메뉴 건너뛰기




Volumn 2, Issue 6, 2008, Pages 291-299

Using whole genome presence/absence data to untangle function in 12 Drosophila genomes

Author keywords

Drosophila; Function; Go categories; Phylogeny; Presence absence

Indexed keywords

DROSOPHILA MELANOGASTER;

EID: 62149086701     PISSN: 19336934     EISSN: 19336942     Source Type: Journal    
DOI: 10.4161/fly.7481     Document Type: Article
Times cited : (10)

References (36)
  • 1
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Drosophila 12 Genomes Consortium
    • Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007; 450:203-18.
    • (2007) Nature , vol.450 , pp. 203-218
  • 2
    • 36048950933 scopus 로고    scopus 로고
    • Gene family evolution across 12 Drosophila genomes
    • Hahn MW, Han MV, Han SG. Gene family evolution across 12 Drosophila genomes. PLoS Genet 2007; 11:197.
    • (2007) PLoS Genet , vol.11 , pp. 197
    • Hahn, M.W.1    Han, M.V.2    Han, S.G.3
  • 4
    • 34247580121 scopus 로고    scopus 로고
    • Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia
    • McBride CS. Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia. Proceedings of the National Academy of Sciences 2007; 104:4996-5001.
    • (2007) Proceedings of the National Academy of Sciences , vol.104 , pp. 4996-5001
    • McBride, C.S.1
  • 5
    • 33744928349 scopus 로고    scopus 로고
    • Genomics of the evolutionary process
    • Clark AG. Genomics of the evolutionary process. TREE 2006; 21:316-21.
    • (2006) TREE , vol.21 , pp. 316-321
    • Clark, A.G.1
  • 6
    • 84883417568 scopus 로고    scopus 로고
    • Characterization of New HAT Transposable Elements In 12 Drosophila Genomes
    • Epub ahead of print
    • de Freitas Ortiz M, Loreto EL. Characterization of new hAT transposable elements in 12 Drosophila genomes. Genetica 2008; [Epub ahead of print].
    • (2008) Genetica
    • de Freitas, O.M.1    Loreto, E.L.2
  • 8
    • 40849138175 scopus 로고    scopus 로고
    • Identification of motifs that are conserved in 12 Drosophila species and regulate midline glia vs. neuron expression
    • Estes P, Fulkerson E, Zhang Y. Identification of motifs that are conserved in 12 Drosophila species and regulate midline glia vs. neuron expression. Genetics 2008; 178:787-99.
    • (2008) Genetics , vol.178 , pp. 787-799
    • Estes, P.1    Fulkerson, E.2    Zhang, Y.3
  • 10
    • 0029107761 scopus 로고
    • Drosophila molecular phylogenies and their uses
    • (edited by M. Hecht, et al
    • Powell J and DeSalle R. Drosophila molecular phylogenies and their uses. In Evolutionary Biology (edited by M. Hecht, et al.,) 1995; 28:87-138.
    • (1995) Evolutionary Biology , vol.28 , pp. 87-138
    • Powell, J.1    Desalle, R.2
  • 11
    • 0028910659 scopus 로고
    • Molecular phylogeny and divergence times of drosophilid species
    • Russo CA, Takezaki M, Nei M. Molecular phylogeny and divergence times of drosophilid species. Molecular Biology and Evolution 1995; 12:391-404.
    • (1995) Molecular Biology and Evolution , vol.12 , pp. 391-404
    • Russo, C.A.1    Takezaki, M.2    Nei, M.3
  • 12
    • 0035201918 scopus 로고    scopus 로고
    • Phylogenetic relationships among species groups of the virilis repleta radiation of Drosophila
    • Tatarenkov A, Ayala FJ. Phylogenetic relationships among species groups of the virilis repleta radiation of Drosophila. Molecular Phylogenetics and Evolution 2001; 21:327-31.
    • (2001) Molecular Phylogenetics and Evolution , vol.21 , pp. 327-331
    • Tatarenkov, A.1    Ayala, F.J.2
  • 13
    • 0033217771 scopus 로고    scopus 로고
    • Phylogeny of Drosophila and related genera: Conflict between molecular and anatomical analyses
    • Kwiatowski J, Ayala FJ. Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses. Molecular Phylogenetics and Evolution 1999; 13:319-28.
    • (1999) Molecular Phylogenetics and Evolution , vol.13 , pp. 319-328
    • Kwiatowski, J.1    Ayala, F.J.2
  • 14
    • 0032041725 scopus 로고    scopus 로고
    • Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae
    • Remsen J, DeSalle R. Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae. Mol Phylogenet Evol 1998; 9:225-35.
    • (1998) Mol Phylogenet Evol , vol.9 , pp. 225-235
    • Remsen, J.1    Desalle, R.2
  • 15
    • 0036039534 scopus 로고    scopus 로고
    • Phylogeny of Drosophilidae (Diptera), with comments on combined analysis and character support
    • Remsen J, O'Grady P. Phylogeny of Drosophilidae (Diptera), with comments on combined analysis and character support. Mol Phylogenet Evol 2002; 24:248-63.
    • (2002) Mol Phylogenet Evol , vol.24 , pp. 248-263
    • Remsen, J.1    O'Grady, P.2
  • 16
    • 33750437728 scopus 로고    scopus 로고
    • Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting
    • Pollard D, Iyer VN, Moses AM, Eisen MB. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genetics 2006; 2:173.
