-
1
-
-
0034721164
-
Error and attack tolerance of complex networks
-
Albert, R, Jeong, H, and Barabási, AL (2000). "Error and attack tolerance of complex networks." Nature (London) 406(6794), 378-382.
-
(2000)
Nature (London)
, vol.406
, Issue.6794
, pp. 378-382
-
-
Albert, R.1
Jeong, H.2
Barabási, A.L.3
-
2
-
-
2442495404
-
Taking the mystery out of biological networks
-
Aloy, P, and Russell, R (2004). "Taking the mystery out of biological networks." EMBO Rep. 5(4), 349-350.
-
(2004)
EMBO Rep
, vol.5
, Issue.4
, pp. 349-350
-
-
Aloy, P.1
Russell, R.2
-
3
-
-
33644550021
-
Structural systems biology: Modeling protein interactions
-
Aloy, P, and Russell, RB (2006). "Structural systems biology: modeling protein interactions." Nat. Rev. Mol. Cell Biol. 7(3), 188-197.
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, Issue.3
, pp. 188-197
-
-
Aloy, P.1
Russell, R.B.2
-
4
-
-
4344715809
-
Comment on 'Network motifs: Simple building blocks of complex networks' and 'Superfamilies of evolved and designed networks.'
-
Artzy-Randrup, Y, Fleishman, S, Ben-Tal, N, and Stone, L (2004). "Comment on 'Network motifs: simple building blocks of complex networks' and 'Superfamilies of evolved and designed networks.'" Science 305(5687), 1107.
-
(2004)
Science
, vol.305
, Issue.5687
, pp. 1107
-
-
Artzy-Randrup, Y.1
Fleishman, S.2
Ben-Tal, N.3
Stone, L.4
-
5
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabási, AL, 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
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabási, AL, and Oltvai, ZN (2004). "Network biology: understanding the cell's functional organization." Nat. Rev. Genet. 5, 101-113.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
7
-
-
1642308591
-
The architecture of complex weighted networks
-
Barrat, A, Barthelemy, M, Pastor-Satorras, R, and Vespignani, A (2004). "The architecture of complex weighted networks." Proc. Natl. Acad. Sci. U.S.A. 101(11), 3747-3752.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A
, vol.101
, Issue.11
, pp. 3747-3752
-
-
Barrat, A.1
Barthelemy, M.2
Pastor-Satorras, R.3
Vespignani, A.4
-
8
-
-
33750238153
-
Stratus not altocumulus: A new view of the yeast protein interaction network
-
Batada, NN, et al. (2006). "Stratus not altocumulus: a new view of the yeast protein interaction network." PLoS Biol. 4, e317.
-
(2006)
PLoS Biol
, vol.4
-
-
Batada, N.N.1
-
9
-
-
42549129218
-
From genotype to phenotype: Systems biology meets natural variation
-
Benfey, PN, and Mitchell-Olds, T (2008). "From genotype to phenotype: systems biology meets natural variation." Science 320(5875), 495-497.
-
(2008)
Science
, vol.320
, Issue.5875
, pp. 495-497
-
-
Benfey, P.N.1
Mitchell-Olds, T.2
-
10
-
-
12444301754
-
Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications
-
Berg, J, Lässig, M, and Wagner, A (2004). "Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications." BMC Evol. Biol. 4, 14689-14694.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 14689-14694
-
-
Berg, J.1
Lässig, M.2
Wagner, A.3
-
11
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
Berman, H, Henrick, K, and Nakamura, H (2003). "Announcing the worldwide Protein Data Bank." Nat. Struct. Biol. 10(12), 980-980.
-
(2003)
Nat. Struct. Biol.
, vol.10
, Issue.12
, pp. 980
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
-
12
-
-
34250345292
-
Confirmation of organized modularity in the yeast interactome
-
Bertin, N, et al. (2007). "Confirmation of organized modularity in the yeast interactome." PLoS Biol. 5, e153.
-
(2007)
PLoS Biol
, vol.5
-
-
Bertin, N.1
-
13
-
-
2942624159
-
Apparent dependence of protein evolutionary rate on the number of interactions is linked to biases in protein-protein interactions data sets
-
Bloom, J, and Adami, C (2003). "Apparent dependence of protein evolutionary rate on the number of interactions is linked to biases in protein-protein interactions data sets." BMC Evol. Biol. 3, 21.
-
(2003)
BMC Evol. Biol.
, vol.3
, pp. 21
-
-
Bloom, J.1
Adami, C.2
-
14
-
-
11944253901
-
-
2nd ed., Cambridge University Press, Cambridge, England
-
Bollobás, B (2001). Random Graphs. 2nd ed., Cambridge University Press, Cambridge, England.
-
(2001)
Random Graphs
-
-
Bollobás, B.1
-
15
-
-
0000025871
-
Science and statistics
-
Box, GEP (1976). "Science and statistics." J. Am. Stat. Assoc. 71(356), 791-799.
-
(1976)
J. Am. Stat. Assoc.
, vol.71
, Issue.356
, pp. 791-799
-
-
Box, G.E.P.1
-
16
-
-
58149242456
-
An experimentally derived confidence score for binary protein-protein interactions
-
Braun, P, et al. (2009). "An experimentally derived confidence score for binary protein-protein interactions." Nat. Methods 6(1), 91-97.
-
(2009)
Nat. Methods
, vol.6
, Issue.1
, pp. 91-97
-
-
Braun, P.1
-
17
-
-
38349088496
-
Coverage and error models of protein-protein interaction data by directed graph analysis
-
Chiang, T, Scholtens, D, Sarkar, D, Gentleman, R, and Huber, W (2007). "Coverage and error models of protein-protein interaction data by directed graph analysis." Genome Biol. 8(9), R186.
-
(2007)
Genome Biol
, vol.8
, Issue.9
-
-
Chiang, T.1
Scholtens, D.2
Sarkar, D.3
Gentleman, R.4
Huber, W.5
-
18
-
-
35348892535
-
Innovation and robustness in complex regulatory gene networks
-
Ciliberti, S, Martin, OC, and Wagner, A (2007). "Innovation and robustness in complex regulatory gene networks." Proc. Natl. Acad. Sci. U.S.A. 104(34), 13591-13596.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, Issue.34
, pp. 13591-13596
-
-
Ciliberti, S.1
Martin, O.C.2
Wagner, A.3
-
19
-
-
84857788275
-
Power-law distributions in empirical data.". Collins, SR, Kemmeren, P, Zhao, X-C, Greenblatt, JF, Spencer, F, Holstege, FCP, Weissman, JS, and Krogan, NJ (2007). "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
-
Clauset, A, Shalizi, C, and Newman, M (2009). "Power-law distributions in empirical data.". Collins, SR, Kemmeren, P, Zhao, X-C, Greenblatt, JF, Spencer, F, Holstege, FCP, Weissman, JS, and Krogan, NJ (2007). "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae." Mol. Cell Proteomics 6(3), 439-450.
