메뉴 건너뛰기




Volumn 21, Issue 11, 2011, Pages 1916-1928

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICRORNA;

EID: 80055024376     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.108753.110     Document Type: Article
Times cited : (70)

References (108)
  • 2
    • 58449116673 scopus 로고    scopus 로고
    • Investigating protein-coding sequence evolution with probabilistic codon substitution models
    • Anisimova M, Kosiol C. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol 26: 255-271.
    • (2009) Mol Biol Evol , vol.26 , pp. 255-271
    • Anisimova, M.1    Kosiol, C.2
  • 3
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • Anisimova M, Bielawski JP, Yang Z. 2001. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18: 1585-1592. (Pubitemid 32735106)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.8 , pp. 1585-1592
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 4
    • 0033962272 scopus 로고    scopus 로고
    • A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing
    • DOI 10.1017/S1355838200991921
    • Aruscavage PJ, Bass BL. 2000. A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing. RNA 6: 257-269. (Pubitemid 30091596)
    • (2000) RNA , vol.6 , Issue.2 , pp. 257-269
    • Aruscavage, P.J.1    Bass, B.L.2
  • 5
    • 24644493193 scopus 로고    scopus 로고
    • Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing
    • DOI 10.1073/pnas.0506139102
    • Baek D, Green P. 2005. Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci 102: 12813-12818. (Pubitemid 41279448)
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.36 , pp. 12813-12818
    • Baek, D.1    Green, P.2
  • 6
    • 0035997389 scopus 로고    scopus 로고
    • RNA editing by adenosine deaminases that act on RNA
    • DOI 10.1146/annurev.biochem.71.110601.135501
    • Bass BL. 2002. RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem 71: 817-846. (Pubitemid 34800236)
    • (2002) Annual Review of Biochemistry , vol.71 , pp. 817-846
    • Bass, B.L.1
  • 8
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser A Stat Soc 57: 289-300.
    • (1995) J R Stat Soc Ser A Stat Soc , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 9
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • DOI 10.1214/aos/1013699998
    • Benjamini Y, Yekutieli D. 2001. The control of the false discovery rate in multiple testing under dependency. Ann Stat 29: 1165-1188. (Pubitemid 33575263)
    • (2001) Annals of Statistics , vol.29 , Issue.4 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 11
    • 0037089146 scopus 로고    scopus 로고
    • Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content
    • Castresana J. 2002. Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content. Nucleic Acids Res 30: 1751-1756. (Pubitemid 34679752)
    • (2002) Nucleic Acids Research , vol.30 , Issue.8 , pp. 1751-1756
    • Castresana, J.1
  • 12
    • 30744432134 scopus 로고    scopus 로고
    • Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    • doi: 10.1186/gb-2005-6-9-r75
    • Chamary JV, Hurst LD. 2005. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol 6: R75. doi: 10.1186/gb-2005-6-9-r75.
    • (2005) Genome Biol , vol.6
    • Chamary, J.V.1    Hurst, L.D.2
  • 13
    • 31144465926 scopus 로고    scopus 로고
    • Hearing silence: Non-neutral evolution at synonymous sites in mammals
    • DOI 10.1038/nrg1770, PII NRG1770
    • Chamary JV, Parmley JL, Hurst LD. 2006. Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7: 98-108. (Pubitemid 43128905)
    • (2006) Nature Reviews Genetics , vol.7 , Issue.2 , pp. 98-108
    • Chamary, J.V.1    Parmley, J.L.2    Hurst, L.D.3
  • 14
    • 34248213721 scopus 로고    scopus 로고
    • Detecting non-coding selective pressure in coding regions
    • doi: 10.1186/1471-2148-7-S1-S9
    • Chen H, Blanchette M. 2007. Detecting non-coding selective pressure in coding regions. BMC Evol Biol 7: S9. doi: 10.1186/1471-2148-7-S1-S9.
