-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
DOI 10.1093/bioinformatics/bti263
-
Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105. (Pubitemid 40668057)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
DOI 10.1093/bioinformatics/btl140
-
Alexa A, Rahnenfuhrer J, Lengauer T. 2006. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22:1600-1607. (Pubitemid 43985293)
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenfuhrer, J.2
Lengauer, T.3
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
4
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner M, Ball CA, Blake JA, et al. (20 co-authors). 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
5
-
-
0002844544
-
Combining trees as a way of combining data sets phylogenetic inference, and the desirability of combining gene trees
-
Baum BR. 1992. Combining trees as a way of combining data sets phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10.
-
(1992)
Taxon
, vol.41
, pp. 3-10
-
-
Baum, B.R.1
-
6
-
-
3142665525
-
GOstat: Find statistically overrepresented Gene Ontologies with a group of genes
-
DOI 10.1093/bioinformatics/bth088
-
Beissbarth T, Speed TP. 2004. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465. (Pubitemid 38931420)
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1464-1465
-
-
Beissbarth, T.1
Speed, T.P.2
-
7
-
-
33747375683
-
Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets
-
Burleigh JG, Driskell AC, Sanderson MJ. 2006. Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Syst Biol. 55: 426-440.
-
(2006)
Syst Biol
, vol.55
, pp. 426-440
-
-
Burleigh, J.G.1
Driskell, A.C.2
Sanderson, M.J.3
-
8
-
-
33847247364
-
From phylogenetics to phylogenomics: The evolutionary relationships of insect endosymbiotic gamma-proteobacteria as a test case
-
Comas I, Moya A, Gonzalez-Candelas F. 2007. From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case. Syst Biol. 56:1-16.
-
(2007)
Syst Biol
, vol.56
, pp. 1-16
-
-
Comas, I.1
Moya, A.2
Gonzalez-Candelas, F.3
-
9
-
-
38849141983
-
Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
-
DOI 10.1101/gr.6531807
-
Cornell MJ, Alam I, Soanes DM, Wong HM, Hedeler C, Paton NW, Rattray M, Hubbard SJ, Talbot NJ, Oliver SG. 2007. Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. Genome Res. 17:1809-1822. (Pubitemid 351360005)
-
(2007)
Genome Research
, vol.17
, Issue.12
, pp. 1809-1822
-
-
Cornell, M.J.1
Alam, I.2
Soanes, D.M.3
Han, M.W.4
Hedeler, C.5
Paton, N.W.6
Rattray, M.7
Hubbard, S.J.8
Talbot, N.J.9
Oliver, S.G.10
-
10
-
-
70649104052
-
Microsporidia: A journey through radical taxonomical revisions
-
Corradi N, Keeling PJ. 2009. Microsporidia: a journey through radical taxonomical revisions. Fung Biol Rev. 23:1-8.
-
(2009)
Fung Biol Rev
, vol.23
, pp. 1-8
-
-
Corradi, N.1
Keeling, P.J.2
-
11
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
DOI 10.1038/nrg1603
-
Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6: 361-375. (Pubitemid 40577180)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.5
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
12
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
DOI 10.1073/pnas.0504070102
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A. 102:14338-14343. (Pubitemid 41429699)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.40
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
13
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
DOI 10.1038/nature06614, PII NATURE06614
-
Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749. (Pubitemid 351522763)
-
(2008)
Nature
, vol.452
, Issue.7188
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
Pang, K.4
Browne, W.E.5
Smith, S.A.6
Seaver, E.7
Rouse, G.W.8
Obst, M.9
Edgecombe, G.D.10
Sorensen, M.V.11
Haddock, S.H.D.12
Schmidt-Rhaesa, A.13
Okusu, A.14
Kristensen, R.M.15
Wheeler, W.C.16
Martindale, M.Q.17
Giribet, G.18
-
15
-
-
24044522270
-
BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis
-
DOI 10.1093/bioinformatics/bti525
-
Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W. 2005. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21:3439-3440. (Pubitemid 41222455)
-
(2005)
Bioinformatics
, vol.21
, Issue.16
, pp. 3439-3440
-
-
Durinck, S.1
Moreau, Y.2
Kasprzyk, A.3
Davis, S.4
De Moor, B.5
Brazma, A.6
Huber, W.7
-
16
-
-
68849131258
-
Hamstr: Profile hidden markov model based search for orthologs in ests
-
Ebersberger I, Strauss S, von Haeseler A. 2009. HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol. 9:157.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 157
-
-
Ebersberger, I.1
Strauss, S.2
Von Haeseler, A.3
-
17
-
-
33845452848
-
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
-
Fitzpatrick DA, Logue ME, Stajich JE, Butler G. 2006. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol. 6:99.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 99
-
-
Fitzpatrick, D.A.1
Logue, M.E.2
Stajich, J.E.3
Butler, G.4
-
18
-
-
80052695664
-
Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata
-
Fong JJ, Fujita MK. 2011. Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata. Mol Phylogenet Evol. 61:300-307.
