메뉴 건너뛰기




Volumn 8, Issue 6, 2007, Pages

The human phylome

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 36448938389     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-6-r109     Document Type: Article
Times cited : (146)

References (95)
  • 3
    • 33646244502 scopus 로고    scopus 로고
    • Transcriptome analyses of human genes and applications for proteome analyses
    • 16611140
    • Suzuki Y Sugano S Transcriptome analyses of human genes and applications for proteome analyses. Curr Protein Pept Sci 2006 7 147-163 16611140
    • (2006) Curr Protein Pept Sci , vol.7 , pp. 147-163
    • Suzuki, Y.1    Sugano, S.2
  • 4
    • 4444311058 scopus 로고    scopus 로고
    • A human proteome project with a beginning and an end
    • 15352225
    • Humphery-Smith I A human proteome project with a beginning and an end. Proteomics 2004 4 2519-2521 15352225
    • (2004) Proteomics , vol.4 , pp. 2519-2521
    • Humphery-Smith, I.1
  • 6
    • 26944471174 scopus 로고    scopus 로고
    • The next wave in metabolome analysis
    • 16154652
    • Nielsen J Oliver S The next wave in metabolome analysis. Trends Biotechnol 2005 23 544-546 16154652
    • (2005) Trends Biotechnol , vol.23 , pp. 544-546
    • Nielsen, J.1    Oliver, S.2
  • 7
    • 0038716425 scopus 로고    scopus 로고
    • Interpretive proteomics - Finding biological meaning in genome and proteome databases
    • 12791396
    • Benner SA Interpretive proteomics - finding biological meaning in genome and proteome databases. Adv Enzyme Regul 2003 43 271-359 12791396
    • (2003) Adv Enzyme Regul , vol.43 , pp. 271-359
    • Benner, S.A.1
  • 8
    • 0035863767 scopus 로고    scopus 로고
    • A phylogenomic approach to microbial evolution
    • 29656 11139625
    • Sicheritz-Ponten T Andersson SG A phylogenomic approach to microbial evolution. Nucleic Acids Res 2001 29 545-552 29656 11139625
    • (2001) Nucleic Acids Res , vol.29 , pp. 545-552
    • Sicheritz-Ponten, T.1    Andersson, S.G.2
  • 9
    • 0042266921 scopus 로고    scopus 로고
    • Reconstruction of the proto-mitochondrial metabolism
    • 12893934
    • Gabaldón T Huynen MA Reconstruction of the proto-mitochondrial metabolism. Science 2003 301 609 12893934
    • (2003) Science , vol.301 , pp. 609
    • Gabaldón, T.1    Huynen, M.A.2
  • 10
    • 85127045455 scopus 로고    scopus 로고
    • Evolution of proteins and proteomes, a phylogenetics approach
    • Gabaldón T Evolution of proteins and proteomes, a phylogenetics approach. Evolutionary Bioinformatics Online 2005 1 51-56
    • (2005) Evolutionary Bioinformatics Online , vol.1 , pp. 51-56
    • Gabaldón, T.1
  • 11
    • 14844314856 scopus 로고    scopus 로고
    • Variation and evolution of biomolecular systems: Searching for functional relevance
    • 15763561
    • Huynen MA Gabaldon T Snel B Variation and evolution of biomolecular systems: Searching for functional relevance. FEBS Lett 2005 579 1839-1845 15763561
    • (2005) FEBS Lett , vol.579 , pp. 1839-1845
    • Huynen, M.A.1    Gabaldon, T.2    Snel, B.3
  • 14
    • 0028247213 scopus 로고
    • HOVERGEN: A database of homologous vertebrate genes
    • 523695 8036164
    • Duret L Mouchiroud D Gouy M HOVERGEN: A database of homologous vertebrate genes. Nucleic Acids Res 1994 22 2360-2365 523695 8036164
    • (1994) Nucleic Acids Res , vol.22 , pp. 2360-2365
    • Duret, L.1    Mouchiroud, D.2    Gouy, M.3
  • 15
    • 13444257876 scopus 로고    scopus 로고
    • The Adaptive Evolution Database (TAED): A phylogeny based tool for comparative genomics
    • 540044 33 Database 15608245
    • Roth C Betts MJ Steffansson P Saelensminde G Liberles DA The Adaptive Evolution Database (TAED): A phylogeny based tool for comparative genomics. Nucleic Acids Res 2005 33 Database D495-497 540044 15608245
    • (2005) Nucleic Acids Res
    • Roth, C.1    Betts, M.J.2    Steffansson, P.3    Saelensminde, G.4    Liberles, D.A.5
