-
3
-
-
33751255087
-
Evaluation of clustering algorithms for protein-protein interaction networks
-
1360682, 16393334
-
Brohee S, van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 2006, 7(488):1-19. 1360682, 16393334.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.488
, pp. 1-19
-
-
Brohee, S.1
van Helden, J.2
-
4
-
-
42749099345
-
Subgraphs in random networks
-
Itzkovitz S, Milo R, Kashtan N, Ziv G, Alon U. Subgraphs in random networks. Physical Review E 2003, 68:026127.
-
(2003)
Physical Review E
, vol.68
, pp. 026127
-
-
Itzkovitz, S.1
Milo, R.2
Kashtan, N.3
Ziv, G.4
Alon, U.5
-
5
-
-
0142059836
-
Protein complexes and functional modules in molecular networks
-
10.1073/pnas.2032324100, 218723, 14517352
-
Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:12123-12128. 10.1073/pnas.2032324100, 218723, 14517352.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, pp. 12123-12128
-
-
Spirin, V.1
Mirny, L.A.2
-
6
-
-
2942544498
-
Protein interaction networks from yeast to human
-
10.1016/j.sbi.2004.05.003, 15193308
-
Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. Protein interaction networks from yeast to human. Current Opinion in Structural Biology 2004, 14:292-299. 10.1016/j.sbi.2004.05.003, 15193308.
-
(2004)
Current Opinion in Structural Biology
, vol.14
, pp. 292-299
-
-
Bork, P.1
Jensen, L.J.2
von Mering, C.3
Ramani, A.K.4
Lee, I.5
Marcotte, E.M.6
-
7
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
10.1038/nature03607, 15944704
-
Palla G, Deranyi I, Farkas I, Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 2005, 435(7043):814-8. 10.1038/nature03607, 15944704.
-
(2005)
Nature
, vol.435
, Issue.7043
, pp. 814-818
-
-
Palla, G.1
Deranyi, I.2
Farkas, I.3
Vicsek, T.4
-
8
-
-
33645830948
-
CFinder: locating cliques and overlapping modules in biological networks
-
10.1093/bioinformatics/btl039, 16473872
-
Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22(8):1021-1023. 10.1093/bioinformatics/btl039, 16473872.
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.J.3
Derenyi, I.4
Vicsek, T.5
-
9
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
140037, 12513700
-
Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4(2):1-27. 140037, 12513700.
-
(2003)
BMC Bioinformatics
, vol.4
, Issue.2
, pp. 1-27
-
-
Bader, G.D.1
Hogue, C.W.2
-
10
-
-
33947219266
-
Large-scale mapping of human protein-protein interactions by mass spectrometry
-
Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson M, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D. Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology 2007, 3(89):1-17.
-
(2007)
Molecular Systems Biology
, vol.3
, Issue.89
, pp. 1-17
-
-
Ewing, R.M.1
Chu, P.2
Elisma, F.3
Li, H.4
Taylor, P.5
Climie, S.6
McBroom-Cerajewski, L.7
Robinson, M.8
O'Connor, L.9
Li, M.10
Taylor, R.11
Dharsee, M.12
Ho, Y.13
Heilbut, A.14
Moore, L.15
Zhang, S.16
Ornatsky, O.17
Bukhman, Y.V.18
Ethier, M.19
Sheng, Y.20
Vasilescu, J.21
Abu-Farha, M.22
Lambert, J.P.23
Duewel, H.S.24
Stewart, I.I.25
Kuehl, B.26
Hogue, K.27
Colwill, K.28
Gladwish, K.29
Muskat, B.30
Kinach, R.31
Adams, S.L.32
Moran, M.F.33
Morin, G.B.34
Topaloglou, T.35
Figeys, D.36
more..
-
11
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
10.1038/nature04209, 16189514
-
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437:1173-1178. 10.1038/nature04209, 16189514.
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
Li, N.6
Berriz, G.F.7
Gibbons, F.D.8
Dreze, M.9
Ayivi-Guedehoussou, N.10
Klitgord, N.11
Simon, C.12
Boxem, M.13
Milstein, S.14
Rosenberg, J.15
Goldberg, D.S.16
Zhang, L.V.17
Wong, S.L.18
Franklin, G.19
Li, S.20
Albala, J.S.21
Lim, J.22
Fraughton, C.23
Llamosas, E.24
Cevik, S.25
Bex, C.26
Lamesch, P.27
Sikorski, R.S.28
Vandenhaute, J.29
Zoghbi, H.Y.30
Smolyar, A.31
Bosak, S.32
Sequerra, R.33
Doucette-Stamm, L.34
Cusick, M.E.35
Hill, D.E.36
Roth, F.P.37
Vidal, M.38
more..