-
(2011)
Mol Phylogenet Evol
, Issue.61
, pp. 300-307
-
-
Fong, J.J.1
Fujita, M.K.2
-
19
-
-
22844438847
-
Hidden likelihood support in genomic data: Can forty-five wrongs make a right?
-
DOI 10.1080/10635150590945368
-
Gatesy J, Baker RH. 2005. Hidden likelihood support in genomic data: can forty-five wrongs make a right? Syst Biol. 54: 483-492. (Pubitemid 41040446)
-
(2005)
Systematic Biology
, vol.54
, Issue.3
, pp. 483-492
-
-
Gatesy, J.1
Baker, R.H.2
-
20
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
(32 co-authors
-
Gavin AC, Aloy P, Grandi P, et al. (32 co-authors). 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
-
21
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
(25 co-authors
-
Gentleman RC, Carey VJ, Bates DM, et al. (25 co-authors). 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
-
22
-
-
10244239321
-
Life with 6000 genes
-
(16 co-authors
-
Goffeau A, Barrell BG, Bussey H, et al. (16 co-authors). 1996. Life with 6000 genes. Science 274:563-567.
-
(1996)
Science
, vol.274
, pp. 563-567
-
-
Goffeau, A.1
Barrell, B.G.2
Bussey, H.3
-
23
-
-
72749099971
-
Assessing the root of bilaterian animals with scalable phylogenomic methods
-
(17 co-authors
-
Hejnol A, Obst M, Stamatakis A, et al. (17 co-authors). 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci. 276:4261-4270.
-
(2009)
Proc Biol Sci
, vol.276
, pp. 4261-4270
-
-
Hejnol, A.1
Obst, M.2
Stamatakis, A.3
-
24
-
-
34247647914
-
A phylogenetic overview of the Agaricomycotina
-
Hibbett DS. 2006. A phylogenetic overview of the Agaricomycotina. Mycologia 98:917-925. (Pubitemid 46683215)
-
(2006)
Mycologia
, vol.98
, Issue.6
, pp. 917-925
-
-
Hibbett, D.S.1
-
25
-
-
34250341823
-
A higher-level phylogenetic classification of the Fungi
-
DOI 10.1016/j.mycres.2007.03.004, PII S0953756207000615
-
Hibbett DS, Binder M, Bischoff JF, et al. (67 co-authors). 2007. A higher-level phylogenetic classification of the Fungi. Mycol Res. 111:509-547. (Pubitemid 46915419)
-
(2007)
Mycological Research
, vol.111
, Issue.5
, pp. 509-547
-
-
Hibbett, D.S.1
Binder, M.2
Bischoff, J.F.3
Blackwell, M.4
Cannon, P.F.5
Eriksson, O.E.6
Huhndorf, S.7
James, T.8
Kirk, P.M.9
Lucking, R.10
Thorsten Lumbsch, H.11
Lutzoni, F.12
Matheny, P.B.13
McLaughlin, D.J.14
Powell, M.J.15
Redhead, S.16
Schoch, C.L.17
Spatafora, J.W.18
Stalpers, J.A.19
Vilgalys, R.20
Aime, M.C.21
Aptroot, A.22
Bauer, R.23
Begerow, D.24
Benny, G.L.25
Castlebury, L.A.26
Crous, P.W.27
Dai, Y.-C.28
Gams, W.29
Geiser, D.M.30
Griffith, G.W.31
Gueidan, C.32
Hawksworth, D.L.33
Hestmark, G.34
Hosaka, K.35
Humber, R.A.36
Hyde, K.D.37
Ironside, J.E.38
Koljalg, U.39
Kurtzman, C.P.40
Larsson, K.-H.41
Lichtwardt, R.42
Longcore, J.43
Miadlikowska, J.44
Miller, A.45
Moncalvo, J.-M.46
Mozley-Standridge, S.47
Oberwinkler, F.48
Parmasto, E.49
Reeb, V.50
Rogers, J.D.51
Roux, C.52
Ryvarden, L.53
Sampaio, J.P.54
Schussler, A.55
Sugiyama, J.56
Thorn, R.G.57
Tibell, L.58
Untereiner, W.A.59
Walker, C.60
Wang, Z.61
Weir, A.62
Weiss, M.63
White, M.M.64
Winka, K.65
Yao, Y.-J.66
Zhang, N.67
more..
