-
1
-
-
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
-
2
-
-
0036078078
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
-
Jordan,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, K.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
3
-
-
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
-
4
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
Wall,D.P., Hirsh,A.E., Fraser,H.B., Kumm,J., Giaever,G., Eisen,M.B. and Feldman,M.W. (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
Kumm, J.4
Giaever, G.5
Eisen, M.B.6
Feldman, M.W.7
-
5
-
-
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. Biol. Evol., 20, 772-774.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 772-774
-
-
Yang, J.1
Gu, Z.2
Li, W.H.3
-
6
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser,H.B., Hirsh,A.E., Steinmetz,L.M., Scharfe,C. and Feldman,M.W. (2002) Evolutionary rate in the protein interaction network. Science, 296, 750-752.
-
(2002)
Science
, vol.296
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
7
-
-
0842291785
-
No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly
-
Jordan,I., Wolf,Y. and Koonin,E. (2003) No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol., 3.
-
(2003)
BMC Evol. Biol.
, vol.3
-
-
Jordan, I.1
Wolf, Y.2
Koonin, E.3
-
8
-
-
0017323923
-
Biochemical evolution
-
Wilson,A.C., Carlson,S.S. and White,T.J. (1977) Biochemical evolution. Annu. Rev. Biochem., 46, 573-639.
-
(1977)
Annu. Rev. Biochem.
, vol.46
, pp. 573-639
-
-
Wilson, A.C.1
Carlson, S.S.2
White, T.J.3
-
9
-
-
84959795073
-
Phylogenetic analysis under dollo's law
-
Farris,J.S. (1977) Phylogenetic analysis under dollo's law. Syst. Zool., 26, 77-88.
-
(1977)
Syst. Zool.
, vol.26
, pp. 77-88
-
-
Farris, J.S.1
-
10
-
-
33745796718
-
A probabilistic model for gene content evolution with duplication, loss and horizontal transfer
-
In Springer, Berlin
-
Csuros,M. and Miklos,I. (2006) A probabilistic model for gene content evolution with duplication, loss and horizontal transfer. In Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB). Springer, Berlin, pp. 206-220.
-
(2006)
Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB)
, pp. 206-220
-
-
Csuros, M.1
Miklos, I.2
-
11
-
-
3042643735
-
Genome phylogeny inference based on gene contents
-
Gu,X. and Zhang,H. (2004) Genome phylogeny inference based on gene contents. Mol. Biol. Evol., 21, 1401-1408.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1401-1408
-
-
Gu, X.1
Zhang, H.2
-
12
-
-
23744452485
-
Estimating the tempo and mode of gene family evolution from comparative genomic data
-
Hahn,M., De Bie,T., Stajich,J., Nguyen,C. and Cristianini,N. (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res., 15, 1153-1160.
-
(2005)
Genome Res.
, vol.15
, pp. 1153-1160
-
-
Hahn, M.1
De Bie, T.2
Stajich, J.3
Nguyen, C.4
Cristianini, N.5
-
13
-
-
35048850026
-
A case study of genome evolution: From continuous to discrete time model
-
Tiuryn,J., Rudnicki,R. and Wojtowicz,D. (2004) A case study of genome evolution: From continuous to discrete time model. Proc. Math. Found. Comput. Sci., 3153, 1-24.
-
(2004)
Proc. Math. Found. Comput. Sci.
, vol.3153
, pp. 1-24
-
-
Tiuryn, J.1
Rudnicki, R.2
Wojtowicz, D.3
-
14
-
-
33746192317
-
Unifying measures of gene function and evolution
-
Wolf,Y., Carmel,L. and Koonin,E. (2006) Unifying measures of gene function and evolution. Proc. Biol. Sci., 273, 1507-1515.
-
(2006)
Proc. Biol. Sci.
, vol.273
, pp. 1507-1515
-
-
Wolf, Y.1
Carmel, L.2
Koonin, E.3
-
15
-
-
0003516147
-
-
Cambridge University Press, Cambridge, UK
-
Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
-
(1998)
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
16
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein,J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol, 17, 368-376.
-
(1981)
J. Mol. Evol.
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
17
-
-
33644876253
-
Database resources of the national center for biotechnology information
-
Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R., Federhen,S. et al. (2006) Database resources of the national center for biotechnology information. Nucleic Acids Res., 34, D173-D180.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
DiCuccio, M.8
Edgar, R.9
Federhen, S.10
-
18
-
-
77952882922
-
Comparative genomics and disorder prediction identify biologically relevant sh3 protein interactions
-
Beltrao,P. and Serrano,L. (2005) Comparative genomics and disorder prediction identify biologically relevant sh3 protein interactions. PLoS Comput. Biol., 1, e26.
-
(2005)
PLoS Comput. Biol.
, vol.1
-
-
Beltrao, P.1
Serrano, L.2
-
19
-
-
0036094818
-
An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks
-
Gaunt,M.W. and Miles,M.A. (2002) An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol. Biol. Evol., 19, 748-761.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 748-761
-
-
Gaunt, M.W.1
Miles, M.A.2
-
20
-
-
0035572722
-
Regions of microsynteny in Magnaporthe grisea and Neurospora crassa
-
Hamer,L., Pan,H., Adachi,K., Orbach,M.J., Page,A., Ramamurthy,L. and Woessner,J.P. (2001) Regions of microsynteny in Magnaporthe grisea and Neurospora crassa. Fungal Genet. Biol., 33, 137-143.
