-
1
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch WM, (1970) Distinguishing homologous from analogous proteins. Syst Zool 19: 99-113.
-
(1970)
Syst Zool
, vol.19
, pp. 99-113
-
-
Fitch, W.M.1
-
2
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
Koonin EV, (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39: 309-338.
-
(2005)
Annu Rev Genet
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
3
-
-
0141519279
-
OrthoMCL: identification of ortholog groups for eukaryotic genomes
-
Li L, Stoeckert CJ Jr, Roos DS, (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert Jr., C.J.2
Roos, D.S.3
-
4
-
-
0032491377
-
Predicting function: From genes to genomes and back
-
Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, et al. (1998) Predicting function: From genes to genomes and back. J Mol Biol 283: 707-725.
-
(1998)
J Mol Biol
, vol.283
, pp. 707-725
-
-
Bork, P.1
Dandekar, T.2
Diaz-Lazcoz, Y.3
Eisenhaber, F.4
Huynen, M.5
-
5
-
-
18144444203
-
Using orthologous and paralogous proteins to identify specificity determining residues
-
preprint0002.0001-preprint0002.0020
-
Mirny LA, Gelfand MS, (2002) Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biol 3: preprint0002.0001-0002.0020.
-
(2002)
Genome Biol
, vol.3
-
-
Mirny, L.A.1
Gelfand, M.S.2
-
6
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov RL, Koonin EV, Lipman DJ, (1997) A genomic perspective on protein families. Science 278: 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
8
-
-
54849436208
-
The quest for orthologs: finding the corresponding gene across genomes
-
Kuzniar A, van Ham RCHJ, Pongor S, Leunissen JAM, (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 24: 539-551.
-
(2008)
Trends Genet
, vol.24
, pp. 539-551
-
-
Kuzniar, A.1
van Ham, R.C.H.J.2
Pongor, S.3
Leunissen, J.A.M.4
-
9
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
10
-
-
33747892409
-
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
-
Alexeyenko A, Tamas I, Liu G, Sonnhammer EL, (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9-15.
-
(2006)
Bioinformatics
, vol.22
-
-
Alexeyenko, A.1
Tamas, I.2
Liu, G.3
Sonnhammer, E.L.4
-
11
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm M, Storm CE, Sonnhammer EL, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
-
(2001)
J Mol Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
12
-
-
0029133912
-
Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology
-
Bork P, Ouzounis C, Casari G, Schneider R, Sander C, et al. (1995) Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol Microbiol 16: 955-967.
-
(1995)
Mol Microbiol
, vol.16
, pp. 955-967
-
-
Bork, P.1
Ouzounis, C.2
Casari, G.3
Schneider, R.4
Sander, C.5
-
13
-
-
0030111235
-
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli
-
Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, et al. (1996) Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol 6: 279-291.
-
(1996)
Curr Biol
, vol.6
, pp. 279-291
-
-
Tatusov, R.L.1
Mushegian, A.R.2
Bork, P.3
Brown, N.P.4
Hayes, W.S.5
-
15
-
-
33747817416
-
Roundup: a multi-genome repository of orthologs and evolutionary distances
-
DeLuca TF, Wu IH, Pu J, Monaghan T, Peshkin L, et al. (2006) Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics 22: 2044-2046.
-
(2006)
Bioinformatics
, vol.22
, pp. 2044-2046
-
-
DeLuca, T.F.1
Wu, I.H.2
Pu, J.3
Monaghan, T.4
Peshkin, L.5
-
16
-
-
33746234722
-
Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
-
Dessimoz C, Boeckmann B, Roth ACJ, Gonnet GH, (2006) Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits. Nucleic Acids Res 34: 3309-3316.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3309-3316
-
-
Dessimoz, C.1
Boeckmann, B.2
Roth, A.C.J.3
Gonnet, G.H.4
-
17
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N, (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 96: 2896-2901.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
18
-
-
33645106540
-
OrthologID: automation of genome-scale ortholog identification within a parsimony framework
-
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, et al. (2006) OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 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
-
20
-
-
0036173130
-
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
-
Storm CEV, Sonnhammer ELL, (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18: 92-99.
-
(2002)
Bioinformatics
, vol.18
, pp. 92-99
-
-
Storm, C.E.V.1
Sonnhammer, E.L.L.2
-
21
-
-
0142028973
-
Comprehensive analysis of orthologous protein domains using the HOPS database
-
Storm CEV, Sonnhammer ELL, (2003) Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 13: 2353-2362.
