-
1
-
-
0032489015
-
The cell as a collection of protein machines: Preparing the next generation of molecular biologists
-
Alberts,B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists, Cell, 92 291-294.
-
(1998)
Cell
, vol.92
, pp. 291-294
-
-
Alberts, B.1
-
2
-
-
0033954256
-
The protein data bank
-
Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res. 28, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
3
-
-
0035023445
-
Predicting protein-protein interactions from primary structure
-
Bock,J.R. and Gough,D.A. (2001) Predicting protein-protein interactions from primary structure. Bioinformatics, 17, 455-460.
-
(2001)
Bioinformatics
, vol.17
, pp. 455-460
-
-
Bock, J.R.1
Gough, D.A.2
-
4
-
-
0037249217
-
Whole proteome interaction mining
-
Bock,J.R. and Gough,D.A. (2003) Whole proteome interaction mining. Bioinformatics, 19 125-135.
-
(2003)
Bioinformatics
, vol.19
, pp. 125-135
-
-
Bock, J.R.1
Gough, D.A.2
-
5
-
-
42749102104
-
Loop series for discrete statistical models on graphs
-
doi: 10.1088/1742-5468/2006/06/P06009
-
Chertkov,M. and Chernyak,V.Y. (2006) Loop series for discrete statistical models on graphs J. Stat. Mech. Theory Exper., doi: 10.1088/1742-5468/2006/06/P06009
-
(2006)
J. Stat. Mech. Theory Exper
-
-
Chertkov, M.1
Chernyak, V.Y.2
-
6
-
-
0036799752
-
Inferring domain-domain interactions from protein-protein interactions
-
Deng,M. et al. (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res., 12, 1540-1548.
-
(2002)
Genome Res
, vol.12
, pp. 1540-1548
-
-
Deng, M.1
-
7
-
-
0034660322
-
Protein function in the post-genomic era
-
Eisenberg,D. et al. (2000) Protein function in the post-genomic era. Nature, 405, 823-826.
-
(2000)
Nature
, vol.405
, pp. 823-826
-
-
Eisenberg, D.1
-
8
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright,A.J. et al. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
-
9
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn,R.D. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Finn, R.D.1
-
10
-
-
33847172327
-
Clustering by passing messages between data points
-
Frey,B.J. and Dueck,D. (2007) Clustering by passing messages between data points. Science, 315, 972.
-
(2007)
Science
, vol.315
, pp. 972
-
-
Frey, B.J.1
Dueck, D.2
-
11
-
-
84898964205
-
A revolution: Belief propagation in graphs with cycles
-
Jordan,M. et al, Eds, MIT Press, Cambridge, MA, USA, pp
-
Frey,B.J. and Mackay,D.J.C. (1997) A revolution: Belief propagation in graphs with cycles. In Jordan,M. et al. (Eds) Advance in Neural Information Processing Systems, Vol. 10. MIT Press, Cambridge, MA, USA, pp. 479-485.
-
(1997)
Advance in Neural Information Processing Systems
, vol.10
, pp. 479-485
-
-
Frey, B.J.1
Mackay, D.J.C.2
-
13
-
-
0034084865
-
Who's your neighbor? New computational approaches for functional genomics
-
Galperin,M.Y. and Koonin,E.V. (2000) Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18, 609-613.
-
(2000)
Nat. Biotechnol
, vol.18
, pp. 609-613
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
14
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin,A.C. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
-
15
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin,A.C. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery.Nature, 440, 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
-
16
-
-
0034595516
-
Co-evolution of Proteins with their Interaction Partners
-
Goh,C. et al. (2000) Co-evolution of Proteins with their Interaction Partners. J. Mol. Biol., 299, 283-293.
-
(2000)
J. Mol. Biol
, vol.299
, pp. 283-293
-
-
Goh, C.1
-
17
-
-
0036435908
-
Co-evolutionary analysis reveals Insights into Protein-Protein Interactions
-
Goh,C. et al. (2002) Co-evolutionary analysis reveals Insights into Protein-Protein Interactions. J. Mol. Biol., 324, 177-192.
-
(2002)
J. Mol. Biol
, vol.324
, pp. 177-192
-
-
Goh, C.1
-
18
-
-
0035798406
-
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
-
Gough,J. et al. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.
-
(2001)
J. Mol. Biol
, vol.313
, pp. 903-919
-
-
Gough, J.1
-
19
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho,Y. 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
-
20
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito,T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4569-4574
-
-
Ito, T.1
-
21
-
-
0142052944
-
-
A Bayesian networks approach for predicting protein-protein interactions from genomic data
-
Jansen,R. et al. (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. science 302, 449-453.
-
(2003)
science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
-
22
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan,N.J. 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
-
23
-
-
33745327144
-
An integrated approach to the prediction of domain-domain interactions
-
Lee,H. et al. (2006) An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics., 7, 269.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 269
-
-
Lee, H.1
-
24
-
-
43549094730
-
Improving domain-based protein interaction prediction using biologically-significant negative dataset
-
Li,X. et al. (2006) Improving domain-based protein interaction prediction using biologically-significant negative dataset. Int. J. Data Min. Bioinform., 1, 138-149.
-
(2006)
Int. J. Data Min. Bioinform
, vol.1
, pp. 138-149
-
-
Li, X.1
-
25
-
-
9144264169
-
A map of the interactome network of the Metazoan C. elegans
-
Li,S. 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
-
26
-
-
0004272772
-
-
Cambridge University Press, Cambridge, UK
-
MacKay,D.J.C. (2003) Information Theory, Inference, and Learning Algorithms. Cambridge University Press, Cambridge, UK.
