메뉴 건너뛰기




Volumn 2008, Issue 4, 2008, Pages 121-137

Strategies for reliable exploitation of evolutionary concepts in high throughput biology

Author keywords

Evolutionary informatics; Functional annotation; Information network; Phylogenetic inference; Systems biology

Indexed keywords

APPLIED RESEARCH; ARTICLE; BIOINFORMATICS; BIOTECHNOLOGY; DRUG RESEARCH; EVOLUTIONARY HOMOLOGY; FUNCTIONAL GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; INFORMATION TECHNOLOGY; LARGE SCALE PRODUCTION; MEDICAL RESEARCH; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; QUALITY CONTROL; RELIABILITY; SPECIES COMPARISON; SYSTEMS BIOLOGY;

EID: 44249108083     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (14)

References (134)
  • 1
    • 0036205874 scopus 로고    scopus 로고
    • Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER
    • Aggarwal, G. and Ramaswamy, R. 2002. Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER. J. Biosci., 27:7-14.
    • (2002) J. Biosci , vol.27 , pp. 7-14
    • Aggarwal, G.1    Ramaswamy, R.2
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S.F., Madden, T.L., Schäffer, A.A. et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25:3389-402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3
  • 3
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M., Ball, C.A., Blake, J.A. et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium: Nat. Genet., 25:25-29.
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 4
    • 33745373606 scopus 로고    scopus 로고
    • Primate segmental duplications: Crucibles of evolution, diversity and disease
    • Bailey, J.A. and Eichler, E.E. 2006. Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat. Rev. Genet., 7:552-64.
    • (2006) Nat. Rev. Genet , vol.7 , pp. 552-564
    • Bailey, J.A.1    Eichler, E.E.2
  • 5
    • 22544457599 scopus 로고    scopus 로고
    • vALId: Validation of protein sequence quality based on multiple alignment data
    • Bianchetti, L., Thompson, J.D., Lecompte, O. et al. 2005. vALId: validation of protein sequence quality based on multiple alignment data. J. Bioinforin. Comput. Biol., 3:929-47.
    • (2005) J. Bioinforin. Comput. Biol , vol.3 , pp. 929-947
    • Bianchetti, L.1    Thompson, J.D.2    Lecompte, O.3
  • 6
    • 33746237567 scopus 로고    scopus 로고
    • Genomic insights into positive selection
    • Biswas, S. and Akey, J.M. 2006. Genomic insights into positive selection. Trends Genet., 22:437-46.
    • (2006) Trends Genet , vol.22 , pp. 437-446
    • Biswas, S.1    Akey, J.M.2
  • 7
    • 0041589546 scopus 로고    scopus 로고
    • Foot Printer: A program designed for phylogenetic foot printing
    • Blanchette, M. and Tompa, M. 2003. Foot Printer: A program designed for phylogenetic foot printing. Nucleic Acids Res., 31:3840-2.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3840-3842
    • Blanchette, M.1    Tompa, M.2
  • 8
    • 10944228197 scopus 로고    scopus 로고
    • Reconstructing large regions of an ancestral mammalian genome in silico
    • Blanchette, M., Green, E.D., Miller, W. et al. 2004. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res., 14:2412-23.
    • (2004) Genome Res , vol.14 , pp. 2412-2423
    • Blanchette, M.1    Green, E.D.2    Miller, W.3
  • 9
    • 33745067419 scopus 로고    scopus 로고
    • The gain and loss of genes during 600 million years of vertebrate evolution
    • Blomme, T., Vandepoele, K., De Bodt, S. et al. 2006. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol., 7:R43.
    • (2006) Genome Biol , vol.7
    • Blomme, T.1    Vandepoele, K.2    De Bodt, S.3
  • 10
    • 0037440008 scopus 로고    scopus 로고
    • Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information
    • Blouin, C., Boucher, Y. and Roger, A.J. 2003. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res., 31:790-7.
    • (2003) Nucleic Acids Res , vol.31 , pp. 790-797
    • Blouin, C.1    Boucher, Y.2    Roger, A.J.3
  • 11
    • 16444378220 scopus 로고    scopus 로고
    • Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication
    • Bos. D.H. 2005. Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication. J. Mol. Evol., 60:221-228.
    • (2005) J. Mol. Evol , vol.60 , pp. 221-228
    • Bos, D.H.1
  • 12
    • 1842768393 scopus 로고    scopus 로고
    • Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes
    • Bourque, G. and Pevzner, P.A. 2004. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res., 14:507-16.
    • (2004) Genome Res , vol.14 , pp. 507-516
    • Bourque, G.1    Pevzner, P.A.2
  • 13
    • 12744263078 scopus 로고    scopus 로고
    • Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    • Bourque, G., Zdobnov, E.M., Bork, P. et al. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res., 15:98-110.
    • (2005) Genome Res , vol.15 , pp. 98-110
    • Bourque, G.1    Zdobnov, E.M.2    Bork, P.3
  • 14
  • 15
    • 0035201828 scopus 로고    scopus 로고
    • Phylogenetic inferences from molecular sequences: Review and critique
    • Brocchieri, L. 2001. Phylogenetic inferences from molecular sequences: review and critique. Theor. Popul. Biol., 59:27-40.
    • (2001) Theor. Popul. Biol , vol.59 , pp. 27-40
    • Brocchieri, L.1
  • 16
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • Brudno, M., Do, C.B., Cooper, G.M. et al. 2003. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13:721-31.