    • (2007) BMC Evol Biol , vol.7
    • Chen, H.1    Blanchette, M.2
  • 15
    • 70350569286 scopus 로고    scopus 로고
    • Mechanisms of alternative splicing regulation: Insights from molecular and genomics approaches
    • Chen M, Manley JL. 2009. Mechanisms of alternative splicing regulation: Insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 10: 741-754.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 741-754
    • Chen, M.1    Manley, J.L.2
  • 16
    • 33244483948 scopus 로고    scopus 로고
    • Alternatively and constitutively spliced exons are subject to different evolutionary forces
    • DOI 10.1093/molbev/msj081
    • Chen F, Wang S, Chen C, Li W, Chuang T. 2006. Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol 23: 675-682. (Pubitemid 43278279)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.3 , pp. 675-682
    • Chen, F.-C.1    Wang, S.-S.2    Chen, C.-J.3    Li, W.-H.4    Chuang, T.-J.5
  • 17
    • 34249719998 scopus 로고    scopus 로고
    • A first look at ARFome: Dual-coding genes in mammalian genomes
    • doi: 10.1371/journal.pcbi.0030091
    • Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A. 2007. A first look at ARFome: Dual-coding genes in mammalian genomes. PLoS Comput Biol 3: e91. doi: 10.1371/journal.pcbi.0030091.
    • (2007) PLoS Comput Biol , vol.3
    • Chung, W.Y.1    Wadhawan, S.2    Szklarczyk, R.3    Pond, S.K.4    Nekrutenko, A.5
  • 18
    • 71049147904 scopus 로고    scopus 로고
    • The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes
    • Cohanim AB, Haran TE. 2009. The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes. Nucleic Acids Res 37: 6466-6476.
    • (2009) Nucleic Acids Res , vol.37 , pp. 6466-6476
    • Cohanim, A.B.1    Haran, T.E.2
  • 19
    • 22244452677 scopus 로고    scopus 로고
    • Distribution and intensity of constraint in mammalian genomic sequence
    • DOI 10.1101/gr.3577405
    • Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15: 901-913. (Pubitemid 40994210)
    • (2005) Genome Research , vol.15 , Issue.7 , pp. 901-913
    • Cooper, G.M.1    Stone, E.A.2    Asimenos, G.3    Green, E.D.4    Batzoglou, S.5    Sidow, A.6
  • 21
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty K, Denise A, Ponty Y. 2009. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25: 1974-1975.
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 24
    • 33749615646 scopus 로고    scopus 로고
    • A machine learning strategy to identify candidate binding sites in human protein-coding sequence
    • doi: 10.1186/1471-2105-7-419
    • Down T, Leong B, Hubbard TJ. 2006. A machine learning strategy to identify candidate binding sites in human protein-coding sequence. BMC Bioinformatics 7: 419. doi: 10.1186/1471-2105-7-419.
    • (2006) BMC Bioinformatics , vol.7 , pp. 419
    • Down, T.1    Leong, B.2    Hubbard, T.J.3
  • 25
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • DOI 10.1126/science.1073774
    • Fairbrother WG, Yeh RF, Sharp PA, Burge CB. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013. (Pubitemid 34856033)
    • (2002) Science , vol.297 , Issue.5583 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.-F.2    Sharp, P.A.3    Burge, C.B.4
  • 27
    • 46749127393 scopus 로고    scopus 로고
    • Measuring the prevalence of regional mutation rates: An analysis of silent substitutions in mammals, fungi, and insects
    • doi: 10.1186/1471-2148-8-186
    • Fox AK, Tuch BB, Chuang JH. 2008. Measuring the prevalence of regional mutation rates: An analysis of silent substitutions in mammals, fungi, and insects. BMC Evol Biol 8: 186. doi: 10.1186/1471-2148-8-186.
    • (2008) BMC Evol Biol , vol.8 , pp. 186
    • Fox, A.K.1    Tuch, B.B.2    Chuang, J.H.3
  • 28
    • 33644784817 scopus 로고    scopus 로고
    • Estimating the "effective number of codons": The wright way of determining codon homozygosity leads to superior estimates
    • DOI 10.1534/genetics.105.049643
    • Fuglsang A. 2006. Estimating the "effective number of codons": The Wright way of determining codon homozygosity leads to superior estimates. Genetics 172: 1301-1307. (Pubitemid 43345459)
    • (2006) Genetics , vol.172 , Issue.2 , pp. 1301-1307
    • Fuglsang, A.1
  • 29
  • 30
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736.
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 31
    • 33745207758 scopus 로고    scopus 로고
    • Comparative analysis identifies exonic splicing regulatory sequences - The complex definition of enhancers and silencers
    • Goren A, Ram O, Amit M, Keren H, Lev-Maor G, Vig I, Pupko T, Ast G. 2006. Comparative analysis identifies exonic splicing regulatory sequences - the complex definition of enhancers and silencers. Mol Cell 22: 769-781.
