-
1
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
Akashi H. 2003. Translational selection and yeast proteome evolution. Genetics 164:1291-303.
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
Akashi, H.1
-
2
-
-
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 215:403-10.
-
(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
-
3
-
-
0016667798
-
The counting and sizing of spermatozoa from ten animal species using a Coulter counter
-
Brotherton J. 1975. The counting and sizing of spermatozoa from ten animal species using a Coulter counter. Andrologia 7:169-85.
-
(1975)
Andrologia
, vol.7
, pp. 169-185
-
-
Brotherton, J.1
-
4
-
-
0242380296
-
Conservation, relocation and duplication in genome evolution
-
Castillo-Davis CI, Hartl DL. 2003. Conservation, relocation and duplication in genome evolution. Trends Genet 19:593-7.
-
(2003)
Trends Genet
, vol.19
, pp. 593-597
-
-
Castillo-Davis, C.I.1
Hartl, D.L.2
-
5
-
-
0036699596
-
Selection for short introns in highly expressed genes
-
Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA. 2002. Selection for short introns in highly expressed genes. Nat Genet 31:415-8.
-
(2002)
Nat Genet
, vol.31
, pp. 415-418
-
-
Castillo-Davis, C.I.1
Mekhedov, S.L.2
Hartl, D.L.3
Koonin, E.V.4
Kondrashov, F.A.5
-
6
-
-
0036263105
-
Population, evolutionary and genomic consequences of interference selection
-
Comeron JM, Kreitman M. 2002. Population, evolutionary and genomic consequences of interference selection. Genetics 161:389-410.
-
(2002)
Genetics
, vol.161
, pp. 389-410
-
-
Comeron, J.M.1
Kreitman, M.2
-
8
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA 102:14338-43.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
9
-
-
30744441602
-
A single determinant dominates the rate of yeast protein evolution
-
Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23:327-37.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 327-337
-
-
Drummond, D.A.1
Raval, A.2
Wilke, C.O.3
-
10
-
-
0033977618
-
Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
-
Duret L, Mouchiroud D. 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
-
11
-
-
0037041441
-
Medicine: Danger-misfolding proteins
-
Ellis RJ, Pinheiro TJ. 2002. Medicine: danger-misfolding proteins. Nature 416:483-4.
-
(2002)
Nature
, vol.416
, pp. 483-484
-
-
Ellis, R.J.1
Pinheiro, T.J.2
-
12
-
-
16844363315
-
Modularity and evolutionary constraint on proteins
-
Fraser HB. 2005. Modularity and evolutionary constraint on proteins. Nat Genet 37:351-2.
-
(2005)
Nat Genet
, vol.37
, pp. 351-352
-
-
Fraser, H.B.1
-
13
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science 296:750-2.
-
(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
-
14
-
-
0027325017
-
Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the epsilon-globin gene
-
Gumucio DL, Shelton DA, Bailey WJ, Slightom JL, Goodman M. 1993. Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the epsilon-globin gene. Proc Natl Acad Sci USA 90:6018-22.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 6018-6022
-
-
Gumucio, D.L.1
Shelton, D.A.2
Bailey, W.J.3
Slightom, J.L.4
Goodman, M.5
-
15
-
-
16344381521
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
-
Hahn MW, Kern AD. 2005. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22:803-6.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
16
-
-
0029888297
-
Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families
-
Hastings KE. 1996. Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families. J Mol Evol 42:631-40.
-
(1996)
J Mol Evol
, vol.42
, pp. 631-640
-
-
Hastings, K.E.1
-
17
-
-
33747817940
-
Toward a molecular understanding of pleiotropy
-
Forthcoming
-
He X, Zhang J. 2006. Toward a molecular understanding of pleiotropy. Genetics. Forthcoming.
-
(2006)
Genetics
-
-
He, X.1
Zhang, J.2
-
18
-
-
0035963414
-
Protein dispensability and rate of evolution
-
Hirsh AE, Fraser HB. 2001. Protein dispensability and rate of evolution. Nature 411:1046-9.
-
(2001)
Nature
, vol.411
, pp. 1046-1049
-
-
Hirsh, A.E.1
Fraser, H.B.2
-
19
-
-
0036947892
-
Robust estimators for expression analysis
-
Hubbell E, Liu WM, Mei R. 2002. Robust estimators for expression analysis. Bioinformatics 18:1585-92.
-
(2002)
Bioinformatics
, vol.18
, pp. 1585-1592
-
-
Hubbell, E.1
Liu, W.M.2
Mei, R.3
-
21
-
-
0023764283
-
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
-
Hughes AL, Nei M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-70.
