-
1
-
-
0035161543
-
Genomes OnLine Database (GOLD): A monitor of genome projects world-wide
-
Bernal, A., Ear, U., and Kyrpides N. (2001) Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 29, 126-127.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 126-127
-
-
Bernal, A.1
Ear, U.2
Kyrpides, N.3
-
2
-
-
0037015858
-
Gene homology resources on the World Wide Web
-
Turchin, A. and Kohane, I. S. (2002) Gene homology resources on the World Wide Web. Physiol Genomics 11, 165-177.
-
(2002)
Physiol Genomics
, vol.11
, pp. 165-177
-
-
Turchin, A.1
Kohane, I.S.2
-
3
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeates, T. O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285-4288.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
4
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte, E. M., Pellegrini, M., Ng, H. L., Rice, D. W., Yeates, T. O., and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
5
-
-
0035900653
-
Reconstructing/deconstructing the earliest eukaryotes: How comparative genomics can help
-
Dacks, J. B. and Doolittle, W. F. (2001) Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help. Cell 107, 419-425.
-
(2001)
Cell
, vol.107
, pp. 419-425
-
-
Dacks, J.B.1
Doolittle, W.F.2
-
6
-
-
0033166097
-
A comparative genomics approach to the evolution of eukaryotes and their mitochondria
-
Lang, B. F., Seif, E., Gray, M. W., O'Kelly, C. J., and Burger, G. (1999) A comparative genomics approach to the evolution of eukaryotes and their mitochondria. J. Eukaryot. Microbiol. 46, 320-326.
-
(1999)
J. Eukaryot. Microbiol
, vol.46
, pp. 320-326
-
-
Lang, B.F.1
Seif, E.2
Gray, M.W.3
O'Kelly, C.J.4
Burger, G.5
-
7
-
-
0034708444
-
Comparative genomics of the eukaryotes
-
Rubin, G. M., Yandell, M. D., Wortman, J. R., et al. (2000) Comparative genomics of the eukaryotes. Science 287, 2204-2215.
-
(2000)
Science
, vol.287
, pp. 2204-2215
-
-
Rubin, G.M.1
Yandell, M.D.2
Wortman, J.R.3
-
8
-
-
0037380723
-
Comparative genomics: Genome-wide analysis in metazoan eukaryotes
-
Ureta-Vidal, A., Ettwiller, L., and Birney, E. (2003) Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4, 251-262.
-
(2003)
Nat. Rev. Genet
, vol.4
, pp. 251-262
-
-
Ureta-Vidal, A.1
Ettwiller, L.2
Birney, E.3
-
9
-
-
18844431588
-
Detecting remotely related proteins by their interactions and sequence similarity
-
Espadaler, J., Aragues, R., Eswar, N., et al. (2005) Detecting remotely related proteins by their interactions and sequence similarity. Proc. Natl. Acad. Sci. USA 102, 7151-7156.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 7151-7156
-
-
Espadaler, J.1
Aragues, R.2
Eswar, N.3
-
10
-
-
24044500970
-
Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships
-
Espadaler, J., Romero-Isart, O., Jackson, R. M., and Oliva, B. (2005) Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships. Bioinformatics 21, 3360-3368.
-
(2005)
Bioinformatics
, vol.21
, pp. 3360-3368
-
-
Espadaler, J.1
Romero-Isart, O.2
Jackson, R.M.3
Oliva, B.4
-
11
-
-
0035211290
-
Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs
-
Matthews, L. R., Vaglio, P., Reboul, J., et al. (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 11, 2120-2126.
-
(2001)
Genome Res
, vol.11
, pp. 2120-2126
-
-
Matthews, L.R.1
Vaglio, P.2
Reboul, J.3
-
12
-
-
2442646432
-
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
-
Kim, W. K., Bolser, D. M., and Park, J. H. (2004) Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics 20, 1138-1150.