    • (2006) Mol Cell , vol.22 , pp. 769-781
    • Goren, A.1    Ram, O.2    Amit, M.3    Keren, H.4    Lev-Maor, G.5    Vig, I.6    Pupko, T.7    Ast, G.8
  • 32
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
    • DOI 10.1016/j.molcel.2007.06.017, PII S1097276507004078
    • Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol Cell 27: 91-105. (Pubitemid 46991392)
    • (2007) Molecular Cell , vol.27 , Issue.1 , pp. 91-105
    • Grimson, A.1    Farh, K.K.-H.2    Johnston, W.K.3    Garrett-Engele, P.4    Lim, L.P.5    Bartel, D.P.6
  • 35
    • 0037440667 scopus 로고    scopus 로고
    • Expression of IGF-I splice variants in young and old human skeletal muscle after high resistance exercise
    • DOI 10.1113/jphysiol.2002.032136
    • Hameed M, Orrell RW, Cobbold M, Goldspink G, Harridge S. 2003. Expression of IGF-I splice variants in young and old human skeletal muscle after high resistance exercise. J Physiol 547: 247-254. (Pubitemid 36285178)
    • (2003) Journal of Physiology , vol.547 , Issue.1 , pp. 247-254
    • Hameed, M.1    Orrell, R.W.2    Cubbold, M.3    Goldspink, G.4    Harridge, S.D.R.5
  • 37
    • 0034646647 scopus 로고    scopus 로고
    • Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA
    • DOI 10.1074/jbc.275.15.11507
    • Hastings ML, Ingle HA, Lazar MA, Munroe SH. 2000. Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. J Biol Chem 275: 11507-11513. (Pubitemid 30212807)
    • (2000) Journal of Biological Chemistry , vol.275 , Issue.15 , pp. 11507-11513
    • Hastings, M.L.1    Ingle, H.A.2    Lazar, M.A.3    Munroe, S.H.4
  • 38
    • 0042528670 scopus 로고    scopus 로고
    • Nervous system targets of RNA editing identified by comparative genomics
    • DOI 10.1126/science.1086763
    • Hoopengardner B, Bhalla T, Staber C, Reenan R. 2003. Nervous system targets of RNA editing identified by comparative genomics. Science 301: 832-836. (Pubitemid 36962624)
    • (2003) Science , vol.301 , Issue.5634 , pp. 832-836
    • Hoopengardner, B.1    Bhalla, T.2    Staber, C.3    Reenan, R.4
  • 39
    • 18444370220 scopus 로고    scopus 로고
    • Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons
    • DOI 10.1038/sj.emboj.7600642
    • Howard MT, Aggarwal G, Anderson CB, Khatri S, Flanigan KM, Atkins JF. 2005. Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons. EMBO J 24: 1596-1607. (Pubitemid 40646449)
    • (2005) EMBO Journal , vol.24 , Issue.8 , pp. 1596-1607
    • Howard, M.T.1    Aggarwal, G.2    Anderson, C.B.3    Khatri, S.4    Flanigan, K.M.5    Atkins, J.F.6
  • 42
    • 33746435693 scopus 로고    scopus 로고
    • Preliminary assessment of the impact of microrna-mediated regulation on coding sequence evolution in mammals
    • DOI 10.1007/s00239-005-0273-2
    • Hurst LD. 2006. Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals. J Mol Evol 63: 174-182. (Pubitemid 44126973)
    • (2006) Journal of Molecular Evolution , vol.63 , Issue.2 , pp. 174-182
    • Hurst, L.D.1
  • 43
    • 0035252561 scopus 로고    scopus 로고
    • Evidence for purifying selection acting on silent sites in BRCA1
    • DOI 10.1016/S0168-9525(00)02173-9, PII S0168952500021739
    • Hurst LD, Pál C. 2001. Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet 17: 62-65. (Pubitemid 32140772)
    • (2001) Trends in Genetics , vol.17 , Issue.2 , pp. 62-65
    • Hurst, L.D.1    Pal, C.2
  • 44
    • 33847032203 scopus 로고    scopus 로고
    • The genetic code is nearly optimal for allowing additional information within protein-coding sequences
    • DOI 10.1101/gr.5987307
    • Itzkovitz S, Alon U. 2007. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res 17: 405-412. (Pubitemid 46556444)