  • 16
    • 0033045528 scopus 로고    scopus 로고
    • The evolution of a mechanism of cell suicide
    • 10070258
    • Blackstone NW Green DR The evolution of a mechanism of cell suicide. Bioessays 1999 21 84-88 10070258
    • (1999) Bioessays , vol.21 , pp. 84-88
    • Blackstone, N.W.1    Green, D.R.2
  • 17
    • 29244467422 scopus 로고    scopus 로고
    • The eloquent ape: Genes, brains and the evolution of language
    • 16369568
    • Fisher SE Marcus GF The eloquent ape: Genes, brains and the evolution of language. Nat Rev Genet 2006 7 9-20 16369568
    • (2006) Nat Rev Genet , vol.7 , pp. 9-20
    • Fisher, S.E.1    Marcus, G.F.2
  • 18
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • 9254330
    • Gascuel O BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 1997 14 685-695 9254330
    • (1997) Mol Biol Evol , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 19
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • 14530136
    • Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003 52 696-704 14530136
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 21
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • 12912839
    • Ronquist F Huelsenbeck JP MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003 19 1572-1574 12912839
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 22
    • 84870640374 scopus 로고    scopus 로고
    • Supplementary material
    • Supplementary material http://bioinfo.cipf.es/data/human_phylome/ human_phylome.html
  • 23
    • 33645816587 scopus 로고    scopus 로고
    • Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    • 1435933 16563161
    • Keane TM Creevey CJ Pentony MM Naughton TJ McLnerney JO Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 2006 6 29 1435933 16563161
    • (2006) BMC Evol Biol , vol.6 , pp. 29
    • Keane, T.M.1    Creevey, C.J.2    Pentony, M.M.3    Naughton, T.J.4    McLnerney, J.O.5
  • 24
    • 0032927161 scopus 로고    scopus 로고
    • Topological bias and inconsistency of maximum likelihood using wrong models
    • 10331281
    • Bruno WJ Halpern AL Topological bias and inconsistency of maximum likelihood using wrong models. Mol Biol Evol 1999 16 564-566 10331281
    • (1999) Mol Biol Evol , vol.16 , pp. 564-566
    • Bruno, W.J.1    Halpern, A.L.2
  • 25
    • 0036213207 scopus 로고    scopus 로고
    • The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support
    • 11919280
    • Buckley TR Cunningham CW The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support. Mol Biol Evol 2002 19 394-405 11919280
    • (2002) Mol Biol Evol , vol.19 , pp. 394-405
    • Buckley, T.R.1    Cunningham, C.W.2
  • 26
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • 1633570
    • Jones DT Taylor WR Thornton JM The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992 8 275-282 1633570
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 27
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • 50453 1438297
    • Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992 89 10915-10919 50453 1438297
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 28
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • 11319253
    • Whelan S Goldman N A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001 18 691-699 11319253
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 29
    • 0034922289 scopus 로고    scopus 로고
    • Modeling amino acid replacement
    • 11382360
    • Müller T Vingron M Modeling amino acid replacement. J Comput Biol 2000 7 761-776 11382360
    • (2000) J Comput Biol , vol.7 , pp. 761-776
    • Müller, T.1    Vingron, M.2
  • 30
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • 8642615
    • Adachi J Hasegawa M Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 1996 42 459-468 8642615
    • (1996) J Mol Evol , vol.42 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 32
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • 15861208