-
(2003)
Information Theory, Inference, and Learning Algorithms
-
-
MacKay, D.J.C.1
-
27
-
-
0347125294
-
The SUPERFAMILY database in 2004: Additions and improvements
-
Madera,M. et al. (2004) The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res., 32, D235-D239.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Madera, M.1
-
28
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte,E.M. et al. (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
-
29
-
-
0036081347
-
MIPS: A database for genomes and protein sequences
-
Mewes,H.W. et al. (2002) MIPS: A database for genomes and protein sequences. Nucleic Acids Res., 30, 31-34.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 31-34
-
-
Mewes, H.W.1
-
30
-
-
33847138173
-
Computer Science - where are the exemplars?
-
Mezard,M. (2007) Computer Science - where are the exemplars? Science 315, 949-951.
-
(2007)
Science
, vol.315
, pp. 949-951
-
-
Mezard, M.1
-
31
-
-
0037008520
-
Analytic and algorithmic solution of random satisfiability problems
-
Mezard,M. et al (2002) Analytic and algorithmic solution of random satisfiability problems. Science, 297, 812.
-
(2002)
Science
, vol.297
, pp. 812
-
-
Mezard, M.1
-
33
-
-
38549154992
-
DOMINE: A database of protein domain interactions
-
Database issue, D656-D661
-
Raghavachari,B. et al. (2008) DOMINE: A database of protein domain interactions. Nucleic Acids Res., 36 (Database issue), D656-D661.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Raghavachari, B.1
-
34
-
-
23444452564
-
Probabilistic model of the human protein-protein interaction network
-
Rhodes,D.R. et al. (2005) Probabilistic model of the human protein-protein interaction network. Nat. Biotechnol., 23, 951-959.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 951-959
-
-
Rhodes, D.R.1
-
35
-
-
34548084807
-
Inferring protein domain interactions from databases of interacting proteins
-
Riley,R. et al. (2005) Inferring protein domain interactions from databases of interacting proteins.Genome Biol., 6, R89.
-
(2005)
Genome Biol
, vol.6
-
-
Riley, R.1
-
36
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual,J.F. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
-
37
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Database Issue, D449-D451
-
Salwinski,L. et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, (Database Issue), D449-D451.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Salwinski, L.1
-
38
-
-
34047202181
-
Deciphering protein - protein interactions. Part-I: Experimental techniques and databases
-
Shoemaker,B.A. and Panchenko,A.R. (2007a) Deciphering protein - protein interactions. Part-I: Experimental techniques and databases. PLoS Comput. Biol., 3, e42.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Shoemaker, B.A.1
Panchenko, A.R.2
-
39
-
-
34247586171
-
Deciphering protein - protein interactions. Part-II: Computational methods to predict protein and domain interaction partners
-
Shoemaker,B.A. and Panchenko,A.R. (2007b) Deciphering protein - protein interactions. Part-II: Computational methods to predict protein and domain interaction partners. PLoS Comput. Biol., 3, e43.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Shoemaker, B.A.1
Panchenko, A.R.2
-
40
-
-
0035943340
-
Correlated sequence-signatures as markers of protein-protein interaction
-
Sprinzak,E. and Margalit,H. (2001) Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol., 311, 681-692.
-
(2001)
J. Mol. Biol
, vol.311
, pp. 681-692
-
-
Sprinzak, E.1
Margalit, H.2
-
41
-
-
13444257903
-
3did: Interacting protein domains of known three-dimensional structure
-
Stein,A. et al. (2005) 3did: Interacting protein domains of known three-dimensional structure. Nucleic Acids Res., 33, D413-D417.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Stein, A.1
-
42
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
-
43
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
Valencia,A. and Pazos,F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12, 368-373.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
44
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering,C. et al. (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
-
45
-
-
0036088133
-
DIP: The database of interacting proteins. A research tool for studying cellular networks of protein interactions
-
Xenarios,I. et al. (2002) DIP: The database of interacting proteins. A research tool for studying cellular networks of protein interactions. Nucleic Acid Res., 30, 303-305.
-
(2002)
Nucleic Acid Res
, vol.30
, pp. 303-305
-
-
Xenarios, I.1
-
46
-
-
19544389868
-
Protein network inference from multiple genomic data: A supervised approach
-
Yamanishi,Y. et al. (2004) Protein network inference from multiple genomic data: A supervised approach. Bioinformatics, 20 (Suppl.1), i363-i370.
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL.1
-
-
Yamanishi, Y.1
-
47
-
-
23744513375
-
-
Yedidia,J.S. et al. (2005) Constructing free-energy approximations and generalized belief propagation algorithms. IEEE Transactions on Information Theory, ISSN; 0018-9448, 51, 2282-2312.
-
Yedidia,J.S. et al. (2005) Constructing free-energy approximations and generalized belief propagation algorithms. IEEE Transactions on Information Theory, ISSN; 0018-9448, 51, 2282-2312.
-
-
-
-
48
-
-
0004031805
-
Understanding belief propagation and its generalizations
-
Technical Report, TR-2001-22. Mitsubishi Electric Research Labratories, Cambridge, Massachusetts
-
Yedidia,J.S. et al. (2002) Understanding belief propagation and its generalizations. Technical Report, TR-2001-22. Mitsubishi Electric Research Labratories, Cambridge, Massachusetts.
-
(2002)
-
-
Yedidia, J.S.1
|