-
1
-
-
50649096663
-
Analyzing protein interaction networks using structural information
-
10.1146/annurev.biochem.77.062706.133317, 18304007
-
Kiel C, Beltrao P, Serrano L. Analyzing protein interaction networks using structural information. Annu Rev Biochem 2008, 77:415-441. 10.1146/annurev.biochem.77.062706.133317, 18304007.
-
(2008)
Annu Rev Biochem
, vol.77
, pp. 415-441
-
-
Kiel, C.1
Beltrao, P.2
Serrano, L.3
-
2
-
-
70449507494
-
Networks in cell biology
-
Kluwer Academic Publishers, Dubitzky W, Granzow M, Berrar D
-
Rodríguez-Caso C, Sole R. Networks in cell biology. Fundamentals of Data Mining in Genomics and Proteomics 2006, Kluwer Academic Publishers, Dubitzky W, Granzow M, Berrar D.
-
(2006)
Fundamentals of Data Mining in Genomics and Proteomics
-
-
Rodríguez-Caso, C.1
Sole, R.2
-
3
-
-
0035889085
-
The concept of self-organization in cellular architecture
-
2198832, 11604416, 10.1083/jcb.200108110
-
Misteli T. The concept of self-organization in cellular architecture. J Cell Biol 2001, 155:181-185. 2198832, 11604416, 10.1083/jcb.200108110.
-
(2001)
J Cell Biol
, vol.155
, pp. 181-185
-
-
Misteli, T.1
-
4
-
-
2942534300
-
Interactome data and databases: different types of protein interaction
-
2447346, 18629062, 10.1002/cfg.377
-
De Las Rivas J, de Luis A. Interactome data and databases: different types of protein interaction. Comp Funct Genomics 2004, 5:173-178. 2447346, 18629062, 10.1002/cfg.377.
-
(2004)
Comp Funct Genomics
, vol.5
, pp. 173-178
-
-
De Las Rivas, J.1
de Luis, A.2
-
5
-
-
42949165604
-
Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases
-
Palotai R, Szalay MS, Csermely P. Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases. IUBMB Life 2008, 60:10-18.
-
(2008)
IUBMB Life
, vol.60
, pp. 10-18
-
-
Palotai, R.1
Szalay, M.S.2
Csermely, P.3
-
6
-
-
43249097241
-
Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system
-
2526548, 18474041, 10.2144/000112797
-
Ratushny V, Golemis E. Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system. Biotechniques 2008, 44:655-662. 2526548, 18474041, 10.2144/000112797.
-
(2008)
Biotechniques
, vol.44
, pp. 655-662
-
-
Ratushny, V.1
Golemis, E.2
-
7
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
-
(2000)
Nat Genet
, vol.25
, 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
-
8
-
-
33846040633
-
GenBank
-
1781245, 17202161, 10.1093/nar/gkl986
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2007, 35:D21-25. 1781245, 17202161, 10.1093/nar/gkl986.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
9
-
-
0043122944
-
ExPASy: The proteomics server for in-depth protein knowledge and analysis
-
168970, 12824418, 10.1093/nar/gkg563
-
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003, 31:3784-3788. 168970, 12824418, 10.1093/nar/gkg563.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3784-3788
-
-
Gasteiger, E.1
Gattiker, A.2
Hoogland, C.3
Ivanyi, I.4
Appel, R.D.5
Bairoch, A.6
-
10
-
-
56649094590
-
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species
-
2582614, 18836191, 10.1093/nar/gkn619
-
Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res 2008, 36(20):e136. 2582614, 18836191, 10.1093/nar/gkn619.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.20
-
-
Lee, K.1
Chuang, H.Y.2
Beyer, A.3
Sung, M.K.4
Huh, W.K.5
Lee, B.6
Ideker, T.7
-
11
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
10.1038/nature750, 12000970
-
Von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403. 10.1038/nature750, 12000970.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
Von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
12
-
-
33747832812
-
BiologicalNetworks: visualization and analysis tool for systems biology
-
1538788, 16845051, 10.1093/nar/gkl308
-
Baitaluk M, Sedova M, Ray A, Gupta A. BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res 2006, 34:W466-471. 1538788, 16845051, 10.1093/nar/gkl308.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Baitaluk, M.1
Sedova, M.2
Ray, A.3
Gupta, A.4
-
13
-
-
33644874819
-
From genomics to chemical genomics: new developments in KEGG
-
1347464, 16381885, 10.1093/nar/gkj102
-
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-357. 1347464, 16381885, 10.1093/nar/gkj102.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
Katayama, T.7
Araki, M.8
Hirakawa, M.9
-
14
-
-
33747853260
-
APID: Agile Protein Interaction DataAnalyzer
-
1538863, 16845013, 10.1093/nar/gkl128
-
Prieto C, De Las Rivas J. APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res 2006, 34:W298-302. 1538863, 16845013, 10.1093/nar/gkl128.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Prieto, C.1
De Las Rivas, J.2
-
15
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
10.1093/bioinformatics/btg015, 12611808
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
-
16
-
-
84888298863
-
Hypergraph
-
Hypergraph. , http://hypergraph.sourceforge.net
-
-
-
-
17
-
-
84885690991
-
Graphviz
-
Graphviz. , http://www.graphviz.org
-
-
-
-
18
-
-
13844264506
-
IPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
-
10.1093/bioinformatics/bti011, 15353450
-
Finn RD, Marshall M, Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 2005, 21:410-412. 10.1093/bioinformatics/bti011, 15353450.