-
12
-
-
25144498379
-
A human protein-protein interaction network: a resource for annotating the proteome
-
10.1016/j.cell.2005.08.029, 16169070
-
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksoz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122(6):957-968. 10.1016/j.cell.2005.08.029, 16169070.
-
(2005)
Cell
, vol.122
, Issue.6
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
Goehler, H.6
Stroedicke, M.7
Zenkner, M.8
Schoenherr, A.9
Koeppen, S.10
Timm, J.11
Mintzlaff, S.12
Abraham, C.13
Bock, N.14
Kietzmann, S.15
Goedde, A.16
Toksoz, E.17
Droege, A.18
Krobitsch, S.19
Korn, B.20
Birchmeier, W.21
Lehrach, H.22
Wanker, E.E.23
more..
-
13
-
-
0035171884
-
BIND - The biomolecular interaction network database
-
10.1093/nar/29.1.242, 29820, 11125103
-
Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. BIND - The biomolecular interaction network database. Nucleic Acids Research 2001, 29:242-245. 10.1093/nar/29.1.242, 29820, 11125103.
-
(2001)
Nucleic Acids Research
, vol.29
, pp. 242-245
-
-
Bader, G.D.1
Donaldson, I.2
Wolting, C.3
Ouellette, B.F.4
Pawson, T.5
Hogue, C.W.6
-
14
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
10.1101/gr.1680803, 403728, 14525934
-
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research 2003, 13:2363-2371. 10.1101/gr.1680803, 403728, 14525934.
-
(2003)
Genome Research
, vol.13
, pp. 2363-2371
-
-
Peri, S.1
Navarro, J.D.2
Amanchy, R.3
Kristiansen, T.Z.4
Jonnalagadda, C.K.5
Surendranath, V.6
Niranjan, V.7
Muthusamy, B.8
Gandhi, T.K.9
Gronborg, M.10
Ibarrola, N.11
Deshpande, N.12
Shanker, K.13
Shivashankar, H.N.14
Rashmi, B.P.15
Ramya, M.A.16
Zhao, Z.17
Chandrika, K.N.18
Padma, N.19
Harsha, H.C.20
Yatish, A.J.21
Kavitha, M.P.22
Menezes, M.23
Choudhury, D.R.24
Suresh, S.25
Ghosh, N.26
Saravana, R.27
Chandran, S.28
Krishna, S.29
Joy, M.30
Anand, S.K.31
Madavan, V.32
Joseph, A.33
Wong, G.W.34
Schiemann, W.P.35
Constantinescu, S.N.36
Huang, L.37
Khosravi-Far, R.38
Steen, H.39
Tewari, M.40
Ghaffari, S.41
Blobe, G.C.42
Dang, C.V.43
Garcia, J.G.44
Pevsner, J.45
Jensen, O.N.46
Roepstorff, P.47
Deshpande, K.S.48
Chinnaiyan, A.M.49
Hamosh, A.50
Chakravarti, A.51
Pandey, A.52
more..
-
15
-
-
25144516911
-
Consolidating the set of known human protein-proteininteractions in prepration for large-scale mapping of the human interactome
-
1175952, 15892868
-
Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM. Consolidating the set of known human protein-proteininteractions in prepration for large-scale mapping of the human interactome. Genome Biology 2005, 6(R40). 1175952, 15892868.
-
(2005)
Genome Biology
, vol.6
, Issue.40
-
-
Ramani, A.K.1
Bunescu, R.C.2
Mooney, R.J.3
Marcotte, E.M.4
-
16
-
-
14744270216
-
A first-draft human protein-interaction map
-
10.1186/gb-2004-5-9-r63, 522870, 15345047
-
Lehner B, Fraser AG. A first-draft human protein-interaction map. Genome Biology 2004, 5:R63. 10.1186/gb-2004-5-9-r63, 522870, 15345047.