-
26
-
-
30744435829
-
Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles)
-
DOI 10.1093/molbev/msj041
-
Hughes J, Longhorn SJ, Papadopoulou A, Theodorides K, de Riva A, Mejia-Chang M, Foster PG, Vogler AP. 2006. Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol Biol Evol. 23:268-278. (Pubitemid 43100041)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.2
, pp. 268-278
-
-
Hughes, J.1
Longhorn, S.J.2
Papadopoulou, A.3
Theodorides, K.4
De Riva, A.5
Mejia-Chang, M.6
Foster, P.G.7
Vogler, A.P.8
-
27
-
-
0031678692
-
SplitsTree: Analyzing and visualizing evolutionary data
-
Huson DH. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14:68-73. (Pubitemid 28397727)
-
(1998)
Bioinformatics
, vol.14
, Issue.1
, pp. 68-73
-
-
Huson, D.H.1
-
28
-
-
33750329972
-
Reconstructing the early evolution of Fungi using a six-gene phylogeny
-
DOI 10.1038/nature05110, PII NATURE05110
-
James TY, Kauff F, Schoch CL, et al. (70 co-authors). 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822. (Pubitemid 44622687)
-
(2006)
Nature
, vol.443
, Issue.7113
, pp. 818-822
-
-
James, T.Y.1
Kauff, F.2
Schoch, C.L.3
Matheny, P.B.4
Hofstetter, V.5
Cox, C.J.6
Celio, G.7
Gueidan, C.8
Fraker, E.9
Miadlikowska, J.10
Lumbsch, H.T.11
Rauhut, A.12
Reeb, V.13
Arnold, A.E.14
Amtoft, A.15
Stajich, J.E.16
Hosaka, K.17
Sung, G.-H.18
Johnson, D.19
O'Rourke, B.20
Crockett, M.21
Binder, M.22
Curtis, J.M.23
Slot, J.C.24
Wang, Z.25
Wilson, A.W.26
Schussler, A.27
Longcore, J.E.28
O'Donnell, K.29
Mozley-Standridge, S.30
Porter, D.31
Letcher, P.M.32
Powell, M.J.33
Taylor, J.W.34
White, M.M.35
Griffith, G.W.36
Davies, D.R.37
Humber, R.A.38
Morton, J.B.39
Sugiyama, J.40
Rossman, A.Y.41
Rogers, J.D.42
Pfister, D.H.43
Hewitt, D.44
Hansen, K.45
Hambleton, S.46
Shoemaker, R.A.47
Kohlmeyer, J.48
Volkmann-Kohlmeyer, B.49
Spotts, R.A.50
Serdani, M.51
Crous, P.W.52
Hughes, K.W.53
Matsuura, K.54
Langer, E.55
Langer, G.56
Untereiner, W.A.57
Lucking, R.58
Budel, B.59
Geiser, D.M.60
Aptroot, A.61
Diederich, P.62
Schmitt, I.63
Schultz, M.64
Yahr, R.65
Hibbett, D.S.66
Lutzoni, F.67
McLaughlin, D.J.68
Spatafora, J.W.69
Vilgalys, R.70
more..
-
29
-
-
34247642095
-
A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)
-
James TY, Letcher PM, Longcore JE, Mozley-Standridge SE, Porter D, Powell MJ, Griffith GW, Vilgalys R. 2006. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98:860-871. (Pubitemid 46683210)
-
(2006)
Mycologia
, vol.98
, Issue.6
, pp. 860-871
-
-
James, T.Y.1
Letcher, P.M.2
Longcore, J.E.3
Mozley-Standridge, S.E.4
Porter, D.5
Powell, M.J.6
Griffith, G.W.7
Vilgalys, R.8
-
31
-
-
79958294748
-
Discovery of novel intermediate forms redefines the fungal tree of life
-
Jones MD, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA. 2011. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:200-203.
