-
1
-
-
33745160404
-
Large-scale identification of protein-protein interaction of Escherichia coli K-12
-
Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.C. et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res., 16, 686-691.
-
(2006)
Genome Res
, vol.16
, pp. 686-691
-
-
Arifuzzaman, M.1
Maeda, M.2
Itoh, A.3
Nishikata, K.4
Takita, C.5
Saito, R.6
Ara, T.7
Nakahigashi, K.8
Huang, H.C.9
-
2
-
-
4644231028
-
Prolinks: A database of protein functional linkages derived from coevolution
-
Bowers, P.M., Pellegrini, M., Thompson, M.J., Fierro, J., Yeates, T.O. and Eisenberg, D. (2004) Prolinks: A database of protein functional linkages derived from coevolution. Genome Biol., 5, R35.
-
(2004)
Genome Biol
, vol.5
-
-
Bowers, P.M.1
Pellegrini, M.2
Thompson, M.J.3
Fierro, J.4
Yeates, T.O.5
Eisenberg, D.6
-
3
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Eschcrichia coli
-
Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B. et al. (2005) Interaction network containing conserved and essential protein complexes in Eschcrichia coli. Nature, 433, 531-537.
-
(2005)
Nature
, vol.433
, pp. 531-537
-
-
Butland, G.1
Peregrin-Alvarez, J.M.2
Li, J.3
Yang, W.4
Yang, X.5
Canadien, V.6
Starostine, A.7
Richards, D.8
Beattie, B.9
-
4
-
-
33846086800
-
recent developments in the integration and prediction of protein interactions
-
STRING 7
-
von Mering, C., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B. and Bork, P. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res., 35, D358-362.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
von Mering, C.1
Jensen, L.J.2
Kuhn, M.3
Chaffron, S.4
Doerks, T.5
Kruger, B.6
Snel, B.7
Bork, P.8
-
5
-
-
13444262374
-
EcoCye: A comprehensive database resource for Escherichia coli
-
Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., Peralta-Gil, M. and Karp, P.D. (2005) EcoCye: A comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33, D334-D337.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
Paulsen, I.T.6
Peralta-Gil, M.7
Karp, P.D.8
-
6
-
-
31544443526
-
Escherichia coli K-12: A cooperatively developed annotation snapshot-2005
-
Riley, M., Abe, T., Arnaud, M.B., Berlyn, M.K., Blattner, F.R., Chaudhuri, R.R., Glasner, J.D., Horiuchi, T., Keseler, I.M. et al. (2006) Escherichia coli K-12: A cooperatively developed annotation snapshot-2005. Nucleic Acids Res., 34, 1-9.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1-9
-
-
Riley, M.1
Abe, T.2
Arnaud, M.B.3
Berlyn, M.K.4
Blattner, F.R.5
Chaudhuri, R.R.6
Glasner, J.D.7
Horiuchi, T.8
Keseler, I.M.9
-
7
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith, J.J., Hayete, B., Thaden, J.T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J.J. and Gardner, T.S. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol., 5, e8.
-
(2007)
PLoS Biol
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
8
-
-
34548440667
-
Genes under positive selection in Escherichia coli
-
Petersen, L., Bollback, J.P., Dimmic, M., Hubisz, M. and Nielsen, R. (2007) Genes under positive selection in Escherichia coli. Genome Res., 17, 1336-1343.
-
(2007)
Genome Res
, vol.17
, pp. 1336-1343
-
-
Petersen, L.1
Bollback, J.P.2
Dimmic, M.3
Hubisz, M.4
Nielsen, R.5
-
9
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark, C., Breitkreutz, B.J., Reguly, T., Boucher, L., Breitkreutz, A. and Tyers, M. (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res., 34, D535-539.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
10
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U. and Eisenberg, D. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, D449-451.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
11
-
-
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
-
12
-
-
27544448536
-
Implementing the iHOP concept for navigation of biomedical literature
-
Hoffmann, R. and Valencia, A. (2005) Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics, 21 Suppl. 2), ii252-ii258.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
-
-
Hoffmann, R.1
Valencia, A.2
-
13
-
-
3042569597
-
Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs
-
Yu, H., Luscombe, N.M., Lu, H.X., Zhu, X., Xia, Y., Han, J.D., Bertin, N., Chung, S., Vidal, M. et al. (2004) Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs. Genome Res., 14, 1107-1118.
