-
1
-
-
13744265233
-
Extreme self-organization in networks constructed from gene expression data
-
Agrawal, H. 2002. Extreme self-organization in networks constructed from gene expression data. Phys. Rev. Lett. 89:268702.
-
(2002)
Phys. Rev. Lett.
, vol.89
, pp. 268702
-
-
Agrawal, H.1
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
The Gene Ontology Consortium
-
Ashburner, M., C. A. Ball, J. A. Blake et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
3
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabasi, A. L., and R. Albert. 1999. Emergence of scaling in random networks. Science 286:509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
4
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabasi, A. L., and Z. N. Oltvai. 2004. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5:101-113.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
5
-
-
19344374050
-
Similarities and differences in genome-wide expression data of six organisms
-
Bergmann, S., J. Ihmels, and N. Barkai. 2004. Similarities and differences in genome-wide expression data of six organisms. PLoS Biol. 2:0085-0093.
-
(2004)
PLoS Biol.
, vol.2
, pp. 0085-0093
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
6
-
-
0036856356
-
A duplication growth model of gene expression networks
-
Bhan, A., D. J. Galas, and T. G. Dewey. 2002. A duplication growth model of gene expression networks. Bioinformatics 18:1486-1493.
-
(2002)
Bioinformatics
, vol.18
, pp. 1486-1493
-
-
Bhan, A.1
Galas, D.J.2
Dewey, T.G.3
-
7
-
-
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
-
8
-
-
0014690698
-
Gene regulation for higher cells: A theory
-
Britten, R. J., and E. H. Davidson. 1969. Gene regulation for higher cells: a theory. Science 165:349-357.
-
(1969)
Science
, vol.165
, pp. 349-357
-
-
Britten, R.J.1
Davidson, E.H.2
-
9
-
-
0242391986
-
Codon adaptation index as a measure of dominating codon bias
-
Carbone, A., A. Zinovyev, and F. Kepes. 2003. Codon adaptation index as a measure of dominating codon bias. Bioinformatics 19:2005-2015.
-
(2003)
Bioinformatics
, vol.19
, pp. 2005-2015
-
-
Carbone, A.1
Zinovyev, A.2
Kepes, F.3
-
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
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-14868.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
13
-
-
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
-
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
-
-
0242284421
-
A simple dependence between protein evolution rate and the number of protein-protein interactions
-
Fraser, H. B., D. P. Wall, and A. E. Hirsh. 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
-
16
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
Giot, L., J. S. Bader, C. Brouwer et al. 2003. A protein interaction map of Drosophila melanogaster. Science 302:1727-1736.
-
(2003)
Science
, vol.302
, pp. 1727-1736
-
-
Giot, L.1
Bader, J.S.2
Brouwer, C.3
-
17
-
-
0036890022
-
Rapid divergence in expression between duplicate genes inferred from microarray data
-
Gu, Z., D. Nicolae, H. H. Lu, and W. H. Li. 2002. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18:609-613.
-
(2002)
Trends Genet.
, vol.18
, pp. 609-613
-
-
Gu, Z.1
Nicolae, D.2
Lu, H.H.3
Li, W.H.4
-
18
-
-
1642534172
-
A genomic timescale for the origin of eukaryotes
-
Hedges, S. B., H. Chen, S. Kumar, D. Y. Wang, A. S. Thompson, and H. Watanabe. 2001. A genomic timescale for the origin of eukaryotes. BMC Evol. Biol. 1:4.
-
(2001)
BMC Evol. Biol.
, vol.1
, pp. 4
-
-
Hedges, S.B.1
Chen, H.2
Kumar, S.3
Wang, D.Y.4
Thompson, A.S.5
Watanabe, H.6
-
20
-
-
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
-
21
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho, Y., A. Gruhler, A. Heilbut et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183.
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
-
22
-
-
0035999981
-
Making sense of microarray data distributions
-
Hoyle, D. C., M. Rattray, R. Jupp, and A. Brass. 2002. Making sense of microarray data distributions. Bioinformatics 18:576-584.
