-
1
-
-
0037174638
-
Systems biology: Life's complexity pyramid
-
Oltvai ZN, Barabasi AL. Systems biology: Life's complexity pyramid. Science 2002;298:763-4.
-
(2002)
Science
, vol.298
, pp. 763-764
-
-
Oltvai, Z.N.1
Barabasi, A.L.2
-
2
-
-
30044440098
-
Molecular interaction maps of bioreglatory networks: A general rubric for systems biology
-
Kohn KW, Aladjem MI, Weinstein JN, et al. Molecular interaction maps of bioreglatory networks: A general rubric for systems biology. Mol Biol Cell 2006;17:1-13.
-
(2006)
Mol Biol Cell
, vol.17
, pp. 1-13
-
-
Kohn, K.W.1
Aladjem, M.I.2
Weinstein, J.N.3
-
3
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E, Somera AL, Mongru DA, et al. Hierarchical organization of modularity in metabolic networks. Science 2002;297:1551-5.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
-
4
-
-
0035905782
-
Modelling cellular behaviour
-
Endy D, Brent R. Modelling cellular behaviour. Nature 2001;409 391-5.
-
(2001)
Nature
, vol.409
, pp. 391-395
-
-
Endy, D.1
Brent, R.2
-
5
-
-
1542316919
-
Control of yeast filamentous-form growth by modules in an integrated molecular network
-
Prinz S, Avila-Campillo I, Aldridge C, et al. Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res 2004;14:380-90.
-
(2004)
Genome Res
, vol.14
, pp. 380-390
-
-
Prinz, S.1
Avila-Campillo, I.2
Aldridge, C.3
-
6
-
-
0142059836
-
Protein complexes and functional modules in molecular networks
-
Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 2003;100:12123-8.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12123-12128
-
-
Spirin, V.1
Mirny, L.A.2
-
8
-
-
0037417817
-
Modular organization of cellular networks
-
Rives AW, Galitski T. Modular organization of cellular networks. Proc Natl Acad Sci USA 2003;100: 1128-33.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1128-1133
-
-
Rives, A.W.1
Galitski, T.2
-
10
-
-
33645241830
-
VANTED: A system for advanced data analysis and visualization in the context of biological networks
-
Junker BH, Klukas C, Schreiber F. VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 2006;7:109.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 109
-
-
Junker, B.H.1
Klukas, C.2
Schreiber, F.3
-
11
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
-
13
-
-
35248849697
-
Integrated network reconstruction, visualization and analysis using YANAsquare
-
Schwarz R, Liang C, Kaleta C, et al. Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics 2007;8:313.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 313
-
-
Schwarz, R.1
Liang, C.2
Kaleta, C.3
-
14
-
-
34547816155
-
Metabolic network visualization eliminating node redundance and preserving metabolic pathways
-
Bourqui R, Cottret L, Lacroix V, et al. Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Syst Biol 2007;1:29.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 29
-
-
Bourqui, R.1
Cottret, L.2
Lacroix, V.3
-
15
-
-
34548358584
-
eXpanda: An integrated platform for network analysis and visualization
-
Negishi Y, Nakamura H, Yachie N, et al. eXpanda: An integrated platform for network analysis and visualization. In Silico Biol 2007;7:141-4.
-
(2007)
In Silico Biol
, vol.7
, pp. 141-144
-
-
Negishi, Y.1
Nakamura, H.2
Yachie, N.3
-
16
-
-
35748962289
-
Tools for visually exploring biological networks
-
Suderman M, Hallett M. Tools for visually exploring biological networks. Bioinformatics 2007;23:2651-9.