-
(2009)
Mol. Cell Proteomics
, vol.6
, Issue.3
, pp. 439-450
-
-
Clauset, A.1
Shalizi, C.2
Newman, M.3
-
20
-
-
56549119570
-
Turning a hobby into a job: How duplicated genes find new functions
-
Conant, G.C, and Wolfe, K.H (2008). "Turning a hobby into a job: how duplicated genes find new functions." Nat. Rev. Genet. 9(12), 938-950.
-
(2008)
Nat. Rev. Genet.
, vol.9
, Issue.12
, pp. 938-950
-
-
Conant, G.C.1
Wolfe, K.H.2
-
21
-
-
33748773071
-
Feed-forward loop circuits as a side effect of genome evolution
-
Cordero, O.X, and Hogeweg, P (2006). "Feed-forward loop circuits as a side effect of genome evolution." Mol. Biol. Evol. 23(10), 1931-1936.
-
(2006)
Mol. Biol. Evol.
, vol.23
, Issue.10
, pp. 1931-1936
-
-
Cordero, O.X.1
Hogeweg, P.2
-
22
-
-
32444446240
-
Gene regulatory networks and the evolution of animal body plans
-
Davidson, EH, and Erwin, DH (2006). "Gene regulatory networks and the evolution of animal body plans." Science 311(5762), 796-800.
-
(2006)
Science
, vol.311
, Issue.5762
, pp. 796-800
-
-
Davidson, E.H.1
Erwin, D.H.2
-
23
-
-
33845262280
-
The effects of incomplete protein interaction data on structural and evolutionary inferences
-
de Silva, E, Thorne, T, Ingram, P, Agrafioti, I, Swire, J, Wiuf, C, and Stumpf, M (2006). "The effects of incomplete protein interaction data on structural and evolutionary inferences." BMC Evol. Biol. 4, 39.
-
(2006)
BMC Evol. Biol.
, vol.4
, pp. 39
-
-
de Silva, E.1
Thorne, T.2
Ingram, P.3
Agrafioti, I.4
Swire, J.5
Wiuf, C.6
Stumpf, M.7
-
24
-
-
31044448435
-
A simple physical model for scaling in protein-protein interaction networks
-
Deeds, EJ, Ashenberg, O, and Shakhnovich, EI (2006). "A simple physical model for scaling in protein-protein interaction networks." Proc. Natl. Acad. Sci. U.S.A. 103(2), 311-316.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, Issue.2
, pp. 311-316
-
-
Deeds, E.J.1
Ashenberg, O.2
Shakhnovich, E.I.3
-
25
-
-
49649114289
-
Escape from adaptive conflict after duplication in an anthocyanin pathway gene
-
Des Marais, DL, and Rausher, MD (2008). "Escape from adaptive conflict after duplication in an anthocyanin pathway gene." Nature (London) 454(7205), 762-765.
-
(2008)
Nature (London)
, vol.454
, Issue.7205
, pp. 762-765
-
-
des Marais, D.L.1
Rausher, M.D.2
-
26
-
-
26844525729
-
The robust yet fragile nature of the internet
-
Doyle, JC, Alderson, DL, Li, L, Low, S, Roughan, M, Shalunov, S, Tanaka, R, and Willinger, W (2005). "The robust yet fragile nature of the internet." Proc. Natl. Acad. Sci. U.S.A. 102(41), 14497-14502.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, Issue.41
, pp. 14497-14502
-
-
Doyle, J.C.1
Alderson, D.L.2
Li, L.3
Low, S.4
Roughan, M.5
Shalunov, S.6
Tanaka, R.7
Willinger, W.8
-
27
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond, DA, Bloom, JD, Adami, C, Wilke, CO, and Arnold, FH (2005). "Why highly expressed proteins evolve slowly." Proc. Natl. Acad. Sci. U.S.A. 102, 14338-14343.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
28
-
-
33645981936
-
A hybrid micromacroevolutionary approach to gene tree reconstruction
-
Durand, D, Halldórsson, BV, and Vernot, B (2006). "A hybrid micromacroevolutionary approach to gene tree reconstruction." J. Comput. Biol. 13(2), 320-335.
-
(2006)
J. Comput. Biol.
, vol.13
, Issue.2
, pp. 320-335
-
-
Durand, D.1
Halldórsson, B.V.2
Vernot, B.3
-
29
-
-
34547840254
-
Identification of functional modules from conserved ancestral protein-protein interactions
-
Dutkowski, J, and Tiuryn, J (2007). "Identification of functional modules from conserved ancestral protein-protein interactions." Bioinformatics 23(13), i149-i158.
-
(2007)
Bioinformatics
, vol.23
, Issue.13
-
-
Dutkowski, J.1
Tiuryn, J.2
-
30
-
-
38849192336
-
Modeling protein network evolution under genome duplication and domain shuffling
-
Evlampiev, K, and Isambert, H (2007). "Modeling protein network evolution under genome duplication and domain shuffling." BMC Systems Biology 1(1), 49.
-
(2007)
BMC Systems Biology
, vol.1
, Issue.1
, pp. 49
-
-
Evlampiev, K.1
Isambert, H.2
-
31
-
-
48249095913
-
Conservation and topology of protein interaction networks under duplication-divergence evolution
-
Evlampiev, K, and Isambert, H (2008). "Conservation and topology of protein interaction networks under duplication-divergence evolution." Proc. Natl. Acad. Sci. U.S.A. 105(29), 9863-9868.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A
, vol.105
, Issue.29
, pp. 9863-9868
-
-
Evlampiev, K.1
Isambert, H.2
-
32
-
-
27644576841
-
High-throughput two-hybrid analysis: The promise and the peril
-
Fields, S (2005). "High-throughput two-hybrid analysis: the promise and the peril." FEBS J. 272(21), 5391-5399.
-
(2005)
FEBS J
, vol.272
, Issue.21
, pp. 5391-5399
-
-
Fields, S.1
-
33
-
-
13844264506
-
IPfam: Visualization of protein-protein interactions in PDB at domain and amino cid resolutions
-
Finn, RD, Marshall, M, and Bateman, A (2005). "iPfam: visualization of protein-protein interactions in PDB at domain and amino cid resolutions." Bioinformatics 21, 410-412.