-
(2004)
Bioinformatics
, vol.20
, pp. 1138-1150
-
-
Kim, W.K.1
Bolser, D.M.2
Park, J.H.3
-
13
-
-
3442889367
-
OrthoDisease: A database of human disease orthologs
-
O'Brien, K. P., Westerlund, I., and Sonnhammer, E. L. (2004) OrthoDisease: a database of human disease orthologs. Hum. Mutat. 24, 112-119.
-
(2004)
Hum. Mutat
, vol.24
, pp. 112-119
-
-
O'Brien, K.P.1
Westerlund, I.2
Sonnhammer, E.L.3
-
14
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (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
-
15
-
-
2942695714
-
Coevolution of gene expression among interacting proteins
-
Fraser, H. B., Hirsh, A. E., Wall, D. P., and Eisen, M. B. (2004) Coevolution of gene expression among interacting proteins. Proc. Natl. Acad. Sci. USA 101, 9033-9038.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 9033-9038
-
-
Fraser, H.B.1
Hirsh, A.E.2
Wall, D.P.3
Eisen, M.B.4
-
16
-
-
9444269272
-
Compensated deleterious mutations in insect genomes
-
Kulathinal, R. J., Bettencourt, B. R., and Hartl, D. L. (2004) Compensated deleterious mutations in insect genomes. Science 306, 1553-1554.
-
(2004)
Science
, vol.306
, pp. 1553-1554
-
-
Kulathinal, R.J.1
Bettencourt, B.R.2
Hartl, D.L.3
-
17
-
-
0037069428
-
Dobzhansky-Muller incompatibilities in protein evolution
-
Kondrashov, A. S., Sunyaev, S., and Kondrashov, F. A. (2002) Dobzhansky-Muller incompatibilities in protein evolution. Proc. Natl. Acad. Sci. USA 99, 14,878-14,883.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
-
-
Kondrashov, A.S.1
Sunyaev, S.2
Kondrashov, F.A.3
-
18
-
-
0348010697
-
Impact of selection, mutation rate and genetic drift on human genetic variation
-
Sunyaev, S., Kondrashov, F. A., Bork, P., and Ramensky, V. (2003) Impact of selection, mutation rate and genetic drift on human genetic variation. Hum. Mol. Genet. 12, 3325-3330.
-
(2003)
Hum. Mol. Genet
, vol.12
, pp. 3325-3330
-
-
Sunyaev, S.1
Kondrashov, F.A.2
Bork, P.3
Ramensky, V.4
-
19
-
-
0035869223
-
Prediction of deleterious human alleles
-
Sunyaev, S., Ramensky, V., Koch, I., Lathe, W., 3rd, Kondrashov, A. S., and Bork, P. (2001) Prediction of deleterious human alleles. Hum. Mol. Genet. 10, 591-597.
-
(2001)
Hum. Mol. Genet
, vol.10
, pp. 591-597
-
-
Sunyaev, S.1
Ramensky, V.2
Koch, I.3
Lathe 3rd, W.4
Kondrashov, A.S.5
Bork, P.6
-
20
-
-
0242284421
-
A simple dependence between protein evolution rate and the number of protein-protein interactions
-
Fraser, H. B., Wall, D. P., and Hirsh, A. E. (2003) A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol. Biol. 3, 11.
-
(2003)
BMC Evol. Biol
, vol.3
, pp. 11
-
-
Fraser, H.B.1
Wall, D.P.2
Hirsh, A.E.3
-
21
-
-
24944526640
-
Converging on a general model of protein evolution
-
Herbeck, J. T. and Wall, D. P. (2005) Converging on a general model of protein evolution. Trends Biotechnol. 23, 485-487.
-
(2005)
Trends Biotechnol
, vol.23
, pp. 485-487
-
-
Herbeck, J.T.1
Wall, D.P.2
-
22
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
Wall, D. P., Hirsh, A. E., Fraser, H. B., et al. (2005) Functional genomic analysis of the rates of protein evolution. Proc. Natl. Acad. Sci. USA 102, 5483-5488.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 5483-5488
-
-
Wall, D.P.1
Hirsh, A.E.2
Fraser, H.B.3
-
23
-
-
0035963414
-
Protein dispensability and rate of evolution
-
Hirsh, A. E. and Fraser, H. B. (2001) Protein dispensability and rate of evolution. Nature 411, 1046-1049.
