-
1
-
-
33745160404
-
Large-scale identification of protein-protein interaction of Escherichia coli K-12
-
Arifuzzaman, M. et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16, 686-691 (2006).
-
(2006)
Genome Res.
, vol.16
, pp. 686-691
-
-
Arifuzzaman, M.1
-
2
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
Butland, G. et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531-537 (2005).
-
(2005)
Nature
, vol.433
, pp. 531-537
-
-
Butland, G.1
-
3
-
-
66049143558
-
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins
-
Hu, P. et al. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7, e96 (2009).
-
(2009)
PLoS Biol.
, vol.7
-
-
Hu, P.1
-
4
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual, J.F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178 (2005).
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
-
5
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu, H. et al. High-quality binary protein interaction map of the yeast interactome network. Science 322, 104-110 (2008).
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
-
6
-
-
48249128882
-
The binary protein interactome of Treponema pallidum-the syphilis spirochete
-
Titz, B. et al. The binary protein interactome of Treponema pallidum-the syphilis spirochete. PLoS ONE 3, e2292 (2008).
-
(2008)
PLoS ONE
, vol.3
-
-
Titz, B.1
-
7
-
-
30844443758
-
Herpesviral protein networks and their interaction with the human proteome
-
Uetz, P. et al. Herpesviral protein networks and their interaction with the human proteome. Science 311, 239-242 (2006).
-
(2006)
Science
, vol.311
, pp. 239-242
-
-
Uetz, P.1
-
8
-
-
77955342525
-
The Escherichia coli K-12 ORFeome: A resource for comparative molecular microbiology
-
Rajagopala, S.V. et al. The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology. BMC Genomics 11, 470 (2010).
-
(2010)
BMC Genomics
, vol.11
, pp. 470
-
-
Rajagopala, S.V.1
-
9
-
-
80054732652
-
Analysis of protein-protein interactions using high-throughput yeast two-hybrid screens
-
Rajagopala, S.V. & Uetz, P. Analysis of protein-protein interactions using high-throughput yeast two-hybrid screens. Methods Mol. Biol. 781, 1-29 (2011).
-
(2011)
Methods Mol. Biol.
, vol.781
, pp. 1-29
-
-
Rajagopala, S.V.1
Uetz, P.2
-
10
-
-
48249112175
-
MPIDB: The microbial protein interaction database
-
Goll, J. et al. MPIDB: the microbial protein interaction database. Bioinformatics 24, 1743-1744 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 1743-1744
-
-
Goll, J.1
-
11
-
-
55749094206
-
MPI-LIT: A literature-curated dataset of microbial binary protein-protein interactions
-
Rajagopala, S.V. et al. MPI-LIT: a literature-curated dataset of microbial binary protein-protein interactions. Bioinformatics 24, 2622-2627 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 2622-2627
-
-
Rajagopala, S.V.1
-
12
-
-
58149242456
-
An experimentally derived confidence score for binary protein-protein interactions
-
Braun, P. et al. An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91-97 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 91-97
-
-
Braun, P.1
-
13
-
-
77956321519
-
Exhaustive benchmarking of the yeast two-hybrid system
-
Chen, Y.C., Rajagopala, S.V., Stellberger, T. & Uetz, P. Exhaustive benchmarking of the yeast two-hybrid system. Nat. Methods 7, 667-668 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 667-668
-
-
Chen, Y.C.1
Rajagopala, S.V.2
Stellberger, T.3
Uetz, P.4
-
14
-
-
1542345539
-
Increasing specificity in high-throughput yeast two-hybrid experiments
-
Vidalain, P.O., Boxem, M., Ge, H., Li, S. & Vidal, M. Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 32, 363-370 (2004).
-
(2004)
Methods
, vol.32
, pp. 363-370
-
-
Vidalain, P.O.1
Boxem, M.2
Ge, H.3
Li, S.4
Vidal, M.5
-
15
-
-
58149305794
-
An empirical framework for binary interactome mapping
-
Venkatesan, K. et al. An empirical framework for binary interactome mapping. Nat. Methods 6, 83-90 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 83-90
-
-
Venkatesan, K.1
-
16
-
-
20144372620
-
High-throughput mapping of a dynamic signaling network in mammalian cells
-
Barrios-Rodiles, M. et al. High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307, 1621-1625 (2005).
-
(2005)
Science
, vol.307
, pp. 1621-1625
-
-
Barrios-Rodiles, M.1
-
17
-
-
84872380683
-
Studying protein complexes by the yeast two-hybrid system
-
Rajagopala, S.V., Sikorski, P., Caufield, J.H., Tovchigrechko, A. & Uetz, P. Studying protein complexes by the yeast two-hybrid system. Methods 58, 392-399 (2012).