-
(2005)
Bioinformatics
, vol.21
, pp. 410-412
-
-
Finn, R.D.1
Marshall, M.2
Bateman, A.3
-
34
-
-
4143058720
-
Predicting specificity in bzip coiled-coil protein interactions
-
Fong, JH, Keating, AE, and Singh, M (2004). "Predicting specificity in bzip coiled-coil protein interactions." Genome Biol. 5(2), R11.
-
(2004)
Genome Biol
, vol.5
, Issue.2
-
-
Fong, J.H.1
Keating, A.E.2
Singh, M.3
-
35
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force, A, Lynch, M, Pickett, F, Amoresa, A, Yana, Y, and Postlethwait, J (1999). "Preservation of duplicate genes by complementary, degenerative mutations." Genetics 151, 1531-1545.
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Pickett, F.3
Amoresa, A.4
Yana, Y.5
Postlethwait, J.6
-
36
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser, H, Hirsh, A, Steinmetz, L, Scharfe, C, and Feldman, M (2002). "Evolutionary rate in the protein interaction network." Science 296, 750-752.
-
(2002)
Science
, vol.296
, pp. 750-752
-
-
Fraser, H.1
Hirsh, A.2
Steinmetz, L.3
Scharfe, C.4
Feldman, M.5
-
37
-
-
16844363315
-
Modularity and evolutionary constraint on proteins
-
Fraser, HB (2005). "Modularity and evolutionary constraint on proteins." Nat. Genet. 37, 351-352.
-
(2005)
Nat. Genet.
, vol.37
, pp. 351-352
-
-
Fraser, H.B.1
-
38
-
-
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 (London) 440(7084), 631-636.
-
(2006)
Nature (London)
, vol.440
, Issue.7084
, pp. 631-636
-
-
Gavin, A.-C.1
-
39
-
-
42949089155
-
Making the most of highthroughput protein-interaction data
-
Gentleman, R, and Huber, W (2007). "Making the most of highthroughput protein-interaction data." Genome Biol. 8(10), 112.
-
(2007)
Genome Biol
, vol.8
, Issue.10
, pp. 112
-
-
Gentleman, R.1
Huber, W.2
-
40
-
-
59049100728
-
Questioning the ubiquity of neofunctionalization
-
Gibson, T.A, and Goldberg, D.S (2009a). "Questioning the ubiquity of neofunctionalization." PLOS Comput. Biol. 5(1), e1000252.
-
(2009)
PLOS Comput. Biol.
, vol.5
, Issue.1
-
-
Gibson, T.A.1
Goldberg, D.S.2
-
41
-
-
61949109355
-
Reverse engineering the evolution of protein interaction networks
-
Gibson, TA, and Goldberg, DS (2009b). "Reverse engineering the evolution of protein interaction networks." Pacific Symposium on Biocomputing, 190-202.
-
(2009)
Pacific Symposium on Biocomputing
, pp. 190-202
-
-
Gibson, T.A.1
Goldberg, D.S.2
-
42
-
-
1842507531
-
A statistical framework for combining and interpreting proteomic datasets
-
Gilchrist, MA, Salter, LA, and Wagner, A (2004). "A statistical framework for combining and interpreting proteomic datasets." Bioinformatics 20(5), 689-700.
-
(2004)
Bioinformatics
, vol.20
, Issue.5
, pp. 689-700
-
-
Gilchrist, M.A.1
Salter, L.A.2
Wagner, A.3
-
43
-
-
34547140875
-
The human disease network
-
Goh, K-I, Cusick, ME, Valle, D, Childs, B, Vidal, M, and Barabasi, A-L (2007). "The human disease network." Proc. Natl. Acad. Sci. U.S.A. 104(21), 8685-8690.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, Issue.21
, pp. 8685-8690
-
-
Goh, K.-I.1
Cusick, M.E.2
Valle, D.3
Childs, B.4
Vidal, M.5
Barabasi, A.-L.6
-
44
-
-
0842290925
-
Molecular evolution in large genetic networks: Does connectivity equal constraint?
-
Hahn, M, Conant, G, and Wagner, A (2004). "Molecular evolution in large genetic networks: does connectivity equal constraint?" J. Mol. Evol. 58, 203-211.
-
(2004)
J. Mol. Evol.
, vol.58
, pp. 203-211
-
-
Hahn, M.1
Conant, G.2
Wagner, A.3
-
45
-
-
34249945479
-
Specificity in protein interactions and its relationship with sequence diversity and coevolution
-
Hakes, L, Lovell, SC, Oliver, SG, and Robertson, DL (2007a). "Specificity in protein interactions and its relationship with sequence diversity and coevolution." Proc. Natl. Acad. Sci. U.S.A. 104(19), 7999-8004.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, Issue.19
, pp. 7999-8004
-
-
Hakes, L.1
Lovell, S.C.2
Oliver, S.G.3
Robertson, D.L.4
-
46
-
-
38049133600
-
All duplicates are not equal: The difference between small-scale and genome duplication
-
Hakes, L, Pinney, JW, Lovell, SC, Oliver, SG, and Robertson, DL (2007b). "All duplicates are not equal: the difference between small-scale and genome duplication." Genome Biol. 8(10), R209.
-
(2007)
Genome Biol
, vol.8
, Issue.10
-
-
Hakes, L.1
Pinney, J.W.2
Lovell, S.C.3
Oliver, S.G.4
Robertson, D.L.5
-
47
-
-
38049079362
-
Proteinprotein interaction networks and biology-what's the connection?
-
Hakes, L, Pinney, JW, Robertson, DL, and Lovell, SC (2008). "Proteinprotein interaction networks and biology-what's the connection?" Nat. Biotechnol. 26(1), 69-72.
-
(2008)
Nat. Biotechnol.
, vol.26
, Issue.1
, pp. 69-72
-
-
Hakes, L.1
Pinney, J.W.2
Robertson, D.L.3
Lovell, S.C.4
-
48
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han, JDJ, 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.D.J.1
-
49
-
-
24944442468
-
Effect of sampling on topology predictions of protein-protein interaction networks
-
Han, JDJ, Dupuy, D, Bertin, N, Cusick, ME, and Vidal, M (2005). "Effect of sampling on topology predictions of protein-protein interaction networks." Nat. Biotechnol. 23, 839-844.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 839-844
-
-
Han, J.D.J.1
Dupuy, D.2
Bertin, N.3
Cusick, M.E.4
Vidal, M.5
-
50
-
-
0033518234
-
From molecular to modular cell biology
-
Hartwell, LH, Hopfield, JJ, Leibler, S, and Murray, AW (1999). "From molecular to modular cell biology." Nature (London) 402(6761), C47-C52.
-
(1999)
Nature (London)
, vol.402
, Issue.6761
, pp. 47-52
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
51
-
-
15544389841
-
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
-
He, X, and Zhang, J (2005). "Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution." Genetics 169(2), 1157-1164.