    • Delsuc F Brinkmann H Philippe H Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005 6 361-375 15861208
    • (2005) Nat Rev Genet , vol.6 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 34
    • 33750810896 scopus 로고    scopus 로고
    • The tree of one percent
    • 1794558 17081279
    • Dagan T Martin W The tree of one percent. Genome Biol 2006 7 118 1794558 17081279
    • (2006) Genome Biol , vol.7 , pp. 118
    • Dagan, T.1    Martin, W.2
  • 36
    • 27844438226 scopus 로고    scopus 로고
    • Genome-scale evidence of the nematode-arthropod clade
    • 1175953 15892869
    • Dopazo H Dopazo J Genome-scale evidence of the nematode-arthropod clade. Genome Biol 2005 6 R41 1175953 15892869
    • (2005) Genome Biol , vol.6
    • Dopazo, H.1    Dopazo, J.2
  • 38
    • 0345874732 scopus 로고    scopus 로고
    • Coelomata and not Ecdysozoa: Evidence from genome-wide phylogenetic analysis
    • 314272 14707168
    • Wolf YI Rogozin IB Koonin EV Coelomata and not Ecdysozoa: Evidence from genome-wide phylogenetic analysis. Genome Res 2004 14 29-36 314272 14707168
    • (2004) Genome Res , vol.14 , pp. 29-36
    • Wolf, Y.I.1    Rogozin, I.B.2    Koonin, E.V.3
  • 40
    • 26444482460 scopus 로고    scopus 로고
    • Molecular phylogeny and divergence times of deuterostome animals
    • 16049193
    • Blair JE Hedges SB Molecular phylogeny and divergence times of deuterostome animals. Mol Biol Evol 2005 22 2275-2284 16049193
    • (2005) Mol Biol Evol , vol.22 , pp. 2275-2284
    • Blair, J.E.1    Hedges, S.B.2
  • 42
    • 33748068074 scopus 로고    scopus 로고
    • Housekeeping genes for phylogenetic analysis of eutherian relationships
    • 16751257
    • Kullberg M Nilsson MA Arnason U Harley EH Janke A Housekeeping genes for phylogenetic analysis of eutherian relationships. Mol Biol Evol 2006 23 1493-1503 16751257
    • (2006) Mol Biol Evol , vol.23 , pp. 1493-1503
    • Kullberg, M.1    Nilsson, M.A.2    Arnason, U.3    Harley, E.H.4    Janke, A.5
  • 43
    • 0141832717 scopus 로고    scopus 로고
    • Revisiting the Glires concept - Phylogenetic analysis of nuclear sequences
    • 12878468
    • Misawa K Janke A Revisiting the Glires concept - phylogenetic analysis of nuclear sequences. Mol Phylogenet Evol 2003 28 320-327 12878468
    • (2003) Mol Phylogenet Evol , vol.28 , pp. 320-327
    • Misawa, K.1    Janke, A.2
  • 45
    • 0028955455 scopus 로고
    • Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory
    • 7714912
    • Ohta T Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 1995 40 56-63 7714912
    • (1995) J Mol Evol , vol.40 , pp. 56-63
    • Ohta, T.1
  • 46
    • 0033921902 scopus 로고    scopus 로고
    • Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes
    • 10654260
    • Zhang J Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J Mol Evol 2000 50 56-68 10654260
    • (2000) J Mol Evol , vol.50 , pp. 56-68
    • Zhang, J.1
  • 47
    • 0036208071 scopus 로고    scopus 로고
    • The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa
    • 11931142
    • Cavalier-Smith T The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 2002 52 297-354 11931142
    • (2002) Int J Syst Evol Microbiol , vol.52 , pp. 297-354
    • Cavalier-Smith, T.1
  • 48
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • 9381173
    • Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families. Science 1997 278 631-637 9381173
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 50
    • 33646909100 scopus 로고    scopus 로고
    • Protein family expansions and biological complexity
    • 1464810 16733546
    • Vogel C Chothia C Protein family expansions and biological complexity. PLoS Comput Biol 2006 2 e48 1464810 16733546
    • (2006) PLoS Comput Biol , vol.2
    • Vogel, C.1    Chothia, C.2
  • 52
    • 0038817812 scopus 로고    scopus 로고
    • New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes
    • 403660 12799346
    • Panopoulou G Hennig S Groth D Krause A Poustka AJ Herwig R Vingron M Lehrach H New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res 2003 13 1056-1066 403660 12799346
    • (2003) Genome Res , vol.13 , pp. 1056-1066
    • Panopoulou, G.1    Hennig, S.2    Groth, D.3    Krause, A.4    Poustka, A.J.5    Herwig, R.6    Vingron, M.7    Lehrach, H.8
  • 54
    • 0037413607 scopus 로고    scopus 로고
    • Molecular evolution: Duplication, duplication
    • 12511940
    • Meyer A Molecular evolution: Duplication, duplication. Nature 2003 421 31-32 12511940
    • (2003) Nature , vol.421 , pp. 31-32
    • Meyer, A.1
  • 55
    • 33745373606 scopus 로고    scopus 로고
    • Primate segmental duplications: Crucibles of evolution, diversity and disease
    • 16770338
    • Bailey JA Eichler EE Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat Rev Genet 2006 7 552-564 16770338
    • (2006) Nat Rev Genet , vol.7 , pp. 552-564
    • Bailey, J.A.1    Eichler, E.E.2
  • 57
    • 13444302764 scopus 로고    scopus 로고
    • FunShift: A database of function shift analysis on protein subfamilies
    • 540021 33 Database 15608176
    • Abhiman S Sonnhammer EL FunShift: A database of function shift analysis on protein subfamilies. Nucleic Acids Res 2005 33 Database D197-200 540021 15608176
    • (2005) Nucleic Acids Res
    • Abhiman, S.1    Sonnhammer, E.L.2
  • 58
    • 0037387451 scopus 로고    scopus 로고
    • Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation
    • 12654935
    • Seoighe C Johnston CR Shields DC Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. Mol Biol Evol 2003 20 484-490 12654935
    • (2003) Mol Biol Evol , vol.20 , pp. 484-490
    • Seoighe, C.1    Johnston, C.R.2    Shields, D.C.3
  • 59
    • 0042191905 scopus 로고    scopus 로고
    • Horizontal gene transfer: A critical view
    • 187805 12902542
    • Kurland CG Canback B Berg OG Horizontal gene transfer: A critical view. Proc Natl Acad Sci USA 2003 100 9658-9662 187805 12902542
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 9658-9662
    • Kurland, C.G.1    Canback, B.2    Berg, O.G.3
  • 60
    • 0037458124 scopus 로고    scopus 로고
    • Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes
    • 12546782
    • Andersson JO Sjogren AM Davis LA Embley TM Roger AJ Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 2003 13 94-104 12546782
    • (2003) Curr Biol , vol.13 , pp. 94-104
    • Andersson, J.O.1    Sjogren, A.M.2    Davis, L.A.3    Embley, T.M.4    Roger, A.J.5
  • 62
    • 12744261287 scopus 로고    scopus 로고
    • The genetics and genomics of the silkworm, Bombyx mori
    • 15355234
    • Goldsmith MR Shimada T Abe H The genetics and genomics of the silkworm, Bombyx mori. Annu Rev Entomol 2005 50 71-100 15355234
    • (2005) Annu Rev Entomol , vol.50 , pp. 71-100
    • Goldsmith, M.R.1    Shimada, T.2    Abe, H.3
  • 63
    • 0037819441 scopus 로고    scopus 로고
    • Widespread horizontal transfer of mitochondrial genes in flowering plants
    • 12853958
    • Bergthorsson U Adams KL Thomason B Palmer JD Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 2003 424 197-201 12853958
    • (2003) Nature , vol.424 , pp. 197-201
    • Bergthorsson, U.1    Adams, K.L.2    Thomason, B.3    Palmer, J.D.4
  • 64
    • 34248350454 scopus 로고    scopus 로고
    • Phylogeographic support for horizontal gene transfer involving sympatric bruchid species
    • 1562361 16872524
    • Alvarez N Benrey B Hossaert-McKey M Grill A McKey D Galtier N Phylogeographic support for horizontal gene transfer involving sympatric bruchid species. Biol Direct 2006 1 21 1562361 16872524
    • (2006) Biol Direct , vol.1 , pp. 21
    • Alvarez, N.1    Benrey, B.2    Hossaert-McKey, M.3    Grill, A.4    McKey, D.5    Galtier, N.6
  • 66
    • 0035827328 scopus 로고    scopus 로고
    • Microbial genes in the human genome: Lateral transfer or gene loss?