-
(2003)
Genome Res
, vol.13
, pp. 2353-2362
-
-
Storm, C.E.V.1
Sonnhammer, E.L.L.2
-
22
-
-
0013017592
-
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
-
Zmasek CM, Eddy SR, (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
-
23
-
-
0037407924
-
Predicting gene function by conserved co-expression
-
van Noort V, Snel B, Huynen MA, (2003) Predicting gene function by conserved co-expression. Trends Genet 19: 238-242.
-
(2003)
Trends Genet
, vol.19
, pp. 238-242
-
-
van Noort, V.1
Snel, B.2
Huynen, M.A.3
-
24
-
-
33745022802
-
Benchmarking ortholog identification methods using functional genomics data
-
Hulsen T, Huynen MA, de Vlieg J, Groenen PM, (2006) Benchmarking ortholog identification methods using functional genomics data. Genome Biol 7: R31.
-
(2006)
Genome Biol
, vol.7
-
-
Hulsen, T.1
Huynen, M.A.2
de Vlieg, J.3
Groenen, P.M.4
-
25
-
-
59149102602
-
Phylogenetic and functional assessment of orthologs inference projects and methods
-
Altenhoff AM, Dessimoz C, (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 5: e1000262.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Altenhoff, A.M.1
Dessimoz, C.2
-
26
-
-
37849023306
-
Assessing performance of orthology detection strategies applied to eukaryotic genomes
-
Chen F, Mackey AJ, Vermunt JK, Roos DS, (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2: e383.
-
(2007)
PLoS ONE
, vol.2
-
-
Chen, F.1
Mackey, A.J.2
Vermunt, J.K.3
Roos, D.S.4
-
27
-
-
33644787447
-
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
-
Chen F, Mackey AJ, Stoeckert CJ, Roos DS, (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 34: D363-D368.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Chen, F.1
Mackey, A.J.2
Stoeckert, C.J.3
Roos, D.S.4
-
28
-
-
75549088687
-
Database resources of the National Center for Biotechnology Information
-
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 38: D5-D16.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bolton, E.4
Bryant, S.H.5
-
29
-
-
0029096506
-
Sampling properties of DNA sequence data in phylogenetic analysis
-
Cummings MP, Otto SP, Wakeley J, (1995) Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol 12: 814-822.
-
(1995)
Mol Biol Evol
, vol.12
, pp. 814-822
-
-
Cummings, M.P.1
Otto, S.P.2
Wakeley, J.3
-
30
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas A, Williams BL, King N, Carroll SB, (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
31
-
-
25844471721
-
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
-
Byrne KP, Wolfe KH, (2005) The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15: 1456-1461.
-
(2005)
Genome Res
, vol.15
, pp. 1456-1461
-
-
Byrne, K.P.1
Wolfe, K.H.2
-
32
-
-
65249107239
-
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
-
Akerborg O, Sennblad B, Arvestad L, Lagergren J, (2009) Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A 106: 5714-5719.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 5714-5719
-
-
Akerborg, O.1
Sennblad, B.2
Arvestad, L.3
Lagergren, J.4
-
33
-
-
67149106149
-
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome
-
Gordon JL, Byrne KP, Wolfe KH, (2009) Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. Plos Genetics 5: e1000485.
-
(2009)
Plos Genetics
, vol.5
-
-
Gordon, J.L.1
Byrne, K.P.2
Wolfe, K.H.3
-
34
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe KH, Shields DC, (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
35
-
-
33645023614
-
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
-
Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH, (2006) Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440: 341-345.
-
(2006)
Nature
, vol.440
, pp. 341-345
-
-
Scannell, D.R.1
Byrne, K.P.2
Gordon, J.L.3
Wong, S.4
Wolfe, K.H.5
-
36
-
-
0344256533
-
Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora
-
Kurtzman CP, (2003) Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS Yeast Res 4: 233-245.
-
(2003)
FEMS Yeast Res
, vol.4
, pp. 233-245
-
-
Kurtzman, C.P.1
-
37
-
-
10244239321
-
Life with 6000 genes
-
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. (1996) Life with 6000 genes. Science 274: 546, 563-567.
-
(1996)
Science
, vol.274
-
-
Goffeau, A.1
Barrell, B.G.2
Bussey, H.3
Davis, R.W.4
Dujon, B.5
-
38
-
-
11144355642
-
The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome
-
Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304: 304-307.