-
(2005)
Genetics
, vol.169
, Issue.2
, pp. 1157-1164
-
-
He, X.1
Zhang, J.2
-
52
-
-
21144433991
-
Gene duplication and the origin of novel proteins
-
Hughes, AL (2005). "Gene duplication and the origin of novel proteins." Proc. Natl. Acad. Sci. U.S.A. 102(25), 8791-8792.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, Issue.25
, pp. 8791-8792
-
-
Hughes, A.L.1
-
53
-
-
33947617347
-
Backup without redundancy: Genetic interactions reveal the cost of duplicate gene loss
-
Ihmels, J, Collins, SR, Schuldiner, M, Krogan, NJ, and Weissman, JS (2007). "Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss." Mol. Syst. Biol. 3, 86.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 86
-
-
Ihmels, J.1
Collins, S.R.2
Schuldiner, M.3
Krogan, N.J.4
Weissman, J.S.5
-
54
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito, TEA (2001). "A comprehensive two-hybrid analysis to explore the yeast protein interactome." Proc. Natl. Acad. Sci. U.S.A. 98, 4569-4574.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A
, vol.98
, pp. 4569-4574
-
-
Ito, T.E.A.1
-
55
-
-
33846404946
-
Macromolecular recognition in the Protein Data Bank
-
Janin, J, Rodier, F, Chakrabarti, P, and Bahadur, RP (2007). "Macromolecular recognition in the Protein Data Bank." Acta Crystallogr., Sect. D: Biol. Crystallogr. 63(1), 1-8.
-
(2007)
Acta Crystallogr., Sect. D: Biol. Crystallogr
, vol.63
, Issue.1
, pp. 1-8
-
-
Janin, J.1
Rodier, F.2
Chakrabarti, P.3
Bahadur, R.P.4
-
56
-
-
67749131001
-
STRING 8-a global view on proteins and their functional interactions in 630 organisms
-
Jensen, LJ, et al. (2008). "STRING 8-a global view on proteins and their functional interactions in 630 organisms." Nucleic Acids Res. http://nar.oxfordjournals.org/cgi/content/abstract/gkn760v1.
-
(2008)
Nucleic Acids Res
-
-
Jensen, L.J.1
-
57
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong, H, Mason, SP, Barabási, A-L, and Oltvai, ZN (2001). "Lethality and centrality in protein networks." Nature (London) 411(6833), 41-42.
-
(2001)
Nature (London)
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabási, A.-L.3
Oltvai, Z.N.4
-
58
-
-
51449104123
-
Approximately sufficient statistics and Bayesian computation
-
Joyce, P, and Marjoram, P (2008). "Approximately sufficient statistics and Bayesian computation." Stat. Appl. Genet. Mol. Biol. 7(1), 26.
-
(2008)
Stat. Appl. Genet. Mol. Biol.
, vol.7
, Issue.1
, pp. 26
-
-
Joyce, P.1
Marjoram, P.2
-
59
-
-
27744432926
-
Revisiting "scale-free" networks
-
Keller, EF (2005). "Revisiting "scale-free" networks." BioEssays 27(10), 1060-1068.
-
(2005)
BioEssays
, vol.27
, Issue.10
, pp. 1060-1068
-
-
Keller, E.F.1
-
60
-
-
3442886313
-
Pathblast: A tool for alignment of protein interaction networks
-
Kelley, BP, Yuan, B, Lewitter, F, Sharan, R, Stockwell, BR, and Ideker, T (2004). "Pathblast: a tool for alignment of protein interaction networks." Nucleic Acids Res. 32, W83-W88.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 83-88
-
-
Kelley, B.P.1
Yuan, B.2
Lewitter, F.3
Sharan, R.4
Stockwell, B.R.5
Ideker, T.6
-
61
-
-
43149092276
-
Principles of protein-protein interactions: What are the preferred ways for proteins to interact?
-
(Washington, D.C.)
-
Keskin, O, Gursoy, A, Ma, B, and Nussinov, R (2008). "Principles of protein-protein interactions: what are the preferred ways for proteins to interact?." Chem. Rev. (Washington, D.C.) 108(4), 1225-1244.
-
(2008)
Chem. Rev.
, vol.108
, Issue.4
, pp. 1225-1244
-
-
Keskin, O.1
Gursoy, A.2
Ma, B.3
Nussinov, R.4
-
62
-
-
38049138722
-
Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context
-
Kim, PM, Korbel, JO, and Gerstein, MB (2007). "Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context." Proc. Natl. Acad. Sci. U.S.A. 104(51), 20274-20279.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, Issue.51
, pp. 20274-20279
-
-
Kim, P.M.1
Korbel, J.O.2
Gerstein, M.B.3
-
63
-
-
33845875196
-
Relating threedimensional structures to protein networks provides evolutionary insights
-
Kim, PM, Lu, LJ, Xia, Y, and Gerstein, MB (2006). "Relating threedimensional structures to protein networks provides evolutionary insights." Science 314(5807), 1938-1941.
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
64
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan, NJ, et al. (2006). "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae." Nature (London) 440(7084),
-
(2006)
Nature (London)
, vol.440
, Issue.7084
-
-
Krogan, N.J.1
-
65
-
-
33746922321
-
Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence
-
Kuo, PD, Banzhaf, W, and Leier, A (2006). "Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence." BioSystems 85(3), 177-200.
-
(2006)
BioSystems
, vol.85
, Issue.3
, pp. 177-200
-
-
Kuo, P.D.1
Banzhaf, W.2
Leier, A.3
-
66
-
-
33947658454
-
Genetic interactions in yeast: Is robustness going bust?
-
Kupiec, M, Sharan, R, and Ruppin, E (2007). "Genetic interactions in yeast: is robustness going bust?." Mol. Syst. Biol. 3.
-
(2007)
Mol. Syst. Biol
, pp. 3
-
-
Kupiec, M.1
Sharan, R.2
Ruppin, E.3
-
67
-
-
0030620646
-
Mathematical and computational challenges in population biology and ecosystems science
-
Levin, SA, Grenfell, B, Hastings, A, and Perelson, AS (1997). "Mathematical and computational challenges in population biology and ecosystems science." Science 275(5298), 334-343.
-
(1997)
Science
, vol.275
, Issue.5298
, pp. 334-343
-
-
Levin, S.A.1
Grenfell, B.2
Hastings, A.3
Perelson, A.S.4
-
68
-
-
46249083761
-
Assembly reflects evolution of protein complexes
-
Levy, ED, Erba, EB, Robinson, CV, and Teichmann, SA (2008). "Assembly reflects evolution of protein complexes." Nature (London) 453(7199), 1262-1265.