-
(2001)
Fungal Genet. Biol.
, vol.33
, pp. 137-143
-
-
Hamer, L.1
Pan, H.2
Adachi, K.3
Orbach, M.J.4
Page, A.5
Ramamurthy, L.6
Woessner, J.P.7
-
21
-
-
2942568227
-
A molecular timescale of eukaryote evolution and the rise of complex multicellular life
-
Hedges,S.B., Blair,J.E., Venturi,M.L. and Shoe,J.L. (2004) A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol. Biol., 4, 2.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 2
-
-
Hedges, S.B.1
Blair, J.E.2
Venturi, M.L.3
Shoe, J.L.4
-
22
-
-
13444306676
-
Cygd: The comprehensive yeast genome database
-
Guldener,U., Munsterkotter,M., Kastenmuller,G., Strack,N., van Helden,J., Lemer,C., Richelles,J., Wodak,S.J., Garcia-Martinez,J., Perez-Ortin,J.E. et al. (2005) Cygd: The comprehensive yeast genome database. Nucleic Acids Res., 33, D364-D368.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Guldener, U.1
Munsterkotter, M.2
Kastenmuller, G.3
Strack, N.4
van Helden, J.5
Lemer, C.6
Richelles, J.7
Wodak, S.J.8
Garcia-Martinez, J.9
Perez-Ortin, J.E.10
-
23
-
-
13844314048
-
Conserved patterns of protein interaction in multiple species
-
Sharan,R., Suthram,S., Kelley,R.M., Kuhn,T., McCuine,S., Uetz,P., Sittler,T., Karp,R.M. and Ideker,T. (2005) Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA, 102, 1974-1979.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 1974-1979
-
-
Sharan, R.1
Suthram, S.2
Kelley, R.M.3
Kuhn, T.4
McCuine, S.5
Uetz, P.6
Sittler, T.7
Karp, R.M.8
Ideker, T.9
-
24
-
-
33747586075
-
A direct comparison of protein interaction confidence assignment schemes
-
Suthram,S., Shlomi,T., Ruppin,E., Sharan,R. and Idekrer,T. (2006) A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics, 7.
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Suthram, S.1
Shlomi, T.2
Ruppin, E.3
Sharan, R.4
Idekrer, T.5
-
25
-
-
0032893083
-
Mips: A database for genomes and protein sequences
-
Mewes,H., Heumann,K., Kaps,A., Mayer,K., Pfeiffer,F., Stocker,S. and Frishman,D. (1999) Mips: A database for genomes and protein sequences. Nucleic Acids Res., 27, 44-48.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 44-48
-
-
Mewes, H.1
Heumann, K.2
Kaps, A.3
Mayer, K.4
Pfeiffer, F.5
Stocker, S.6
Frishman, D.7
-
26
-
-
33644883005
-
A global view of pleiotropy and phenotypically derived gene function in yeast
-
doi:10.1038/msb4100004
-
Dudley,A., Janse,D., Tanay,A., Shamir,R. and Church,G. (2005) A global view of pleiotropy and phenotypically derived gene function in yeast. Mol. Syst. Biol. doi:10.1038/msb4100004.
-
(2005)
Mol. Syst. Biol.
-
-
Dudley, A.1
Janse, D.2
Tanay, A.3
Shamir, R.4
Church, G.5
-
27
-
-
0037482108
-
Assessment of the reliability of protein-protein interactions and protein function prediction
-
Deng,M., Sun,F. and Chen,T. (2003) Assessment of the reliability of protein-protein interactions and protein function prediction. Pac. Symp. Biocomput., 140-151.
-
(2003)
Pac. Symp. Biocomput.
, pp. 140-151
-
-
Deng, M.1
Sun, F.2
Chen, T.3
-
28
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini,M., Marcotte,E., Thompson,M., Eisenberg,D. and Yeates,T. (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.2
Thompson, M.3
Eisenberg, D.4
Yeates, T.5
-
29
-
-
0035046878
-
Lineage-specific gene expansions in bacterial and archaeal genomes
-
Jordan,I. Makarova,K., Spouge,J., Wolf,Y. and Koonin,E. (2001) Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res., 11, 555-565.
-
(2001)
Genome Res.
, vol.11
, pp. 555-565
-
-
Jordan, I.1
Makarova, K.2
Spouge, J.3
Wolf, Y.4
Koonin, E.5
-
30
-
-
0033918311
-
Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels
-
Lin,J. and Gerstein,M. (2000) Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels. Genome Res., 10, 808-818.
-
(2000)
Genome Res.
, vol.10
, pp. 808-818
-
-
Lin, J.1
Gerstein, M.2
-
31
-
-
33646182934
-
An integrated view of protein evolution
-
Pal,C., Papp,B. and Lercher,M. (2006) An integrated view of protein evolution. Nat. Rev. Genet., 7, 337-348.
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.3
-
32
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
Jansen,R., Greenbaum,D. and Gerstein,M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res., 12, 37-46.
-
(2002)
Genome Res.
, vol.12
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
33
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm,M., Storm,C. and Sonnhammer,E. (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.2
Sonnhammer, E.3
-
34
-
-
0034117082
-
A fast algorithm for joint reconstruction of ancestral amino acid sequences
-
Pupko,T., Pe'er,I. Shamir,R. and Graur,D. (2000) A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol., 17, 890-896.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 890-896
-
-
Pupko, T.1
Pe'er, I.2
Shamir, R.3
Graur, D.4
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