    • (2007) Genome Research , vol.17 , Issue.4 , pp. 405-412
    • Itzkovitz, S.1    Alon, U.2
  • 46
    • 0035898609 scopus 로고    scopus 로고
    • Two overlapping reading frames in a single exon encode interacting proteins - A novel way of gene usage
    • DOI 10.1093/emboj/20.14.3849
    • Klemke M, Kehlenbach RH, Huttner WB. 2001. Two overlapping reading frames in a single exon encode interacting proteins - a novel way of gene usage. EMBO J 20: 3849-3860. (Pubitemid 32691796)
    • (2001) EMBO Journal , vol.20 , Issue.14 , pp. 3849-3860
    • Klemke, M.1    Kehlenbach, R.H.2    Huttner, W.B.3
  • 47
    • 34547675965 scopus 로고    scopus 로고
    • An empirical codon model for protein sequence evolution
    • DOI 10.1093/molbev/msm064
    • Kosiol C, Holmes I, Goldman N. 2007. An empirical codon model for protein sequence evolution. Mol Biol Evol 24: 1464-1479. (Pubitemid 47216596)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.7 , pp. 1464-1479
    • Kosiol, C.1    Holmes, I.2    Goldman, N.3
  • 48
    • 76249090744 scopus 로고    scopus 로고
    • COMIT: Identification of noncoding motifs under selection in coding sequences
    • doi: 10.1186/gb-2009-10-11-r133
    • Kural D, Ding Y, Wu J, Korpi A, Chuang J. 2009. COMIT: Identification of noncoding motifs under selection in coding sequences. Genome Biol 10: R133. doi: 10.1186/gb-2009-10-11-r133.
    • (2009) Genome Biol , vol.10
    • Kural, D.1    Ding, Y.2    Wu, J.3    Korpi, A.4    Chuang, J.5
  • 50
    • 45549100203 scopus 로고    scopus 로고
    • An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4
    • DOI 10.1093/nar/gkn148
    • Lampe X, Samad OA, Guiguen A, Matis C, Remacle S, Picard JJ, Rijli FM, Rezsohazy R. 2008. An ultraconserved hox-pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4. Nucleic Acids Res 36: 3214-3225. (Pubitemid 351858991)
    • (2008) Nucleic Acids Research , vol.36 , Issue.10 , pp. 3214-3225
    • Lampe, X.1    Samad, O.A.2    Guiguen, A.3    Matis, C.4    Remacle, S.5    Picard, J.J.6    Rijli, F.M.7    Rezsohazy, R.8
  • 51
    • 11144294108 scopus 로고    scopus 로고
    • A transcriptional regulatory element in the coding sequence of the human Bcl-2 gene
    • DOI 10.1111/j.1365-2567.2004.02073.x
    • Lang G, Gombert WM, Gould HJ. 2005. A transcriptional regulatory element in the coding sequence of the human bcl-2 gene. Immunology 114: 25-36. (Pubitemid 40030290)
    • (2005) Immunology , vol.114 , Issue.1 , pp. 25-36
    • Lang, G.1    Gombert, W.M.2    Gould, H.J.3
  • 52
    • 0034748984 scopus 로고    scopus 로고
    • Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: Implications for understanding the mechanistic basis of the male mutation bias
    • Lercher MJ, Williams EJB, Hurst LD. 2001. Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: Implications for understanding the mechanistic basis of the male mutation bias. Mol Biol Evol 18: 2032-2039. (Pubitemid 33026774)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.11 , pp. 2032-2039
    • Lercher, M.J.1    Williams, E.J.B.2    Hurst, L.D.3
  • 53
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • DOI 10.1016/j.cell.2004.12.035, PII S0092867404012607
    • Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20. (Pubitemid 40094598)
    • (2005) Cell , vol.120 , Issue.1 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 55
    • 53849094809 scopus 로고    scopus 로고
    • Ultraconserved coding regions outside the homeobox of mammalian hox genes
    • doi: 10.1186/1471-2148-8-260
    • Lin Z, Ma H, Nei M. 2008. Ultraconserved coding regions outside the homeobox of mammalian hox genes. BMC Evol Biol 8: 260. doi: 10.1186/1471-2148-8- 260.