    • (2003) Genome Res , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.B.2    Cooper, G.M.3
  • 17
    • 0000303438 scopus 로고
    • The Multiple Sequence Alignment Problem in Biology
    • Carrillo, H. and Lipman, D. 1988. The Multiple Sequence Alignment Problem in Biology. SIAM Appl. Math., 48:1073-82.
    • (1988) SIAM Appl. Math , vol.48 , pp. 1073-1082
    • Carrillo, H.1    Lipman, D.2
  • 18
    • 0042121237 scopus 로고    scopus 로고
    • Multiple sequence alignment with the Clustal series of programs
    • Chenna, R., Sugawara, H., Koike, T. et al. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31:3497-500.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3497-3500
    • Chenna, R.1    Sugawara, H.2    Koike, T.3
  • 19
    • 2942604504 scopus 로고    scopus 로고
    • Bioinformatics tools for single nucleotide polymorphism discovery and analysis
    • Clifford, R.J., Edmonson, M.N., Nguyen, C. et al. 2004. Bioinformatics tools for single nucleotide polymorphism discovery and analysis, Ann. N. Y. Acad. Sci., 1020:101-9.
    • (2004) Ann. N. Y. Acad. Sci , vol.1020 , pp. 101-109
    • Clifford, R.J.1    Edmonson, M.N.2    Nguyen, C.3
  • 20
    • 0038305140 scopus 로고    scopus 로고
    • A co-evolution perspective of the TNFSF and TNFRSF families in the immune system
    • Collette, Y., Gilles, A., Pontarotti, P. et al. 2003. A co-evolution perspective of the TNFSF and TNFRSF families in the immune system. Trends Immunol., 24:387-94.
    • (2003) Trends Immunol , vol.24 , pp. 387-394
    • Collette, Y.1    Gilles, A.2    Pontarotti, P.3
  • 21
    • 0344898488 scopus 로고    scopus 로고
    • GIMS: An integrated data storage and analysis environment for genomic and functional data
    • Cornell, M., Paton, N.W., Hedeler, C. et al. 2003. GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast, 20:1291-306.
    • (2003) Yeast , vol.20 , pp. 1291-1306
    • Cornell, M.1    Paton, N.W.2    Hedeler, C.3
  • 22
    • 33846476262 scopus 로고    scopus 로고
    • Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
    • Dagan, T. and Martin, W. 2007. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl. Acad. Sci. U.S.A., 104:870-5.
    • (2007) Proc. Natl. Acad. Sci. U.S.A , vol.104 , pp. 870-875
    • Dagan, T.1    Martin, W.2
  • 23
    • 33644557410 scopus 로고    scopus 로고
    • Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
    • Danchin, E.G., Gouret, P. and Pontarotti, P. 2006. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals. BMC Evol. Biol., 6:5.
    • (2006) BMC Evol. Biol , vol.6 , pp. 5
    • Danchin, E.G.1    Gouret, P.2    Pontarotti, P.3
  • 24
    • 44249100806 scopus 로고    scopus 로고
    • Danchin, E.G., Gaucher, E.A. and Pontarotti, P. 2007. Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters In Liberles D, ed. Ancestral Sequence Reconstruction. Oxfond University Press.
    • Danchin, E.G., Gaucher, E.A. and Pontarotti, P. 2007. Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters In Liberles D, ed. Ancestral Sequence Reconstruction. Oxfond University Press.
  • 25
    • 0036061865 scopus 로고    scopus 로고
    • A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
    • Daubin, V., Gouy, M. and Perrière, G. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res., 12:1080-90.
    • (2002) Genome Res , vol.12 , pp. 1080-1090
    • Daubin, V.1    Gouy, M.2    Perrière, G.3
  • 26
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • Delsue, F., Brinkmann, H. and Philippe, H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev Genet., 6:361-75.
    • (2005) Nat. Rev Genet , vol.6 , pp. 361-375
    • Delsue, F.1    Brinkmann, H.2    Philippe, H.3
  • 27
    • 44249110160 scopus 로고    scopus 로고
    • The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species
    • in press
    • Descorps-Declere, S., Lemoine, F., Sculo, Q. et al. 2007. The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species. Biochimie (in press).
    • (2007) Biochimie
    • Descorps-Declere, S.1    Lemoine, F.2    Sculo, Q.3
  • 28
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • Devos, D. and Valencia, A. 2001. Intrinsic errors in genome annotation. Trends Genet., 17:429-31.
    • (2001) Trends Genet , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 29
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do, C.B., Mahabhashyam, M.S., Brudno, M. et al. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15:330-40.
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3
  • 31
    • 20444500847 scopus 로고    scopus 로고
    • Evolutionary aspects of whole-genome biology
    • Doolittle, R.F. 2005. Evolutionary aspects of whole-genome biology. Curr. Opin. Struct. Biol., 15:248-53.
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 248-253
    • Doolittle, R.F.1
  • 32
    • 20744436518 scopus 로고    scopus 로고
    • Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases
    • Dufayard, J.F., Duret, L., Penel, S. et al. 2005. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics, 21:2596-603.