-
(2004)
Genome Biology
, vol.5
-
-
Lehner, B.1
Fraser, A.G.2
-
17
-
-
18744376914
-
Online predicted human interaction database
-
10.1093/bioinformatics/bti273, 15657099
-
Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics 2005, 21:2076-2082. 10.1093/bioinformatics/bti273, 15657099.
-
(2005)
Bioinformatics
, vol.21
, pp. 2076-2082
-
-
Brown, K.R.1
Jurisica, I.2
-
18
-
-
58149178567
-
PIPs: human protein-protein interaction prediction database
-
10.1093/nar/gkn870, 2686497, 18988626
-
McDowall MD, Scott MS, Barton GJ. PIPs: human protein-protein interaction prediction database. Nucleic Acids Research 2009, 37:D651-D656. 10.1093/nar/gkn870, 2686497, 18988626.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
McDowall, M.D.1
Scott, M.S.2
Barton, G.J.3
-
19
-
-
58149183207
-
Functional and transcriptional coherency of modules in the human protein interaction network
-
Chaurasia G, Tschaut A, Russ J, Herzel H. Functional and transcriptional coherency of modules in the human protein interaction network. Journal of Integrative Bioinformatics 2007, 4(3):76.
-
(2007)
Journal of Integrative Bioinformatics
, vol.4
, Issue.3
, pp. 76
-
-
Chaurasia, G.1
Tschaut, A.2
Russ, J.3
Herzel, H.4
-
20
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
10.1038/nature04532, 16429126
-
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440:631-636. 10.1038/nature04532, 16429126.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dumpelfeld, B.10
Edelmann, A.11
Heurtier, M.A.12
Hoffman, V.13
Hoefert, C.14
Klein, K.15
Hudak, M.16
Michon, A.M.17
Schelder, M.18
Schirle, M.19
Remor, M.20
Rudi, T.21
Hooper, S.22
Bauer, A.23
Bouwmeester, T.24
Casari, G.25
Drewes, G.26
Neubauer, G.27
Rick, J.M.28
Kuster, B.29
Bork, P.30
Russell, R.B.31
Superti-Furga, G.32
more..
-
21
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces Cerevisiae
-
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis A, Punna T, Peregrin-Alvarez JM, Zhang X, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, F GJ. Global landscape of protein complexes in the yeast Saccharomyces Cerevisiae. Nature 2006, 30(440):637-643.
-
(2006)
Nature
, vol.30
, Issue.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
Tikuisis, A.10
Punna, T.11
Peregrin-Alvarez, J.M.12
Zhang, X.13
Paccanaro, A.14
Bray, J.E.15
Sheung, A.16
Beattie, B.17
Richards, D.P.18
Canadien, V.19
Lalev, A.20
Mena, F.21
Wong, P.22
Starostine, A.23
Canete, M.M.24
Vlasblom, J.25
Wu, S.26
Orsi, C.27
Collins, S.R.28
Chandran, S.29
Haw, R.30
Rilstone, J.J.31
Gandi, K.32
Thompson, N.J.33
Musso, G.34
St Onge, P.35
Ghanny, S.36
Lam, M.H.37
Butland, G.38
Altaf-Ul, A.M.39
Kanaya, S.40
Shilatifard, A.41
O'Shea, E.42
Weissman, J.S.43
Ingles, C.J.44
Hughes, T.R.45
Parkinson, J.46
Gerstein, M.47
Wodak, S.J.48
Emili, A.49
F, G.J.50
more..
-
22
-
-
33847744247
-
How complete are current yeast and human protein-interaction networks?
-
10.1186/gb-2006-7-11-120, 1794583, 17147767
-
Hart GT, Ramani AK, Marcotte EM. How complete are current yeast and human protein-interaction networks?. Genome Biology 2006, 7(11):120. 10.1186/gb-2006-7-11-120, 1794583, 17147767.
-
(2006)
Genome Biology
, vol.7
, Issue.11
, pp. 120
-
-
Hart, G.T.1
Ramani, A.K.2
Marcotte, E.M.3
-
23
-
-
25444448797
-
Fromthe Cover: Spontaneous evolution ofmodularity and network motifs
-
10.1073/pnas.0503610102, 1236541, 16174729
-
Kashtan N, Alon U. Fromthe Cover: Spontaneous evolution ofmodularity and network motifs. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:13773-13778. 10.1073/pnas.0503610102, 1236541, 16174729.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 13773-13778
-
-
Kashtan, N.1
Alon, U.2
-
24
-
-
33846048729
-
UniHI: an entry gate to the human protein interactome
-
Chaurasia G, Iqbal Y, Hanig C, Herzel H, Wanker E, Futschik E. UniHI: an entry gate to the human protein interactome. Nucleic Acids Research 2007, DB(D):590-594.