-
(1988)
Nature
, vol.335
, pp. 167-170
-
-
Hughes, A.L.1
Nei, M.2
-
22
-
-
0033565762
-
Do essential genes evolve slowly?
-
Hurst LD, Smith NG. 1999. Do essential genes evolve slowly? Curr Biol 9:747-50.
-
(1999)
Curr Biol
, vol.9
, pp. 747-750
-
-
Hurst, L.D.1
Smith, N.G.2
-
23
-
-
0036078078
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
-
Jordan IK, Rogozin IB, Wolf YI, Koonin EV. 2002. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 12:962-8.
-
(2002)
Genome Res
, vol.12
, pp. 962-968
-
-
Jordan, I.K.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
24
-
-
9144269670
-
EnsMart: A generic system for fast and flexible access to biological data
-
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E. 2004. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 14:160-9.
-
(2004)
Genome Res
, vol.14
, pp. 160-169
-
-
Kasprzyk, A.1
Keefe, D.2
Smedley, D.3
London, D.4
Spooner, W.5
Melsopp, C.6
Hammond, M.7
Rocca-Serra, P.8
Cox, T.9
Birney, E.10
-
26
-
-
0016087667
-
On some principles governing molecular evolution
-
Kimura M, Ohta T. 1974. On some principles governing molecular evolution. Proc Natl Acad Sci USA 71:2848-52.
-
(1974)
Proc Natl Acad Sci USA
, vol.71
, pp. 2848-2852
-
-
Kimura, M.1
Ohta, T.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, Bettencourt BR, Meiklejohn CD, Hartl DL. 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 22:1345-54.
-
(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
-
-
0003421005
-
-
Sunderland: Sinauer Associates
-
Li WH. 1997. Molecular evolution. Sunderland: Sinauer Associates.
-
(1997)
Molecular Evolution
-
-
Li, W.H.1
-
30
-
-
33646882591
-
Low rates of expression-profile divergence in highly-expressed genes and tissue-specific genes during mammalian evolution
-
Liao BY, Zhang J. 2006a. Low rates of expression-profile divergence in highly-expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 23:1119-28.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1119-1128
-
-
Liao, B.Y.1
Zhang, J.2
-
31
-
-
33244455951
-
Evolutionary conservation of expression profiles between human and mouse orthologous genes
-
Liao BY, Zhang J. 2006b. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 23:530-40.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 530-540
-
-
Liao, B.Y.1
Zhang, J.2
-
32
-
-
15244356879
-
Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee
-
Lu J, Wu CI. 2005. Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci USA 102:4063-7.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4063-4067
-
-
Lu, J.1
Wu, C.I.2
-
33
-
-
33644909094
-
The evolutionary rate of a protein is influenced by features of the interacting partners
-
Makino T, Gojobori T. 2006. The evolutionary rate of a protein is influenced by features of the interacting partners. Mol Biol Evol 23:784-9.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 784-789
-
-
Makino, T.1
Gojobori, T.2
-
34
-
-
0347601042
-
Genic mutation rates in mammals: Local similarity, chromosomal heterogeneity, and X-versus-autosome disparity
-
Malcom CM, Wyckoff GJ, Lahn BT. 2003. Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X-versus-autosome disparity. Mol Biol Evol 20:1633-41.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1633-1641
-
-
Malcom, C.M.1
Wyckoff, G.J.2
Lahn, B.T.3
-
35
-
-
0033969150
-
Implications of macromolecular crowding for protein assembly
-
Minton AP. 2000. Implications of macromolecular crowding for protein assembly. Curr Opin Struct Biol 10:34-9.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 34-39
-
-
Minton, A.P.1
-
36
-
-
0036737630
-
Impact of the presence of paralogs on sequence divergence in a set of mousehuman orthologs
-
Nembaware V, Crum K, Kelso J, Seoighe C. 2002. Impact of the presence of paralogs on sequence divergence in a set of mousehuman orthologs. Genome Res 12:1370-6.
-
(2002)
Genome Res
, vol.12
, pp. 1370-1376
-
-
Nembaware, V.1
Crum, K.2
Kelso, J.3
Seoighe, C.4
-
37
-
-
0027020232
-
The nearly neutral theory of molecular evolution
-
Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263-86.
-
(1992)
Annu Rev Ecol Syst
, vol.23
, pp. 263-286
-
-
Ohta, T.1
-
38
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pal C, Papp B, Hurst LD. 2001a. Highly expressed genes in yeast evolve slowly. Genetics 158:927-31.