-
(2008)
Nature (London)
, vol.453
, Issue.7199
, pp. 1262-1265
-
-
Levy, E.D.1
Erba, E.B.2
Robinson, C.V.3
Teichmann, S.A.4
-
69
-
-
26444488575
-
Expression divergence between duplicate genes
-
Li, W-H, Yang, J, and Gu, X (2005). "Expression divergence between duplicate genes." Trends Genet. 21(11), 602-607.
-
(2005)
Trends Genet
, vol.21
, Issue.11
, pp. 602-607
-
-
Li, W.-H.1
Yang, J.2
Gu, X.3
-
70
-
-
34548724489
-
The evolution of genetic networks by non-adaptive processes
-
Lynch, M (2007a). "The evolution of genetic networks by non-adaptive processes." Nat. Rev. Genet. 8(10), 803-813.
-
(2007)
Nat. Rev. Genet
, vol.8
, Issue.10
, pp. 803-813
-
-
Lynch, M.1
-
71
-
-
34547396004
-
The frailty of adaptive hypotheses for the origins of organismal complexity
-
Lynch, M (2007b). "The frailty of adaptive hypotheses for the origins of organismal complexity." Proc. Natl. Acad. Sci. U.S.A. 104, 8597-8604.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, pp. 8597-8604
-
-
Lynch, M.1
-
73
-
-
33748799967
-
Modern computational approaches for analysing molecular genetic variation data
-
Marjoram, P, and Tavaré, S (2006). "Modern computational approaches for analysing molecular genetic variation data." Nat. Rev. Genet. 7(10), 759-770.
-
(2006)
Nat. Rev. Genet.
, vol.7
, Issue.10
, pp. 759-770
-
-
Marjoram, P.1
Tavaré, S.2
-
74
-
-
0037012880
-
Specificity and stability in topology of protein networks
-
Masloy, S, and Sneppen, K (2002). "Specificity and stability in topology of protein networks." Science 296(5569), 910-913.
-
(2002)
Science
, vol.296
, Issue.5569
, pp. 910-913
-
-
Masloy, S.1
Sneppen, K.2
-
75
-
-
2942615357
-
Upstream plasticity and downstream robustness in evolution of molecular networks
-
Maslov, S, Sneppen, K, Eriksen, K, and Yan, K (2004). "Upstream plasticity and downstream robustness in evolution of molecular networks." BMC Evol. Biol. 4, 9.
-
(2004)
BMC Evol. Biol.
, vol.4
, pp. 9
-
-
Maslov, S.1
Sneppen, K.2
Eriksen, K.3
Yan, K.4
-
76
-
-
33947619951
-
Graph theory and networks in biology
-
Mason, O, and Verwoerd, M (2007). "Graph theory and networks in biology." Syst. Biol. 4(2), 89-119.
-
(2007)
Syst. Biol.
, vol.4
, Issue.2
, pp. 89-119
-
-
Mason, O.1
Verwoerd, M.2
-
77
-
-
0842309879
-
Uses and abuses of mathematics in biology
-
May, RM (2004). "Uses and abuses of mathematics in biology." Science 303(5659), 790-793.
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 790-793
-
-
May, R.M.1
-
78
-
-
28844434073
-
An evolutionary and functional assessment of regulatory network motifs
-
Mazurie, A, Bottani, S, and Vergassola, M (2005). "An evolutionary and functional assessment of regulatory network motifs." Genome Biol 6, R35.
-
(2005)
Genome Biol
, vol.6
-
-
Mazurie, A.1
Bottani, S.2
Vergassola, M.3
-
79
-
-
13244299158
-
Discriminative topological features reveal biological network mechanisms
-
Middendorf, M, Ziv, E, Adams, C, Hom, J, Koytcheff, R, Levovitz, C, Woods, G, Chen, I, and Wiggins, C (2004). "Discriminative topological features reveal biological network mechanisms." BMC Bioinf. 5(1), 181.
-
(2004)
BMC Bioinf
, vol.5
, Issue.1
, pp. 181
-
-
Middendorf, M.1
Ziv, E.2
Adams, C.3
Hom, J.4
Koytcheff, R.5
Levovitz, C.6
Woods, G.7
Chen, I.8
Wiggins, C.9
-
80
-
-
14744273317
-
Inferring network mechanisms: The Drosophila melanogaster protein interaction network
-
Middendorf, M, Ziv, E, and Wiggins, C (2005). "Inferring network mechanisms: the Drosophila melanogaster protein interaction network." Proc. Natl. Acad. Sci. U.S.A. 102(9), 3192-3197.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, Issue.9
, pp. 3192-3197
-
-
Middendorf, M.1
Ziv, E.2
Wiggins, C.3
-
81
-
-
1542287343
-
Superfamilies of evolved and designed networks
-
Milo, R, Itzkovitz, S, Kashtan, N, Levitt, R, Shen-Orr, S, Ayzenshtat, I, Sheffer, M, and Alon, U (2004). "Superfamilies of evolved and designed networks." Science 303, 1538-1542.
-
(2004)
Science
, vol.303
, pp. 1538-1542
-
-
Milo, R.1
Itzkovitz, S.2
Kashtan, N.3
Levitt, R.4
Shen-Orr, S.5
Ayzenshtat, I.6
Sheffer, M.7
Alon, U.8
-
82
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo, R, Shen-Orr, S, Itzkovitz, S, Kashtan, N, Chklovskii, D, and Alon, U (2002). "Network motifs: simple building blocks of complex networks." Science 298(5594), 824-827.
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
83
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris, J, and Weng, Z (2005). "Structure, function, and evolution of transient and obligate protein-protein interactions." Proc. Natl. Acad. Sci. U.S.A. 102(31), 10930-10935.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, Issue.31
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
84
-
-
18244408824
-
Genomes, phylogeny, and evolutionary systems biology
-
Monica, M (2005). "Genomes, phylogeny, and evolutionary systems biology." Proc. Natl. Acad. Sci. U.S.A. 102, 6630-6635.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, pp. 6630-6635
-
-
Monica, M.1
-
85
-
-
34547616501
-
The new mutation theory of phenotypic evolution
-
Nei, M (2007). "The new mutation theory of phenotypic evolution." Proc. Natl. Acad. Sci. U.S.A. 104(30), 12235-12242.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, Issue.30
, pp. 12235-12242
-
-
Nei, M.1
-
86
-
-
27944477670
-
Concerted and birth-and-death evolution of multigene families
-
Nei, M, and Rooney, AP (2005). "Concerted and birth-and-death evolution of multigene families." Annu. Rev. Genet. 39(1), 121-152.
-
(2005)
Annu. Rev. Genet.
