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Volumn 6, Issue , 2012, Pages

CellNOptR: A flexible toolkit to train protein signaling networks to data using multiple logic formalisms

Author keywords

Logic modeling; Perturbation data; Phosphoproteomics; Signaling networks; Systems biology

Indexed keywords

PROTEIN;

EID: 84867537553     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-133     Document Type: Article
Times cited : (158)

References (50)
  • 1
    • 77956554551 scopus 로고    scopus 로고
    • Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes
    • Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK. Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Molecular & Cellular Proteomics: MCP 2010, 9:1849-1865.
    • (2010) Molecular & Cellular Proteomics: MCP , vol.9 , pp. 1849-1865
    • Alexopoulos, L.G.1    Saez-Rodriguez, J.2    Cosgrove, B.D.3    Lauffenburger, D.A.4    Sorger, P.K.5
  • 3
    • 75849156133 scopus 로고    scopus 로고
    • Simplistic pathways or complex networks?
    • Jorgensen C, Linding R. Simplistic pathways or complex networks?. Curr Opin Genet Dev 2010, 20:15-22.
    • (2010) Curr Opin Genet Dev , vol.20 , pp. 15-22
    • Jorgensen, C.1    Linding, R.2
  • 4
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis : current approaches and outstanding challenges
    • Khatri P, Sirota M, Butte A. Ten years of pathway analysis : current approaches and outstanding challenges. Plos Comp Bio 2012, 8:15-22.
    • (2012) Plos Comp Bio , vol.8 , pp. 15-22
    • Khatri, P.1    Sirota, M.2    Butte, A.3
  • 5
    • 68749099453 scopus 로고    scopus 로고
    • Pathway databases and tools for their exploitation: benefits, current limitations and challenges
    • Bauer-Mehren A, Furlong L, Sanz F. Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 2009, 5:290.
    • (2009) Mol Syst Biol , vol.5 , pp. 290
    • Bauer-Mehren, A.1    Furlong, L.2    Sanz, F.3
  • 11
    • 71449120701 scopus 로고    scopus 로고
    • Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
    • Saez-Rodriguez J, Alexopoulos L, Epperlein J, Samaga R, Lauffenburger D, Klamt S, Sorger P. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol 2009, 5:331.
    • (2009) Mol Syst Biol , vol.5 , pp. 331
    • Saez-Rodriguez, J.1    Alexopoulos, L.2    Epperlein, J.3    Samaga, R.4    Lauffenburger, D.5    Klamt, S.6    Sorger, P.7
  • 13
    • 84862167967 scopus 로고    scopus 로고
    • Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks
    • Kirouac D, Saez-Rodriguez J, Swantek J, Burke J, Lauffenburger D, Sorger P. Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol 2012, 6:29.
    • (2012) BMC Syst Biol , vol.6 , pp. 29
    • Kirouac, D.1    Saez-Rodriguez, J.2    Swantek, J.3    Burke, J.4    Lauffenburger, D.5    Sorger, P.6
  • 14
    • 84855921201 scopus 로고    scopus 로고
    • Modeling signaling networks using high-throughput phospho-proteomics
    • Terfve C, Saez-Rodriguez J. Modeling signaling networks using high-throughput phospho-proteomics. Adv Exp Med Biol 2012, 736:19-57.
    • (2012) Adv Exp Med Biol , vol.736 , pp. 19-57
    • Terfve, C.1    Saez-Rodriguez, J.2
  • 15
    • 84875366717 scopus 로고    scopus 로고
    • Crowdsourcing network inference: the DREAM predictive signaling network challenge science signaling 2011
    • Prill R, Saez-Rodriguez J, Alexopoulos L, Sorger P, Stolovitzky G. Crowdsourcing network inference: the DREAM predictive signaling network challenge science signaling 2011. Sci Signal 2011, 30:189.
    • (2011) Sci Signal , vol.30 , pp. 189
    • Prill, R.1    Saez-Rodriguez, J.2    Alexopoulos, L.3    Sorger, P.4    Stolovitzky, G.5
  • 18
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman J. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 1969, 22:437-467.
    • (1969) J Theor Biol , vol.22 , pp. 437-467
    • Kauffman, J.1
  • 21
    • 49549099084 scopus 로고    scopus 로고
    • Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc
    • Gonzalez A, Chaouiya C, Thieffry D. Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. Bioinformatics 2008, 24:234-240.
    • (2008) Bioinformatics , vol.24 , pp. 234-240
    • Gonzalez, A.1    Chaouiya, C.2    Thieffry, D.3
  • 24
    • 84859838760 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with CellNetAnalyzer
    • Klamt S, Saez-Rodriguez J, Gilles E. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 2007, 8:1.
    • (2007) BMC Syst Biol , vol.8 , pp. 1