    • (2008) BMC Evol Biol , vol.8 , pp. 260
    • Lin, Z.1    Ma, H.2    Nei, M.3
  • 58
    • 17444412589 scopus 로고    scopus 로고
    • Detecting amino acid sites under positive selection and purifying selection
    • DOI 10.1534/genetics.104.032144
    • MassinghamT, Goldman N. 2005. Detecting amino acid sites under positive selection and purifying selection. Genetics 169: 1753-1762. (Pubitemid 40547480)
    • (2005) Genetics , vol.169 , Issue.3 , pp. 1753-1762
    • Massingham, T.1    Goldman, N.2
  • 59
    • 36349016790 scopus 로고    scopus 로고
    • Prominent Roles for Odorant Receptor Coding Sequences in Allelic Exclusion
    • DOI 10.1016/j.cell.2007.10.050, PII S0092867407014043
    • Nguyen MQ, Zhou Z, Marks CA, Ryba NJP, Belluscio L. 2007. Prominent roles for odorant receptor coding sequences in allelic exclusion. Cell 131: 1009-1017. (Pubitemid 350148208)
    • (2007) Cell , vol.131 , Issue.5 , pp. 1009-1017
    • Nguyen, M.Q.1    Zhou, Z.2    Marks, C.A.3    Ryba, N.J.P.4    Belluscio, L.5
  • 60
    • 66149086564 scopus 로고    scopus 로고
    • Reliabilities of identifying positive selection by the branch-site and the site-prediction methods
    • Nozawa M, Suzuki Y, Nei M. 2009. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci 106: 6700-6705.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 6700-6705
    • Nozawa, M.1    Suzuki, Y.2    Nei, M.3
  • 61
    • 0034106726 scopus 로고    scopus 로고
    • Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters
    • Ota R, Waddell PJ, Hasegawa M, Shimodaira H, Kishino H. 2000. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol Biol Evol 17: 798-803. (Pubitemid 30252267)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.5 , pp. 798-803
    • Ota, R.1    Waddell, P.J.2    Hasegawa, M.3    Shimodaira, H.4    Kishino, H.5
  • 63
    • 34547709593 scopus 로고    scopus 로고
    • Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals
    • DOI 10.1093/molbev/msm104
    • Parmley JL, Hurst LD. 2007a. Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol 24: 1600-1603. (Pubitemid 47236703)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1600-1603
    • Parmley, J.L.1    Hurst, L.D.2
  • 64
    • 34250205655 scopus 로고    scopus 로고
    • S owing to purifying selection on synonymous mutations?
    • DOI 10.1007/s00239-006-0207-7
    • Parmley JL, Hurst LD. 2007b. How common are intragene windows with KA > KS owing to purifying selection on synonymous mutations? J Mol Evol 64: 646-655. (Pubitemid 46956757)
    • (2007) Journal of Molecular Evolution , vol.64 , Issue.6 , pp. 646-655
    • Parmley, J.L.1    Hurst, L.D.2
  • 65
    • 30744469841 scopus 로고    scopus 로고
    • Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
    • DOI 10.1093/molbev/msj035
    • Parmley JL, Chamary JV, Hurst LD. 2006. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23: 301-309. (Pubitemid 43100044)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.2 , pp. 301-309
    • Parmley, J.L.1    Chamary, J.V.2    Hurst, L.D.3
  • 67
    • 4944234045 scopus 로고    scopus 로고
    • An evolutionary model for protein-coding regions with conserved RNA structure
    • DOI 10.1093/molbev/msh199
    • Pedersen JS, Forsberg R, Meyer IM, Hein J. 2004a. An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol 21: 1913-1922. (Pubitemid 39331638)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.10 , pp. 1913-1922
    • Pedersen, J.S.1    Forsberg, R.2    Meyer, I.M.3    Hein, J.4
  • 68
    • 4644228621 scopus 로고    scopus 로고
    • A comparative method for finding and folding RNA secondary structures within protein-coding regions
    • DOI 10.1093/nar/gkh839
    • Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J. 2004b. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res 32: 4925-4936. (Pubitemid 39429696)
    • (2004) Nucleic Acids Research , vol.32 , Issue.16 , pp. 4925-4936
