-
1
-
-
0036013593
-
Statistical mechanics of complex networks
-
Albert, R. and Barabási, A.-L. (2002) Statistical mechanics of complex networks. Rev. Modern Phys., 74, 47-97.
-
(2002)
Rev. Modern Phys.
, vol.74
, pp. 47-97
-
-
Albert, R.1
Barabási, A.-L.2
-
2
-
-
84975860562
-
Biomolecular network motif counting and discovery by color coding
-
Alon, N. et al. (2008) Biomolecular network motif counting and discovery by color coding. Bioinformatics, 24, i241-i249.
-
(2008)
Bioinformatics
, vol.24
-
-
Alon, N.1
-
3
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
Ashburner, M. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
4
-
-
0036789265
-
Analyzing yeast protein-protein interaction data obtained from different sources
-
Bader, G. and Hogue, C. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol., 20, 991-997.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 991-997
-
-
Bader, G.1
Hogue, C.2
-
5
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabási, A.-L. and Albert, R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabási, A.-L.1
Albert, R.2
-
6
-
-
33750991092
-
The degree distribution of the generalized duplication model
-
Bebek, G. et al. (2006) The degree distribution of the generalized duplication model. Theor. Comput. Sci., 369, 239-249.
-
(2006)
Theor. Comput. Sci.
, vol.369
, pp. 239-249
-
-
Bebek, G.1
-
7
-
-
0742275434
-
Mathematical results on scale-free random graphs
-
Bornholdt, S. and Schuster, H.G. (eds) Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG
-
Bollobás, B. and Riordan, O.M. (2005) Mathematical results on scale-free random graphs. In Bornholdt, S. and Schuster, H.G. (eds) Handbook of Graphs and Networks: From the Genome to the Internet, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG.
-
(2005)
Handbook of Graphs and Networks: From the Genome to the Internet
-
-
Bollobás, B.1
Riordan, O.M.2
-
8
-
-
0038074373
-
Topological structure analysis of the protein-protein interaction network in budding yeast
-
Bu, D. et al. (2003) Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res., 31, 2443-2450.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 2443-2450
-
-
Bu, D.1
-
9
-
-
61949235526
-
Dense graphlet statistics of protein interaction and random networks
-
Colak, R. et al. (2009) Dense graphlet statistics of protein interaction and random networks. In 14th Pac. Symp. Biocomput., 14, 178-189.
-
(2009)
14th Pac. Symp. Biocomput.
, vol.14
, pp. 178-189
-
-
Colak, R.1
-
10
-
-
34547533699
-
Emergence of tempered preferential attachment from optimization
-
D'Souza, R.M. et al. (2007) Emergence of tempered preferential attachment from optimization. Proc. Natl Acad. Sci. USA, 104, 6112-6117.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 6112-6117
-
-
D'Souza, R.M.1
-
11
-
-
31044448435
-
A simple physical model for scaling in protein-protein interaction networks
-
Deeds, E.J. et al. (2006) A simple physical model for scaling in protein-protein interaction networks. Proc. Natl Acad. Sci. USA, 103, 311-316.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 311-316
-
-
Deeds, E.J.1
-
14
-
-
33644617753
-
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
-
Gandhi, T. et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet., 38, 285-293.
-
(2006)
Nat. Genet.
, vol.38
, pp. 285-293
-
-
Gandhi, T.1
-
15
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A.P. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
-
(2000)
Mol. Biol. Cell.
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
-
16
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin, A. 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.1
-
17
-
-
33644878150
-
MPact: the MIPS protein interaction resource on yeast
-
Guldener, U. et al. (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res., 34, D436-D441.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Guldener, U.1
-
18
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han, J. et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.1
-
19
-
-
34547558890
-
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution
-
Hormozdiari, F. et al. (2007) Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PLoS Comput. Biol., 3, e118.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Hormozdiari, F.1
-
20
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang da, W. et al. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang da, W.1
-
21
-
-
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
-
22
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
Jenssen, T.K. et al. (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28, 21-28.
-
(2001)
Nat. Genet.
, vol.28
, pp. 21-28
-
-
Jenssen, T.K.1
-
23
-
-
33744473304
-
How scale-free are biological networks
-
Khanin, R. and Wit, E. (2006) How scale-free are biological networks. J. Comput. Biol., 13, 810-818.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 810-818
-
-
Khanin, R.1
Wit, E.2
-
24
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan, 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.1
-
25
-
-
15544377794
-
Molecular and evolutionary basis of the cellular stress response
-
Kultz, D. (2005) Molecular and evolutionary basis of the cellular stress response. Annu. Rev. Physiol., 67, 225-257.
-
(2005)
Annu. Rev. Physiol.
, vol.67
, pp. 225-257
-
-
Kultz, D.1
-
27
-
-
33645857372
-
Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale
-
Li, H. et al. (2006) Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale. Bioinformatics, 22, 989-996.
-
(2006)
Bioinformatics
, vol.22
, pp. 989-996
-
-
Li, H.1
-
28
-
-
35649007860
-
Maximal biclique subgraphs and closed pattern pairs of the adjacency matrix: a one-to-one correspondence and mining algorithms
-
Li, J. et al. (2007) Maximal biclique subgraphs and closed pattern pairs of the adjacency matrix: a one-to-one correspondence and mining algorithms. IEEE Trans. Knowl. Data Eng., 19, 1625-1637.
-
(2007)
IEEE Trans. Knowl. Data Eng.
, vol.19
, pp. 1625-1637
-
-
Li, J.1
-
29
-
-
72949090589
-
The powerful law of the power law and other myths in network biology
-
Lima-Mendez, G. and van Helden, J. (2009) The powerful law of the power law and other myths in network biology. Mol. Biosyst., 5, 1482-1493.