    • (2005) Bioinformatics , vol.21 , pp. 2596-2603
    • Dufayard, J.F.1    Duret, L.2    Penel, S.3
  • 33
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32:1792-7.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 34
    • 22044443709 scopus 로고    scopus 로고
    • Eilbeck, K, Lewis, S.E., Mungall, C.J. et al. 2005. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol., 6:R.44.
    • Eilbeck, K, Lewis, S.E., Mungall, C.J. et al. 2005. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol., 6:R.44.
  • 35
    • 0031976258 scopus 로고    scopus 로고
    • Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
    • Eisen, J.A. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res., 8:163-7.
    • (1998) Genome Res , vol.8 , pp. 163-167
    • Eisen, J.A.1
  • 36
    • 0036595632 scopus 로고    scopus 로고
    • Phylogenetic analysis and gene functional predictions: Phylogenomics in action
    • Eisen, J.A. and Wu, M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor. Popul. Biol., 61:481-7.
    • (2002) Theor. Popul. Biol , vol.61 , pp. 481-487
    • Eisen, J.A.1    Wu, M.2
  • 37
    • 33645310990 scopus 로고    scopus 로고
    • Protein molecular function prediction by Bayesian phylogenomics
    • Engelhardt, B.E., Jordan, M.I., Muratore, K.E. et al. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput. Biol., 1:e45.
    • (2005) PLoS Comput. Biol , vol.1
    • Engelhardt, B.E.1    Jordan, M.I.2    Muratore, K.E.3
  • 38
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright, A.J., Iliopoulos, I., Kyrpides, N.C. et al. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature, 402:86-90.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3
  • 39
    • 33747844623 scopus 로고    scopus 로고
    • FootPrinter3: Phylogenetic footprinting in partially alignable sequences
    • Fang, F. and Blanchette, M. 2006. FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res., 34: W617-20.
    • (2006) Nucleic Acids Res , vol.34
    • Fang, F.1    Blanchette, M.2
  • 40
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17:368-76.
    • (1981) J. Mol. Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 41
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng, D.F. and Doolittle, R.F. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25:351-60
    • (1987) J. Mol. Evol , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 42
    • 33846266906 scopus 로고    scopus 로고
    • Modeling the evolution of protein domain architectures using maximum parsimony
    • Fong, J.H., Geer, L.Y., Panchenko, A.R. et al. 2007. Modeling the evolution of protein domain architectures using maximum parsimony. J. Mol. Biol., 366:307-15.
    • (2007) J. Mol. Biol , vol.366 , pp. 307-315
    • Fong, J.H.1    Geer, L.Y.2    Panchenko, A.R.3
  • 43
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force, A., Lynch, M., Pickett, F.B. et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 151:1531-45.
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3
  • 44
    • 0032229196 scopus 로고    scopus 로고
    • Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
    • Galperin, M.Y. and Koonin, E.V. 1998. Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol., 1:55-67.
    • (1998) In Silico Biol , vol.1 , pp. 55-67
    • Galperin, M.Y.1    Koonin, E.V.2
  • 45
    • 17844386108 scopus 로고    scopus 로고
    • A benchmark of multiple sequence alignment programs upon structural RNAs
    • Gardner, P.P.; Wilm, A. and Washietl, S. 2005. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res., 33:2433-9.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2433-2439
    • Gardner, P.P.1    Wilm, A.2    Washietl, S.3
  • 46
    • 0036606898 scopus 로고    scopus 로고
    • Predicting functional divergence in protein evolution by site-specific rate shifts
    • Gaucher, E.A., Gu, X., Miyamoto, M.M. et al. 2002. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci., 27:315-21.
    • (2002) Trends Biochem Sci , vol.27 , pp. 315-321
    • Gaucher, E.A.1    Gu, X.2    Miyamoto, M.M.3
  • 47
    • 0034923923 scopus 로고    scopus 로고
    • Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
    • Gerlt, J.A. and Babbitt, P.C. 2001. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem., 70:209-46.
    • (2001) Annu. Rev. Biochem , vol.70 , pp. 209-246
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 48
    • 33746684967 scopus 로고    scopus 로고
    • Phylogeny based discovery of regulatory elements
    • Gertz, J., Fay, J. and Cohen, B. 2006. Phylogeny based discovery of regulatory elements. BMC Bioinformatics, 7:266.
    • (2006) BMC Bioinformatics , vol.7 , pp. 266
    • Gertz, J.1    Fay, J.2    Cohen, B.3
  • 49
    • 12244283680 scopus 로고    scopus 로고
    • Modeling the percolation of annotation errors in a database of protein sequences
    • Gilks, W.R., Audit, B., De Angelis, D. et al. 2002. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics, 18:1641-9.
    • (2002) Bioinformatics , vol.18 , pp. 1641-1649
    • Gilks, W.R.1    Audit, B.2    De Angelis, D.3
  • 50
    • 30344483214 scopus 로고    scopus 로고
    • Nexplorer: Phylogeny-based exploration of sequence family data
    • Gopalan, V., Qiu, W.G., Chen, M.Z. et al. 2006. Nexplorer: phylogeny-based exploration of sequence family data. Bioinformatics, 22:120-1.
    • (2006) Bioinformatics , vol.22 , pp. 120-121
    • Gopalan, V.1    Qiu, W.G.2    Chen, M.Z.3
  • 51
    • 25444473119 scopus 로고    scopus 로고
    • FIGENIX: Intelligent automation of genomic annotation expertise integration in a new software platform
    • Gouret, P., Vitiello, V., Balandraud, N. et al. 2005. FIGENIX: intelligent automation of genomic annotation expertise integration in a new software platform. BMC Bioinformatics, 6:198.