    • Pedersen, J.S.1    Meyer, I.M.2    Forsberg, R.3    Simmonds, P.4    Hein, J.5
  • 70
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard KS, Hubisz MJ, Rosenbloom KR, 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
  • 71
    • 27844569825 scopus 로고    scopus 로고
    • Site-to-site variation of synonymous substitution rates
    • DOI 10.1093/molbev/msi232
    • Pond SK, Muse SV. 2005. Site-to-site variation of synonymous substitution rates. Mol Biol Evol 22: 2375-2385. (Pubitemid 41661376)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.12 , pp. 2375-2385
    • Pond, S.K.1    Muse, S.V.2
  • 72
    • 0346732315 scopus 로고    scopus 로고
    • Gene Fusion and Overlapping Reading Frames in the Mammalian Genes for 4E-BP3 and MASK
    • DOI 10.1074/jbc.M310761200
    • Poulin F, Brueschke A, Sonenberg N. 2003. Gene fusion and overlapping reading frames in the mammalian genes for 4E-BP3 and MASK. J Biol Chem 278: 52290-52297. (Pubitemid 38035817)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.52 , pp. 52290-52297
    • Poulin, F.1    Brueschke, A.2    Sonenberg, N.3
  • 73
    • 33845752004 scopus 로고    scopus 로고
    • Intron size in mammals: complexity comes to terms with economy
    • DOI 10.1016/j.tig.2006.10.003, PII S0168952506003465
    • Pozzoli U, Menozzi G, Comi GP, Cagliani R, Bresolin N, Sironi M. 2007. Intron size in mammals: Complexity comes to terms with economy. Trends Genet 23: 20-24. (Pubitemid 46001690)
    • (2007) Trends in Genetics , vol.23 , Issue.1 , pp. 20-24
    • Pozzoli, U.1    Menozzi, G.2    Comi, G.P.3    Cagliani, R.4    Bresolin, N.5    Sironi, M.6
  • 76
    • 42549161129 scopus 로고    scopus 로고
    • Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts
    • doi: 10.1186/1471-2164-9-122
    • Ribrioux S, Brungger A, Baumgarten B, Seuwen K, John M. 2008. Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts. BMC Genomics 9: 122. doi: 10.1186/1471-2164-9-122.
    • (2008) BMC Genomics , vol.9 , pp. 122
    • Ribrioux, S.1    Brungger, A.2    Baumgarten, B.3    Seuwen, K.4    John, M.5
  • 77
    • 46449089502 scopus 로고    scopus 로고
    • The computational detection of functional nucleotide sequence motifs in the coding regions of organisms
    • Robins H, Krasnitz M, Levine AJ. 2008. The computational detection of functional nucleotide sequence motifs in the coding regions of organisms. Exp Biol Med 233: 665-673.
    • (2008) Exp Biol Med , vol.233 , pp. 665-673
    • Robins, H.1    Krasnitz, M.2    Levine, A.J.3
  • 78
    • 58449095670 scopus 로고    scopus 로고
    • Bayesian comparisons of codon substitution models
    • Rodrigue N, Lartillot N, Philippe H. 2008. Bayesian comparisons of codon substitution models. Genetics 180: 1579-1591.
    • (2008) Genetics , vol.180 , pp. 1579-1591
    • Rodrigue, N.1    Lartillot, N.2    Philippe, H.3
  • 79
    • 0033529064 scopus 로고    scopus 로고
    • Regulation of alternative splicing by RNA editing
    • Rueter SM, Dawson TR, Emeson RB. 1999. Regulation of alternative splicing by RNA editing. Nature 399: 75-80.
    • (1999) Nature , vol.399 , pp. 75-80
    • Rueter, S.M.1    Dawson, T.R.2    Emeson, R.B.3
  • 80
    • 33645508511 scopus 로고    scopus 로고
    • Regions of extreme synonymous codon selection in mammalian genes
    • Schattner P, Diekhans M. 2006. Regions of extreme synonymous codon selection in mammalian genes. Nucleic Acids Res 34: 1700-1710.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1700-1710
    • Schattner, P.1    Diekhans, M.2
  • 81
    • 56749103771 scopus 로고    scopus 로고
    • The trouble with sliding windows and the selective pressure in BRCA1
    • doi: 10.1371/journal.pone.0003746
    • Schmid K, Yang Z. 2008. The trouble with sliding windows and the selective pressure in BRCA1. PLoS ONE 3: e3746. doi: 10.1371/journal.pone. 0003746.