-
(2001)
Genetics
, vol.158
, pp. 927-931
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
39
-
-
0035207792
-
Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer
-
Pal C, Papp B, Hurst LD. 2001b. Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Mol Biol Evol 18:2323-6.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 2323-2326
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
40
-
-
0037472928
-
Genomic function: Rate of evolution and gene dispensability
-
Pal C, Papp B, Hurst LD. 2003. Genomic function: rate of evolution and gene dispensability. Nature 421:496-7.
-
(2003)
Nature
, vol.421
, pp. 496-497
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
41
-
-
1242284655
-
An analysis of determinants of amino acids substitution rates in bacterial proteins
-
Rocha EP, Danchin A. 2004. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol Biol Evol 21:108-16.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 108-116
-
-
Rocha, E.P.1
Danchin, A.2
-
42
-
-
0025978949
-
Getting started with yeast
-
Sherman F. 1991. Getting started with yeast. Methods Enzymol 194:3-21.
-
(1991)
Methods Enzymol
, vol.194
, pp. 3-21
-
-
Sherman, F.1
-
43
-
-
0242285634
-
Human disease genes: Patterns and predictions
-
Smith NG, Eyre-Walker A. 2003. Human disease genes: patterns and predictions. Gene 318:169-75.
-
(2003)
Gene
, vol.318
, pp. 169-175
-
-
Smith, N.G.1
Eyre-Walker, A.2
-
44
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su AI, Wiltshire T, Batalov S, et al. (13 co-authors). 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062-7.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
-
45
-
-
5044252972
-
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
-
Subramanian S, Kumar S. 2004. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-81.
-
(2004)
Genetics
, vol.168
, pp. 373-381
-
-
Subramanian, S.1
Kumar, S.2
-
46
-
-
10744227931
-
Mammalian overlapping genes: The comparative perspective
-
Veeramachaneni V, Makalowski W, Galdzicki M, Sood R, Makalowska I. 2004. Mammalian overlapping genes: the comparative perspective. Genome Res 14:280-6.
-
(2004)
Genome Res
, vol.14
, pp. 280-286
-
-
Veeramachaneni, V.1
Makalowski, W.2
Galdzicki, M.3
Sood, R.4
Makalowska, I.5
-
47
-
-
4744355710
-
Compactness of human housekeeping genes: Selection for economy or genomic design?
-
Vinogradov AE. 2004. Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet 20:248-53.
-
(2004)
Trends Genet
, vol.20
, pp. 248-253
-
-
Vinogradov, A.E.1
-
48
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. 2005. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci USA 102:5483-8.
-
(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
-
49
-
-
0035071815
-
An abundance of X-linked genes expressed in spermatogonia
-
Wang PJ, McCarrey JR, Yang F, Page DC. 2001. An abundance of X-linked genes expressed in spermatogonia. Nat Genet 27:422-6.
-
(2001)
Nat Genet
, vol.27
, pp. 422-426
-
-
Wang, P.J.1
McCarrey, J.R.2
Yang, F.3
Page, D.C.4
-
51
-
-
0347766006
-
Elevated rates of protein secretion, evolution, and disease among tissue-specific genes
-
Winter EE, Goodstadt L, Ponting CP. 2004. Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res 14:54-61.
-
(2004)
Genome Res
, vol.14
, pp. 54-61
-
-
Winter, E.E.1
Goodstadt, L.2
Ponting, C.P.3
-
52
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai I, Benjamin H, Shmoish M, et al. (12 co-authors). 2005. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650-9.
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
-
53
-
-
0038708556
-
Rate of protein evolution versus fitness effect of gene deletion
-
Yang J, Gu Z, Li WH. 2003. Rate of protein evolution versus fitness effect of gene deletion. Mol Biol Evol 20:772-4.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 772-774
-
-
Yang, J.1
Gu, Z.2
Li, W.H.3
-
54
-
-
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 13:555-6.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
55
-
-
0034161476
-
Protein-length distributions for the three domains of life
-
Zhang J. 2001. Protein-length distributions for the three domains of life. Trends Genet 16:107-9.
-
(2001)
Trends Genet
, vol.16
, pp. 107-109
-
-
Zhang, J.1
-
56
-
-
16344369543
-
Significant impact of protein dispensability on the instantaneous rate of protein evolution
-
Zhang J, He X. 2005. Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol Biol Evol 22:1147-55.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1147-1155
-
-
Zhang, J.1
He, X.2
-
57
-
-
1542286776
-
Mammalian housekeeping genes evolve more slowly than tissue-specific genes
-
Zhang L, Li WH. 2004. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 21:236-9.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 236-239
-
-
Zhang, L.1
Li, W.H.2
|