-
1
-
-
17444387503
-
Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks
-
Agrafioti, I., J. Swire, J. Abbott, D. Huntley, S. Butcher, and M. P. Stumpf. 2005. Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. BMC Evol. Biol. 5:23.
-
(2005)
BMC Evol. Biol.
, vol.5
, pp. 23
-
-
Agrafioti, I.1
Swire, J.2
Abbott, J.3
Huntley, D.4
Butcher, S.5
Stumpf, M.P.6
-
2
-
-
0028220048
-
Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
-
Akashi, H. 1994. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136:927-935.
-
(1994)
Genetics
, vol.136
, pp. 927-935
-
-
Akashi, H.1
-
3
-
-
0035546157
-
Gene expression and molecular evolution
-
_. 2001. Gene expression and molecular evolution. Curr. Opin. Genet. Dev. 11:660-666.
-
(2001)
Curr. Opin. Genet. Dev.
, vol.11
, pp. 660-666
-
-
-
4
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
_. 2003. Translational selection and yeast proteome evolution. Genetics 164:1291-1303.
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
-
5
-
-
0037162469
-
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
-
USA
-
Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99:9697-9702.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 9697-9702
-
-
Bernstein, J.A.1
Khodursky, A.B.2
Lin, P.H.3
Lin-Chao, S.4
Cohen, S.N.5
-
6
-
-
2942624159
-
Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets
-
Bloom, J. D., and C. Adami. 2003. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol. Biol. 3:21.
-
(2003)
BMC Evol. Biol.
, vol.3
, pp. 21
-
-
Bloom, J.D.1
Adami, C.2
-
7
-
-
2942683220
-
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response
-
_. 2004. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response. BMC Evol. Biol. 4:14.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 14
-
-
-
8
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho, R. J., M. J. Campbell, E. A. Winzeler et al. (11 co-authors). 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2:65-73.
-
(1998)
Mol. Cell
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
Campbell, M.J.2
Winzeler, E.A.3
-
9
-
-
0034666040
-
Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
-
Coghlan, A., and K. H. Wolfe. 2000. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16:1131-1145.
-
(2000)
Yeast
, vol.16
, pp. 1131-1145
-
-
Coghlan, A.1
Wolfe, K.H.2
-
10
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
USA
-
Drummond, D. A., J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold. 2005. Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA 102:14338-14343.
-
(2005)
Proc. Natl. Acad. Sci.
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
11
-
-
0033977618
-
Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
-
Duret, L., and D. Mouchiroud. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17:68-74.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 68-74
-
-
Duret, L.1
Mouchiroud, D.2
-
12
-
-
16844363315
-
Modularity and evolutionary constraint on proteins
-
Fraser, H. B. 2005. Modularity and evolutionary constraint on proteins. Nat. Genet. 37:351-352.
-
(2005)
Nat. Genet.
, vol.37
, pp. 351-352
-
-
Fraser, H.B.1
-
13
-
-
2942678187
-
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
-
Fraser, H. B., and A. E. Hirsh. 2004. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol. Biol. 4:13.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 13
-
-
Fraser, H.B.1
Hirsh, A.E.2
-
14
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser, H. B., A. E. Hirsh, L. M. Steinmetz, C. Scharfe, and M. W. Feldman. 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
-
15
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami, S., W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O'Shea, and J. S. Weissman. 2003. Global analysis of protein expression in yeast. Nature 425:737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
16
-
-
0346727127
-
Protein degradation and protection against misfolded or damaged proteins
-
Goldberg, A. L. 2003. Protein degradation and protection against misfolded or damaged proteins. Nature 426:895-899.
-
(2003)
Nature
, vol.426
, pp. 895-899
-
-
Goldberg, A.L.1
-
17
-
-
0347033256
-
Role of duplicate genes in genetic robustness against null mutations
-
Gu, Z., L. M. Steinmetz, X. Gu, C. Scharfe, R. W. Davis, and W. H. Li. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421:63-66.
-
(2003)
Nature
, vol.421
, pp. 63-66
-
-
Gu, Z.1
Steinmetz, L.M.2
Gu, X.3
Scharfe, C.4
Davis, R.W.5
Li, W.H.6
-
18
-
-
0017467860
-
Advantages of examining multicollinearities in regression analysis
-
Gunst, R. F., and R. L. Mason. 1977a. Advantages of examining multicollinearities in regression analysis. Biometrics 33:249-260.
-
(1977)
Biometrics
, vol.33
, pp. 249-260
-
-
Gunst, R.F.1
Mason, R.L.2
-
19
-
-
84881435143
-
Biased estimation in regression:an evaluation using mean squared error
-
_. 1977b. Biased estimation in regression:an evaluation using mean squared error. J. Am. Stat. Assoc. 72:616-628.