    • (2005) BMC Bioinformatics , vol.6 , pp. 198
    • Gouret, P.1    Vitiello, V.2    Balandraud, N.3
  • 52
    • 0037968852 scopus 로고    scopus 로고
    • Functional Divergence in Protein (Family) Sequence Evolution
    • Gu, X. 2003. Functional Divergence in Protein (Family) Sequence Evolution. Genetica, 118:133-41.
    • (2003) Genetica , vol.118 , pp. 133-141
    • Gu, X.1
  • 54
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz, G.Z. and Stormo, G.D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15:563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 55
    • 33847324470 scopus 로고    scopus 로고
    • Imputing supertrees and supernetworks from quartets
    • Holland, B., Conner, G., Huber, K. et al. 2007. Imputing supertrees and supernetworks from quartets. Syst. Biol., 56:57-67.
    • (2007) Syst. Biol , vol.56 , pp. 57-67
    • Holland, B.1    Conner, G.2    Huber, K.3
  • 56
    • 7244259101 scopus 로고    scopus 로고
    • Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate protokaryotype
    • Jaillon, O., Aury, J.M., Brunet, F. et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate protokaryotype. Nature, 431:946-57.
    • (2004) Nature , vol.431 , pp. 946-957
    • Jaillon, O.1    Aury, J.M.2    Brunet, F.3
  • 57
    • 33750298722 scopus 로고    scopus 로고
    • Prediction of genomic functional elements
    • Jones, S.J. 2006. Prediction of genomic functional elements. Annu. Rev. Genomics Hum. Genet., 7:315-38.
    • (2006) Annu. Rev. Genomics Hum. Genet , vol.7 , pp. 315-338
    • Jones, S.J.1
  • 58
    • 0037370478 scopus 로고    scopus 로고
    • Bioinformatics in the post-sequence era
    • Kanehisa, M. and Bork, P. 2003. Bioinformatics in the post-sequence era. Nat. Genet., 33:305-10.
    • (2003) Nat. Genet , vol.33 , pp. 305-310
    • Kanehisa, M.1    Bork, P.2
  • 59
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplas, K., Barrett, C. and Hughey, R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14:846-56.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplas, K.1    Barrett, C.2    Hughey, R.3
  • 60
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT. a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K. et al. 2002. MAFFT. a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30:3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3
  • 61
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - the BLAST-like alignment tool
    • Kent, W.J. 2002. BLAT - the BLAST-like alignment tool. Genome Res., 12:656-64.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 62
    • 34248153777 scopus 로고    scopus 로고
    • Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
    • Kikuta, H., Laplante, M., Navratilova, P. et al. 2007. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res., 17:545-55.
    • (2007) Genome Res , vol.17 , pp. 545-555
    • Kikuta, H.1    Laplante, M.2    Navratilova, P.3
  • 63
    • 33644845048 scopus 로고    scopus 로고
    • Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
    • Kim, Y. and Subramaniam, S. 2006. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins, 62:1115-24.
    • (2006) Proteins , vol.62 , pp. 1115-1124
    • Kim, Y.1    Subramaniam, S.2
  • 64
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
    • Kishino, H. and Hasegawa, M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol., 29:170-9.
    • (1989) J. Mol. Evol , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 65
    • 33645865251 scopus 로고    scopus 로고
    • Reconstruction of a 450-My-old ancestral vertebrate protokaryotype
    • Kohn, M., Höogel, J., Vogel, W. et al. 2006. Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet., 22:203-10.
    • (2006) Trends Genet , vol.22 , pp. 203-210
    • Kohn, M.1    Höogel, J.2    Vogel, W.3
  • 66
    • 16444381885 scopus 로고    scopus 로고
    • A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    • Koonin, E.V., Federova, N.D., Jackson, J.D. et al. 2004. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol., 5:R-7.
    • (2004) Genome Biol , vol.5
    • Koonin, E.V.1    Federova, N.D.2    Jackson, J.D.3
  • 67
    • 27644472372 scopus 로고    scopus 로고
    • Orthologs, paralogs, and evolutionary genomics
    • Koonin, E.V. 2005. Orthologs, paralogs, and evolutionary genomics. Annu Rev. Genet., 39:309-38.
    • (2005) Annu Rev. Genet , vol.39 , pp. 309-338
    • Koonin, E.V.1
  • 68
    • 33748980210 scopus 로고    scopus 로고
    • Evolutionary systems biology: Links between gene evolution and function
    • Koonin, E.V. and Wolf, Y.I. 2006. Evolutionary systems biology: links between gene evolution and function. Curr. Opin. Biotechnol., 17:481-7.
    • (2006) Curr. Opin. Biotechnol , vol.17 , pp. 481-487
    • Koonin, E.V.1    Wolf, Y.I.2
  • 69
    • 31144442881 scopus 로고    scopus 로고
    • Automatic assessment of alignment quality
    • Lassmann, T. and Sonnhammer, E.L. 2005. Automatic assessment of alignment quality. Nucleic Acids Res., 33:7120-8.
    • (2005) Nucleic Acids Res , vol.33 , pp. 7120-7128
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 70
    • 33646468497 scopus 로고    scopus 로고
    • Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters
    • Lee, A.P., Koh, E.G., Tay, A. et al. 2006. Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters. Proc. Natl. Acad. Sci., U.S.A., 103:6994-9.