-
(2009)
Mol. Biosyst.
, vol.5
, pp. 1482-1493
-
-
Lima-Mendez, G.1
van Helden, J.2
-
30
-
-
33845276522
-
Limits of dense graph sequences
-
Lovász, L. and Szegedy, B. (2006) Limits of dense graph sequences. J. Comb. Theory Ser. B, 96, 933-957.
-
(2006)
J. Comb. Theory Ser. B
, vol.96
, pp. 933-957
-
-
Lovász, L.1
Szegedy, B.2
-
31
-
-
13244299158
-
Discriminative topological features reveal biological network mechanisms
-
Middendorf, M. et al. (2004) Discriminative topological features reveal biological network mechanisms. BMC Bioinformatics, 5, 181.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 181
-
-
Middendorf, M.1
-
32
-
-
79960601554
-
A brief history of generative models for power law and lognormal distributions
-
Mitzenmacher, M. (2004) A brief history of generative models for power law and lognormal distributions. Internet Math., 1, 226-251.
-
(2004)
Internet Math.
, vol.1
, pp. 226-251
-
-
Mitzenmacher, M.1
-
33
-
-
0038718854
-
The structure and function of complex networks
-
Newman, M.E.J. (2003) The structure and function of complex networks. SIAM Rev., 45, 167-256.
-
(2003)
SIAM Rev.
, vol.45
, pp. 167-256
-
-
Newman, M.E.J.1
-
35
-
-
0037460091
-
-
Pastor-Satorras, R. et al. (2003) Evolving protein interaction networks through gene duplication. J. Theor. Biol., 222, 199-210.
-
(2003)
J. Theor. Biol.
, vol.222
, pp. 199-210
-
-
Pastor-Satorras, R.1
-
36
-
-
12344273375
-
Modeling interactome: scale-free or geometric
-
Pržulj, N. (2004) Modeling interactome: scale-free or geometric. Bioinformatics, 20, 3508-3515.
-
(2004)
Bioinformatics
, vol.20
, pp. 3508-3515
-
-
Pržulj, N.1
-
37
-
-
0035843145
-
The protein-protein interaction map of Helicobacter pylori
-
Rain, J.C. 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
-
38
-
-
33847064282
-
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
-
Reguly, T. et al. (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol., 5, 11.
-
(2006)
J. Biol.
, vol.5
, pp. 11
-
-
Reguly, T.1
-
39
-
-
24944565272
-
Some protein interaction data do not exhibit power law statistics
-
Reiko, T. et al. (2005) Some protein interaction data do not exhibit power law statistics. FEBS Lett., 579, 5140-5144.
-
(2005)
FEBS Lett.
, vol.579
, pp. 5140-5144
-
-
Reiko, T.1
-
40
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski, L. et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Salwinski, L.1
-
41
-
-
1642314524
-
A novel proteomic screen for peptide-protein interactions
-
Schulze, W.X. and Mann, M. (2004) A novel proteomic screen for peptide-protein interactions. J. Biol. Chem., 279, 10756-10764.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 10756-10764
-
-
Schulze, W.X.1
Mann, M.2
-
42
-
-
33947252154
-
Network-based prediction of protein function
-
Sharan, R. et al. (2007) Network-based prediction of protein function. Mol. Syst. Biol., 3, 88.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 88
-
-
Sharan, R.1
-
43
-
-
33644873184
-
BioGRID: a general repository for interaction datasets
-
Stark, C. et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Stark, C.1
-
44
-
-
33646730795
-
Statistical model selection methods applied to biological networks
-
Priami, C. et al. (eds) Springer, Weinheim, FRG
-
Stumpf, M., et al. (2005) Statistical model selection methods applied to biological networks. In Priami,C. et al. (eds) Transactions on Computational Systems Biology 3. Springer, Weinheim, FRG, pp. 65-77.
-
(2005)
Transactions on Computational Systems Biology
, vol.3
, pp. 65-77
-
-
Stumpf, M.1
-
45
-
-
44349113144
-
Estimating the size of the human interactome
-
Stumpf, M. et al. (2008) Estimating the size of the human interactome. Proc. Natl Acad. Sci. USA, 105, 6959-6964.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 6959-6964
-
-
Stumpf, M.1
-
46
-
-
15444372528
-
Subnets of scale-free networks are not scale free: the sampling properties of networks
-
Stumpf, M.P. (2005) Subnets of scale-free networks are not scale free: the sampling properties of networks. Proc. Natl Acad. Sci. USA, 102, 4221-4224.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4221-4224
-
-
Stumpf, M.P.1
-
47
-
-
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
-
48
-
-
34247193051
-
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
-
Ulitsky, I. and Shamir, R. (2007) Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol. Syst. Biol., 3, 104.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 104
-
-
Ulitsky, I.1
Shamir, R.2
-
49
-
-
49549121813
-
High confidence determination of specific protein-protein interactions using quantitative mass spectrometry
-
Vermeulen, M. et al. (2008) High confidence determination of specific protein-protein interactions using quantitative mass spectrometry. Curr. Opin. Biotechnol., 19, 331-337.
-
(2008)
Curr. Opin. Biotechnol.
, vol.19
, pp. 331-337
-
-
Vermeulen, M.1
-
50
-
-
0037161731
-
Comparative assessment of large-scale data sets of proteinprotein interactions
-
von Mering, C. et al. (2002) Comparative assessment of large-scale data sets of proteinprotein interactions. Nature, 417, 399-403.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
von Mering, C.1
-
52
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu, H. et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science, 322, 104-110.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
-
53
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu, H. et al. (2008) High-quality binary protein interaction map of the yeast interactome network, Science, 322, 104-110.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
|