-
(2005)
Bioinformatics
, vol.21
, pp. 410-412
-
-
Finn, R.D.1
Marshall, M.2
Bateman, A.3
-
19
-
-
13444309633
-
ProViz: protein interaction visualization and exploration
-
10.1093/bioinformatics/bth494, 15347570
-
Iragne F, Nikolski M, Mathieu B, Auber D, Sherman D. ProViz: protein interaction visualization and exploration. Bioinformatics 2005, 21:272-274. 10.1093/bioinformatics/bth494, 15347570.
-
(2005)
Bioinformatics
, vol.21
, pp. 272-274
-
-
Iragne, F.1
Nikolski, M.2
Mathieu, B.3
Auber, D.4
Sherman, D.5
-
20
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
403769, 14597658, 10.1101/gr.1239303
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 403769, 14597658, 10.1101/gr.1239303.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
21
-
-
29144470990
-
Topology, tinkering and evolution of the human transcription factor network
-
10.1111/j.1742-4658.2005.05041.x, 16336278
-
Rodriguez-Caso C, Medina MA, Sole RV. Topology, tinkering and evolution of the human transcription factor network. FEBS J 2005, 272:6423-6434. 10.1111/j.1742-4658.2005.05041.x, 16336278.
-
(2005)
FEBS J
, vol.272
, pp. 6423-6434
-
-
Rodriguez-Caso, C.1
Medina, M.A.2
Sole, R.V.3
-
22
-
-
0038699629
-
The p53-Mdm2 pathway: targets for the development of new anticancer therapeutics
-
10.2174/1389557033488178, 12698949
-
Zheleva DI, Lane DP, Fischer PM. The p53-Mdm2 pathway: targets for the development of new anticancer therapeutics. Mini Rev Med Chem 2003, 3:257-270. 10.2174/1389557033488178, 12698949.
-
(2003)
Mini Rev Med Chem
, vol.3
, pp. 257-270
-
-
Zheleva, D.I.1
Lane, D.P.2
Fischer, P.M.3
-
23
-
-
9144248312
-
IntAct: an open source molecular interaction database
-
308786, 14681455, 10.1093/nar/gkh052
-
Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A. IntAct: an open source molecular interaction database. Nucleic Acids Res 2004, 32:D452-455. 308786, 14681455, 10.1093/nar/gkh052.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Lewington, C.3
Mudali, S.4
Kerrien, S.5
Orchard, S.6
Vingron, M.7
Roechert, B.8
Roepstorff, P.9
Valencia, A.10
-
24
-
-
3042786293
-
A gene network for navigating the literature
-
10.1038/ng0704-664, 15226743
-
Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004, 36:664. 10.1038/ng0704-664, 15226743.
-
(2004)
Nat Genet
, vol.36
, pp. 664
-
-
Hoffmann, R.1
Valencia, A.2
-
25
-
-
0037208166
-
TRANSFAC: transcriptional regulation, from patterns to profiles
-
165555, 12520026, 10.1093/nar/gkg108
-
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31:374-378. 165555, 12520026, 10.1093/nar/gkg108.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
-
26
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
403728, 14525934, 10.1101/gr.1680803
-
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13:2363-2371. 403728, 14525934, 10.1101/gr.1680803.