    • (2006) Proc. Natl. Acad. Sci., U.S.A , vol.103 , pp. 6994-6999
    • Lee, A.P.1    Koh, E.G.2    Tay, A.3
  • 71
    • 33751414256 scopus 로고    scopus 로고
    • Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family
    • Levasseur, A, Gouret, P., Lesage-Meessen, L. et al. 2006. Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family. BMC Evol. Biol., 8:6:92.
    • (2006) BMC Evol. Biol , vol.8 , Issue.6 , pp. 92
    • Levasseur, A.1    Gouret, P.2    Lesage-Meessen, L.3
  • 72
    • 35349010004 scopus 로고    scopus 로고
    • Conceptual bases for quantifying the role of the environment on gene evolution: The participation of positive selection and neutral evolution
    • Levasseur, A., Orlando, L., Bailly, X. et al. 2007. Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution. Biol. Rev. Camb. Philos. Soc., 82:551-72.
    • (2007) Biol. Rev. Camb. Philos. Soc , vol.82 , pp. 551-572
    • Levasseur, A.1    Orlando, L.2    Bailly, X.3
  • 73
    • 28044457401 scopus 로고    scopus 로고
    • Reliable prediction of transcription factor binding sites by phylogenetic verification
    • Li, X., Zhong, S. and Wong, W.H. 2005. Reliable prediction of transcription factor binding sites by phylogenetic verification. Proc. Natl. Acad. Sci., U.S.A., 102:16945-50.
    • (2005) Proc. Natl. Acad. Sci., U.S.A , vol.102 , pp. 16945-16950
    • Li, X.1    Zhong, S.2    Wong, W.H.3
  • 74
    • 33244455951 scopus 로고    scopus 로고
    • Evolutionary conservation of expression profiles between human and mouse orthologous genes
    • Liao, B.Y. and Zhang, J.Z. 2006. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Molecular Biology and Evolution, 23:530-40.
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 530-540
    • Liao, B.Y.1    Zhang, J.Z.2
  • 75
    • 0036075245 scopus 로고    scopus 로고
    • Tracking adaptive evolutionary events in genomic sequences
    • 3:REVIEWS1018
    • Liberles, D.A. and Wayne, M.L. 2002. Tracking adaptive evolutionary events in genomic sequences. Genome Biol., 3:REVIEWS1018.
    • (2002) Genome Biol
    • Liberles, D.A.1    Wayne, M.L.2
  • 76
    • 0027764344 scopus 로고
    • Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
    • Livingstone, C.D. and Barton, G.J. 1993. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9:745-56.
    • (1993) Comput. Appl. Biosci , vol.9 , pp. 745-756
    • Livingstone, C.D.1    Barton, G.J.2
  • 77
    • 0036134757 scopus 로고    scopus 로고
    • Heterotachy, an important process of protein evolution
    • Lopez, P., Casane, D. and Philippe, H. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol., 19:1-7.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 1-7
    • Lopez, P.1    Casane, D.2    Philippe, H.3
  • 78
    • 34547664096 scopus 로고    scopus 로고
    • Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes
    • Lupski, J.R. and Stankiewicz, P. 2005. Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet., 1:e49.
    • (2005) PLoS Genet , vol.1
    • Lupski, J.R.1    Stankiewicz, P.2
  • 79
    • 0036202921 scopus 로고    scopus 로고
    • PatternHunter: Faster and more sensitive homology search
    • Ma, B., Tromp, J. and Li, M. 2002. PatternHunter: faster and more sensitive homology search. Bioinformatics, 18:440-5.
    • (2002) Bioinformatics , vol.18 , pp. 440-445
    • Ma, B.1    Tromp, J.2    Li, M.3
  • 80
    • 33750386912 scopus 로고    scopus 로고
    • Reconstructing contiguous regions of an ancestial genome
    • Ma, J., Zhang, L., Suh, B.B. et al. 2006. Reconstructing contiguous regions of an ancestial genome. Genome Res., 16:1557-65.
    • (2006) Genome Res , vol.16 , pp. 1557-1565
    • Ma, J.1    Zhang, L.2    Suh, B.B.3
  • 81
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte, E.M., Pellegrini, M., Ho-Leung, N. et al. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science, 30:751-3.
    • (1999) Science , vol.30 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ho-Leung, N.3
  • 82
    • 0036796369 scopus 로고    scopus 로고
    • Current methods of gene prediction, their strengths and weaknesses
    • Mathe, C., Sagot, M.F., Schiex, T. et al. 2002. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res., 30:4103-17.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4103-4117
    • Mathe, C.1    Sagot, M.F.2    Schiex, T.3
  • 83
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the GenTHREADER. method for genomic fold recognition
    • McGuffin, L.J. and Jones, D.T. 2003. Improvement of the GenTHREADER. method for genomic fold recognition. Bioinformatics, 19:874-81.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • McGuffin, L.J.1    Jones, D.T.2
  • 84
    • 2942622384 scopus 로고    scopus 로고
    • Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
    • Mirkin, B.G., Fenner, T.I., Galperin, M.Y. et al. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol., 3:2.