-
(2007)
Nucleic Acids Research
, pp. 590-594
-
-
Chaurasia, G.1
Iqbal, Y.2
Hanig, C.3
Herzel, H.4
Wanker, E.5
Futschik, E.6
-
25
-
-
0242659154
-
Bioinformatics analysis of experimentally determined protein complexes in the Yeast Saccharomyces Cerevisiae
-
10.1101/gr.1073603, 403764, 14559778
-
Dezso Z, Oltvai ZN, Barabasi AL. Bioinformatics analysis of experimentally determined protein complexes in the Yeast Saccharomyces Cerevisiae. Genome Research 2003, 13:2450-2454. 10.1101/gr.1073603, 403764, 14559778.
-
(2003)
Genome Research
, vol.13
, pp. 2450-2454
-
-
Dezso, Z.1
Oltvai, Z.N.2
Barabasi, A.L.3
-
26
-
-
57749210454
-
An in silico method for detecting overlapping functional modules from composite biological networks
-
2600641, 18976494
-
Maraziotis IA, Dimitrakopoulou K, Bezerianos A. An in silico method for detecting overlapping functional modules from composite biological networks. BMC Systems Biology 2008, 2(93). 2600641, 18976494.
-
(2008)
BMC Systems Biology
, vol.2
, Issue.93
-
-
Maraziotis, I.A.1
Dimitrakopoulou, K.2
Bezerianos, A.3
-
27
-
-
35349016017
-
Flexible web-based integration of distributed large-scale human protein interaction maps
-
Chaurasia G, Iqbal Y, Hanig C, Herzel H, Wanker EE, Futschik ME. Flexible web-based integration of distributed large-scale human protein interaction maps. Journal of Integrative Bioinformatics 2007, 4(3).
-
(2007)
Journal of Integrative Bioinformatics
, vol.4
, Issue.3
-
-
Chaurasia, G.1
Iqbal, Y.2
Hanig, C.3
Herzel, H.4
Wanker, E.E.5
Futschik, M.E.6
-
28
-
-
66249092826
-
Information flow analysis of interactome networks
-
10.1371/journal.pcbi.1000350, 2685719, 19503817
-
Missiuro PV, Liu K, Zou L, Ross BC, Zhao G, Liu JS, Ge H. Information flow analysis of interactome networks. PLos Computational Biology 2009, 5(4):e1000350. 10.1371/journal.pcbi.1000350, 2685719, 19503817.
-
(2009)
PLos Computational Biology
, vol.5
, Issue.4
-
-
Missiuro, P.V.1
Liu, K.2
Zou, L.3
Ross, B.C.4
Zhao, G.5
Liu, J.S.6
Ge, H.7
-
29
-
-
0033518234
-
From molecular to modular cell biology
-
10.1038/35011540, 10591225
-
Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402:c47-c52. 10.1038/35011540, 10591225.
-
(1999)
Nature
, vol.402
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
30
-
-
27244456660
-
Finding local community structure in networks
-
Clauset A. Finding local community structure in networks. Physical Review E 2005, 72:026132.
-
(2005)
Physical Review E
, vol.72
, pp. 026132
-
-
Clauset, A.1
-
31
-
-
33846126275
-
Resolution limit in community detection
-
10.1073/pnas.0605965104, 1765466, 17190818
-
Fortunato S, Barthelemy M. Resolution limit in community detection. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:36-41. 10.1073/pnas.0605965104, 1765466, 17190818.
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, pp. 36-41
-
-
Fortunato, S.1
Barthelemy, M.2
-
32
-
-
34250655368
-
An information-theoretic framework for resolving community structure in complex networks
-
10.1073/pnas.0611034104, 1855072, 17452639
-
Roswall M, Bergstrom CT. An information-theoretic framework for resolving community structure in complex networks. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(18):7327-7331. 10.1073/pnas.0611034104, 1855072, 17452639.