-
(2004)
Genome Res
, vol.14
, pp. 1107-1118
-
-
Yu, H.1
Luscombe, N.M.2
Lu, H.X.3
Zhu, X.4
Xia, Y.5
Han, J.D.6
Bertin, N.7
Chung, S.8
Vidal, M.9
-
14
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
Lee, I., Date, S.V., Adai, A.T. and Marcotte, E.M. (2004) A probabilistic functional network of yeast genes. Science, 356 1555-1558.
-
(2004)
Science
, vol.356
, pp. 1555-1558
-
-
Lee, I.1
Date, S.V.2
Adai, A.T.3
Marcotte, E.M.4
-
15
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M. and Hirakawa, M. (2006) From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res., 34, D354-D357.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
Katayama, T.7
Araki, M.8
Hirakawa, M.9
-
16
-
-
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. 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
-
17
-
-
33644875286
-
The Gene Ontology (GO) project in 2006
-
Gene Ontology Consortium
-
Gene Ontology Consortium. (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res., 34, D322-D326.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
-
18
-
-
34147121646
-
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
-
Collins, S.R., Kemmeren, P., Zhao, X.C., Greenblatt, J.F., Spencer, F., Holstege, F.C., Weissman, J.S. and Krogar, N.J., (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell Proteomics; 6, 439-450.
-
(2007)
Mol. Cell Proteomics
, vol.6
, pp. 439-450
-
-
Collins, S.R.1
Kemmeren, P.2
Zhao, X.C.3
Greenblatt, J.F.4
Spencer, F.5
Holstege, F.C.6
Weissman, J.S.7
Krogar, N.J.8
-
19
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
-
20
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D. and Yeates, T.O. (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.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
21
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O. and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
22
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215 403-410.
-
(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
-
23
-
-
0035843145
-
The protein-protein interaction map of Helicobacter pylori
-
Rain, J.C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J. et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-215.
-
(2001)
Nature
, vol.409
, pp. 211-215
-
-
Rain, J.C.1
Selig, L.2
De Reuse, H.3
Battaglia, V.4
Reverdy, C.5
Simon, S.6
Lenzen, G.7
Petel, F.8
Wojcik, J.9
-
24
-
-
38549161592
-
A proteome-wide protein interaction map for Campylobacter jejuni
-
Parrish, J.R., Yu, J., Liu, G., Hines, J.A., Chan, J.E., Mangiola, B.A., Zhang, H., Pacifico, S., Fotouhi, F. et al. (2007) A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol., 8, R130.
-
(2007)
Genome Biol
, vol.8
-
-
Parrish, J.R.1
Yu, J.2
Liu, G.3
Hines, J.A.4
Chan, J.E.5
Mangiola, B.A.6
Zhang, H.7
Pacifico, S.8
Fotouhi, F.9
-
25
-
-
33748672677
-
GenePro: A Cytoscape plug-in for advanced visualization and analysis of interaction networks
-
Vlasblom, J., Wu, S., Pu, S., Superina, M., Liu, G., Orsi, C. and Wodak, S.J. (2006) GenePro: A Cytoscape plug-in for advanced visualization and analysis of interaction networks. Bioinformatics, 22, 2178-2179.
-
(2006)
Bioinformatics
, vol.22
, pp. 2178-2179
-
-
Vlasblom, J.1
Wu, S.2
Pu, S.3
Superina, M.4
Liu, G.5
Orsi, C.6
Wodak, S.J.7
-
26
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
|