-
(2011)
Nature
, vol.474
, pp. 200-203
-
-
Jones, M.D.1
Forn, I.2
Gadelha, C.3
Egan, M.J.4
Bass, D.5
Massana, R.6
Richards, T.A.7
-
32
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
DOI 10.1159/000084979
-
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110:462-467. (Pubitemid 41159923)
-
(2005)
Cytogenetic and Genome Research
, vol.110
, Issue.1-4
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
Walichiewicz, J.6
-
33
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
DOI 10.1093/nar/gki198
-
Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518. (Pubitemid 40360980)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.2
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.-I.2
Toh, H.3
Miyata, T.4
-
34
-
-
0033977617
-
Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi
-
Keeling PJ, Luker MA, Palmer JD. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol Biol Evol. 17:23-31. (Pubitemid 30056989)
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.1
, pp. 23-31
-
-
Keeling, P.J.1
Luker, M.A.2
Palmer, J.D.3
-
35
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
DOI 10.1038/nature02424
-
Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624. (Pubitemid 38524797)
-
(2004)
Nature
, vol.428
, Issue.6983
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
36
-
-
79954732034
-
Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination
-
Koestler T, Ebersberger I. 2011. Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination. Genome Biol Evol. 3:186-194.
-
(2011)
Genome Biol Evol
, Issue.3
, pp. 186-194
-
-
Koestler, T.1
Ebersberger, I.2
-
37
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
DOI 10.1093/molbev/msh112
-
Lartillot N, Philippe H. 2004. A Bayesian mixture model for acrosssite heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109. (Pubitemid 38658218)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.6
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
38
-
-
45849154166
-
An improved general amino acid replacement matrix
-
DOI 10.1093/molbev/msn067
-
Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320. (Pubitemid 351882003)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.7
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
39
-
-
55249086237
-
Microsporidia evolved from ancestral sexual fungi
-
Lee SC, Corradi N, Byrnes EJ 3rd, Torres-Martinez S, Dietrich FS, Keeling PJ, Heitman J. 2008. Microsporidia evolved from ancestral sexual fungi. Curr Biol. 18:1675-1679.
-
(2008)
Curr Biol
, vol.18
, pp. 1675-1679
-
-
Lee, S.C.1
Corradi, N.2
Byrnes III, E.J.3
Torres-Martinez, S.4
Dietrich, F.S.5
Keeling, P.J.6
Heitman, J.7
-
40
-
-
62649089109
-
Population genomics of domestic and wild yeasts
-
(26 co-authors
-
Liti G, Carter DM, Moses AM, et al. (26 co-authors). 2009. Population genomics of domestic and wild yeasts. Nature 458:337-341.
-
(2009)
Nature
, vol.458
, pp. 337-341
-
-
Liti, G.1
Carter, D.M.2
Moses, A.M.3
-
41
-
-
57749183675
-
Phylogenomic analyses support the monophyly of taphrinomycotina, including schizosaccharomyces fission yeasts
-
Liu Y, Leigh JW, Brinkmann H, Cushion MT, Rodriguez-Ezpeleta N, Philippe H, Lang BF. 2009. Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts. Mol Biol Evol. 26:27-34.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 27-34
-
-
Liu, Y.1
Leigh, J.W.2
Brinkmann, H.3
Cushion, M.T.4
Rodriguez-Ezpeleta, N.5
Philippe, H.6
Lang, B.F.7
-
42
-
-
72249109366
-
Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support
-
Liu Y, Steenkamp ET, Brinkmann H, Forget L, Philippe H, Lang BF. 2009. Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support. BMC Evol Biol. 9:272.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 272
-
-
Liu, Y.1
Steenkamp, E.T.2
Brinkmann, H.3
Forget, L.4
Philippe, H.5
Lang, B.F.6
-
43
-
-
32044471897
-
Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits
-
Lutzoni F, Kauff F, Cox C, et al. (46 co-authors). 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot. 91:1446-1480. (Pubitemid 43193713)
-
(2004)
American Journal of Botany
, vol.91
, Issue.10
, pp. 1446-1480
-
-
Lutzoni, F.1
Kauff, F.2
Cox, C.J.3
McLaughlin, D.4
Celio, G.5
Dentinger, C.6
Padamsee, M.7
Hibbett, D.8
James, T.Y.9
Baloch, E.10
Grube, M.11
Reeb, V.12
Hofstetter, V.13
Schoch, C.14
Arnold, A.E.15
Miadlikowska, J.16
Spatafora, J.17
Johnson, D.18
Hambleton, S.19
Crockett, M.20
Shoemaker, R.21
Sung, G.-H.22
Lucking, R.23
Lumbsch, T.24
O'Donnell, K.25
Binder, M.26
Diederich, P.27
Ertz, D.28
Gueidan, C.29
Hansen, K.30
Harris, R.C.31
Hosaka, K.32
Lim, Y.-W.33
Matheny, B.34
Nishida, H.35
Pfister, D.36
Rogers, J.37
Rossman, A.38
Schmitt, I.39
Sipman, H.40
Stone, J.41
Sugiyama, J.42
Yahr, R.43
Vilgalys, R.44
more..