    • 11358996
    • Salzberg SL White O Peterson J Eisen JA Microbial genes in the human genome: Lateral transfer or gene loss? Science 2001 292 1903-1906 11358996
    • (2001) Science , vol.292 , pp. 1903-1906
    • Salzberg, S.L.1    White, O.2    Peterson, J.3    Eisen, J.A.4
  • 67
    • 0036468355 scopus 로고    scopus 로고
    • The human zoo: Endogenous retroviruses in the human genome
    • Bromham L The human zoo: Endogenous retroviruses in the human genome. Trends Ecol Evol 2002 17 160
    • (2002) Trends Ecol Evol , vol.17 , pp. 160
    • Bromham, L.1
  • 69
    • 23044437168 scopus 로고    scopus 로고
    • What tangled web: Barriers to rampant horizontal gene transfer
    • 15954096
    • Kurland CG What tangled web: Barriers to rampant horizontal gene transfer. Bioessays 2005 27 741-747 15954096
    • (2005) Bioessays , vol.27 , pp. 741-747
    • Kurland, C.G.1
  • 70
    • 17444385984 scopus 로고    scopus 로고
    • Tracing the evolution of a large protein complex in the eukaryotes, NADH: Ubiquinone oxidoreductase (Complex I)
    • 15843018
    • Gabaldón T Rainey D Huynen MA Tracing the evolution of a large protein complex in the eukaryotes, NADH:uBiquinone oxidoreductase (Complex I). J Mol Biol 2005 348 857-870 15843018
    • (2005) J Mol Biol , vol.348 , pp. 857-870
    • Gabaldón, T.1    Rainey, D.2    Huynen, M.A.3
  • 71
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • 5449325
    • Fitch WM Distinguishing homologous from analogous proteins. Syst Zool 1970 19 99-113 5449325
    • (1970) Syst Zool , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 72
    • 2442423854 scopus 로고    scopus 로고
    • Prediction of protein function and pathways in the genome era
    • 15095013
    • Gabaldón T Huynen MA Prediction of protein function and pathways in the genome era. Cell Mol Life Sci 2004 61 930-944 15095013
    • (2004) Cell Mol Life Sci , vol.61 , pp. 930-944
    • Gabaldón, T.1    Huynen, M.A.2
  • 73
    • 0032568582 scopus 로고    scopus 로고
    • Measuring genome evolution
    • 34486 9600883
    • Huynen MA Bork P Measuring genome evolution. Proc Natl Acad Sci USA 1998 95 5849-5856 34486 9600883
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 5849-5856
    • Huynen, M.A.1    Bork, P.2
  • 74
    • 13444256478 scopus 로고    scopus 로고
    • Inparanoid: A comprehensive database of eukaryotic orthologs
    • 540061 33 Database 15608241
    • O'Brien KP Remm M Sonnhammer EL Inparanoid: A comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005 33 Database D476-480 540061 15608241
    • (2005) Nucleic Acids Res
    • O'Brien, K.P.1    Remm, M.2    Sonnhammer, E.L.3
  • 75
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • 403725 12952885
    • Li L Stoeckert CJ Jr Roos DS OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 2003 13 2178-2189 403725 12952885
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 76
    • 0031976258 scopus 로고    scopus 로고
    • Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
    • 9521918
    • Eisen JA Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 1998 8 163-167 9521918
    • (1998) Genome Res , vol.8 , pp. 163-167
    • Eisen, J.A.1
  • 77
    • 27644472372 scopus 로고    scopus 로고
    • Orthologs, paralogs, and evolutionary genomics
    • 16285863
    • Koonin EV Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 2005 39 309-338 16285863
    • (2005) Annu Rev Genet , vol.39 , pp. 309-338
    • Koonin, E.V.1
  • 78
    • 0034791426 scopus 로고    scopus 로고
    • A simple algorithm to infer gene duplication and speciation events on a gene tree
    • 11590098
    • Zmasek CM Eddy SR A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 2001 17 821-828 11590098
    • (2001) Bioinformatics , vol.17 , pp. 821-828
    • Zmasek, C.M.1    Eddy, S.R.2
  • 79
    • 0013017592 scopus 로고    scopus 로고
    • RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
    • 116988 12028595
    • Zmasek CM Eddy SR RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 2002 3 14 116988 12028595
    • (2002) BMC Bioinformatics , vol.3 , pp. 14
    • Zmasek, C.M.1    Eddy, S.R.2
  • 80
    • 33746582319 scopus 로고    scopus 로고
    • A phylogenomic gene cluster resource: The Phylogenetically Inferred Groups (PhIGs) database
    • 1523372 16608522
    • Dehal PS Boore JL A phylogenomic gene cluster resource: The Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics 2006 7 201 1523372 16608522
    • (2006) BMC Bioinformatics , vol.7 , pp. 201
    • Dehal, P.S.1    Boore, J.L.2