-
(2012)
Methods
, vol.58
, pp. 392-399
-
-
Rajagopala, S.V.1
Sikorski, P.2
Caufield, J.H.3
Tovchigrechko, A.4
Uetz, P.5
-
18
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
19
-
-
67749140118
-
Scale-free networks: A decade and beyond
-
Barabasi, A.L. Scale-free networks: a decade and beyond. Science 325, 412-413 (2009).
-
(2009)
Science
, vol.325
, pp. 412-413
-
-
Barabasi, A.L.1
-
20
-
-
34147217542
-
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map
-
Collins, S.R. et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446, 806-810 (2007).
-
(2007)
Nature
, vol.446
, pp. 806-810
-
-
Collins, S.R.1
-
21
-
-
34447294237
-
A new method to measure the semantic similarity of GO terms
-
Wang, J., Du, Z., Payattakool, R., Yu, P.S. & Chen, C.J. A new method to measure the semantic similarity of GO terms. Bioinformatics 23, 1274-1281 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 1274-1281
-
-
Wang, J.1
Du, Z.2
Payattakool, R.3
Yu, P.S.4
Chen, C.J.5
-
22
-
-
12144290243
-
Structure-based assembly of protein complexes in yeast
-
Aloy, P. et al. Structure-based assembly of protein complexes in yeast. Science 303, 2026-2029 (2004).
-
(2004)
Science
, vol.303
, pp. 2026-2029
-
-
Aloy, P.1
-
23
-
-
77955388349
-
Integrative structure modeling of macromolecular assemblies from proteomics data
-
Lasker, K. et al. Integrative structure modeling of macromolecular assemblies from proteomics data. Mol. Cell. Proteomics 9, 1689-1702 (2010).
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 1689-1702
-
-
Lasker, K.1
-
24
-
-
81755177857
-
Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways
-
Babu, M. et al. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 7, e1002377 (2011).
-
(2011)
PLoS Genet.
, vol.7
-
-
Babu, M.1
-
25
-
-
43249117094
-
Functional maps of protein complexes from quantitative genetic interaction data
-
Bandyopadhyay, S., Kelley, R., Krogan, N.J. & Ideker, T. Functional maps of protein complexes from quantitative genetic interaction data. PLOS Comput. Biol. 4, e1000065 (2008).
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Bandyopadhyay, S.1
Kelley, R.2
Krogan, N.J.3
Ideker, T.4
-
26
-
-
77953236579
-
Quantitative genetic interactions reveal biological modularity
-
Beltrao, P., Cagney, G. & Krogan, N.J. Quantitative genetic interactions reveal biological modularity. Cell 141, 739-745 (2010).
-
(2010)
Cell
, vol.141
, pp. 739-745
-
-
Beltrao, P.1
Cagney, G.2
Krogan, N.J.3
-
27
-
-
34249041230
-
Exploring genetic interactions and networks with yeast
-
Boone, C., Bussey, H. & Andrews, B.J. Exploring genetic interactions and networks with yeast. Nat. Rev. Genet. 8, 437-449 (2007).
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 437-449
-
-
Boone, C.1
Bussey, H.2
Andrews, B.J.3
-
28
-
-
75649111192
-
The genetic landscape of a cell
-
Costanzo, M. et al. The genetic landscape of a cell. Science 327, 425-431 (2010).
-
(2010)
Science
, vol.327
, pp. 425-431
-
-
Costanzo, M.1
-
29
-
-
50849098825
-
ESGA: E. Coli synthetic genetic array analysis
-
Butland, G. et al. eSGA: E. coli synthetic genetic array analysis. Nat. Methods 5, 789-795 (2008).
-
(2008)
Nat. Methods
, vol.5
, pp. 789-795
-
-
Butland, G.1
-
30
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
Brohee, S. & van Helden, J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 488
-
-
Brohee, S.1
Van Helden, J.2
-
31
-
-
85006068329
-
Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli
-
(in the press
-
Babu, M. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet. (in the press).
-
PLoS Genet
-
-
Babu, M.1
-
32
-
-
0019413905
-
E. Coli mutant pleiotropically defective in the export of secreted proteins
-
Oliver, D.B. & Beckwith, J. E. coli mutant pleiotropically defective in the export of secreted proteins. Cell 25, 765-772 (1981).