-
44
-
-
84857229990
-
The tree versus the forest: The fungal tree of life and the topological diversity within the yeast phylome
-
Marcet-Houben M, Gabaldon T. 2009. The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PLoS One 4:e4357.
-
(2009)
PLoS One
, vol.4
-
-
Marcet-Houben, M.1
Gabaldon, T.2
-
45
-
-
40449120632
-
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
-
DOI 10.1038/nature06556, PII NATURE06556
-
Martin F, Aerts A, Ahren D, et al. (68 co-authors). 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88-92. (Pubitemid 351355085)
-
(2008)
Nature
, vol.452
, Issue.7183
, pp. 88-92
-
-
Martin, F.1
Aerts, A.2
Ahren, D.3
Brun, A.4
Danchin, E.G.J.5
Duchaussoy, F.6
Gibon, J.7
Kohler, A.8
Lindquist, E.9
Pereda, V.10
Salamov, A.11
Shapiro, H.J.12
Wuyts, J.13
Blaudez, D.14
Buee, M.15
Brokstein, P.16
Canback, B.17
Cohen, D.18
Courty, P.E.19
Coutinho, P.M.20
Delaruelle, C.21
Detter, J.C.22
Deveau, A.23
DiFazio, S.24
Duplessis, S.25
Fraissinet-Tachet, L.26
Lucic, E.27
Frey-Klett, P.28
Fourrey, C.29
Feussner, I.30
Gay, G.31
Grimwood, J.32
Hoegger, P.J.33
Jain, P.34
Kilaru, S.35
Labbe, J.36
Lin, Y.C.37
Legue, V.38
Le Tacon, F.39
Marmeisse, R.40
Melayah, D.41
Montanini, B.42
Muratet, M.43
Nehls, U.44
Niculita-Hirzel, H.45
Secq, M.P.O.-L.46
Peter, M.47
Quesneville, H.48
Rajashekar, B.49
Reich, M.50
Rouhier, N.51
Schmutz, J.52
Yin, T.53
Chalot, M.54
Henrissat, B.55
Kues, U.56
Lucas, S.57
Van De Peer, Y.58
Podila, G.K.59
Polle, A.60
Pukkila, P.J.61
Richardson, P.M.62
Rouze, P.63
Sanders, I.R.64
Stajich, J.E.65
Tunlid, A.66
Tuskan, G.67
Grigoriev, I.V.68
more..
-
46
-
-
79955754400
-
Sequencing the fungal tree of life
-
Martin F, Cullen D, Hibbett D, Pisabarro A, Spatafora JW, Baker SE, Grigoriev IV. 2011. Sequencing the fungal tree of life. New Phytol. 190:818-821.
-
(2011)
New Phytol
, vol.190
, pp. 818-821
-
-
Martin, F.1
Cullen, D.2
Hibbett, D.3
Pisabarro, A.4
Spatafora, J.W.5
Baker, S.E.6
Grigoriev, I.V.7
-
47
-
-
77958144939
-
A phylogenomic approach to resolve the arthropod tree of life
-
(16 co-authors
-
Meusemann K, von Reumont BM, Simon S, et al. (16 co-authors). 2010. A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol. 27:2451-2464.
-
(2010)
Mol Biol Evol
, Issue.27
, pp. 2451-2464
-
-
Meusemann, K.1
Von Reumont, B.M.2
Simon, S.3
-
48
-
-
77956685978
-
Genome sequence of the model mushroom Schizophyllum commune
-
(32 co-authors
-
Ohm RA, de Jong JF, Lugones LG, et al. (32 co-authors). 2010. Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol. 28:957-963.
