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Volumn 5, Issue MAY2016, 2016, Pages

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

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EID: 84979503828     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.13328     Document Type: Article
Times cited : (109)

References (55)
  • 2
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch A, Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28:45-48. doi: 10.1093/nar/28.1.45
    • (2000) Nucleic Acids Research , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 3
    • 84884660617 scopus 로고    scopus 로고
    • Gene expression regulation by upstream open reading frames and human disease
    • Barbosa C, Peixeiro I, Romäo L. 2013. Gene expression regulation by upstream open reading frames and human disease. PLoS Genetics 9:e1003529. doi: 10.1371/journal.pgen.1003529
    • (2013) PLoS Genetics , vol.9
    • Barbosa, C.1    Peixeiro, I.2    Romäo, L.3
  • 8
    • 33749556658 scopus 로고    scopus 로고
    • Galectin-1: A small protein with major functions
    • Camby I, Le Mercier M, Lefranc F, Kiss R. 2006. Galectin-1: a small protein with major functions. Glycobiology 16:137R-157. doi: 10.1093/glycob/cwl025
    • (2006) Glycobiology , vol.16 , pp. 137R-157R
    • Camby, I.1    Le Mercier, M.2    Lefranc, F.3    Kiss, R.4
  • 10
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology 26:1367-1372. doi: 10.1038/nbt.1511
    • (2008) Nature Biotechnology , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 14
    • 33750971421 scopus 로고    scopus 로고
    • Non-equilibrium theory of the allele frequency spectrum
    • Evans SN, Shvets Y, Slatkin M. 2007. Non-equilibrium theory of the allele frequency spectrum. Theoretical Population Biology 71:109-119. doi: 10.1016/j.tpb.2006.06.005
    • (2007) Theoretical Population Biology , vol.71 , pp. 109-119
    • Evans, S.N.1    Shvets, Y.2    Slatkin, M.3
  • 16
    • 34249021370 scopus 로고    scopus 로고
    • Peptides encoded by short ORFs control development and define a new eukaryotic gene family
    • Galindo MI, Pueyo JI, Fouix S, Bishop SA, Couso JP. 2007. Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biology 5:e106. doi: 10.1371/journal.pbio. 0050106
    • (2007) PLoS Biology , vol.5
    • Galindo, M.I.1    Pueyo, J.I.2    Fouix, S.3    Bishop, S.A.4    Couso, J.P.5
  • 17
    • 84879969127 scopus 로고    scopus 로고
    • Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
    • Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. 2013. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154:240-251. doi: 10.1016/j.cell.2013.06.009
    • (2013) Cell , vol.154 , pp. 240-251
    • Guttman, M.1    Russell, P.2    Ingolia, N.T.3    Weissman, J.S.4    Lander, E.S.5
  • 18
    • 84879671055 scopus 로고    scopus 로고
    • Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs
    • Hangauer MJ, Vaughn IW, McManus MT. 2013. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genetics 9:e1003569. doi: 10. 1371/journal.pgen.1003569
    • (2013) PLoS Genetics , vol.9
    • Hangauer, M.J.1    Vaughn, I.W.2    McManus, M.T.3
  • 22
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223. doi: 10.1126/science.1168978
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.3    Weissman, J.S.4
  • 23
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • Ingolia NT, Lareau LF, Weissman JS. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789-802. doi: 10.1016/j.cell.2011.10.002
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 27
    • 84888838351 scopus 로고    scopus 로고
    • Primate transcript and protein expression levels evolve under compensatory selection pressures
    • Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y. 2013. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science 342:1100-1104. doi: 10.1126/science.1242379
    • (2013) Science , vol.342 , pp. 1100-1104
    • Khan, Z.1    Ford, M.J.2    Cusanovich, D.A.3    Mitrano, A.4    Pritchard, J.K.5    Gilad, Y.6
  • 28
    • 46049107404 scopus 로고    scopus 로고
    • Alternative translation start sites and hidden coding potential of eukaryotic mRNAs
    • Kochetov AV. 2008. Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. BioEssays 30:683-691. doi: 10.1002/bies.20771
    • (2008) BioEssays , vol.30 , pp. 683-691
    • Kochetov, A.V.1
  • 29
    • 34447573973 scopus 로고    scopus 로고
    • Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA
    • Kondo T, Hashimoto Y, Kato K, Inagaki S, Hayashi S, Kageyama Y. 2007. Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nature Cell Biology 9:660-665. doi: 10.1038/ncb1595
    • (2007) Nature Cell Biology , vol.9 , pp. 660-665
    • Kondo, T.1    Hashimoto, Y.2    Kato, K.3    Inagaki, S.4    Hayashi, S.5    Kageyama, Y.6
  • 31
    • 0023665902 scopus 로고
    • An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs
    • Kozak M. 1987. An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Research 15:8125-8148. doi: 10.1093/nar/15.20.8125
    • (1987) Nucleic Acids Research , vol.15 , pp. 8125-8148
    • Kozak, M.1
  • 32
    • 4344681535 scopus 로고    scopus 로고
    • Expression of the Alzheimer protease BACE1 is suppressed via its 5'-untranslated region
    • Lammich S, Schöbel S, Zimmer AK, Lichtenthaler SF, Haass C. 2004. Expression of the Alzheimer protease BACE1 is suppressed via its 5'-untranslated region. EMBO Reports 5:620-625. doi: 10.1038/sj.embor.7400166
    • (2004) EMBO Reports , vol.5 , pp. 620-625
    • Lammich, S.1    Schöbel, S.2    Zimmer, A.K.3    Lichtenthaler, S.F.4    Haass, C.5
  • 33
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359. doi:10.1038/nmeth.1923
    • (2012) Nature Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 38
    • 79959446962 scopus 로고    scopus 로고
    • PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions
    • Lin MF, Jungreis I, Kellis M. 2011. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27:i275-282. doi: 10.1093/bioinformatics/btr209
    • (2011) Bioinformatics , vol.27 , pp. i275-i282
    • Lin, M.F.1    Jungreis, I.2    Kellis, M.3
  • 39
    • 84957881805 scopus 로고    scopus 로고
    • Novor: Real-time peptide de novo sequencing software
    • Ma B. 2015. Novor: Real-time peptide de novo sequencing software. Journal of the American Society for Mass Spectrometry 26:1885-1894. doi: 10.1007/s13361-015-1204-0
    • (2015) Journal of the American Society for Mass Spectrometry , vol.26 , pp. 1885-1894
    • Ma, B.1
  • 41
    • 0034459468 scopus 로고    scopus 로고
    • Upstream open reading frames as regulators of mRNA translation
    • Morris DR, Geballe AP. 2000. Upstream open reading frames as regulators of mRNA translation. Molecular and Cellular Biology 20:8635-8642. doi: 10.1128/MCB.20.23.8635-8642.2000
    • (2000) Molecular and Cellular Biology , vol.20 , pp. 8635-8642
    • Morris, D.R.1    Geballe, A.P.2
  • 42
    • 84908540871 scopus 로고    scopus 로고
    • Proteogenomics: Concepts, applications and computational strategies
    • Nesvizhskii AI. 2014. Proteogenomics: concepts, applications and computational strategies. Nature Methods 11:1114-1125. doi: 10.1038/nmeth.3144
    • (2014) Nature Methods , vol.11 , pp. 1114-1125
    • Nesvizhskii, A.I.1
  • 43
    • 29444452921 scopus 로고    scopus 로고
    • Molecular signatures of natural selection
    • Nielsen R. 2005. Molecular signatures of natural selection. Annual Review of Genetics 39:197-218. doi: 10.1146/annurev.genet.39.073003.112420
    • (2005) Annual Review of Genetics , vol.39 , pp. 197-218
    • Nielsen, R.1
  • 49
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111. doi: 10.1093/bioinformatics/btp120
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 50
    • 77952905505 scopus 로고    scopus 로고
    • Most "dark matter" transcripts are associated with known genes
    • van Bakel H, Nislow C, Blencowe BJ, Hughes TR. 2010. Most "dark matter" transcripts are associated with known genes. PLoS Biology 8:e1000371. doi: 10.1371/journal.pbio.1000371
    • (2010) PLoS Biology , vol.8
    • van Bakel, H.1    Nislow, C.2    Blencowe, B.J.3    Hughes, T.R.4
  • 52
    • 84959149884 scopus 로고    scopus 로고
    • Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation
    • Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP. 2016. Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation. Cell Reports 14:\. doi: 10.1016/j.celrep.2016.01.043
    • (2016) Cell Reports , vol.14 , pp. 1787-1799
    • Weinberg, D.E.1    Shah, P.2    Eichhorn, S.W.3    Hussmann, J.A.4    Plotkin, J.B.5    Bartel, D.P.6
  • 55
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24:1586-1591. doi: 10.1093/molbev/msm088
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1586-1591
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.