    • (2003) BMC Evol. Biol , vol.3 , pp. 2
    • Mirkin, B.G.1    Fenner, T.I.2    Galperin, M.Y.3
  • 85
    • 0019134329 scopus 로고
    • Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application
    • Miyata, T. and Yasunaga, T. 1980. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J. Mol. Evol., 16:23-36.
    • (1980) J. Mol. Evol , vol.16 , pp. 23-36
    • Miyata, T.1    Yasunaga, T.2
  • 86
    • 0642368358 scopus 로고    scopus 로고
    • Position specific variation in the rate of evolutibn in trancription factor binding sites
    • Moses, A.M., Chiang, D.Y., Kellis, M. et a. 2003. Position specific variation in the rate of evolutibn in trancription factor binding sites. BMC Evol. Biol., 3:19.
    • (2003) BMC Evol. Biol , vol.3 , pp. 19
    • Moses, A.M.1    Chiang, D.Y.2    Kellis, M.3    et a4
  • 87
    • 22744440499 scopus 로고    scopus 로고
    • Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
    • Murphy, W.J., Larkin, D.M., Everts-van der Wind, A. et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science, 309:613-617.
    • (2005) Science , vol.309 , pp. 613-617
    • Murphy, W.J.1    Larkin, D.M.2    Everts-van der Wind, A.3
  • 88
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D.G. and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302:205-217.
    • (2000) J. Mol. Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 89
    • 0031110886 scopus 로고    scopus 로고
    • From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem
    • Page, R.D. and Charleston, M.A. 1997. From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem. Mol. Phylogenet. Evol., 7:231-40.
    • (1997) Mol. Phylogenet. Evol , vol.7 , pp. 231-240
    • Page, R.D.1    Charleston, M.A.2
  • 90
    • 0030821675 scopus 로고    scopus 로고
    • Correlated mutations contain information about protein-protein interaction
    • Pazos, F., Helmer-Citterich, M., Ausiello, G. et al. 1997. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271:511-23.
    • (1997) J. Mol. Biol , vol.271 , pp. 511-523
    • Pazos, F.1    Helmer-Citterich, M.2    Ausiello, G.3
  • 91
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • Pazos, F. and Valencia, A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng., 14:609-14.
    • (2001) Protein Eng , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 92
    • 0036568319 scopus 로고    scopus 로고
    • In silico two-hybrid system for the selection of physically interacting protein pairs
    • Pazos, F. and Valencia, A. 2002. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins, 47:219-27.
    • (2002) Proteins , vol.47 , pp. 219-227
    • Pazos, F.1    Valencia, A.2
  • 93
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calcilation of positional conservation in a protein sequence alignment
    • Pei, J. and Grishin, N.V. 2001. AL2CO: calcilation of positional conservation in a protein sequence alignment. Bioinformatics, 17:700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 94
    • 0033551248 scopus 로고    scopus 로고
    • Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
    • Pellegrini, M., Marcotte, E.M., Thompson, M.J. et al. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci., U.S.A., 96:4285-8.
    • (1999) Proc. Natl. Acad. Sci., U.S.A , vol.96 , pp. 4285-4288
    • Pellegrini, M.1    Marcotte, E.M.2    Thompson, M.J.3
  • 95
    • 0037264074 scopus 로고    scopus 로고
    • Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
    • Pevzner, P. and Tesler, G. 2003. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res., 13:37-45.
    • (2003) Genome Res , vol.13 , pp. 37-45
    • Pevzner, P.1    Tesler, G.2
  • 97
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm, M., Storm, C.E. and Sonnhammer, E.L. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314:1041-52.
    • (2001) J. Mol. Biol , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 98
    • 12344324765 scopus 로고    scopus 로고
    • DIVAA: Analysis of amino acid diversity in multiple aligned protein sequences
    • Rodi, D.J., Mandava, S. and Makowski, L. 2004. DIVAA: analysis of amino acid diversity in multiple aligned protein sequences. Bioinformatics, 20:3481-9.
    • (2004) Bioinformatics , vol.20 , pp. 3481-3489
    • Rodi, D.J.1    Mandava, S.2    Makowski, L.3
  • 99
    • 0344824014 scopus 로고    scopus 로고
    • Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene
    • Rodriguez-Trelles, F., Tarrío, R. and Ayala, F.J. 2003. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proc. Natl. Acad. Sci., U.SA., 100:13413-7.
    • (2003) Proc. Natl. Acad. Sci., U.SA , vol.100 , pp. 13413-13417
    • Rodriguez-Trelles, F.1    Tarrío, R.2    Ayala, F.J.3
  • 100
    • 33645470450 scopus 로고    scopus 로고
    • Genome-wide scans for loci under selection in humans
    • Ronald, J. and Akey, J.M. 2005. Genome-wide scans for loci under selection in humans. Hum. Genomics, 2:113-25.
    • (2005) Hum. Genomics , vol.2 , pp. 113-125
    • Ronald, J.1    Akey, J.M.2
  • 101
    • 23944525773 scopus 로고    scopus 로고
    • Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
    • Rossnes, R., Eidhammer, I. and Liberles, D.A. 2005. Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data. BMC Bioinformatics, 6:127.
    • (2005) BMC Bioinformatics , vol.6 , pp. 127
    • Rossnes, R.1    Eidhammer, I.2    Liberles, D.A.3
  • 102
    • 0030045281 scopus 로고    scopus 로고
    • Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
    • Russo, C.A., Takezaki, N. and Nei, M. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol., 13:525-36.