    • (2008) PLoS ONE , vol.3
    • Schmid, K.1    Yang, Z.2
  • 82
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic Regulation of Nucleosome Positioning in the Human Genome
    • DOI 10.1016/j.cell.2008.02.022, PII S0092867408002705
    • Schones DE, Cui K, Cuddapah S, Roh T, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898. (Pubitemid 351312809)
    • (2008) Cell , vol.132 , Issue.5 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3    Roh, T.-Y.4    Barski, A.5    Wang, Z.6    Wei, G.7    Zhao, K.8
  • 83
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exon-intron structure
    • Schwartz S, Meshorer E, Ast G. 2009. Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16: 990-995.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 990-995
    • Schwartz, S.1    Meshorer, E.2    Ast, G.3
  • 84
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:DT) tracts: Major determinants of nucleosome organization
    • Segal E, Widom J. 2009. Poly(dA:DT) tracts: Major determinants of nucleosome organization. Curr. Opin. Struct. Biol. 19: 65-71.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 85
    • 33646838978 scopus 로고    scopus 로고
    • A periodic pattern of mRNA secondary structure created by the genetic code
    • DOI 10.1093/nar/gkl287
    • Shabalina SA, Ogurtsov AY, Spiridonov NA. 2006. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res 34: 2428-2437. (Pubitemid 43985680)
    • (2006) Nucleic Acids Research , vol.34 , Issue.8 , pp. 2428-2437
    • Shabalina, S.A.1    Ogurtsov, A.Y.2    Spiridonov, N.A.3
  • 88
    • 0032714307 scopus 로고    scopus 로고
    • The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents
    • Smith NGC, Hurst LD. 1999. The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. Genetics 153: 1395-1402. (Pubitemid 29522150)
    • (1999) Genetics , vol.153 , Issue.3 , pp. 1395-1402
    • Smith, N.G.C.1    Hurst, L.D.2
  • 89
    • 33645224575 scopus 로고    scopus 로고
    • GONOME: Measuring correlations between GO terms and genomic positions
    • doi: 10.1186/1471-2105-7-94
    • Stanley S, Bailey T, Mattick J. 2006. GONOME: Measuring correlations between GO terms and genomic positions. BMC Bioinformatics 7: 94. doi: 10.1186/1471-2105-7-94.
    • (2006) BMC Bioinformatics , vol.7 , pp. 94
    • Stanley, S.1    Bailey, T.2    Mattick, J.3
  • 91
    • 0036855372 scopus 로고    scopus 로고
    • Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
    • Suzuki Y, Nei M. 2002. Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol Biol Evol 19: 1865-1869. (Pubitemid 35388109)
    • (2002) Molecular Biology and Evolution , vol.19 , Issue.11 , pp. 1865-1869
    • Suzuki, Y.1    Nei, M.2
  • 93
    • 77649245858 scopus 로고    scopus 로고
    • Translation efficiency is determined by both codon bias and folding energy
    • Tuller T, Waldman YY, Kupiec M, Ruppin E. 2010. Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci 107: 3645-3650.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 3645-3650
    • Tuller, T.1    Waldman, Y.Y.2    Kupiec, M.3    Ruppin, E.4
  • 94
    • 58149512003 scopus 로고    scopus 로고
    • A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2
    • Tümpel S, Cambronero F, Sims C, Krumlauf R, Wiedemann LM. 2008. A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2. Proc Natl Acad Sci 105: 20077-20082.
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 20077-20082
    • Tümpel, S.1    Cambronero, F.2    Sims, C.3    Krumlauf, R.4    Wiedemann, L.M.5
  • 95
    • 0142092546 scopus 로고    scopus 로고
    • The signature of selection mediated by expression on human genes
    • DOI 10.1101/gr.641103
    • Urrutia AO, Hurst LD. 2003. The signature of selection mediated by expression on human genes. Genome Res 13: 2260-2264. (Pubitemid 37265991)
    • (2003) Genome Research , vol.13 , Issue.10 , pp. 2260-2264
    • Urrutia, A.O.1    Hurst, L.D.2
  • 96
    • 57849138429 scopus 로고    scopus 로고
    • Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes
    • doi: 10.1186/gb-2008-9-12-r169
    • Wang P, Yin S, Zhang Z, Xin D, Hu L, Kong X, Hurst L. 2008. Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes. Genome Biol 9: R169. doi: 10.1186/gb-2008-9-12-r169.