  • 81
    • 33645106540 scopus 로고    scopus 로고
    • OrthologID: Automation of genome-scale ortholog identification within a parsimony framework
    • 16410324
    • Chiu JC Lee EK Egan MG Sarkar IN Coruzzi GM DeSalle R OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 2006 22 699-707 16410324
    • (2006) Bioinformatics , vol.22 , pp. 699-707
    • Chiu, J.C.1    Lee, E.K.2    Egan, M.G.3    Sarkar, I.N.4    Coruzzi, G.M.5    DeSalle, R.6
  • 82
    • 33745022802 scopus 로고    scopus 로고
    • Benchmarking ortholog identification methods using functional genomics data
    • 1557999 16613613
    • Hulsen T Huynen MA de Vlieg J Groenen PM Benchmarking ortholog identification methods using functional genomics data. Genome Biol 2006 7 R31 1557999 16613613
    • (2006) Genome Biol , vol.7
    • Hulsen, T.1    Huynen, M.A.2    de Vlieg, J.3    Groenen, P.M.4
  • 83
    • 33746433923 scopus 로고    scopus 로고
    • Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
    • 16830091
    • Berglund-Sonnhammer AC Steffansson P Betts MJ Liberles DA Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J Mol Evol 2006 63 240-250 16830091
    • (2006) J Mol Evol , vol.63 , pp. 240-250
    • Berglund-Sonnhammer, A.C.1    Steffansson, P.2    Betts, M.J.3    Liberles, D.A.4
  • 84
    • 2342651581 scopus 로고    scopus 로고
    • Bayesian gene/species tree reconciliation and orthology analysis using MCMC
    • 12855432
    • Arvestad L Berglund AC Lagergren J Sennblad B Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 2003 19 Suppl 1 I7-I15 12855432
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Arvestad, L.1    Berglund, A.C.2    Lagergren, J.3    Sennblad, B.4
  • 85
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • 14574403
    • Rokas A Williams BL King N Carroll SB Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003 425 798-804 14574403
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 86
    • 0019951634 scopus 로고
    • Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences
    • 7078635
    • Penny D Foulds LR Hendy MD Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 1982 297 197-200 7078635
    • (1982) Nature , vol.297 , pp. 197-200
    • Penny, D.1    Foulds, L.R.2    Hendy, M.D.3
  • 87
    • 33751039720 scopus 로고    scopus 로고
    • Bushes in the tree of life
    • 1637082 17105342
    • Rokas A Carroll SB Bushes in the tree of life. PLoS Biol 2006 4 e352 1637082 17105342
    • (2006) PLoS Biol , vol.4
    • Rokas, A.1    Carroll, S.B.2
  • 88
    • 27544434211 scopus 로고    scopus 로고
    • Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes
    • 16204094
    • Gabaldón T Huynen MA Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Bioinformatics 2005 21 Suppl 2 ii144-ii150 16204094
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Gabaldón, T.1    Huynen, M.A.2
  • 89
    • 22144452209 scopus 로고    scopus 로고
    • The Integr8 project - A resource for genomic and proteomic data
    • 15972013
    • Pruess M Kersey P Apweiler R The Integr8 project - a resource for genomic and proteomic data. In Silico Biol 2005 5 179-185 15972013
    • (2005) In Silico Biol , vol.5 , pp. 179-185
    • Pruess, M.1    Kersey, P.2    Apweiler, R.3
  • 90
    • 46149126950 scopus 로고    scopus 로고
    • Candida Genome Database http://www.candidagenome.org
  • 91
    • 46149125346 scopus 로고    scopus 로고
    • Neurospora Crassa at MIT
    • Neurospora crassa at MIT http://www.broad.mit.edu/annotation/fungi/ neurospora
  • 92
    • 46149124833 scopus 로고    scopus 로고
    • Chlamydomonas Genome at JGI
    • Chlamydomonas genome at JGI http://genome.jgi-psf.org/chlamy
  • 93
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • 7265238
    • Smith TF Waterman MS Identification of common molecular subsequences. J Mol Biol 1981 147 195-197 7265238
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 94
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • 517706 15318951
    • Edgar RC MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004 5 113 517706 15318951
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 95
    • 0037407924 scopus 로고    scopus 로고
    • Predicting gene function by conserved co-expression
    • 12711213
    • van Noort V Snel B Huynen MA Predicting gene function by conserved co-expression. Trends Genet 2003 19 238-242 12711213
    • (2003) Trends Genet , vol.19 , pp. 238-242
    • van Noort, V.1    Snel, B.2    Huynen, M.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.