    • (1996) Mol. Biol. Evol , vol.13 , pp. 525-536
    • Russo, C.A.1    Takezaki, N.2    Nei, M.3
  • 103
    • 3242891274 scopus 로고    scopus 로고
    • ConSite: Web-based prediction of regulatory elements using cross-species comparison
    • Sandelin, A., Wasserman, W.W. and Lenhard, B. 2004. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Reg., 32:W249-52.
    • (2004) Nucleic Acids Reg , vol.32
    • Sandelin, A.1    Wasserman, W.W.2    Lenhard, B.3
  • 104
    • 0042695888 scopus 로고    scopus 로고
    • The challenge of constructing large phylogenetic trees
    • Sanderson, M.J. and Driskell, A.C. 2003. The challenge of constructing large phylogenetic trees. Trends Plant Sci., 8:374-9.
    • (2003) Trends Plant Sci , vol.8 , pp. 374-379
    • Sanderson, M.J.1    Driskell, A.C.2
  • 105
    • 33847741060 scopus 로고    scopus 로고
    • The origins of polypeptide domains
    • Schmidt, E.E. and Davies, C.J. 2007. The origins of polypeptide domains. Bioessays, 29:262-70.
    • (2007) Bioessays , vol.29 , pp. 262-270
    • Schmidt, E.E.1    Davies, C.J.2
  • 106
    • 1842507574 scopus 로고    scopus 로고
    • Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments
    • Shah, N., Couronne, O., Pennacchio, L.A. et al. 2004. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics, 20:636-43.
    • (2004) Bioinformatics , vol.20 , pp. 636-643
    • Shah, N.1    Couronne, O.2    Pennacchio, L.A.3
  • 107
    • 28944450584 scopus 로고    scopus 로고
    • Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    • Shapiro, B., Rambaut, A. and Drummond, A.J. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol., 23:7-9.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 7-9
    • Shapiro, B.1    Rambaut, A.2    Drummond, A.J.3
  • 108
    • 0035863767 scopus 로고    scopus 로고
    • A phylogenomic approach to microbial evolution
    • Sicheritz-Pontén, T. and Andersson, S.G. 2001. A phylogenomic approach to microbial evolution. Nucleic Acids Res., 29:545-52.
    • (2001) Nucleic Acids Res , vol.29 , pp. 545-552
    • Sicheritz-Pontén, T.1    Andersson, S.G.2
  • 109
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny
    • Siddharthan, R., Siggia, E.D. and van Nimwegen, E. 2005. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput. Biol., 1:e67.
    • (2005) PLoS Comput. Biol , vol.1
    • Siddharthan, R.1    Siggia, E.D.2    van Nimwegen, E.3
  • 110
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel, A., Bejerano, G., Pedersen, J.S. et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15:1034-50.
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1    Bejerano, G.2    Pedersen, J.S.3
  • 111
    • 13244260826 scopus 로고    scopus 로고
    • PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
    • Sinha, S., Blanchette, M. and Tompa, M. 2004. PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics, 5:170.
    • (2004) BMC Bioinformatics , vol.5 , pp. 170
    • Sinha, S.1    Blanchette, M.2    Tompa, M.3
  • 112
    • 0037267806 scopus 로고    scopus 로고
    • Human-Mouse Alignments with BLASTZ
    • Schwartz, S., Kent, W.J., Smith, A. et al. 2003. Human-Mouse Alignments with BLASTZ. Genome Research, 13:103-7.
    • (2003) Genome Research , vol.13 , pp. 103-107
    • Schwartz, S.1    Kent, W.J.2    Smith, A.3
  • 113
    • 1042280957 scopus 로고    scopus 로고
    • Phylogenomic inference of protein molecular function: Advances and challenges
    • Sjölander, K. 2004. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics, 20:170-9.
    • (2004) Bioinformatics , vol.20 , pp. 170-179
    • Sjölander, K.1
  • 114
    • 28944438378 scopus 로고    scopus 로고
    • ConFind: A robust tool for conserved sequence identification
    • Smagala, J.A., Dawson, E.D., Mehlmann, M. et al. 2005. ConFind: a robust tool for conserved sequence identification. Bioinformatics, 21:4420-2.
    • (2005) Bioinformatics , vol.21 , pp. 4420-4422
    • Smagala, J.A.1    Dawson, E.D.2    Mehlmann, M.3
  • 115
    • 27144493223 scopus 로고    scopus 로고
    • Genome trees and the nature of genome evolution
    • Snel, B., Huynen, M.A. and Dutilh, B.E. 2005. Genome trees and the nature of genome evolution. Annu Rev. Microbiol., 59:191-209.
    • (2005) Annu Rev. Microbiol , vol.59 , pp. 191-209
    • Snel, B.1    Huynen, M.A.2    Dutilh, B.E.3
  • 116
    • 0038658640 scopus 로고    scopus 로고
    • Efficient algorithms for multichromosomal genome rearrangements
    • Tesler, G. 2002a. Efficient algorithms for multichromosomal genome rearrangements. J. Comp. Sys. Sci., 65:587-609.
    • (2002) J. Comp. Sys. Sci , vol.65 , pp. 587-609
    • Tesler, G.1
  • 117
    • 0036211065 scopus 로고    scopus 로고
    • GRIMM: Genome rearrangements web server
    • Tesler, G. 2002b. GRIMM: genome rearrangements web server. Bioinformatics, 18:492-3.