-
(2004)
Science
, vol.304
, pp. 304-307
-
-
Dietrich, F.S.1
Voegeli, S.2
Brachat, S.3
Lerch, A.4
Gates, K.5
-
39
-
-
3042720475
-
Genome evolution in yeasts
-
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, et al. (2004) Genome evolution in yeasts. Nature 430: 35-44.
-
(2004)
Nature
, vol.430
, pp. 35-44
-
-
Dujon, B.1
Sherman, D.2
Fischer, G.3
Durrens, P.4
Casaregola, S.5
-
40
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
Kellis M, Birren BW, Lander ES, (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
41
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
-
(2003)
Science
, vol.301
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
-
42
-
-
13444256478
-
Inparanoid: a comprehensive database of eukaryotic orthologs
-
O'Brien KP, Remm M, Sonnhammer EL, (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33: D476-480.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
O'Brien, K.P.1
Remm, M.2
Sonnhammer, E.L.3
-
43
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
44
-
-
77951887222
-
The diversity and evolution of circadian clock proteins in fungi
-
Salichos L, Rokas A, (2010) The diversity and evolution of circadian clock proteins in fungi. Mycologia 102: 269-278.
-
(2010)
Mycologia
, vol.102
, pp. 269-278
-
-
Salichos, L.1
Rokas, A.2
-
45
-
-
77649130916
-
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology
-
Grossetete S, Labedan B, Lespinet O, (2010) FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. BMC Genomics 11: 81.
-
(2010)
BMC Genomics
, vol.11
, pp. 81
-
-
Grossetete, S.1
Labedan, B.2
Lespinet, O.3
-
46
-
-
79954577654
-
Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture
-
Kent BN, Salichos L, Gibbons JG, Rokas A, Newton IL, et al. (2011) Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol Evol 3: 209-218.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 209-218
-
-
Kent, B.N.1
Salichos, L.2
Gibbons, J.G.3
Rokas, A.4
Newton, I.L.5
-
47
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, et al. (2005) Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A 102: 5483-5488.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 5483-5488
-
-
Wall, D.P.1
Hirsh, A.E.2
Fraser, H.B.3
Kumm, J.4
Giaever, G.5
-
48
-
-
0004249246
-
Biometry: the principles and practice of statistics in biological research
-
New York, Freeman. xix
-
Sokal RR, Rohlf FJ, (1995) Biometry: the principles and practice of statistics in biological research. New York Freeman. xix pp. 887 p.
-
(1995)
, pp. 887
-
-
Sokal, R.R.1
Rohlf, F.J.2
-
49
-
-
39049134682
-
Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data
-
Lemoine F, Lespinet O, Labedan B, (2007) Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. BMC Evol Biol 7: 237.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 237
-
-
Lemoine, F.1
Lespinet, O.2
Labedan, B.3
-
51
-
-
77951948657
-
Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
-
Fitzpatrick DA, O'Gaora P, Byrne KP, Butler G, (2010) Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. BMC Genomics 11: 290.
-
(2010)
BMC Genomics
, vol.11
, pp. 290
-
-
Fitzpatrick, D.A.1
O'Gaora, P.2
Byrne, K.P.3
Butler, G.4
-
52
-
-
0035814904
-
Computational genomics
-
Koonin EV, (2001) Computational genomics. Curr Biol 11: R155-158.
-
(2001)
Curr Biol
, vol.11
-
-
Koonin, E.V.1
-
53
-
-
1842861592
-
Structure, function and evolution of multidomain proteins
-
Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA, (2004) Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 14: 208-216.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 208-216
-
-
Vogel, C.1
Bashton, M.2
Kerrison, N.D.3
Chothia, C.4
Teichmann, S.A.5
-
54
-
-
0030884401
-
Synteny conservation and chromosome rearrangements during mammalian evolution
-
Ehrlich J, Sankoff D, Nadeau JH, (1997) Synteny conservation and chromosome rearrangements during mammalian evolution. Genetics 147: 289-296.
-
(1997)
Genetics
, vol.147
, pp. 289-296
-
-
Ehrlich, J.1
Sankoff, D.2
Nadeau, J.H.3
-
55
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski LB, Golding GB, (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52: 540-542.
-
(2001)
J Mol Evol
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
56
-
-
34548501747
-
Natural history and evolutionary principles of gene duplication in fungi
-
Wapinski I, Pfeffer A, Friedman N, Regev A, (2007) Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54-61.
-
(2007)
Nature
, vol.449
, pp. 54-61
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
|