-
1
-
-
0033150836
-
Protein families in multicellular organisms
-
Copley,R.R., Schultz,J., Ponting,C.P. and Bork,P. (1999) Protein families in multicellular organisms. Curr. Opin. Struct. Biol. 9, 408-415.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 408-415
-
-
Copley, R.R.1
Schultz, J.2
Ponting, C.P.3
Bork, P.4
-
2
-
-
0036338127
-
Alternative splicing and genome complexity
-
Brett,D., Pospisil,H., Valcarcel,J., Reich,J. and Bork,P. (2002) Alternative splicing and genome complexity. Nature Genet., 30, 29-30.
-
(2002)
Nature Genet.
, vol.30
, pp. 29-30
-
-
Brett, D.1
Pospisil, H.2
Valcarcel, J.3
Reich, J.4
Bork, P.5
-
3
-
-
0037819447
-
Transcription regulation and animal diversity
-
Levine,M. and Tjian,R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
-
(2003)
Nature
, vol.424
, pp. 147-151
-
-
Levine, M.1
Tjian, R.2
-
4
-
-
0036772367
-
Conservation of gene co-regulation in prokaryotes and eukaryotes
-
discussion 410
-
Teichmann,S.A. and Babu,M.M. (2002) Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol., 20, 407-410; discussion 410.
-
(2002)
Trends Biotechnol.
, vol.20
, pp. 407-410
-
-
Teichmann, S.A.1
Babu, M.M.2
-
5
-
-
19344374050
-
Similarities and differences in genome-wide expression data of six organisms
-
Bergmann,S., Ihmels,J. and Barkai,N. (2004) Similarities and differences in genome-wide expression data of six organisms. PLoS Biol., 2, E9.
-
(2004)
PLoS Biol.
, vol.2
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
6
-
-
0037464547
-
Genetics and the making of Homo sapiens
-
Carroll,S.B. (2003) Genetics and the making of Homo sapiens. Nature, 422, 849-857.
-
(2003)
Nature
, vol.422
, pp. 849-857
-
-
Carroll, S.B.1
-
7
-
-
0034943378
-
The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
-
Wagner,A. (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol., 18, 1283-1292.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1283-1292
-
-
Wagner, A.1
-
8
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
Wray,G.A., Hahn,M.W., Abouheif,E., Balhoff,J.P., Pizer,M., Rockman,M.V. and Romano,L.A. (2003) The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol., 20, 1377-1419.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
Rockman, M.V.6
Romano, L.A.7
-
9
-
-
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
-
10
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee,T.I., Rinaldi,N.J., Robert,F., Odom,D.T., Bar-Joseph,Z., Gerber,G.K., Hannett,N.M., Harbison,C.T., Thompson,C.M., Simon,I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
-
11
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes,T.R., Marton,M.J., Jones,A.R., Roberts,C.J., Stoughton,R., Armour,C.D., Bennett,H.A., Coffey,E., Dai,H., He,Y.D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
-
12
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
13
-
-
0037452966
-
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms
-
Alter,O., Brown,P.O. and Botstein,D. (2003) Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc. Natl Acad. Sci. USA, 100, 3351-3356.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3351-3356
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
14
-
-
1642287458
-
Universality and flexibility in gene expression from bacteria to human
-
Ueda,H.R., Hayashi,S., Matsuyama,S., Yomo,T., Hashimoto,S., Kay,S.A., Hogenesch,J.B. and Iino,M. (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
Hayashi, S.2
Matsuyama, S.3
Yomo, T.4
Hashimoto, S.5
Kay, S.A.6
Hogenesch, J.B.7
Iino, M.8
-
15
-
-
0842267618
-
Comparing genomic expression patterns across species identifies shared transcriptional profile in aging
-
McCarroll,S.A., Murphy,C.T., Zou,S., Pletcher,S.D., Chin,C.S., Jan,Y.N., Kenyon,C., Bargmann,C.I. and Li,H. (2004) Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nature Genet., 36, 197-204.
-
(2004)
Nature Genet.