, vol.39
, Issue.1
, pp. 121-152
-
-
Nei, M.1
Rooney, A.P.2
-
87
-
-
18744389789
-
Assortative mixing in networks
-
Newman, MEJ (2002). "Assortative mixing in networks." Phys. Rev. Lett. 89, 208701.
-
(2002)
Phys. Rev. Lett.
, vol.89
, pp. 208701
-
-
Newman, M.E.J.1
-
88
-
-
27944480531
-
Intensity and coherence of motifs in weighted complex networks
-
Onnela, J-P, Saramäki, J, Kertész, J, and Kaski, K (2005). "Intensity and coherence of motifs in weighted complex networks." Phys. Rev. E 71(6), 065103.
-
(2005)
Phys. Rev. E
, vol.71
, Issue.6
, pp. 065103
-
-
Onnela, J.-P.1
Saramäki, J.2
Kertész, J.3
Kaski, K.4
-
89
-
-
34249107988
-
The minimum information required for reporting a molecular interaction experiment (MIMIx)
-
Orchard, S, et al. (2007). "The minimum information required for reporting a molecular interaction experiment (MIMIx)." Nat. Biotechnol. 25(8), 894-898.
-
(2007)
Nat. Biotechnol.
, vol.25
, Issue.8
, pp. 894-898
-
-
Orchard, S.1
-
90
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pal, C, Papp, B, and Hurst, LD (2001). "Highly expressed genes in yeast evolve slowly." Genetics 158, 927-931.
-
(2001)
Genetics
, vol.158
, pp. 927-931
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
91
-
-
33646182934
-
An integrated view of protein evolution
-
Pal, C, Papp, B, and Lercher, MJ (2006). "An integrated view of protein evolution." Nat. Rev. Genet. 7(5), 337-348.
-
(2006)
Nat. Rev. Genet.
, vol.7
, Issue.5
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
92
-
-
38549161592
-
A proteome-wide protein interaction map for Campylobacter jejuni
-
Parrish, J, et al. (2007). "A proteome-wide protein interaction map for Campylobacter jejuni." Genome Biol. 8(7), R130.
-
(2007)
Genome Biol
, vol.8
, Issue.7
-
-
Parrish, J.1
-
93
-
-
0037460091
-
Evolving protein interaction networks through gene duplication
-
Pastor-Satorras, R, Smith, E, and Solé, RV (2003). "Evolving protein interaction networks through gene duplication." J. Theor. Biol. 222(2), 199-210.
-
(2003)
J. Theor. Biol.
, vol.222
, Issue.2
, pp. 199-210
-
-
Pastor-Satorras, R.1
Smith, E.2
Solé, R.V.3
-
94
-
-
34848913963
-
Evolution of protein complexes by duplication of homomeric interactions
-
Pereira-Leal, J, Levy, E, Kamp, C, and Teichmann, S (2007). "Evolution of protein complexes by duplication of homomeric interactions." Genome Biol. 8(4), R51.
-
(2007)
Genome Biol
, vol.8
, Issue.4
-
-
Pereira-Leal, J.1
Levy, E.2
Kamp, C.3
Teichmann, S.4
-
95
-
-
22744439567
-
The evolution of connectivity in metabolic networks
-
Pfeiffer, T, Soyer, OS, and Bonhoeffer, S (2005). "The evolution of connectivity in metabolic networks." PLoS Biol. 3(7).
-
(2005)
PLoS Biol
, vol.3
, Issue.7
-
-
Pfeiffer, T.1
Soyer, O.S.2
Bonhoeffer, S.3
-
96
-
-
38049136510
-
Reconstruction of ancestral protein interaction networks for the bZIP transcription factors
-
Pinney, JW, Amoutzias, GD, Rattray, M, and Robertson, DL (2007). "Reconstruction of ancestral protein interaction networks for the bZIP transcription factors." Proc. Natl. Acad. Sci. U.S.A. 104, 20449-20453.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, pp. 20449-20453
-
-
Pinney, J.W.1
Amoutzias, G.D.2
Rattray, M.3
Robertson, D.L.4
-
97
-
-
38949107398
-
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
-
Presser, A, Elowitz, MB, Kellis, M, and Kishony, R (2008). "The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication." Proc. Natl. Acad. Sci. U.S.A. 105(3), 950-954.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A
, vol.105
, Issue.3
, pp. 950-954
-
-
Presser, A.1
Elowitz, M.B.2
Kellis, M.3
Kishony, R.4
-
98
-
-
33846672214
-
Biological network comparison using graphlet degree distribution
-
Przulj, N (2007). "Biological network comparison using graphlet degree distribution." Bioinformatics 23(2), e177-e183.
-
(2007)
Bioinformatics
, vol.23
, Issue.2
-
-
Przulj, N.1
-
99
-
-
0035843145
-
The protein-protein interaction map of Helicobacter pylori
-
Rain, J-C, et al. (2001). "The protein-protein interaction map of Helicobacter pylori." Nature (London) 409, 211-215.
-
(2001)
Nature (London)
, vol.409
, pp. 211-215
-
-
Rain, J.-C.1
-
100
-
-
67649819681
-
Model criticism with likelihood-free inference, with an application to protein network evolution
-
Ratmann, O, Andrieu, C, Wiuf, C, and Richardson, S (2009). "Model criticism with likelihood-free inference, with an application to protein network evolution." Proc. Nat. Acad. Sci. U.S.A., 106, 10576-10581.
-
(2009)
Proc. Nat. Acad. Sci. U.S.A
, vol.106
, pp. 10576-10581
-
-
Ratmann, O.1
Andrieu, C.2
Wiuf, C.3
Richardson, S.4
-
101
-
-
36949017519
-
Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H pylori and P. falciparum
-
Ratmann, O, Jørgensen, O, Hinkley, T, Stumpf, MP, Richardson, S, and Wiuf, C (2007). "Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H pylori and P. falciparum." PLOS Comput. Biol. 3(2007), 11.
-
(2007)
PLOS Comput. Biol.
, vol.3
, Issue.2007
, pp. 11
-
-
Ratmann, O.1
Jørgensen, O.2
Hinkley, T.3
Stumpf, M.P.4
Richardson, S.5
Wiuf, C.6
-
102
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz, E, Somera, AL, Mongru, DA, Oltvai, ZN, and Barabasi, AL (2002). "Hierarchical organization of modularity in metabolic networks." Science 297, 1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
103
-
-
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(4), 11.
-
(2006)
J. Biol.
, vol.5
, Issue.4
, pp. 11
-
-
Reguly, T.1
-
104
-
-
84857789809
-
Statistical selection of relevant features to classify random, scale free and exponential networks
-
Reyes, L, Conde, E, Lopez, T, Santillán, C, and Izaguirre, R (2008) "Statistical selection of relevant features to classify random, scale free and exponential networks." Innovations in Hybrid Intelligent Systems, 454-461.