    • (2002) Bioinformatics , vol.18 , pp. 492-493
    • Tesler, G.1
  • 118
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson, J.D., Plewniak, F. and Poch, O. 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27:2682-90.
    • (1999) Nucleic Acids Res , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 119
    • 0034255358 scopus 로고    scopus 로고
    • DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
    • Thompson, J.D., Plewniak, F., Thierry, J.C. et al. 2000. DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res., 28:2919-26.
    • (2000) Nucleic Acids Res , vol.28 , pp. 2919-2926
    • Thompson, J.D.1    Plewniak, F.2    Thierry, J.C.3
  • 120
    • 0035824873 scopus 로고    scopus 로고
    • Towards a reliable objective function for multiple sequence alignments
    • Thompson, J.D., Plewniak, F., Ripp, R. et al. 2001. Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol., 314:937-51.
    • (2001) J. Mol. Biol , vol.314 , pp. 937-951
    • Thompson, J.D.1    Plewniak, F.2    Ripp, R.3
  • 121
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
    • Thompson, J.D., Koehl, P., Ripp, R. et al. 2005a. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins, 61:127-36.
    • (2005) Proteins , vol.61 , pp. 127-136
    • Thompson, J.D.1    Koehl, P.2    Ripp, R.3
  • 122
    • 23444442072 scopus 로고    scopus 로고
    • b. MAO: A Multiple Alignment Ontology for nucleic acid and protein sequences
    • Thompson, J.D., Holbrook, S.R., Katoh, K. et al. 2005b. MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res., 33:4164-71.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4164-4171
    • Thompson, J.D.1    Holbrook, S.R.2    Katoh, K.3
  • 123
    • 33847138105 scopus 로고    scopus 로고
    • MACSIMS: Multiple alignment of complete sequences information management system
    • Thompson, J.D., Muller, A., Waterhouse, A. et al. 2006. MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics, 7:318.
    • (2006) BMC Bioinformatics , vol.7 , pp. 318
    • Thompson, J.D.1    Muller, A.2    Waterhouse, A.3
  • 124
    • 0033674329 scopus 로고    scopus 로고
    • Models of protein sequence evolution and their applications
    • Thorne, J.L. 2000. Models of protein sequence evolution and their applications. Curr. Opin. Genet. Dev., 10:602-5.
    • (2000) Curr. Opin. Genet. Dev , vol.10 , pp. 602-605
    • Thorne, J.L.1
  • 125
    • 0043074672 scopus 로고    scopus 로고
    • Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region
    • Vienne, A., Rasmussen, J., Abi-Rached, L. et al. 2003. Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region. Mol. Biol, Evol., 20:1290-8.
    • (2003) Mol. Biol, Evol , vol.20 , pp. 1290-1298
    • Vienne, A.1    Rasmussen, J.2    Abi-Rached, L.3
  • 126
    • 0037250152 scopus 로고    scopus 로고
    • A database of predicted functional associations between proteins
    • STRING
    • von Mering, C., Huynen, M., Jaeggi, D. et al. 2003. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res., 31:258-61.
    • (2003) Nucleic Acids Res , vol.31 , pp. 258-261
    • von Mering, C.1    Huynen, M.2    Jaeggi, D.3
  • 128
  • 129
    • 0037370306 scopus 로고    scopus 로고
    • Molecular evolution meets the genomics revolution
    • Wolfe, K.H. and Li, W.H. 2003. Molecular evolution meets the genomics revolution. Nat. Genet., 33:255-65.
    • (2003) Nat. Genet , vol.33 , pp. 255-265
    • Wolfe, K.H.1    Li, W.H.2
  • 130
    • 20044366725 scopus 로고    scopus 로고
    • Highly Conserved Non Coding Sequences Are Associated with Vertebrate Development
    • Woolfe, A., Goodson, M., Goode, D.K. et al. 2005. Highly Conserved Non Coding Sequences Are Associated with Vertebrate Development. PLoS Biol., 3:e7.
    • (2005) PLoS Biol , vol.3
    • Woolfe, A.1    Goodson, M.2    Goode, D.K.3
  • 131
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • Yang, Z.H. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol., 11:367-72.
    • (1996) Trends Ecol. Evol , vol.11 , pp. 367-372
    • Yang, Z.H.1
  • 132
    • 14744275703 scopus 로고    scopus 로고
    • The power of phylogenetic comparison in revealing protein function
    • Yang, Z. 2005. The power of phylogenetic comparison in revealing protein function. Proc. Natl. Acad. Sci., U.S.A., 102:3179-80.
    • (2005) Proc. Natl. Acad. Sci., U.S.A , vol.102 , pp. 3179-3180
    • Yang, Z.1
  • 133
    • 0036733640 scopus 로고    scopus 로고
    • Computational prediction of eukaryotic protein-coding genes
    • Zhang, M.Q. 2002. Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet., 3:698-709.
    • (2002) Nat. Rev. Genet , vol.3 , pp. 698-709
    • Zhang, M.Q.1
  • 134
    • 0013017592 scopus 로고    scopus 로고
    • RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
    • Zmasek, C.M. and Eddy, S.R. 2002. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 3:14.
    • (2002) BMC Bioinformatics , vol.3 , pp. 14
    • Zmasek, C.M.1    Eddy, S.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.