-
1
-
-
77955505357
-
Protein-protein interactions essentials: Key concepts to building and analyzing interactome networks
-
De Las Rivas, J. and Fontanillo, C. (2010) Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput. Biol., 60, e1000807.
-
(2010)
PLoS Comput. Biol.
, vol.60
-
-
De Las Rivas, J.1
Fontanillo, C.2
-
2
-
-
78651328883
-
The biogrid interaction database: 2011 update
-
Database issue
-
Stark, C., Breitkreutz, B.-J., Chatr-Aryamontri, A. et al. (2011) The BioGRID interaction database: 2011 update. Nucleic Acids. Res., 39(Database issue), D698-D704.
-
(2011)
Nucleic Acids. Res.
, vol.39
-
-
Stark, C.1
Breitkreutz, B.-J.2
Chatr-Aryamontri, A.3
-
3
-
-
75549087047
-
The intact molecular interaction database in 2010
-
Database issue
-
Aranda, B., Achuthan, P., Alam-Faruque, Y. et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids. Res., 38(Database issue), D525-D531.
-
(2010)
Nucleic Acids. Res.
, vol.38
-
-
Aranda, B.1
Achuthan, P.2
Alam-Faruque, Y.3
-
4
-
-
75549083295
-
Mint, the molecular interaction database: 2009 update
-
Database issue
-
Ceol, A., Chatr-Aryamontri, A., Licata, L. et al. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids. Res., 38(Database issue), D532-D539.
-
(2010)
Nucleic Acids. Res.
, vol.38
-
-
Ceol, A.1
Chatr-Aryamontri, A.2
Licata, L.3
-
5
-
-
0347755535
-
The Database of Interacting Proteins: 2004 update
-
Salwinski, L., Miller, C. S., Smith, A. J. et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids. Res., 32(Database issue), D449-D451. (Pubitemid 38081696)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
6
-
-
13444272070
-
The Biomolecular Interaction Network Database and related tools 2005 update
-
DOI 10.1093/nar/gki051
-
Alfarano, C., Andrade, C. E., Anthony, K. et al. (2005) The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res., 33(Database issue), D418-D424. (Pubitemid 40207907)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Alfarano, C.1
Andrade, C.E.2
Anthony, K.3
Bahroos, N.4
Bajec, M.5
Bantoft, K.6
Betel, D.7
Bobechko, B.8
Boutilier, K.9
Burgess, E.10
Buzadzija, K.11
Cavero, R.12
D'Abreo, C.13
Donaldson, I.14
Dorairajoo, D.15
Dumontier, M.J.16
Dumontier, M.R.17
Earles, V.18
Farrall, R.19
Feldman, H.20
Garderman, E.21
Gong, Y.22
Gonzaga, R.23
Grytsan, V.24
Gryz, E.25
Gu, V.26
Haldorsen, E.27
Halupa, A.28
Haw, R.29
Hrvojic, A.30
Hurrell, L.31
Isserlin, R.32
Jack, F.33
Juma, F.34
Khan, A.35
Kon, T.36
Konopinsky, S.37
Le, V.38
Lee, E.39
Ling, S.40
Magidin, M.41
Moniakis, J.42
Montojo, J.43
Moore, S.44
Muskat, B.45
Ng, I.46
Paraiso, J.P.47
Parker, B.48
Pintilie, G.49
Pirone, R.50
Salama, J.J.51
Sgro, S.52
Shan, T.53
Shu, Y.54
Siew, J.55
Skinner, D.56
Snyder, K.57
Stasiuk, R.58
Strumpf, D.59
Tuekam, B.60
Tao, S.61
Wang, Z.62
White, M.63
Willis, R.64
Wolting, C.65
Wong, S.66
Wrong, A.67
Xin, C.68
Yao, R.69
Yates, B.70
Zhang, S.71
Zheng, K.72
Pawson, T.73
Ouellette, B.F.F.74
Hogue, C.W.V.75
more..
-
8
-
-
58149193222
-
Human protein reference database-2009 update
-
Database issue
-
Keshava Prasad, T. S., Goel, R., Kandasamy, K. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids. Res., 37(Database issue), D767-D772.
-
(2009)
Nucleic Acids. Res.