-
(2008)
Innovations in Hybrid Intelligent Systems
, pp. 454-461
-
-
Reyes, L.1
Conde, E.2
Lopez, T.3
Santillán, C.4
Izaguirre, R.5
-
105
-
-
14744271727
-
Lasting impressions: Motifs in protein-protein maps may provide footprints of evolutionary events
-
Rice, J, Kershenbaum, A, and Stolovitzky, G (2005). "Lasting impressions: motifs in protein-protein maps may provide footprints of evolutionary events." Proc. Natl. Acad. Sci. U.S.A. 102(9), 3173-3174.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, Issue.9
, pp. 3173-3174
-
-
Rice, J.1
Kershenbaum, A.2
Stolovitzky, G.3
-
106
-
-
0036245438
-
Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
-
Rosenberg, NA, and Nordborg, M (2002). "Genealogical trees, coalescent theory and the analysis of genetic polymorphisms." Nat. Rev. Genet. 3(5), 380-390.
-
(2002)
Nat. Rev. Genet.
, vol.3
, Issue.5
, pp. 380-390
-
-
Rosenberg, N.A.1
Nordborg, M.2
-
107
-
-
27144530248
-
Towards a proteome-scale map of the human proteinprotein interaction network
-
Rual, J, et al. (2005). "Towards a proteome-scale map of the human proteinprotein interaction network." Nature (London) 437, 1173-1178.
-
(2005)
Nature (London)
, vol.437
, pp. 1173-1178
-
-
Rual, J.1
-
108
-
-
54249117223
-
Targeting and tinkering with interaction networks
-
Russell, RB, and Aloy, P (2008). "Targeting and tinkering with interaction networks." Nat. Chem. Biol. 4(11), 666-673.
-
(2008)
Nat. Chem. Biol.
, vol.4
, Issue.11
, pp. 666-673
-
-
Russell, R.B.1
Aloy, P.2
-
109
-
-
39749105401
-
A large-scale protein protein interaction analysis in Synechocystis sp. PCC6803
-
Sato, S, Shimoda, Y, Muraki, A, Kohara, M, Nakamura, Y, and Tabata, S (2007). "A large-scale protein protein interaction analysis in Synechocystis sp. PCC6803." DNA Res. 14(5), 207-216.
-
(2007)
DNA Res
, vol.14
, Issue.5
, pp. 207-216
-
-
Sato, S.1
Shimoda, Y.2
Muraki, A.3
Kohara, M.4
Nakamura, Y.5
Tabata, S.6
-
110
-
-
84857784882
-
Estimating node degree in bait-prey graphs
-
Scholtens D., Chiang T., Huber W., and Gentleman R. (2007). "Estimating node degree in bait-prey graphs." Bioinformatics, http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm565v1.
-
(2007)
Bioinformatics
-
-
Scholtens, D.1
Chiang, T.2
Huber, W.3
Gentleman, R.4
-
111
-
-
33645595576
-
Making sense of high-throughput protein-protein interaction data
-
Scholtens, D, and Gentleman, R (2004). "Making sense of high-throughput protein-protein interaction data." Stat. Appl. Genet. Mol. Biol. 3(1), 39, http://www.bepress.com/sagmb/vol3/iss1/art39.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
, Issue.1
, pp. 39
-
-
Scholtens, D.1
Gentleman, R.2
-
112
-
-
73549094892
-
A large scale analysis of protein protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti
-
Shimoda Y., Shinpo S., Kohara M., Nakamura Y., Tabata S., and Sato S. (2008). "A large scale analysis of protein protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti." DNA Res., http://dnaresearch.oxfordjournals.org/cgi/content/abstract/dsm028v1.
-
(2008)
DNA Res
-
-
Shimoda, Y.1
Shinpo, S.2
Kohara, M.3
Nakamura, Y.4
Tabata, S.5
Sato, S.6
-
113
-
-
33750805181
-
Evolution of complexity in signaling pathways
-
Soyer, O, and Bonhoeffer, S (2006). "Evolution of complexity in signaling pathways." Proc. Natl. Acad. Sci. U.S.A. 103, 16337-16342.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, pp. 16337-16342
-
-
Soyer, O.1
Bonhoeffer, S.2
-
114
-
-
25144498379
-
A human protein-protein interaction network: A resource for annotating the proteome
-
Stelzl, U, et al. (2005). "A human protein-protein interaction network: a resource for annotating the proteome." Cell 122(6), 957-968.
-
(2005)
Cell
, vol.122
, Issue.6
, pp. 957-968
-
-
Stelzl, U.1
-
115
-
-
33646730795
-
Statistical model selection methods applied to biological networks
-
Stumpf, M, Ingram, P, Nouvel, I, and Wiuf, C (2005). "Statistical model selection methods applied to biological networks." Trans. Comp. Sys. Biol. 3, 65-77.
-
(2005)
Trans. Comp. Sys. Biol.
, vol.3
, pp. 65-77
-
-
Stumpf, M.1
Ingram, P.2
Nouvel, I.3
Wiuf, C.4
-
116
-
-
34250322596
-
Evolution at the system level: The natural history of protein interaction networks
-
Stumpf, M, Kelly, W, Thorne, T, and Wiuf, C, (2007). "Evolution at the system level: the natural history of protein interaction networks." Trends Ecol. Evol. 22, 366-373.
-
(2007)
Trends Ecol. Evol.
, vol.22
, pp. 366-373
-
-
Stumpf, M.1
Kelly, W.2
Thorne, T.3
Wiuf, C.4
-
117
-
-
44449159032
-
Multimodel inference of network properties from incomplete data
-
Stumpf, MP H, and Thorne, T (2007). "Multimodel inference of network properties from incomplete data." J. Integr. Bioinformatics 3(32).
-
(2007)
J. Integr. Bioinformatics
, vol.3
, Issue.32
-
-
Stumpf, M.P.H.1
Thorne, T.2
-
118
-
-
0036443972
-
The constraints protein-protein interactions place on sequence divergence
-
Teichmann, S (2002). "The constraints protein-protein interactions place on sequence divergence." J. Mol. Biol. 324, 399-407.
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 399-407
-
-
Teichmann, S.1
-
119
-
-
2442537233
-
Gene regulatory network growth by duplication
-
Teichmann, SA, and Babu, M (2004). "Gene regulatory network growth by duplication." Nat. Genet. 36, 492-496.
-
(2004)
Nat. Genet.