-
(2001)
Nature
, vol.411
, pp. 1046-1049
-
-
Hirsh, A.E.1
Fraser, H.B.2
-
24
-
-
0033565762
-
Do essential genes evolve slowly?
-
Hurst, L. D. and Smith, N. G. (1999) Do essential genes evolve slowly? Curr. Biol. 9, 747-750.
-
(1999)
Curr. Biol
, vol.9
, pp. 747-750
-
-
Hurst, L.D.1
Smith, N.G.2
-
25
-
-
0036078078
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
-
Jordan, I. K., Rogozin, I. B., Wolf, Y. I., and Koonin, E. V. (2002) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12, 962-968.
-
(2002)
Genome Res
, vol.12
, pp. 962-968
-
-
Jordan, I.K.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
26
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
Krylov, D. M., Wolf, Y. I., Rogozin, I. B., and Koonin, E. V. (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13, 2229-2235.
-
(2003)
Genome Res
, vol.13
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
27
-
-
0038708556
-
Rate of protein evolution versus fitness effect of gene deletion
-
Yang, J., Gu, Z., and Li, W. H. (2003) Rate of protein evolution versus fitness effect of gene deletion. Mol. Bol. Evol. 20, 772-774.
-
(2003)
Mol. Bol. Evol
, vol.20
, pp. 772-774
-
-
Yang, J.1
Gu, Z.2
Li, W.H.3
-
28
-
-
16344369543
-
Significant impact of protein dispensability on the instantaneous rate of protein evolution
-
Zhang, J. and He, X. (2005) Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol. Biol. Evol. 22, 1147-1155.
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 1147-1155
-
-
Zhang, J.1
He, X.2
-
29
-
-
1242284655
-
An analysis of determinants of amino acids substitution rates in bacterial proteins
-
Rocha, E. P. and Danchin, A. (2004) An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol. Biol. Evol. 21, 108-116.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 108-116
-
-
Rocha, E.P.1
Danchin, A.2
-
30
-
-
0034625235
-
The impact of comparative genomics on our understanding of evolution
-
Koonin, E. V., Aravind, L., and Kondrashov, A. S. (2000) The impact of comparative genomics on our understanding of evolution. Cell 101, 573-576.
-
(2000)
Cell
, vol.101
, pp. 573-576
-
-
Koonin, E.V.1
Aravind, L.2
Kondrashov, A.S.3
-
31
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski, L. B. and Golding, G. B. (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
-
32
-
-
0033956060
-
The COG database: A tool for genome-scale analysis of protein functions and evolution
-
Tatusov, R. L., Galperin, M. Y., Natale, D. A., and Koonin, E. V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 33-36
-
-
Tatusov, R.L.1
Galperin, M.Y.2
Natale, D.A.3
Koonin, E.V.4
-
33
-
-
13444256478
-
Inparanoid: A comprehensive database of eukaryotic orthologs
-
O'Brien, K. P., Remm, M., and Sonnhammer, E. L. (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33, D476-D480.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
O'Brien, K.P.1
Remm, M.2
Sonnhammer, E.L.3
-
34
-
-
0035861990
-
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, 1041-1052.
-
(2001)
J. Mol. Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
35
-
-
13444293344
-
Database resources of the National Center for Biotechnology Information
-
Wheeler, D. L., Barrett, T., Benson, D. A., et al. (2005) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 33, D39-D45.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
-
36
-
-
0141626909
-
Detecting putative orthologs
-
Wall, D. P., Fraser, H. B., and Hirsh, A. E. (2003) Detecting putative orthologs. Bioinformatics 19, 1710-1711.