-
(2010)
Nat Biotechnol
, Issue.28
, pp. 957-963
-
-
Ohm, R.A.1
De Jong, J.F.2
Lugones, L.G.3
-
49
-
-
0037460985
-
TIGR gene indices clustering tools (TGICL): A software system for fast clustering of large EST datasets
-
DOI 10.1093/bioinformatics/btg034
-
Pertea G, Huang X, Liang F, et al. (12 co-authors). 2003. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651-652. (Pubitemid 36417060)
-
(2003)
Bioinformatics
, vol.19
, Issue.5
, pp. 651-652
-
-
Pertea, G.1
Huang, X.2
Liang, F.3
Antonescu, V.4
Sultana, R.5
Karamycheva, S.6
Lee, Y.7
White, J.8
Cheung, F.9
Parvizi, B.10
Tsai, J.11
Quackenbush, J.12
-
50
-
-
79953716259
-
Resolving difficult phylogenetic questions: Why more sequences are not enough
-
Philippe H, Brinkmann H, Lavrov DV, Littlewood DT, Manuel M, Worheide G, Baurain D. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
-
(2011)
PLoS Biol
, Issue.9
-
-
Philippe, H.1
Brinkmann, H.2
Lavrov, D.V.3
Littlewood, D.T.4
Manuel, M.5
Worheide, G.6
Baurain, D.7
-
51
-
-
65249099546
-
Phylogenomics revives traditional views on deep animal relationships
-
(20 co-authors
-
Philippe H, Derelle R, Lopez P, et al. (20 co-authors). 2009. Phylogenomics revives traditional views on deep animal relationships. Curr Biol. 19:706-712.
-
(2009)
Curr Biol
, vol.19
, pp. 706-712
-
-
Philippe, H.1
Derelle, R.2
Lopez, P.3
-
52
-
-
17744386162
-
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and protostomia
-
DOI 10.1093/molbev/msi111
-
Philippe H, Lartillot N, Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol. 22: 1246-1253. (Pubitemid 40577762)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.5
, pp. 1246-1253
-
-
Philippe, H.1
Lartillot, N.2
Brinkmann, H.3
-
53
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
Ragan MA. 1992. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol. 1:53-58.
-
(1992)
Mol Phylogenet Evol
, vol.1
, pp. 53-58
-
-
Ragan, M.A.1
-
54
-
-
77952904253
-
Basidiomycete mating type genes and pheromone signaling
-
Raudaskoski M, Kothe E. 2010. Basidiomycete mating type genes and pheromone signaling. Eukaryot Cell 9:847-859.
-
(2010)
Eukaryot Cell
, vol.9
, pp. 847-859
-
-
Raudaskoski, M.1
Kothe, E.2
-
55
-
-
33747884042
-
A phylogenomic analysis of the Ascomycota
-
DOI 10.1016/j.fgb.2006.05.001, PII S108718450600096X
-
Robbertse B, Reeves JB, Schoch CL, Spatafora JW. 2006. A phylogenomic analysis of the Ascomycota. Fungal Genet Biol. 43:715-725. (Pubitemid 44292552)
-
(2006)
Fungal Genetics and Biology
, vol.43
, Issue.10
, pp. 715-725
-
-
Robbertse, B.1
Reeves, J.B.2
Schoch, C.L.3
Spatafora, J.W.4
-
56
-
-
36148929776
-
EST sequencing of Onychophora and phylogenomic analysis of Metazoa
-
DOI 10.1016/j.ympev.2007.09.002, PII S1055790307003156
-
Roeding F, Hagner-Holler S, Ruhberg H, Ebersberger I, von Haeseler A, Kube M, Reinhardt R, Burmester T. 2007. EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol Phylogenet Evol. 45:942-951. (Pubitemid 350110621)
-
(2007)
Molecular Phylogenetics and Evolution
, vol.45
, Issue.3
, pp. 942-951
-
-
Roeding, F.1
Hagner-Holler, S.2
Ruhberg, H.3
Ebersberger, I.4
Von Haeseler, A.5
Kube, M.6
Reinhardt, R.7
Burmester, T.8
-
58
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
DOI 10.1038/nature02053
-
Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804. (Pubitemid 37355944)
-
(2003)
Nature
, vol.425
, Issue.6960
, pp. 798-804
-
-
Rokas, A.1
Williams, B.I.2
King, N.3
Carroll, S.B.4
-
59
-
-
34248217100
-
Inferring angiosperm phylogeny from est data with widespread gene duplication
-
Sanderson MJ, McMahon MM. 2007. Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol Biol. 7(Suppl 1):S3.