, vol.37
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
-
9
-
-
58149213932
-
Literature-curated protein interaction data sets
-
Cusick, M. E., Yu, H., Smolyar, A. et al. (2009) Literature-curated protein interaction data sets. Nat. Methods, 6, 39-46.
-
(2009)
Nat. Methods
, vol.6
, pp. 39-46
-
-
Cusick, M.E.1
Yu, H.2
Smolyar, A.3
-
10
-
-
41649106470
-
Submit your interaction data the IMEx way: A step by step guide to trouble-free deposition
-
DOI 10.1002/pmic.200700286
-
Orchard, S., Kerrien, S., Jones, P. et al. (2007) Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics, 7 (Suppl. 1), 28-34. (Pubitemid 351547767)
-
(2007)
Proteomics - Practical Proteomics
, vol.2
, Issue.1
, pp. 28-34
-
-
Orchard, S.1
Kerrien, S.2
Jones, P.3
Ceol, A.4
Chatr-Aryamontri, A.5
Salwinski, L.6
Nerothin, J.7
Hermjakob, H.8
-
11
-
-
35348976204
-
Broadening the horizon-level 2.5 of the hupo-psi format for molecular interactions
-
Kerrien, S., Orchard, S., Montecchi-Palazzi, L. et al. (2007) Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol., 5, 44.
-
(2007)
BMC Biol.
, vol.5
, pp. 44
-
-
Kerrien, S.1
Orchard, S.2
Montecchi-Palazzi, L.3
-
12
-
-
38449088751
-
Inferring cellular networks-A review
-
Markowetz, F. and Spang, R. (2007) Inferring cellular networks-A review. BMC Bioinformatics, 8 (Suppl. 6), S5.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 6
-
-
Markowetz, F.1
Spang, R.2
-
13
-
-
57549085034
-
Prediction of protein-protein interaction networks
-
Gomez, S. M., Choi, K. and Wu, Y. (2008) Prediction of protein-protein interaction networks. Current Protocols in Bioinformatics, 22, 8.2.1-8.2.14.
-
(2008)
Current Protocols in Bioinformatics
, vol.22
, pp. 821-8214
-
-
Gomez, S.M.1
Choi, K.2
Wu, Y.3
-
14
-
-
67149143183
-
Inferring protein-protein interactions from multiple protein domain combinations
-
Kanaan, S. P., Huang, C., Wuchty, S. et al. (2009) Inferring protein-protein interactions from multiple protein domain combinations. Methods Mol. Biol., 541, 43-59.
-
(2009)
Methods Mol. Biol.
, vol.541
, pp. 43-59
-
-
Kanaan, S.P.1
Huang, C.2
Wuchty, S.3
-
15
-
-
72949117638
-
Predicting protein-protein interactions in the context of protein evolution
-
Lewis, A. C. F., Saeed, R. and Deane, C. M. (2010) Predicting protein-protein interactions in the context of protein evolution. Mol. Biosyst., 6, 55-64.
-
(2010)
Mol. Biosyst.
, vol.6
, pp. 55-64
-
-
Lewis, A.C.F.1
Saeed, R.2
Deane, C.M.3
-
16
-
-
67349200229
-
Interaction networks: From protein functions to drug discovery. A review
-
Chautard, E., Thierry-Mieg, N. and Ricard-Blum, S. (2009) Interaction networks: from protein functions to drug discovery. A review. Pathol. Biol., 57, 324-333.
-
(2009)
Pathol. Biol.
, vol.57
, pp. 324-333
-
-
Chautard, E.1
Thierry-Mieg, N.2
Ricard-Blum, S.3
-
17
-
-
77950353931
-
Toward the dynamic interactome: It's about time
-
Przytycka, T. M., Singh, M. and Slonim, D. K. (2010) Toward the dynamic interactome: it's about time. Brief. Bioinform., 11, 15-29.
-
(2010)
Brief. Bioinform.