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.18
, pp. 7327-7331
-
-
Roswall, M.1
Bergstrom, C.T.2
-
33
-
-
34848890341
-
Extracting the hierarchical organization of complex systems
-
10.1073/pnas.0703740104, 2000510, 17881571
-
Sales-Pardo M, Guimera' R, Moreira AA, Amaral AN. Extracting the hierarchical organization of complex systems. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(39):15224-15229. 10.1073/pnas.0703740104, 2000510, 17881571.
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.39
, pp. 15224-15229
-
-
Sales-Pardo, M.1
Guimera', R.2
Moreira, A.A.3
Amaral, A.N.4
-
34
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
10.1038/nature02555, 15190252
-
Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93. 10.1038/nature02555, 15190252.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
35
-
-
2442477788
-
Genomic analysis of essentiality within protein networks
-
10.1016/j.tig.2004.04.008, 15145574
-
Yu H, Greenbaum D, Lu HX, Zhu X, Gerstein M. Genomic analysis of essentiality within protein networks. Trends in Genetics 2004, 20(6):227-231. 10.1016/j.tig.2004.04.008, 15145574.
-
(2004)
Trends in Genetics
, vol.20
, Issue.6
, pp. 227-231
-
-
Yu, H.1
Greenbaum, D.2
Lu, H.X.3
Zhu, X.4
Gerstein, M.5
-
36
-
-
0035799707
-
Lethality and centrality in protein networks
-
10.1038/35075138, 11333967
-
Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
37
-
-
33745712594
-
Why do hubs tend to be essential in protein networks?
-
10.1371/journal.pgen.0020088, 1473040,1473040, 16751849
-
He X, Zhang J. Why do hubs tend to be essential in protein networks?. PLoS Genetics 2006, 2(6):e88. 10.1371/journal.pgen.0020088, 1473040,1473040, 16751849.
-
(2006)
PLoS Genetics
, vol.2
, Issue.6
-
-
He, X.1
Zhang, J.2
-
38
-
-
50949092459
-
Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
-
10.1371/journal.pcbi.1000140, 2467474, 18670624
-
Zotenko E, Mestre J, O'Leary DP, Przytycka TM. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Computational Biology 2008, 4(8):e1000140. 10.1371/journal.pcbi.1000140, 2467474, 18670624.
-
(2008)
PLoS Computational Biology
, vol.4
, Issue.8
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
40
-
-
37649028224
-
Finding and evaluating community structure in networks
-
Newman MEJ, Girvan M. Finding and evaluating community structure in networks. Physical Review E 2004, 69:026113.
-
(2004)
Physical Review E
, vol.69
, pp. 026113
-
-
Newman, M.E.J.1
Girvan, M.2
-
42
-
-
33947724499
-
Characterization of complex networks: a survey of measurements
-
Costa L, Rodrigues FA, Travieso G, Villas Boas PR. Characterization of complex networks: a survey of measurements. Advances in Physics 2007, 56:167-242.
-
(2007)
Advances in Physics
, vol.56
, pp. 167-242
-
-
Costa, L.1
Rodrigues, F.A.2
Travieso, G.3
Villas Boas, P.R.4
-
43
-
-
38849162343
-
Computing communities in large networks using random walks
-
Pons P, Latapy M. Computing communities in large networks using random walks. Journal of Graph Algorithms and Applications 2006, 10(2):191-218.
-
(2006)
Journal of Graph Algorithms and Applications
, vol.10
, Issue.2
, pp. 191-218
-
-
Pons, P.1
Latapy, M.2
-
44
-
-
77951138987
-
The performance of modularity maximization in practical contexts
-
Good BH, Montjoye YA, Clauset A. The performance of modularity maximization in practical contexts. Physical Review E 2010, 81:046106.
-
(2010)
Physical Review E
, vol.81
, pp. 046106
-
-
Good, B.H.1
Montjoye, Y.A.2
Clauset, A.3
-
46
-
-
34047168855
-
Comparison of human protein-protein interaction maps
-
10.1093/bioinformatics/btl683, 17237052
-
Futschik ME, Chaurasia G, Herzel H. Comparison of human protein-protein interaction maps. Bioinformatics 2007, 23(5):605-611. 10.1093/bioinformatics/btl683, 17237052.