-
(2007)
Bioinformatics
, vol.23
, pp. 2651-2659
-
-
Suderman, M.1
Hallett, M.2
-
17
-
-
33645151090
-
PathSys: Integrating molecular interacaon graphs for systems biology
-
Baitaluk M, Qian X, Godbole S, et al. PathSys: Integrating molecular interacaon graphs for systems biology. BMC Bioinformatics 2006;7:55.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 55
-
-
Baitaluk, M.1
Qian, X.2
Godbole, S.3
-
18
-
-
13444309633
-
ProViz: Protein interaction visualization and exploration
-
Iragne F, Nikolski M, Mathieu B, et al. ProViz: Protein interaction visualization and exploration. Bioinformatics 2005; 21:272-4.
-
(2005)
Bioinformatics
, vol.21
, pp. 272-274
-
-
Iragne, F.1
Nikolski, M.2
Mathieu, B.3
-
19
-
-
33645119902
-
Analyzing networks with VisANT
-
eds, New Jersey: John Wiley & Sons, Inc, 8.8.1-24
-
Hu Z, Mellor J, DeLisi C. Analyzing networks with VisANT. In: Baxevanis A, Davison D, Page R, et al. (eds). Current Protocols in Bioinformatics. New Jersey: John Wiley & Sons, Inc., 2004,8.8.1-24.
-
(2004)
Current Protocols in Bioinformatics
-
-
Hu, Z.1
Mellor, J.2
DeLisi, C.3
-
20
-
-
2942609149
-
VisANT: An online visualization and analysis tool for biological interaction data
-
Hu Z, Mellor J, Wu J, et al. VisANT: An online visualization and analysis tool for biological interaction data. BMC Bioinformatics 2004;5:17.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 17
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
-
21
-
-
34249653071
-
Towards zoomable multidimensional maps of the cell
-
Hu Z, Mellor J, Wu J, et al. Towards zoomable multidimensional maps of the cell. Nat Biotechnol 2007;25: 547-54.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 547-554
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
-
22
-
-
23144466889
-
VisANT: Data-integrating visual framework for biological networks and modules
-
Hu Z, Mellor J, Wu J, et al. VisANT: Data-integrating visual framework for biological networks and modules. Nucleic Acids Res 2005;33:W352-7.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
-
23
-
-
34547586817
-
VisANT 3.0: New modules for pathway visualization, editing, prediction and construction
-
Hu Z, Ng DM, Yamada T, et al. VisANT 3.0: New modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res 2007;35:W625-32.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Hu, Z.1
Ng, D.M.2
Yamada, T.3
-
24
-
-
0742323374
-
The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data
-
Hermjakob H, Montecchi-Palazzi L, Bader G, et al. The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat Biotechnol 2004; 22:177-83.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Bader, G.3
-
25
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007;2:2366-82.
-
(2007)
Nat Protoc
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
-
26
-
-
0036081482
-
Predictome: A database of putative functional links between proteins
-
Mellor JC, Yanai I, Clodfelter KH, et al. Predictome: A database of putative functional links between proteins. Nucleic Acids Res 2002;30:306-9.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 306-309
-
-
Mellor, J.C.1
Yanai, I.2
Clodfelter, K.H.3
-
27
-
-
0034595516
-
Co-evolution of proteins with their interaction partners
-
Goh CS, Bogan AA, Joachimiak M, et al. Co-evolution of proteins with their interaction partners. J Mol Biol 2000;299: 283-93.
-
(2000)
J Mol Biol
, vol.299
, pp. 283-293
-
-
Goh, C.S.1
Bogan, A.A.2
Joachimiak, M.3
-
28
-
-
33846086800
-
STRING 7 - recent developments in the integration and prediction of protein interactions
-
von Meting C, Jensen LJ, Kuhn M, et al. STRING 7 - recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 2007;35: D358-62.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
von Meting, C.1
Jensen, L.J.2
Kuhn, M.3
-
29
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008;36:D480-4.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
-
30
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
31
-
-
38549170927
-
MIPS: Analysis and annotation of genome information in 2007
-
Mewes HW, Dietmann S, Frishman D, et al. MIPS: Analysis and annotation of genome information in 2007. Nucleic Acids Res 2008;36:D196-201.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Mewes, H.W.1
Dietmann, S.2
Frishman, D.3
-
32
-
-
0037245913
-
The biomolecular interaction network database
-
Bader GD, Betel D, Hogue CW. BIND: The biomolecular interaction network database. Nucleic Acids Res 2003;31: 248-50.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.B.3
-
34
-
-
34547844158
-
Supervised reconstruction of biological networks with local models
-
Bleakley K, Biau G, Vert JP. Supervised reconstruction of biological networks with local models. Bioinformatics 2007; 23:i57-65.