-
(2003)
Bioinformatics
, vol.19
, pp. 1710-1711
-
-
Wall, D.P.1
Fraser, H.B.2
Hirsh, A.E.3
-
37
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (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
-
38
-
-
0042121237
-
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, 3497-3500.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
-
39
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang, Z. (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
-
(1997)
Comput. Appl. Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
40
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D. T., Taylor, W. R., and Thornton, J. M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
-
(1992)
Comput. Appl. Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
41
-
-
0035956856
-
Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms
-
Nei, M., Xu, P., and Glazko G. (2001) Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc. Natl. Acad. Sci. USA 98, 2497-2502.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 2497-2502
-
-
Nei, M.1
Xu, P.2
Glazko, G.3
-
42
-
-
23744515783
-
Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects
-
Degnan, P. H., Lazarus, A. B., and Wernegreen, J. J. (2005) Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Res. 15, 1023-1033.
-
(2005)
Genome Res
, vol.15
, pp. 1023-1033
-
-
Degnan, P.H.1
Lazarus, A.B.2
Wernegreen, J.J.3
-
43
-
-
14044252090
-
Conservation and evolution of cis-regulatory systems in ascomycete fungi
-
Gasch, A. P., Moses, A. M., Chiang, D. Y., Fraser, H. B., Berardini, M., and Eisen, M. B. (2004) Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2, e398.
-
(2004)
PLoS Biol
, vol.2
-
-
Gasch, A.P.1
Moses, A.M.2
Chiang, D.Y.3
Fraser, H.B.4
Berardini, M.5
Eisen, M.B.6
-
44
-
-
14644429103
-
fog-2 and the evolution of self-fertile hermaphroditism in Caenorhabditis
-
Nayak, S., Goree, J., and Schedl T. (2005) fog-2 and the evolution of self-fertile hermaphroditism in Caenorhabditis. PLoS Biol. 3, e6.
-
(2005)
PLoS Biol
, vol.3
-
-
Nayak, S.1
Goree, J.2
Schedl, T.3
-
45
-
-
19144367138
-
Prediction of functional modules based on comparative genome analysis and Gene Ontology application
-
Wu, H., Su, Z., Mao, F., Olman, V., and Xu, Y. (2005) Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Res. 33, 2822-2837.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2822-2837
-
-
Wu, H.1
Su, Z.2
Mao, F.3
Olman, V.4
Xu, Y.5
-
46
-
-
3543099834
-
Evolution and topology in the yeast protein interaction network
-
Wuchty, S. (2004) Evolution and topology in the yeast protein interaction network. Genome Res. 14, 1310-1314.
-
(2004)
Genome Res
, vol.14
, pp. 1310-1314
-
-
Wuchty, S.1
-
47
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
48
-
-
33644876924
-
Ensembl 2006
-
Birney, E., Andrews, D., and Caccamo, M. (2006) Ensembl 2006. Nucleic Acids Res. 34, D556-D5561.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Birney, E.1
Andrews, D.2
Caccamo, M.3
-
49
-
-
33644520519
-
The Genomes On Line Database (GOLD) v.2: A monitor of genome projects worldwide
-
Liolios, K., Tavernarakis, N., Hugenholtz, P., and Kyrpides, N. C. (2006) The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34, D332-D334.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Liolios, K.1
Tavernarakis, N.2
Hugenholtz, P.3
Kyrpides, N.C.4
-
50
-
-
18144420835
-
Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions
-
Bastien, O., Roy, S., and Marechal, E. (2005) Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions. C R Biol. 328, 445-453.
-
(2005)
C R Biol
, vol.328
, pp. 445-453
-
-
Bastien, O.1
Roy, S.2
Marechal, E.3
-
51
-
-
27744607026
-
A collection of amino acid replacement matrices derived from clusters of orthologs
-
Olsen, R. and Loomis, W. F. (2005) A collection of amino acid replacement matrices derived from clusters of orthologs. J. Mol. Evol. 61, 659-665.
-
(2005)
J. Mol. Evol
, vol.61
, pp. 659-665
-
-
Olsen, R.1
Loomis, W.F.2
-
52
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch, W. M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool. 19, 99-113.
-
(1970)
Syst. Zool
, vol.19
, pp. 99-113
-
-
Fitch, W.M.1
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