-
(1981)
Cell
, vol.25
, pp. 765-772
-
-
Oliver, D.B.1
Beckwith, J.2
-
33
-
-
34547556624
-
The protein network of bacterial motility
-
Rajagopala, S.V. et al. The protein network of bacterial motility. Mol. Syst. Biol. 3, 128 (2007).
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 128
-
-
Rajagopala, S.V.1
-
34
-
-
84872272432
-
Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness
-
Bershtein, S., Mu, W., Serohijos, A.W., Zhou, J. & Shakhnovich, E.I. Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. Mol. Cell 49, 133-144 (2013).
-
(2013)
Mol. Cell
, vol.49
, pp. 133-144
-
-
Bershtein, S.1
Mu, W.2
Serohijos, A.W.3
Zhou, J.4
Shakhnovich, E.I.5
-
35
-
-
73349095048
-
Systematic mapping of genetic interaction networks
-
Dixon, S.J., Costanzo, M., Baryshnikova, A., Andrews, B. & Boone, C. Systematic mapping of genetic interaction networks. Annu. Rev. Genet. 43, 601-625 (2009).
-
(2009)
Annu. Rev. Genet.
, vol.43
, pp. 601-625
-
-
Dixon, S.J.1
Costanzo, M.2
Baryshnikova, A.3
Andrews, B.4
Boone, C.5
-
36
-
-
78650431707
-
Regulation of peptidoglycan synthesis by outer-membrane proteins
-
Typas, A. et al. Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell 143, 1097-1109 (2010).
-
(2010)
Cell
, vol.143
, pp. 1097-1109
-
-
Typas, A.1
-
37
-
-
0035211290
-
Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or interologs
-
Matthews, L.R. et al. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 11, 2120-2126 (2001).
-
(2001)
Genome Res.
, vol.11
, pp. 2120-2126
-
-
Matthews, L.R.1
-
38
-
-
13844314048
-
Conserved patterns of protein interaction in multiple species
-
Sharan, R. et al. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102, 1974-1979 (2005).
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 1974-1979
-
-
Sharan, R.1
-
39
-
-
9144271294
-
Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks
-
Singleton, M.R., Dillingham, M.S., Gaudier, M., Kowalczykowski, S.C. & Wigley, D.B. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature 432, 187-193 (2004).
-
(2004)
Nature
, vol.432
, pp. 187-193
-
-
Singleton, M.R.1
Dillingham, M.S.2
Gaudier, M.3
Kowalczykowski, S.C.4
Wigley, D.B.5
-
40
-
-
79958858245
-
Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation
-
Cingolani, G. & Duncan, T.M. Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation. Nat. Struct. Mol. Biol. 18, 701-707 (2011).
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 701-707
-
-
Cingolani, G.1
Duncan, T.M.2
-
41
-
-
33847205020
-
Gateway-based destination vectors for functional analyses of bacterial ORFeomes: Application to the Min system in Brucella abortus
-
Hallez, R., Letesson, J.J., Vandenhaute, J. & De Bolle, X. Gateway-based destination vectors for functional analyses of bacterial ORFeomes: application to the Min system in Brucella abortus. Appl. Environ. Microbiol. 73, 1375-1379 (2007).
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 1375-1379
-
-
Hallez, R.1
Letesson, J.J.2
Vandenhaute, J.3
De Bolle, X.4
-
42
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin, A.C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
-
43
-
-
38549134505
-
Many Microbe Microarrays Database: Uniformly normalized Affymetrix compendia with structured experimental metadata
-
Faith, J.J. et al. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res. 36, D866-D870 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Faith, J.J.1
-
44
-
-
78650475398
-
Phenotypic landscape of a bacterial cell
-
Nichols, R.J. et al. Phenotypic landscape of a bacterial cell. Cell 144, 143-156 (2011).
-
(2011)
Cell
, vol.144
, pp. 143-156
-
-
Nichols, R.J.1
-
46
-
-
67849101838
-
CVTree update: A newly designed phylogenetic study platform using composition vectors and whole genomes
-
Xu, Z. & Hao, B. CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res. 37, W174-W178 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Xu, Z.1
Hao, B.2
-
47
-
-
84864489995
-
A web server for inferring validating and visualizing phylogenetic trees and networks
-
Alix, B., Boubacar, D.A. & Vladimir, M.T.-R.E.X. A web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res. 40, W573-W579 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Alix, B.1
Boubacar, D.A.2
Vladimir, M.T.-R.E.X.3
-
48
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm, M., Storm, C.E. & Sonnhammer, E.L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041-1052 (2001).
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
|