-
(2002)
Bioinformatics
, vol.18
, pp. 576-584
-
-
Hoyle, D.C.1
Rattray, M.2
Jupp, R.3
Brass, A.4
-
23
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong, H., S. P. Mason, A. L. Barabasi, and Z. N. Oltvai. 2001. Lethality and centrality in protein networks. Nature 411:41-42.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
24
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong, H., B. Tombor, R. Albert, Z. N. Oltvai, and A. L. Barabasi. 2000. The large-scale organization of metabolic networks. Nature 407:651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
25
-
-
0036078078
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
-
Jordan, I. K., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. 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
-
-
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. K., Y. I. Wolf, and E. V. Koonin. 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. 3:1.
-
(2003)
BMC Evol. Biol.
, vol.3
, pp. 1
-
-
Jordan, I.K.1
Wolf, Y.I.2
Koonin, E.V.3
-
27
-
-
0000732090
-
Evolution of protein molecules
-
H. N. Munro. ed. Academic, New York
-
Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. Munro. ed. Mammalian protein metabolism. Academic, New York.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
28
-
-
0037448540
-
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
-
Kamath, R. S., A. G. Fraser, Y. Dong et al. 2003. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231-237.
-
(2003)
Nature
, vol.421
, pp. 231-237
-
-
Kamath, R.S.1
Fraser, A.G.2
Dong, Y.3
-
29
-
-
0041718387
-
Birth and death of protein domains: A simple model of evolution explains power law behavior
-
Karev, G. P., Y. I. Wolf, A. Y. Rzhetsky, F. S. Berezovskaya, and E. V. Koonin. 2002. Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol. Biol. 2:18.
-
(2002)
BMC Evol. Biol.
, vol.2
, pp. 18
-
-
Karev, G.P.1
Wolf, Y.I.2
Rzhetsky, A.Y.3
Berezovskaya, F.S.4
Koonin, E.V.5
-
30
-
-
19344372220
-
A neutral model of transcriptome evolution
-
Khaitovich, P., G. Weiss, M. Lachmann, I. Hellman, W. Enard, B. Muetzel, U. Wiekner, W. Ansorge, and S. Paabo. 2004. A neutral model of transcriptome evolution. PLOS Biol. 2:0682-0689.
-
(2004)
PLOS Biol.
, vol.2
, pp. 0682-0689
-
-
Khaitovich, P.1
Weiss, G.2
Lachmann, M.3
Hellman, I.4
Enard, W.5
Muetzel, B.6
Wiekner, U.7
Ansorge, W.8
Paabo, S.9
-
31
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King, M. C., and A. C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
32
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
Koonin, E. V., N. D. Fedorova, J. D. Jackson et al. 2004. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5:R7.
-
(2004)
Genome Biol.
, vol.5
-
-
Koonin, E.V.1
Fedorova, N.D.2
Jackson, J.D.3
-
33
-
-
0037079014
-
The structure of the protein universe and genome evolution
-
Koonin, E. V., Y. I. Wolf, and G. P. Karev. 2002. The structure of the protein universe and genome evolution. Nature 420:218-223.
-
(2002)
Nature
, vol.420
, pp. 218-223
-
-
Koonin, E.V.1
Wolf, Y.I.2
Karev, G.P.3
-
34
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
Krylov, D. M., Y. I. Wolf, I. B. Rogozin, and E. V. Koonin. 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
-
35
-
-
0036021408
-
General statistics of stochastic process of gene expression in eukaryotic cells
-
Kuznetsov, V. A., G. D. Knott, and R. F. Bonner. 2002. General statistics of stochastic process of gene expression in eukaryotic cells. Genetics 161:1321-1332.
-
(2002)
Genetics
, vol.161
, pp. 1321-1332
-
-
Kuznetsov, V.A.1
Knott, G.D.2
Bonner, R.F.3
-
36
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander, E., S. L. M. Linton, B. Birren et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.1
Linton, S.L.M.2
Birren, B.3
-
37
-
-
9144264169
-
A map of the interactome network of the metazoan C. elegans
-
Li, S., C. M. Armstrong, N. Berlin et al. 2004. A map of the interactome network of the metazoan C. elegans. Science 303:540-543.
-
(2004)
Science
, vol.303
, pp. 540-543
-
-
Li, S.1
Armstrong, C.M.2
Berlin, N.3
-
38
-
-
0003421005
-
-
Sinauer Associates, Sunderland, Mass.