-
(2007)
Bioinformatics
, vol.23
, Issue.5
, pp. 605-611
-
-
Futschik, M.E.1
Chaurasia, G.2
Herzel, H.3
-
47
-
-
0142184341
-
Global analysis of protein localization in budding yeast
-
10.1038/nature02026, 14562095
-
Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature 2003, 425(6959):686-91. 10.1038/nature02026, 14562095.
-
(2003)
Nature
, vol.425
, Issue.6959
, pp. 686-691
-
-
Huh, W.K.1
Falvo, J.V.2
Gerke, L.C.3
Carroll, A.S.4
Howson, R.W.5
Weissman, J.S.6
O'Shea, E.K.7
-
48
-
-
33749508463
-
Characterization and prediction of protein-protein interations within and between complexes
-
10.1073/pnas.0603352103, 1595418, 17003128
-
Sprinzak E, Altuvia Y, Margalit H. Characterization and prediction of protein-protein interations within and between complexes. Proceedings of the National Academy of Sciences of the United States of America 2006, 103(40):14718-14723. 10.1073/pnas.0603352103, 1595418, 17003128.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.40
, pp. 14718-14723
-
-
Sprinzak, E.1
Altuvia, Y.2
Margalit, H.3
-
49
-
-
38549163153
-
CORUM: the comprehensive resource of mammalian protein complexes
-
2238909, 17965090
-
Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stumpflen V, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Research 2008, 36(DB):D646-50. 2238909, 17965090.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 646-50
-
-
Ruepp, A.1
Brauner, B.2
Dunger-Kaltenbach, I.3
Frishman, G.4
Montrone, C.5
Stransky, M.6
Waegele, B.7
Schmidt, T.8
Doudieu, O.N.9
Stumpflen, V.10
Mewes, H.W.11
-
50
-
-
67849118790
-
COFECO: composite function annotation enriched by protein complex data
-
10.1093/nar/gkp331, 2703949, 19429688
-
Sun CH, Kim MS, Han Y, Yi GS. COFECO: composite function annotation enriched by protein complex data. Nucleic Acids Research 2009, 37(2):W350-W355. 10.1093/nar/gkp331, 2703949, 19429688.
-
(2009)
Nucleic Acids Research
, vol.37
, Issue.2
-
-
Sun, C.H.1
Kim, M.S.2
Han, Y.3
Yi, G.S.4
-
51
-
-
76749084811
-
Protein interaction networks - More than mere modules
-
10.1371/journal.pcbi.1000659, 2813263, 20126533
-
Pinkert S, Schultz J, Reichardt J. Protein interaction networks - More than mere modules. PLoS Computational Biology 2010, 6:e1000659. 10.1371/journal.pcbi.1000659, 2813263, 20126533.
-
(2010)
PLoS Computational Biology
, vol.6
-
-
Pinkert, S.1
Schultz, J.2
Reichardt, J.3
-
53
-
-
46149108150
-
Using indirect protein-protein interactions for protein complex prediction
-
10.1142/S0219720008003497, 18574858
-
Chua HN, Ning K, Sung WK, Leong HW, Wong L. Using indirect protein-protein interactions for protein complex prediction. Journal of Bioinformatics and Computational Biology 2008, 6(3):435-466. 10.1142/S0219720008003497, 18574858.
-
(2008)
Journal of Bioinformatics and Computational Biology
, vol.6
, Issue.3
, pp. 435-466
-
-
Chua, H.N.1
Ning, K.2
Sung, W.K.3
Leong, H.W.4
Wong, L.5
-
54
-
-
65549085067
-
Power-law distributions in empirical data
-
[ArXiv:0706.1062]
-
Clauset A, Shalizi CR. Power-law distributions in empirical data. SIAM Review 2009, 51:661-703. [ArXiv:0706.1062].
-
(2009)
SIAM Review
, vol.51
, pp. 661-703
-
-
Clauset, A.1
Shalizi, C.R.2
-
55
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Research 2004, DB1(32):277-80.
-
(2004)
Nucleic Acids Research
, Issue.32
, pp. 277-280
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
56
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
10.1101/gr.205602, 155252, 11779829
-
Jansen R, Greenbaum D, Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Research 2002, 12:37-46. 10.1101/gr.205602, 155252, 11779829.
-
(2002)
Genome Research
, vol.12
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
57
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
10.1126/science.1105103, 15692050
-
de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science 2005, 307:724-727. 10.1126/science.1105103, 15692050.
