고
    • Cotranslational response to proteotoxic stress by elongation pausing of ribosomes
    • Liu, B., Han, Y. and Qian, S.B. (2013) Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol. Cell, 49, 453-463.
    • (2013) Mol. Cell , vol.49 , pp. 453-463
    • Liu, B.1    Han, Y.2    Qian, S.B.3
  • 11
    • 84876093209 scopus 로고    scopus 로고
    • P53 induces transcriptional and translational programs to suppress cell proliferation and growth
    • Loayza-Puch, F., Drost, J., Rooijers, K., Lopes, R., Elkon, R. and Agami, R. (2013) p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol., 14, R32.
    • (2013) Genome Biol. , vol.14
    • Loayza-Puch, F.1    Drost, J.2    Rooijers, K.3    Lopes, R.4    Elkon, R.5    Agami, R.6
  • 12
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • Ingolia, N.T., Lareau, L.F. and Weissman, J.S. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147, 789-802.
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 14
    • 84862778053 scopus 로고    scopus 로고
    • Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
    • Bazzini, A.A., Lee, M.T. and Giraldez, A.J. (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science, 336, 233-237.
    • (2012) Science , vol.336 , pp. 233-237
    • Bazzini, A.A.1    Lee, M.T.2    Giraldez, A.J.3
  • 15
    • 84870527178 scopus 로고    scopus 로고
    • Contributions of mRNA abundance, ribosome loading, and post-or peri-translational effects to temporal repression of C. Elegans heterochronic miRNA targets
    • Stadler, M., Artiles, K., Pak, J. and Fire, A. (2012) Contributions of mRNA abundance, ribosome loading, and post-or peri-translational effects to temporal repression of C. Elegans heterochronic miRNA targets. Genome Res., 22, 2418-2426.
    • (2012) Genome Res. , vol.22 , pp. 2418-2426
    • Stadler, M.1    Artiles, K.2    Pak, J.3    Fire, A.4
  • 16
    • 84856625798 scopus 로고    scopus 로고
    • High-resolution view of the yeast meiotic program revealed by ribosome profiling
    • Brar, G.A., Yassour, M., Friedman, N., Regev, A., Ingolia, N.T. and Weissman, J.S. (2012) High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science, 335, 552-557.
    • (2012) Science , vol.335 , pp. 552-557
    • Brar, G.A.1    Yassour, M.2    Friedman, N.3    Regev, A.4    Ingolia, N.T.5    Weissman, J.S.6
  • 17
    • 84867919856 scopus 로고    scopus 로고
    • Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress
    • Gerashchenko, M.V., Lobanov, A.V. and Gladyshev, V.N. (2012) Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress. Proc. Natl Acad. Sci. USA, 109, 17394-17399.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 17394-17399
    • Gerashchenko, M.V.1    Lobanov, A.V.2    Gladyshev, V.N.3
  • 19
    • 84860231100 scopus 로고    scopus 로고
    • The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    • Li, G.W., Oh, E. and Weissman, J.S. (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature, 484, 538-541.
    • (2012) Nature , vol.484 , pp. 538-541
    • Li, G.W.1    Oh, E.2    Weissman, J.S.3
  • 21
    • 84880372200 scopus 로고    scopus 로고
    • Highresolution view of bacteriophage lambda gene expression by ribosome profiling
    • Liu, X., Jiang, H., Gu, Z. and Roberts, J.W. (2013) Highresolution view of bacteriophage lambda gene expression by ribosome profiling. Proc. Natl Acad. Sci. USA, 110, 11928-11933.
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 11928-11933
    • Liu, X.1    Jiang, H.2    Gu, Z.3    Roberts, J.W.4
  • 22
    • 84882258295 scopus 로고    scopus 로고
    • Ribosome profiling: A Hi-Def monitor for protein synthesis at the genome-wide scale
    • Michel, A.M. and Baranov, P.V. (2013) Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale. Wiley Interdiscip. Rev. RNA, 4, 473-490.
    • (2013) Wiley Interdiscip. Rev. RNA , vol.4 , pp. 473-490
    • Michel, A.M.1    Baranov, P.V.2
  • 24
    • 84865226981 scopus 로고    scopus 로고
    • Next-generation sequencing data interpretation: Enhancing reproducibility and accessibility
    • Nekrutenko, A. and Taylor, J. (2012) Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat. Rev. Genet., 13, 667-672.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 667-672
    • Nekrutenko, A.1    Taylor, J.2
  • 27
    • 84868324214 scopus 로고    scopus 로고
    • Observation of dually decoded regions of the human genome using ribosome profiling data
    • Michel, A.M., Choudhury, K.R., Firth, A.E., Ingolia, N.T., Atkins, J.F. and Baranov, P.V. (2012) Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res., 22, 2219-2229.
    • (2012) Genome Res. , vol.22 , pp. 2219-2229
    • Michel, A.M.1    Choudhury, K.R.2    Firth, A.E.3    Ingolia, N.T.4    Atkins, J.F.5    Baranov, P.V.6
  • 28
    • 0031559590 scopus 로고    scopus 로고
    • Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: Programmed efficiency of 50%
    • Larsen, B., Gesteland, R.F. and Atkins, J.F. (1997) Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%. J. Mol. Biol., 271, 47-60.
    • (1997) J. Mol. Biol. , vol.271 , pp. 47-60
    • Larsen, B.1    Gesteland, R.F.2    Atkins, J.F.3
  • 29
    • 0025355475 scopus 로고
    • Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme
    • Tsuchihashi, Z. and Kornberg, A. (1990) Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme. Proc. Natl Acad. Sci. USA, 87, 2516-2520.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 2516-2520
    • Tsuchihashi, Z.1    Kornberg, A.2
  • 30
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
    • Pruitt, K.D., Tatusova, T., Brown, G.R. and Maglott, D.R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
    • (2012) Nucleic Acids Res. , vol.40
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 33
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. and Siepel, A. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res., 20, 110-121.
    • (2010) Genome Res. , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 36
    • 58149189877 scopus 로고    scopus 로고
    • GtRNAdb: A database of transfer RNA genes detected in genomic sequence
    • Chan, P.P. and Lowe, T.M. (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res., 37, D93-D97.
    • (2009) Nucleic Acids Res. , vol.37
    • Chan, P.P.1    Lowe, T.M.2
  • 38
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17, 10-12.
    • (2011) EMBnet J. , vol.17 , pp. 10-12
    • Martin, M.1
  • 39
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C, Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 40
    • 0036226603 scopus 로고    scopus 로고
    • BLAT the blast-like alignment tool
    • Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 41
    • 77955895425 scopus 로고    scopus 로고
    • BigWig and BigBed: Enabling browsing of large distributed datasets
    • Kent, W.J., Zweig, A.S., Barber, G, Hinrichs, A.S. and Karolchik, D. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26, 2204-2207.
    • (2010) Bioinformatics , vol.26 , pp. 2204-2207
    • Kent, W.J.1    Zweig, A.S.2    Barber, G.3    Hinrichs, A.S.4    Karolchik, D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.