-
(2007)
Bioinformatics
, vol.23
, Issue.I57-65
-
-
Bleakley, K.1
Biau, G.2
Vert, J.P.3
-
35
-
-
0142052944
-
A Bayesian networks approach for predicting protein-protein interactions from genornic data
-
Jansen R, Yu H, Greenbaum D, et al. A Bayesian networks approach for predicting protein-protein interactions from genornic data. Science 2003;302:449-53.
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
Yu, H.2
Greenbaum, D.3
-
37
-
-
0035998736
-
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh A, Scott AF, Amberger J, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2002;30:52-5.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 52-55
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.3
-
38
-
-
38549097071
-
The universal protein resource (UniProt)
-
The universal protein resource (UniProt). Nucleic Acids Res 2008;36:D190-5.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
-
39
-
-
38549117309
-
The HGNC Database in 2008: A resource for the human genome
-
Bruford EA, Lush MJ, Wright MW, et al. The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res 2008;36 D445-8.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Bruford, E.A.1
Lush, M.J.2
Wright, M.W.3
-
41
-
-
45949108954
-
Protein interactions in human genetic diseases
-
Schuster-Bockler B, Bateman A. Protein interactions in human genetic diseases. Genome Biol 2008;9:R9.
-
(2008)
Genome Biol
, vol.9
-
-
Schuster-Bockler, B.1
Bateman, A.2
-
42
-
-
1942469444
-
Network motifs in integrated cellular networks of transcription- regulation and protein-protein interaction
-
Yeger-Lotem E, Sattath S, Kashtan N, et al. Network motifs in integrated cellular networks of transcription- regulation and protein-protein interaction. Proc Natl Acad Sci USA 2004;101 5934-9.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 5934-5939
-
-
Yeger-Lotem, E.1
Sattath, S.2
Kashtan, N.3
-
43
-
-
33847051248
-
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
-
Zhang LV, King OD, Wong SL, et al. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 2005;4:6.
-
(2005)
J Biol
, vol.4
, pp. 6
-
-
Zhang, L.V.1
King, O.D.2
Wong, S.L.3
-
49
-
-
36249031117
-
Gene set enrichment analysis reveals several globally affected pathways due to SKI-1/S1P inhibition in HepG2 cells
-
De Windt A, Rai M, Bernier L, et al. Gene set enrichment analysis reveals several globally affected pathways due to SKI-1/S1P inhibition in HepG2 cells. DNA Cell Biol 2007; 26:765-72.
-
(2007)
DNA Cell Biol
, vol.26
, pp. 765-772
-
-
De Windt, A.1
Rai, M.2
Bernier, L.3
-
50
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005;102 15545-50.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
-
51
-
-
33750580714
-
Grouping Gene Ontology terms to improve the assessment of gene set enrichment in micro-array data
-
Lewin A, Grieve IC. Grouping Gene Ontology terms to improve the assessment of gene set enrichment in micro-array data. BMC Bioinformatics 2006;7:426.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 426
-
-
Lewin, A.1
Grieve, I.C.2
-
52
-
-
35348826675
-
A multivariate extension of the gene set enrichment analysis
-
Klebanov L, Glazko G, Salzman P, et al. A multivariate extension of the gene set enrichment analysis. J Bioinform Comput Biol 2007;5:1139-53.
-
(2007)
J Bioinform Comput Biol
, vol.5
, pp. 1139-1153
-
-
Klebanov, L.1
Glazko, G.2
Salzman, P.3
|