    • (2008) Genome Biol , vol.9
    • Wang, P.1    Yin, S.2    Zhang, Z.3    Xin, D.4    Hu, L.5    Kong, X.6    Hurst, L.7
  • 97
    • 57149100569 scopus 로고    scopus 로고
    • The impact of the nucleosome code on protein-coding sequence evolution in yeast
    • doi: 10.1371/journal.pgen.1000250
    • Warnecke T, Batada NN, Hurst LD. 2008. The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 4: e1000250. doi: 10.1371/journal.pgen.1000250.
    • (2008) PLoS Genet , vol.4
    • Warnecke, T.1    Batada, N.N.2    Hurst, L.D.3
  • 98
    • 56649089682 scopus 로고    scopus 로고
    • Evolutionary footprints of nucleosome positions in yeast
    • Washietl S, Machné R, Goldman N. 2008. Evolutionary footprints of nucleosome positions in yeast. Trends Genet 24: 583-587.
    • (2008) Trends Genet , vol.24 , pp. 583-587
    • Washietl, S.1    Machné, R.2    Goldman, N.3
  • 99
    • 0032843848 scopus 로고    scopus 로고
    • Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics
    • Whelan S, Goldman N. 1999. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics. Mol Biol Evol 16: 1292-1299. (Pubitemid 29409873)
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.9 , pp. 1292-1299
    • Whelan, S.1    Goldman, N.2
  • 100
    • 0036667703 scopus 로고    scopus 로고
    • Is the synonymous substitution rate in mammals gene-specific?
    • Williams EJ, Hurst LD. 2002. Is the synonymous substitution rate in mammals gene-specific? Mol Biol Evol 19: 1395-1398.
    • (2002) Mol Biol Evol , vol.19 , pp. 1395-1398
    • Williams, E.J.1    Hurst, L.D.2
  • 101
    • 66749176636 scopus 로고    scopus 로고
    • Conserved elements within open reading frames of mammalian Hox genes
    • doi: 10.1186/jbiol116
    • Woltering J, Duboule D. 2009. Conserved elements within open reading frames of mammalian Hox genes. J Biol 8: 17. doi: 10.1186/jbiol116.
    • (2009) J Biol , vol.8 , pp. 17
    • Woltering, J.1    Duboule, D.2
  • 102
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • DOI 10.1016/0378-1119(90)90491-9
    • Wright F. 1990. The 'effective number of codons' used in a gene. Gene 87: 23-29. (Pubitemid 20139850)
    • (1990) Gene , vol.87 , Issue.1 , pp. 23-29
    • Wright, F.1
  • 103
    • 26444593981 scopus 로고    scopus 로고
    • Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
    • DOI 10.1073/pnas.0501213102
    • Xing Y, Lee C. 2005. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci 102: 13526-13531. (Pubitemid 41420882)
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.38 , pp. 13526-13531
    • Xing, Y.1    Lee, C.2
  • 104
    • 33644853819 scopus 로고    scopus 로고
    • Can RNA selection pressure distort the measurement of Ka / Ks?
    • DOI 10.1016/j.gene.2005.12.015, PII S0378111906000205
    • Xing Y, Lee C. 2006. Can RNA selection pressure distort the measurement of Ka/Ks? Gene 370: 1-5. (Pubitemid 43375893)
    • (2006) Gene , vol.370 , Issue.1-2 , pp. 1-5
    • Xing, Y.1    Lee, C.2
  • 105
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang Z, Bielawski JP. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15: 496-503.
    • (2000) Trends Ecol Evol , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2
  • 106
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen AK. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449. (Pubitemid 30257141)
    • (2000) Genetics , vol.155 , Issue.1 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.-M.K.4
  • 107
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • DOI 10.1089/1066527041410418
    • Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394. (Pubitemid 38901668)
    • (2004) Journal of Computational Biology , vol.11 , Issue.2-3 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 108
    • 0035966269 scopus 로고    scopus 로고
    • XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor
    • DOI 10.1016/S0092-8674(01)00611-0
    • Yoshida H, Matsui T, Yamamoto A, Okada T, Mori K. 2001. XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. Cell 107: 881-891. (Pubitemid 34084979)
    • (2001) Cell , vol.107 , Issue.7 , pp. 881-891
    • Yoshida, H.1    Matsui, T.2    Yamamoto, A.3    Okada, T.4    Mori, K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.