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.2
-
120
-
-
48249128882
-
The binary protein interactome of Treponema pallidum-the Syphilis spirochete
-
Titz, B, Rajagopala, SV, Goll, J, Häuser, R, McKevitt, MT, Palzkill, T, and Uetz, P (2008). "The binary protein interactome of Treponema pallidum-the Syphilis spirochete." PLoS ONE 3(5), e2292, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2386257.
-
(2008)
PLoS ONE
, vol.3
, Issue.5
-
-
Titz, B.1
Rajagopala, S.V.2
Goll, J.3
Häuser, R.4
McKevitt, M.T.5
Palzkill, T.6
Uetz, P.7
-
121
-
-
0034628508
-
A comprehensive analysis of protein-protein interaction networks in Saccharomyces cerevisiae
-
Uetz, PEA (2000). "A comprehensive analysis of protein-protein interaction networks in Saccharomyces cerevisiae." Nature (London) 403, 623-627.
-
(2000)
Nature (London)
, vol.403
, pp. 623-627
-
-
Uetz, P.E.A.1
-
122
-
-
33645124787
-
Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication
-
van Hoof, A (2005). "Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication." Genetics 171, 1455-1461.
-
(2005)
Genetics
, vol.171
, pp. 1455-1461
-
-
van Hoof, A.1
-
123
-
-
11144248635
-
The topological relationship between the largescale attributes and local interaction patterns of complex networks
-
Vazquez, A, et al. (2004). "The topological relationship between the largescale attributes and local interaction patterns of complex networks." Proc. Natl. Acad. Sci. U.S.A. 101, 17940-17945.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A
, vol.101
, pp. 17940-17945
-
-
Vazquez, A.1
-
124
-
-
0013173298
-
Modeling of protein interaction networks
-
Vazquez, A, Flammini, A, Maritan, A, and Vespignani, A (2003). "Modeling of protein interaction networks." ComPlexUs 1, 38-44.
-
(2003)
ComPlexUs
, vol.1
, pp. 38-44
-
-
Vazquez, A.1
Flammini, A.2
Maritan, A.3
Vespignani, A.4
-
125
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering, C, Krause, R, Snel, B, Cornell, M, Oliver, S, Fields, S, and Bork, P (2002). "Comparative assessment of large-scale data sets of protein-protein interactions." Nature (London) 417, 399-403.
-
(2002)
Nature (London)
, vol.417
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.5
Fields, S.6
Bork, P.7
-
126
-
-
0034612214
-
Decoupled evolution of coding region and mRNA expression patterns after gene duplication: Implication for the neutralist-selectionist debate
-
Wagner, A (2000). "Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implication for the neutralist-selectionist debate." Proc. Natl. Acad. Sci. U.S.A. 97(12), 6579-6584.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, Issue.12
, pp. 6579-6584
-
-
Wagner, A.1
-
127
-
-
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(7) 1283-1292.
-
(2001)
Mol. Biol. Evol.
, vol.18
, Issue.7
, pp. 1283-1292
-
-
Wagner, A.1
-
128
-
-
0142198920
-
Does Selection Mold Molecular Networks?
-
2003
-
Wagner, A (2003a). "Does Selection Mold Molecular Networks?." Sci. STKE 2003(202), pe41.
-
(2003)
Sci. STKE
, Issue.202
-
-
Wagner, A.1
-
129
-
-
0037423828
-
How the global structure of protein interaction networks evolves
-
Wagner, A (2003b). "How the global structure of protein interaction networks evolves." Proc. R. Soc. London, Ser. B 270(1514), 457-466.
-
(2003)
Proc. R. Soc. London, Ser. B
, vol.270
, Issue.1514
, pp. 457-466
-
-
Wagner, A.1
-
130
-
-
56549087988
-
Neutralism and selectionism: A network-based reconciliation?
-
Wagner, A (2008). "Neutralism and selectionism: a network-based reconciliation?." Nat. Rev. Genet. 9(12), 965-974.
-
(2008)
Nat. Rev. Genet.
, vol.9
, Issue.12
, pp. 965-974
-
-
Wagner, A.1
-
131
-
-
34347329333
-
In search of the biological significance of modular structures in protein networks
-
Wang, Z, and Zhang, J (2007). "In search of the biological significance of modular structures in protein networks." PLoS Computational Biology, 3.
-
(2007)
PLoS Computational Biology
, pp. 3
-
-
Wang, Z.1
Zhang, J.2
-
132
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
Watts, DJ, and Strogatz, SH (1998). "Collective dynamics of 'small-world' networks." Nature 393 440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
133
-
-
58149203228
-
Superfamily-sophisticated comparative genomics, data mining, visualization and phylogeny
-
Wilson, D, et al. (2009). "Superfamily-sophisticated comparative genomics, data mining, visualization and phylogeny." Nucleic Acids Res. 37, D380-386.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Wilson, D.1
-
134
-
-
33644876493
-
SCOPPI: A structural classification of protein-protein interfaces
-
Winter, C, Henschel, A, Kim, WK, and Schroeder, M (2006). "SCOPPI: a structural classification of protein-protein interfaces." Nuc. Acids Res. 34, D310-314.
-
(2006)
Nuc. Acids Res.
, vol.34
-
-
Winter, C.1
Henschel, A.2
Kim, W.K.3
Schroeder, M.4
-
135
-
-
33646745354
-
A likelihood approach to analysis of network data
-
Wiuf, C, Brameier, M, Hagberg, O, and Stumpf, M (2006). "A likelihood approach to analysis of network data." Proc. Natl. Acad. Sci. U.S.A. 103(20), 7566-7570.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, Issue.20
, pp. 7566-7570
-
-
Wiuf, C.1
Brameier, M.2
Hagberg, O.3
Stumpf, M.4
-
137
-
-
59149103076
-
Challenges and rewards of interaction proteomics
-
Wodak, SJ, Pu, S, Vlasblom, J, and Seraphin, B (2009). "Challenges and rewards of interaction proteomics." Mol. Cell Proteomics 8(1), 3-18.
-
(2009)
Mol. Cell Proteomics
, vol.8
, Issue.1
, pp. 3-18
-
-
Wodak, S.J.1
Pu, S.2
Vlasblom, J.3
Seraphin, B.4
-
138
-
-
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(5898), 104-110.
-
(2008)
Science
, vol.322
, Issue.5898
, pp. 104-110
-
-
Yu, H.1
-
139
-
-
33747379012
-
Design principles of molecular networks revealed by global comparisons and composite motifs
-
Yu, H, Xia, Y, Trifonov, V, and Gerstein, M (2006). "Design principles of molecular networks revealed by global comparisons and composite motifs." Genome Biol. 7(7), R55.
-
(2006)
Genome Biol
, vol.7
, Issue.7
-
-
Yu, H.1
Xia, Y.2
Trifonov, V.3
Gerstein, M.4
|