, vol.11
, pp. 15-29
-
-
Przytycka, T.M.1
Singh, M.2
Slonim, D.K.3
-
18
-
-
75549091794
-
Corum: The comprehensive resource of mammalian protein complexes-2009
-
Database issue
-
Ruepp, A., Waegele, B., Lechner, M. et al. (2010) CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res., 38(Database issue), D497-D501.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Ruepp, A.1
Waegele, B.2
Lechner, M.3
-
19
-
-
33644878150
-
Mpact: The mips protein interaction resource on yeast
-
Database issue
-
Gldener, U., Mnsterktter, M., Oesterheld, M. et al. (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res., 34(Database issue), D436-D441.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Gldener, U.1
Mnsterktter, M.2
Oesterheld, M.3
-
20
-
-
20144387067
-
The MIPS mammalian protein-protein interaction database
-
DOI 10.1093/bioinformatics/bti115
-
Pagel, P., Kovac, S., Oesterheld, M. et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834. (Pubitemid 40439425)
-
(2005)
Bioinformatics
, vol.21
, Issue.6
, pp. 832-834
-
-
Pagel, P.1
Kovac, S.2
Oesterheld, M.3
Brauner, B.4
Dunger-Kaltenbach, I.5
Frishman, G.6
Montrone, C.7
Mark, P.8
Stumpflen, V.9
Mewes, H.-W.10
Ruepp, A.11
Frishman, D.12
-
21
-
-
18744376914
-
Online predicted human interaction database
-
DOI 10.1093/bioinformatics/bti273
-
Brown, K. R. and Jurisica, I. (2005) Online predicted human interaction database. Bioinformatics, 21, 2076-2082. (Pubitemid 40668047)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2076-2082
-
-
Brown, K.R.1
Jurisica, I.2
-
22
-
-
54949127160
-
Irefindex: A consolidated protein interaction database with provenance
-
Razick, S., Magklaras, G. and Donaldson, I. M. (2008) iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics, 9, 405.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 405
-
-
Razick, S.1
Magklaras, G.2
Donaldson, I.M.3
-
23
-
-
79952052352
-
Irefweb: Interactive analysis of consolidated protein interaction data and their supporting evidence
-
doi:10.1093/database/baq023
-
Turner, B., Razick, S., Turinsky, A. L. et al. (2010) iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database, doi:10.1093/database/baq023.
-
(2010)
Database
-
-
Turner, B.1
Razick, S.2
Turinsky, A.L.3
-
24
-
-
79952676403
-
Literature curation of protein interactions: Measuring agreement across major public databases
-
doi:10.1093/database/baq026
-
Turinsky, A. L., Razick, S., Turner, B. et al. (2010) Literature curation of protein interactions: measuring agreement across major public databases. Database, doi:10.1093/database/baq026.
-
(2010)
Database
-
-
Turinsky, A.L.1
Razick, S.2
Turner, B.3
-
25
-
-
69849111694
-
Itm probe: Analyzing information flow in protein networks
-
Stojmirović, A. and Yu, Y.-K. (2009) ITM Probe: analyzing information flow in protein networks. Bioinformatics, 25, 2447-2449.
-
(2009)
Bioinformatics
, vol.25
, pp. 2447-2449
-
-
Stojmirović, A.1
Yu, Y.-K.2
-
26
-
-
78651317908
-
Entrez gene: Gene-centered information at ncbi
-
Database issue
-
Maglott, D., Ostell, J., Pruitt, K. D. et al. (2011) Entrez Gene: gene-centered information at NCB I. Nucleic Acids Res, 39(Database issue), D52-D577.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Maglott, D.1
Ostell, J.2
Pruitt, K.D.3
-
27
-
-
75849153303
-
The universal protein resource (uniprot) in 2010
-
Database issue
-
UniProt Consortium (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38(Database issue), D142-D148.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
UniProt Consortium1
-
28
-
-
35948989284
-
The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
-
DOI 10.1038/nbt1346, PII NBT1346
-
Smith, B., Ashburner, M., Rosse, C. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251-1255. (Pubitemid 350076511)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.11
, pp. 1251-1255