-
(2007)
BMC Evol Biol
, vol.7
, Issue.SUPPL. 1
-
-
Sanderson, M.J.1
McMahon, M.M.2
-
60
-
-
58849142045
-
Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis
-
Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R. 2009. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol. 7:e20.
-
(2009)
PLoS Biol
, vol.7
-
-
Schierwater, B.1
Eitel, M.2
Jakob, W.3
Osigus, H.J.4
Hadrys, H.5
Dellaporta, S.L.6
Kolokotronis, S.O.7
Desalle, R.8
-
61
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. (Pubitemid 34284960)
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
62
-
-
67749119915
-
The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits
-
(64 co-authors
-
Schoch CL, Sung GH, Lopez-Giraldez F, et al. (64 co-authors). 2009. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol. 58:224-239.
-
(2009)
Syst Biol
, vol.58
, pp. 224-239
-
-
Schoch, C.L.1
Sung, G.H.2
Lopez-Giraldez, F.3
-
63
-
-
0035711692
-
A new fungal phylum, the Glomeromycota: Phylogeny and evolution
-
Schüßler A, Schwarzott D, Walker C. 2001. A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res. 105:1413-1421. (Pubitemid 34134580)
-
(2001)
Mycological Research
, vol.105
, Issue.12
, pp. 1413-1421
-
-
Schussler, A.1
Schwarzott, D.2
Walker, C.3
-
64
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
DOI 10.1101/gr.1239303
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-2504. (Pubitemid 37428274)
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
65
-
-
70450270772
-
A phylogenomic approach to resolve the basal pterygote divergence
-
Simon S, Strauss S, von Haeseler A, Hadrys H. 2009. A phylogenomic approach to resolve the basal pterygote divergence. Mol Biol Evol. 26:2719-2730.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2719-2730
-
-
Simon, S.1
Strauss, S.2
Von Haeseler, A.3
Hadrys, H.4
-
66
-
-
70349490066
-
Comparative genomics of protoploid saccharomycetaceae
-
(54 co-authors
-
Souciet JL, Dujon B, Gaillardin C, et al. (54 co-authors). 2009. Comparative genomics of protoploid Saccharomycetaceae. Genome Res. 19:1696-1709.
-
(2009)
Genome Res
, vol.19
, pp. 1696-1709
-
-
Souciet, J.L.1
Dujon, B.2
Gaillardin, C.3
-
67
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
DOI 10.1093/bioinformatics/btl446
-
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
68
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
DOI 10.1080/10635150701472164, PII 780704285
-
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577. (Pubitemid 47171631)
-
(2007)
Systematic Biology
, vol.56
, Issue.4
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
69
-
-
36048980287
-
Phylogenomics
-
DOI 10.1016/j.cub.2007.09.023, PII S0960982207019823
-
Telford MJ. 2007. Phylogenomics. Curr Biol. 17:R945-R946. (Pubitemid 350090019)
-
(2007)
Current Biology
, vol.17
, Issue.22
-
-
Telford, M.J.1
-
70
-
-
0027241482
-
Monophyletic origins of the metazoa: An evolutionary link with fungi
-
Wainright PO, Hinkle G, Sogin ML, Stickel SK. 1993. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science 260:340-342. (Pubitemid 23160139)
-
(1993)
Science
, vol.260
, Issue.5106
, pp. 340-342
-
-
Wainright, P.O.1
Hinkle, G.2
Sogin, M.L.3
Stickel, S.K.4
-
71
-
-
33746080839
-
Phylogenetic distribution and evolution of mycorrhizas in land plants
-
DOI 10.1007/s00572-005-0033-6
-
Wang B, Qiu YL. 2006. Phylogenetic distribution and evolution of mycorrhizas in land plants. Mycorrhiza 16:299-363. (Pubitemid 44078603)
-
(2006)
Mycorrhiza
, vol.16
, Issue.5
, pp. 299-363
-
-
Wang, B.1
Qiu, Y.-L.2
|