    • (2006) PLoS Genetics , vol.2 , pp. 173
    • Pollard, D.1    Iyer, V.N.2    Moses, A.M.3    Eisen, M.B.4
  • 17
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003; 425:798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 19
    • 33645106540 scopus 로고    scopus 로고
    • Ortholog ID: Automation of genome-scale ortholog identification within a parsimony framework
    • Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R. Ortholog ID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 2006; 22:699-707.
    • (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
  • 20
    • 36049018312 scopus 로고    scopus 로고
    • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    • Harvard FlyBase curators; Berkeley Drosophila Genome Project
    • Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007; 450:219-32.
    • (2007) Nature , vol.450 , pp. 219-232
    • Stark, A.1    Lin, M.F.2    Kheradpour, P.3    Pedersen, J.S.4    Parts, L.5    Carlson, J.W.6    Crosby, M.A.7    Rasmussen, M.D.8    Roy, S.9    Deoras, A.N.10    Ruby, J.G.11    Brennecke, J.12
  • 21
    • 37249041403 scopus 로고    scopus 로고
    • Drosophila Biology in the Genomic Age
    • Markow TA, O'Grady PM. Drosophila Biology in the Genomic Age. Genetics 2006; 177:1269-76.
    • (2006) Genetics , vol.177 , pp. 1269-1276
    • Markow, T.A.1    O'Grady, P.M.2
  • 22
    • 0032805771 scopus 로고    scopus 로고
    • Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher-level artiodactyl taxa
    • Gatesy J, O'Grady P, Baker RH. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher-level artiodactyl taxa. Cladistics 1999; 15:271-313.
    • (1999) Cladistics , vol.15 , pp. 271-313
    • Gatesy, J.1    O'Grady, P.2    Baker, R.H.3
  • 23
    • 4143074629 scopus 로고    scopus 로고
    • Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila
    • Holloway AK, Begun DJ. Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila. Mol Biol Evol 2004; 21:1625-8.
    • (2004) Mol Biol Evol , vol.21 , pp. 1625-1628
    • Holloway, A.K.1    Begun, D.J.2
  • 24
    • 2942678704 scopus 로고    scopus 로고
    • Early events in speciation: Polymorphism for hybrid male sterility in Drosophila mojavensis
    • Reed LK, Markow TA. Early events in speciation: polymorphism for hybrid male sterility in Drosophila mojavensis. Proceedings of the National Academy of Sciences 2004; 101:9009-12.
    • (2004) Proceedings of the National Academy of Sciences , vol.101 , pp. 9009-9012
    • Reed, L.K.1    Markow, T.A.2
  • 25
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-The BLAST-Like Alignment Tool
    • Kent WJ. BLAT-The BLAST-Like Alignment Tool. Genome Research 2002; 12:656-64.
    • (2002) Genome Research , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 27
    • 38549102535 scopus 로고    scopus 로고
    • The FlyBase Consortium. FlyBase:Integration and improvements to query tools
    • Wilson RJ, Goodman JL, Strelets VB. The FlyBase Consortium. FlyBase:integration and improvements to query tools. Nucleic Acids Research 2008; 36:588-93.
    • (2008) Nucleic Acids Research , vol.36 , pp. 588-593
    • Wilson, R.J.1    Goodman, J.L.2    Strelets, V.B.3
  • 30
    • 41049110434 scopus 로고    scopus 로고
    • Automated simultaneous analysis phylogenetics (ASAP): An enabling tool for phylogenomics
    • Sarkar IN, Egan MG, Coruzzi G, Lee EK, DeSalle R. Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phylogenomics. BMC Bioinf 2008; 9:103.
    • (2008) BMC Bioinf , vol.9 , pp. 103
    • Sarkar, I.N.1    Egan, M.G.2    Coruzzi, G.3    Lee, E.K.4    Desalle, R.5
  • 31
    • 14244268694 scopus 로고    scopus 로고
    • Uppsala, Sweden, Evolutionary Biology Centre, Uppsala University
    • Huelsenbeck J, Ronquist F. Mr Bayes Version 3.0. Uppsala, Sweden, Evolutionary Biology Centre, Uppsala University 2003.
    • (2003) Mr Bayes Version 3.0
    • Huelsenbeck, J.1    Ronquist, F.2
  • 32
    • 0031371067 scopus 로고    scopus 로고
    • Multiple sources of molecular characters and the phylogeny of Hawaiian drosophilids
    • Baker R, DeSalle R. Multiple sources of molecular characters and the phylogeny of Hawaiian drosophilids. Syst Biol 1997; 46:654-73.
    • (1997) Syst Biol , vol.46 , pp. 654-673
    • Baker, R.1    Desalle, R.2
  • 33
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
    • Al-Shahrour F, Díaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 2004; 20:578-80.
    • (2004) Bioinformatics , vol.20 , pp. 578-580
    • Al-Shahrour, F.1    Díaz-Uriarte, R.2    Dopazo, J.3
  • 36
    • 4444344022 scopus 로고    scopus 로고
    • Genomic data visualization on the Web
    • Wu W, Noble WS. Genomic data visualization on the Web. Bioinformatics 2004; 20:1804-5.
    • (2004) Bioinformatics , vol.20 , pp. 1804-1805
    • Wu, W.1    Noble, W.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.