-
(2003)
Genome Res
, 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
-
27
-
-
0033971642
-
DIP: the database of interacting proteins
-
102387, 10592249, 10.1093/nar/28.1.289
-
Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Res 2000, 28:289-291. 102387, 10592249, 10.1093/nar/28.1.289.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 289-291
-
-
Xenarios, I.1
Rice, D.W.2
Salwinski, L.3
Baron, M.K.4
Marcotte, E.M.5
Eisenberg, D.6
-
28
-
-
33947419351
-
An evaluation of human protein-protein interaction data in the public domain
-
1764475, 17254303, 10.1186/1471-2105-7-S5-S19
-
Mathivanan S, Periaswamy B, Gandhi TK, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A. An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics 2006, 7(Suppl 5):S19. 1764475, 17254303, 10.1186/1471-2105-7-S5-S19.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 5
-
-
Mathivanan, S.1
Periaswamy, B.2
Gandhi, T.K.3
Kandasamy, K.4
Suresh, S.5
Mohmood, R.6
Ramachandra, Y.L.7
Pandey, A.8
-
29
-
-
34248403166
-
Information integration of protein-protein interactions as essential tools for immunomics
-
10.1016/j.cellimm.2006.12.008, 17442285
-
Montanez R, Navas-Delgado I, Medina MA, Aldana-Montes JF, Sanchez-Jimenez F. Information integration of protein-protein interactions as essential tools for immunomics. Cell Immunol 2006, 244:84-86. 10.1016/j.cellimm.2006.12.008, 17442285.
-
(2006)
Cell Immunol
, vol.244
, pp. 84-86
-
-
Montanez, R.1
Navas-Delgado, I.2
Medina, M.A.3
Aldana-Montes, J.F.4
Sanchez-Jimenez, F.5
-
30
-
-
34247098818
-
The usefulness of post-genomics tools for characterization of the amine cross-talk in mammalian cells
-
10.1042/BST0350381, 17371282
-
Sanchez-Jimenez F, Montanez R, Correa-Fiz F, Chaves P, Rodriguez-Caso C, Urdiales JL, Aldana-Montes JF, Medina MA. The usefulness of post-genomics tools for characterization of the amine cross-talk in mammalian cells. Biochem Soc Trans 2007, 35:381-385. 10.1042/BST0350381, 17371282.
-
(2007)
Biochem Soc Trans
, vol.35
, pp. 381-385
-
-
Sanchez-Jimenez, F.1
Montanez, R.2
Correa-Fiz, F.3
Chaves, P.4
Rodriguez-Caso, C.5
Urdiales, J.L.6
Aldana-Montes, J.F.7
Medina, M.A.8
-
31
-
-
34249709500
-
Complexities of targeting innate immunity to treat infection
-
10.1016/j.it.2007.04.005, 17468048
-
Brown KL, Cosseau C, Gardy JL, Hancock RE. Complexities of targeting innate immunity to treat infection. Trends Immunol 2007, 28:260-266. 10.1016/j.it.2007.04.005, 17468048.
-
(2007)
Trends Immunol
, vol.28
, pp. 260-266
-
-
Brown, K.L.1
Cosseau, C.2
Gardy, J.L.3
Hancock, R.E.4
-
32
-
-
70349761106
-
A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining
-
2567339, 18823570, 10.1186/1755-8794-1-46
-
Chen BS, Yang SK, Lan CY, Chuang YJ. A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med Genomics 2008, 1:46. 2567339, 18823570, 10.1186/1755-8794-1-46.
-
(2008)
BMC Med Genomics
, vol.1
, pp. 46
-
-
Chen, B.S.1
Yang, S.K.2
Lan, C.Y.3
Chuang, Y.J.4
-
33
-
-
33644875750
-
PSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
-
1347407, 16381926, 10.1093/nar/gkj044
-
Ng A, Bursteinas B, Gao Q, Mollison E, Zvelebil M. pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res 2006, 34:D527-534. 1347407, 16381926, 10.1093/nar/gkj044.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Ng, A.1
Bursteinas, B.2
Gao, Q.3
Mollison, E.4
Zvelebil, M.5
-
34
-
-
38849203273
-
TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders
-
10.1093/bioinformatics/btm588, 18048394
-
Masotti D, Nardini C, Rossi S, Bonora E, Romeo G, Volinia S, Benini L. TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders. Bioinformatics 2008, 24:428-429. 10.1093/bioinformatics/btm588, 18048394.
-
(2008)
Bioinformatics
, vol.24
, pp. 428-429
-
-
Masotti, D.1
Nardini, C.2
Rossi, S.3
Bonora, E.4
Romeo, G.5
Volinia, S.6
Benini, L.7
-
35
-
-
77956392214
-
Roles of biogenic amines in emergent and rare diseases
-
Research Signpost, Dandrifosse, Pandalai S
-
Correa-fiz F, Reyes-Palomares A, Ruiz-Pérez MV, Medina MA, Sanchez-Jiménez F. Roles of biogenic amines in emergent and rare diseases. Biological aspects of biogenic amines and polyamine conjugates 2008, 16. Research Signpost, Dandrifosse, Pandalai S.
-
(2008)
Biological aspects of biogenic amines and polyamine conjugates
, vol.16
-
-
Correa-fiz, F.1
Reyes-Palomares, A.2
Ruiz-Pérez, M.V.3
Medina, M.A.4
Sanchez-Jiménez, F.5
|