-
Li, W. H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
-
(1997)
Molecular Evolution
-
-
Li, W.H.1
-
39
-
-
0242713700
-
The dominance of the population by a selected few: Power-law behaviour applies to a wide variety of genomic properties
-
RESEARCH0040
-
Luscombe, N. M., J. Qian, Z. Zhang, T. Johnson, and M. Gerstein. 2002. The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol. 3:RESEARCH0040.
-
(2002)
Genome Biol.
, pp. 3
-
-
Luscombe, N.M.1
Qian, J.2
Zhang, Z.3
Johnson, T.4
Gerstein, M.5
-
40
-
-
0038486898
-
Divergence in the spatial pattern of gene expression between human duplicate genes
-
Makova, K. D., and W. H. Li. 2003. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 13:1638-1645.
-
(2003)
Genome Res.
, vol.13
, pp. 1638-1645
-
-
Makova, K.D.1
Li, W.H.2
-
41
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
-
(1986)
Mol. Biol. Evol.
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
42
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pal, 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
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
43
-
-
0037472928
-
Genomic function: Rate of evolution and gene dispensability
-
-. 2003. Genomic function: rate of evolution and gene dispensability. Nature 421:496-497.
-
(2003)
Nature
, vol.421
, pp. 496-497
-
-
-
44
-
-
0344738015
-
Systems biology: Tracing life's circuitry
-
Pennisi, E. 2003. Systems biology: tracing life's circuitry. Science 302:1646-1649.
-
(2003)
Science
, vol.302
, pp. 1646-1649
-
-
Pennisi, E.1
-
45
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz, E., A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabasi. 2002. Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
46
-
-
0034777716
-
Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome
-
Rzhetsky, A., and S. M. Gomez. 2001. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics 17:988-996.
-
(2001)
Bioinformatics
, vol.17
, pp. 988-996
-
-
Rzhetsky, A.1
Gomez, S.M.2
-
47
-
-
0037007048
-
Large-scale analysis of the human and mouse transcriptomes
-
Su, A. I., M. P. Cooke, K. A. Ching et al. 2002. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. USA 99:4465-4470.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4465-4470
-
-
Su, A.I.1
Cooke, M.P.2
Ching, K.A.3
-
49
-
-
1642287458
-
Universality and flexibility in gene expression from bacteria to human
-
Ueda, H. R., S. Hayshi, S. Matsuyama, T. Yomo, S. Hashimoto, S. A. Kay, J. B. Hogenesch, and M. Iino. 2004. Universality and flexibility in gene expression from bacteria to human. Proc. Natl. Acad. Sci. USA 101:3765-3769.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3765-3769
-
-
Ueda, H.R.1
Hayshi, S.2
Matsuyama, S.3
Yomo, T.4
Hashimoto, S.5
Kay, S.A.6
Hogenesch, J.B.7
Iino, M.8
-
50
-
-
0034612214
-
Decoupled evolution of coding region and mRNA expression patterns after gene duplication: Implications for the neutralist-selectionist debate
-
Wagner, A. 2000. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. USA 97:6579-6584.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 6579-6584
-
-
Wagner, A.1
-
51
-
-
0037423828
-
How the global structure of protein interaction networks evolves
-
-. 2003. How the global structure of protein interaction networks evolves. Proc. R. Soc. Loncd B Biol. Sci. 270:457-466.
-
(2003)
Proc. R. Soc. Loncd B Biol. Sci.
, vol.270
, pp. 457-466
-
-
-
52
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston, R. H. K. Lindblad-Toh, E. Birney et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston1
Lindblad-Toh, R.H.K.2
Birney, E.3
-
53
-
-
1842631448
-
Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control
-
Yanai, I., D. Graur, and R. Ophir. 2004. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS 8:15-24.
-
(2004)
OMICS
, vol.8
, pp. 15-24
-
-
Yanai, I.1
Graur, D.2
Ophir, R.3
-
54
-
-
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
-
55
-
-
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
-
56
-
-
1542286776
-
Mammalian housekeeping genes evolve more slowly than tissue-specific genes
-
Zhang, L., and W. H. Li. 2004. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol. Biol. Evol. 21:236-239.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 236-239
-
-
Zhang, L.1
Li, W.H.2
|