-
(2005)
Science
, vol.307
, pp. 724-727
-
-
de Lichtenberg, U.1
Jensen, L.J.2
Brunak, S.3
Bork, P.4
-
58
-
-
58149193234
-
STRING 8 - a global view on proteins and their functional interactions in 630 organisms
-
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research 2008, 1(5).
-
(2008)
Nucleic Acids Research
, vol.1
, Issue.5
-
-
Jensen, L.J.1
Kuhn, M.2
Stark, M.3
Chaffron, S.4
Creevey, C.5
Muller, J.6
Doerks, T.7
Julien, P.8
Roth, A.9
Simonovic, M.10
Bork, P.11
von Mering, C.12
-
59
-
-
0347473809
-
Gaining confidence in high-throughput protein interaction networks
-
10.1038/nbt924, 14704708
-
Bader JS, Chaudhuri A, Rothberg JM, Chant J. Gaining confidence in high-throughput protein interaction networks. Nature Biotechnology 2004, 22:78-85. 10.1038/nbt924, 14704708.
-
(2004)
Nature Biotechnology
, vol.22
, pp. 78-85
-
-
Bader, J.S.1
Chaudhuri, A.2
Rothberg, J.M.3
Chant, J.4
-
60
-
-
33747586075
-
A direct comparison of protein interaction confidence assignment schemes
-
Sulthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics 2006, 26(7):360.
-
(2006)
BMC Bioinformatics
, vol.26
, Issue.7
, pp. 360
-
-
Sulthram, S.1
Shlomi, T.2
Ruppin, E.3
Sharan, R.4
Ideker, T.5
-
61
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
-
10.1093/bioinformatics/btn161, 2718639, 18586718
-
Dittrich MT. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24:i223-i231. 10.1093/bioinformatics/btn161, 2718639, 18586718.
-
(2008)
Bioinformatics
, vol.24
-
-
Dittrich, M.T.1
-
62
-
-
58149213932
-
Literature-curated protein interaction datasets
-
10.1038/nmeth.1284, 2683745, 19116613
-
Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, Vandenhaute J, Yazaki J, Hill DE, Ecker JR, Roth FP. Literature-curated protein interaction datasets. Nature Methods 2009, 6:39-46. 10.1038/nmeth.1284, 2683745, 19116613.
-
(2009)
Nature Methods
, vol.6
, pp. 39-46
-
-
Cusick, M.E.1
Yu, H.2
Smolyar, A.3
Venkatesan, K.4
Carvunis, A.R.5
Simonis, N.6
Rual, J.F.7
Borick, H.8
Braun, P.9
Dreze, M.10
Vandenhaute, J.11
Yazaki, J.12
Hill, D.E.13
Ecker, J.R.14
Roth, F.P.15
-
63
-
-
0036497195
-
Self-organization of theWeb and identification of communities
-
Flake GW, Lawrence S, Giles CL, Coetzee FM. Self-organization of theWeb and identification of communities. IEEE Computer 2002, 35:66-71.
-
(2002)
IEEE Computer
, vol.35
, pp. 66-71
-
-
Flake, G.W.1
Lawrence, S.2
Giles, C.L.3
Coetzee, F.M.4
-
64
-
-
0007015178
-
Finding a maximum density subgraph
-
[Technical report]
-
Goldberg AV. Finding a maximum density subgraph. UCB/CSD, UC Berkeley, CA 1984, 84. [Technical report].
-
(1984)
UCB/CSD, UC Berkeley, CA
, vol.84
-
-
Goldberg, A.V.1
-
65
-
-
0032482432
-
Collective dynamics of "small-world" networks
-
10.1038/30918, 9623998
-
Watts DJ, Strogatz SH. Collective dynamics of "small-world" networks. Nature 1998, 393:440-442. 10.1038/30918, 9623998.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
66
-
-
2942564706
-
Detecting community structure in networks
-
Newman MEJ. Detecting community structure in networks. European Physical Journal B 2004, 38:321-330.
-
(2004)
European Physical Journal B
, vol.38
, pp. 321-330
-
-
Newman, M.E.J.1
-
67
-
-
42749100809
-
Fast algorithm for detecting community structure in networks
-
Newman MEJ. Fast algorithm for detecting community structure in networks. Physical Review E 2004, 69:066133.
-
(2004)
Physical Review E
, vol.69
, pp. 066133
-
-
Newman, M.E.J.1
|