-
(1977)
J. Am. Stat. Assoc.
, vol.72
, pp. 616-628
-
-
-
20
-
-
16344381521
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
-
Hahn, M. W., and A. D. Kern. 2005. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol. Biol. Evol. 22:803-806.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
21
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han, J. D., N. Bertin, T. Hao et al. (11 co-authors). 2004. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430:88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
-
22
-
-
0035963414
-
Protein dispensability and rate of evolution
-
Hirsh, A. E., and H. B. Fraser. 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
-
23
-
-
0141576852
-
Rate of evolution and gene dispensability: Reply
-
_. 2003. Rate of evolution and gene dispensability: reply. Nature 421:497-498.
-
(2003)
Nature
, vol.421
, pp. 497-498
-
-
-
24
-
-
10344224528
-
Adjusting for selection on synonymous sites in estimates of evolutionary distance
-
Hirsh, A. E., H. B. Fraser, and D. P. Wall. 2005. Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol. Biol. Evol. 22:174-177.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 174-177
-
-
Hirsh, A.E.1
Fraser, H.B.2
Wall, D.P.3
-
25
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka, R., and R. Gentleman. 1996. R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5:299-314.
-
(1996)
J. Comput. Graph. Stat.
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
26
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura, T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:13-34.
-
(1985)
Mol. Biol. Evol.
, vol.2
, pp. 13-34
-
-
Ikemura, T.1
-
27
-
-
0037540048
-
Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses
-
Kurtzman, C. P., and C. J. Robnett. 2003. Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res. 3:417-432.
-
(2003)
FEMS Yeast Res.
, vol.3
, pp. 417-432
-
-
Kurtzman, C.P.1
Robnett, C.J.2
-
28
-
-
17744376961
-
Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions
-
Lemos, B., B. R. Bettencourt, C. D. Meiklejohn, and D. L. Hartl. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol. Biol. Evol. 22:1345-1354.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1345-1354
-
-
Lemos, B.1
Bettencourt, B.R.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
29
-
-
0002226671
-
Use of the singular value decomposition in regression analysis
-
Mandel, J. 1982. Use of the singular value decomposition in regression analysis. Am. Stat. 36:15-24.
-
(1982)
Am. Stat.
, vol.36
, pp. 15-24
-
-
Mandel, J.1
-
30
-
-
0035012056
-
Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans
-
Marais, G., and L. Duret. 2001. Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J. Mol. Evol. 52:275-280.
-
(2001)
J. Mol. Evol.
, vol.52
, pp. 275-280
-
-
Marais, G.1
Duret, L.2
-
31
-
-
0000547160
-
Principal component regression in NIR analysis: Viewpoints, background details, and selection of components
-
Naes, T., and H. Martens. 1988. Principal component regression in NIR analysis: viewpoints, background details, and selection of components. J. Chemometrics 2:155-167.
-
(1988)
J. Chemometrics
, vol.2
, pp. 155-167
-
-
Naes, T.1
Martens, H.2
-
33
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pál, C., B. Papp, and L. D. Hurst. 2001. Highly expressed genes in yeast evolve slowly. Genetics 158:927-931.
-
(2001)
Genetics
, vol.158
, pp. 927-931
-
-
Pál, C.1
Papp, B.2
Hurst, L.D.3
-
34
-
-
0037472928
-
Genomic function: Rate of evolution and gene dispensability
-
_. 2003. Genomic function: rate of evolution and gene dispensability. Nature 421:496-497[discussion 497-498].
-
(2003)
Nature
, vol.421
, pp. 496-497
-
-
-
35
-
-
0035166979
-
The comprehensive microbial resource
-
Peterson, J. D., L. A. Umayam, T. Dickinson, E. K. Hickey, and O. White. 2001. The comprehensive microbial resource. Nucleic Acids Res. 29:123-125.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.3
Hickey, E.K.4
White, O.5
-
36
-
-
1242284655
-
An analysis of determinants of amino acids substitution rates in bacterial proteins
-
Rocha, E. P., and A. Danchin. 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
-
37
-
-
5044252972
-
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
-
Subramanian, S., and S. Kumar. 2004. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381.
-
(2004)
Genetics
, vol.168
, pp. 373-381
-
-
Subramanian, S.1
Kumar, S.2
-
39
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
USA
-
Wall, D. P., A. E. Hirsh, H. B. Fraser, J. Kumm, G. Giaever, M. B. Eisen, and M. W. Feldman. 2005. Functional genomic analysis of the rates of protein evolution. Proc. Natl. Acad. Sci. USA 102:5483-5488.
-
(2005)
Proc. Natl. Acad. Sci.
, 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
-
40
-
-
4143122090
-
Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
-
Wright, S. I., C. B. Yau, M. Looseley, and B. C. Meyers. 2004. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol. Biol. Evol. 21:1719-1726.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1719-1726
-
-
Wright, S.I.1
Yau, C.B.2
Looseley, M.3
Meyers, B.C.4
-
41
-
-
0038708556
-
Rate of protein evolution versus fitness effect of gene deletion
-
Yang, J., Z. Gu, and W. H. Li. 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
-
42
-
-
16344369543
-
Significant impact of protein dispensability on the instantaneous rate of protein evolution
-
Zhang, J., and X. He. 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
|