, vol.36
, pp. 197-204
-
-
McCarroll, S.A.1
Murphy, C.T.2
Zou, S.3
Pletcher, S.D.4
Chin, C.S.5
Jan, Y.N.6
Kenyon, C.7
Bargmann, C.I.8
Li, H.9
-
16
-
-
0037407924
-
Predicting gene function by conserved co-expression
-
van Noort,V., Snel,B. and Huynen,M.A. (2003) Predicting gene function by conserved co-expression. Trends Genet., 19, 238-242.
-
(2003)
Trends Genet.
, vol.19
, pp. 238-242
-
-
van Noort, V.1
Snel, B.2
Huynen, M.A.3
-
17
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart,J.M., Segal,E., Koller,D. and Kim,S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
18
-
-
0042706147
-
Genomic analysis of gene expression relationships in transcriptional regulatory networks
-
Yu,H., Luscombe,N.M., Qian,J. and Gerstein,M. (2003) Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet., 19, 422-427.
-
(2003)
Trends Genet.
, vol.19
, pp. 422-427
-
-
Yu, H.1
Luscombe, N.M.2
Qian, J.3
Gerstein, M.4
-
19
-
-
0036889686
-
Orthology, paralogy and proposed classification for paralog subtypes
-
Sonnhammer,E.L. and Koonin,E.V. (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet., 18, 619-620.
-
(2002)
Trends Genet.
, vol.18
, pp. 619-620
-
-
Sonnhammer, E.L.1
Koonin, E.V.2
-
20
-
-
9144233545
-
The EMBL Nucleotide Sequence Database
-
(Database issue)
-
Kulikova,T., Aldebert,P., Althorpe,N., Baker,W., Bates,K., Browne,P., van den Broek,A., Cochrane,G., Duggan,K., Eberhardt,R. et al. (2004) The EMBL Nucleotide Sequence Database. Nucleic Acids Res., 32 (Database issue), D27-D30.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kulikova, T.1
Aldebert, P.2
Althorpe, N.3
Baker, W.4
Bates, K.5
Browne, P.6
van den Broek, A.7
Cochrane, G.8
Duggan, K.9
Eberhardt, R.10
-
21
-
-
0346494826
-
WormBase: A multi-species resource for nematode biology and genomics
-
(Database issue)
-
Harris,T.W., Chen,N., Cunningham,F., Tello-Ruiz,M., Antoshechkin,I., Bastiani,C., Bieri,T., Blasiar,D., Bradnam,K., Chan,J. et al. (2004) WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res., 32 (Database issue), D411-D417.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Harris, T.W.1
Chen, N.2
Cunningham, F.3
Tello-Ruiz, M.4
Antoshechkin, I.5
Bastiani, C.6
Bieri, T.7
Blasiar, D.8
Bradnam, K.9
Chan, J.10
-
22
-
-
0032919364
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Ogata,H., Goto,S., Sato,K., Fujibuchi,W., Bono,H. and Kanehisa,M. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res., 27, 29-34.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
23
-
-
0042266921
-
Reconstruction of the proto-mitochondrial metabolism
-
Gabaldon,T. and Huynen,M.A. (2003) Reconstruction of the proto-mitochondrial metabolism. Science, 301, 609.
-
(2003)
Science
, vol.301
, pp. 609
-
-
Gabaldon, T.1
Huynen, M.A.2
-
24
-
-
0035860551
-
A gene expression map for Caenorhabditis elegans
-
Kim,S.K., Lund,J., Kiraly,M., Duke,K., Jiang,M., Stuart,J.M., Eizinger,A., Wylie,B.N. and Davidson,G.S. (2001) A gene expression map for Caenorhabditis elegans. Science, 293, 2087-2092.