-
-
Smith, B.1
Ashburner, M.2
Rosse, C.3
Bard, J.4
Bug, W.5
Ceusters, W.6
Goldberg, L.J.7
Eilbeck, K.8
Ireland, A.9
Mungall, C.J.10
Leontis, N.11
Rocca-Serra, P.12
Ruttenberg, A.13
Sansone, S.-A.14
Scheuermann, R.H.15
Shah, N.16
Whetzel, P.L.17
Lewis, S.18
-
29
-
-
10744230485
-
Global mapping of the yeast genetic interaction network
-
DOI 10.1126/science.1091317
-
Tong, A. H. Y., Lesage, G., Bader, G. D. et al. (2004) Global mapping of the yeast genetic interaction network. Science, 303, 808-813. (Pubitemid 38174652)
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 808-813
-
-
Tong, A.H.Y.1
Lesage, G.2
Bader, G.D.3
Ding, H.4
Xu, H.5
Xin, X.6
Young, J.7
Berriz, G.F.8
Brost, R.L.9
Chang, M.10
Chen, Y.11
Cheng, X.12
Chua, G.13
Friesen, H.14
Goldberg, D.S.15
Haynes, J.16
Humphries, C.17
He, G.18
Hussein, S.19
Ke, L.20
Krogan, N.21
Li, Z.22
Levinson, J.N.23
Lu, H.24
Menard, P.25
Munyana, C.26
Parsons, A.B.27
Ryan, O.28
Tonikian, R.29
Roberts, T.30
Sdicu, A.-M.31
Shapiro, J.32
Sheikh, B.33
Suter, B.34
Wong, S.L.35
Zhang, L.V.36
Zhu, H.37
Burd, C.G.38
Munro, S.39
Sander, C.40
Rine, J.41
Greenblatt, J.42
Peter, M.43
Bretscher, A.44
Bell, G.45
Roth, F.P.46
Brown, G.W.47
Andrews, B.48
Bussey, H.49
Boone, C.50
more..
-
30
-
-
34147121646
-
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
-
DOI 10.1074/mcp.M600381-MCP200
-
Collins, S. R., Kemmeren, P., Zhao, X.-C. et al. (2007) Toward a comprehensive atlas of the physical interactome of saccharomyces cerevisiae. Mol. Cell. Proteomics., 6, 439-450. (Pubitemid 46554539)
-
(2007)
Molecular and Cellular Proteomics
, vol.6
, Issue.3
, pp. 439-450
-
-
Collins, S.R.1
Kemmeren, P.2
Zhao, X.-C.3
Greenblatt, J.F.4
Spencer, F.5
Hoolstege, F.C.P.6
Weissman, J.S.7
Krogan, N.J.8
-
31
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin, A.-C., Aloy, P., Grandi, P. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.-C.1
Aloy, P.2
Grandi, P.3
-
32
-
-
33645453254
-
Global landscape of protein complexes in the yeast saccharomyces cerevisiae
-
Krogan, N. J., Cagney, G., Yu, H. et al. (2006) Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature, 440, 637-643.
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
-
33
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner, M., Ball, C. A., Blake, J. A. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
34
-
-
57949094762
-
Raid-dbs: Massspectrometry based peptide identification web server with knowledge integration
-
Alves, G., Ogurtsov, A. Y. and Yu, Y.-K. (2008) RAId-DbS: massspectrometry based peptide identification web server with knowledge integration. BMC Genomics, 9, 505.
-
(2008)
BMC Genomics
, vol.9
, pp. 505
-
-
Alves, G.1
Ogurtsov, A.Y.2
Yu, Y.-K.3
-
35
-
-
14244260623
-
Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae
-
DOI 10.1074/jbc.M413209200
-
Hannich, J. T., Lewis, A., Kroetz, M. B. et al. (2005) Defining the sumo-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem., 280, 4102-4110. (Pubitemid 40288574)
-
(2005)
Journal of Biological Chemistry
, vol.280
, Issue.6
, pp. 4102-4110
-
-
Hannich, J.T.1
Lewis, A.2
Kroetz, M.B.3
Li, S.-J.4
Heide, H.5
Emili, A.6
Hochstrasser, M.7
-
36
-
-
78651275182
-
Reactome: A database of reactions, pathways and biological processes
-
Database issue
-
Croft, D., O'Kelly, G., Wu, G. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39(Database issue), D691-D697.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Croft, D.1
O'Kelly, G.2
Wu, G.3
-
37
-
-
0032476584
-
Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA
-
DOI 10.1093/emboj/17.21.6327
-
Blaiseau, P. L. and Thomas, D. (1998) Multiple transcriptional activation complexes tether the yeast activator Met4 to DN A. EMBO J., 17, 6327-6336. (Pubitemid 28497804)
-
(1998)
EMBO Journal
, vol.17
, Issue.21
, pp. 6327-6336
-
-
Blaiseau, P.-L.1
Thomas, D.2
|