-
(2001)
Science
, vol.293
, pp. 2087-2092
-
-
Kim, S.K.1
Lund, J.2
Kiraly, M.3
Duke, K.4
Jiang, M.5
Stuart, J.M.6
Eizinger, A.7
Wylie, B.N.8
Davidson, G.S.9
-
25
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen,M.B., Spellman,P.T., Brown,P.O. and Botstein,D. (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
-
26
-
-
0033058895
-
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes
-
Itoh,T., Takemoto,K., Mori,H. and Gojobori,T. (1999) Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol., 16 332-346.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 332-346
-
-
Itoh, T.1
Takemoto, K.2
Mori, H.3
Gojobori, T.4
-
27
-
-
0035162782
-
RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12
-
Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., Millan-Zarate,D., Diaz-Peredo,E., Sanchez-Solano,F., Perez-Rueda,E., Bonavides-Martinez,C. and Collado-Vides,J. (2001) RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res., 29, 72-74.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 72-74
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Millan-Zarate, D.4
Diaz-Peredo, E.5
Sanchez-Solano, F.6
Perez-Rueda, E.7
Bonavides-Martinez, C.8
Collado-Vides, J.9
-
28
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
-
29
-
-
0037252718
-
The Proteome Analysis database: A tool for the in silico analysis of whole proteomes
-
Pruess,M., Fleischmann,W., Kanapin,A., Karavidopoulou,Y., Kersey,P., Kriventseva,E., Mittard,V., Mulder,N., Phan,I., Servant,F. et al. (2003) The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res., 31 414-417.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 414-417
-
-
Pruess, M.1
Fleischmann, W.2
Kanapin, A.3
Karavidopoulou, Y.4
Kersey, P.5
Kriventseva, E.6
Mittard, V.7
Mulder, N.8
Phan, I.9
Servant, F.10
-
30
-
-
0032861774
-
SCPD: A promoter database of the yeast Saccharomyces cerevisiae
-
Zhu,J. and Zhang,M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.
-
(1999)
Bioinformatics
, vol.15
, pp. 607-611
-
-
Zhu, J.1
Zhang, M.Q.2
-
31
-
-
0036716752
-
Adaptive evolution after gene duplication
-
Hughes,A.L. (2002) Adaptive evolution after gene duplication. Trends Genet., 18, 433-434.
-
(2002)
Trends Genet.
, vol.18
, pp. 433-434
-
-
Hughes, A.L.1
-
32
-
-
0034669669
-
Predicting regulons and their cis-regulatory motifs by comparative genomics
-
Manson McGuire,A. and Church,G.M. (2000) Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res., 28, 4523-4530.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4523-4530
-
-
Manson McGuire, A.1
Church, G.M.2
-
33
-
-
0030210340
-
Gene order is not conserved in bacterial evolution
-
Mushegian,A.R. and Koonin,E.V. (1996) Gene order is not conserved in bacterial evolution. Trends Genet., 12, 289-290.
-
(1996)
Trends Genet.
, vol.12
, pp. 289-290
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
34
-
-
0031024670
-
Conserved clusters of functionally related genes in two bacterial genomes
-
Tamames,J., Casari,G., Ouzounis,C. and Valencia,A. (1997) Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol., 44, 66-73.
-
(1997)
J. Mol. Evol.
, vol.44
, pp. 66-73
-
-
Tamames, J.1
Casari, G.2
Ouzounis, C.3
Valencia, A.4
-
36
-
-
0031035094
-
Genome plasticity as a paradigm of eubacteria evolution
-
Watanabe,H., Mori,H., Itoh,T. and Gojobori,T. (1997) Genome plasticity as a paradigm of eubacteria evolution. J. Mol. Evol., 44 (Suppl. 1), S57-S64.
-
(1997)
J. Mol. Evol.
, vol.44
, Issue.SUPPL. 1
-
-
Watanabe, H.1
Mori, H.2
Itoh, T.3
Gojobori, T.4
-
37
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
38
-
-
0002269482
-
Use of contiguity on the chromosome to predict functional coupling
-
Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1998) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol., 1, 0009.
-
(1998)
Silico Biol.
, vol.1
, pp. 0009
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
39
-
-
0033593549
-
Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi
-
Wang,D.Y., Kumar,S. and Hedges,S.B. (1999) Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. R. Soc. Lond., B. Biol. Sci., 266, 163-171.
-
(1999)
Proc. R. Soc. Lond. B. Biol. Sci.
, vol.266
, pp. 163-171
-
-
Wang, D.Y.1
Kumar, S.2
Hedges, S.B.3
-
40
-
-
1542286745
-
Quantifying modularity in the evolution of biomolecular systems
-
Snel,B. and Huynen,M.A. (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res., 14, 391-397.
-
(2004)
Genome Res.
, vol.14
, pp. 391-397
-
-
Snel, B.1
Huynen, M.A.2
|