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.3
  • 25
    • 46249090099 scopus 로고    scopus 로고
    • MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data
    • Ulitsky I, Gat-Viks I, Shamir R. MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. Genome Biol 2008, 9:1.
    • (2008) Genome Biol , vol.9 , pp. 1
    • Ulitsky, I.1    Gat-Viks, I.2    Shamir, R.3
  • 27
    • 77952851181 scopus 로고    scopus 로고
    • BoolNet-an R package for generation, reconstruction and analysis of Boolean networks
    • Mussel C, Hopfensitz M, Kestler H. BoolNet-an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 2010, 26:1378-1380.
    • (2010) Bioinformatics , vol.26 , pp. 1378-1380
    • Mussel, C.1    Hopfensitz, M.2    Kestler, H.3
  • 28
    • 67650351960 scopus 로고    scopus 로고
    • ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists
    • Helikar T, Rogers J. ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. BMC Syst Biol 2009, 6:58.
    • (2009) BMC Syst Biol , vol.6 , pp. 58
    • Helikar, T.1    Rogers, J.2
  • 29
    • 33646352954 scopus 로고    scopus 로고
    • GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks
    • Gonzalez A, Naldi A, Sanchez L, Thieffry D, Chaouiya C. GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems 2006, 84:91-100.
    • (2006) Biosystems , vol.84 , pp. 91-100
    • Gonzalez, A.1    Naldi, A.2    Sanchez, L.3    Thieffry, D.4    Chaouiya, C.5
  • 32
    • 0345269975 scopus 로고    scopus 로고
    • Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
    • de Jong H, Geiselmann J, Hernandez C, Page M. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 2003, 19:336-344.
    • (2003) Bioinformatics , vol.19 , pp. 336-344
    • de Jong, H.1    Geiselmann, J.2    Hernandez, C.3    Page, M.4
  • 33
    • 84874595620 scopus 로고    scopus 로고
    • The Bioconductor project
    • The Bioconductor project. [http://www.bioconductor.org].
  • 35
    • 79953668247 scopus 로고    scopus 로고
    • Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli
    • Morris M, Saez-Rodriguez J, Clarke D, Sorger P, Lauffenburger D. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput Biol 2011, 7:e1001099.
    • (2011) PLoS Comput Biol , vol.7
    • Morris, M.1    Saez-Rodriguez, J.2    Clarke, D.3    Sorger, P.4    Lauffenburger, D.5
  • 36
    • 70449481350 scopus 로고    scopus 로고
    • Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
    • Wittmann D, Krumsiek J, Saez-Rodriguez J, Lauffenburger D, Klamt S, Theis F. Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst Biol 2009, 28:98.
    • (2009) BMC Syst Biol , vol.28 , pp. 98
    • Wittmann, D.1    Krumsiek, J.2    Saez-Rodriguez, J.3    Lauffenburger, D.4    Klamt, S.5    Theis, F.6
  • 37
    • 84875369129 scopus 로고    scopus 로고
    • Genalg: R Based Genetic Algorithm, E Willighagen
    • genalg: R Based Genetic Algorithm, E Willighagen. http://cran.r-project.org/web/packages/genalg/.
  • 38
    • 69549124230 scopus 로고    scopus 로고
    • An evolutionary method for complex-process optimization
    • Egea J, Marti R, Banga J. An evolutionary method for complex-process optimization. Computers & Operations Research 2010, 37:315-324.
    • (2010) Computers & Operations Research , vol.37 , pp. 315-324
    • Egea, J.1    Marti, R.2    Banga, J.3
  • 39
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: new features for data integration and network visualization
    • Smoot M, Ono K, Ruscheinski J, Wang P, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27:431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.1    Ono, K.2    Ruscheinski, J.3    Wang, P.4    Ideker, T.5
  • 41
    • 33646337667 scopus 로고    scopus 로고
    • A methodology for the structural and functional analysis of signaling and regulatory networks
    • Klamt S, Saez-Rodriguez J, Lindquist J, Simeoni L, Gilles E. A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinf 2006, 7:56.
    • (2006) BMC Bioinf , vol.7 , pp. 56
    • Klamt, S.1    Saez-Rodriguez, J.2    Lindquist, J.3    Simeoni, L.4    Gilles, E.5
  • 42
    • 13944252487 scopus 로고    scopus 로고
    • Activity-dependent neuroprotection and cAMP response element-binding protein (CREB): kinase coupling, stimulus intensity, and temporal regulation of CREB phosphorylation at serine 133
    • Lee B, Butcher G, Hoyt K, Impey S, Obrietan K. Activity-dependent neuroprotection and cAMP response element-binding protein (CREB): kinase coupling, stimulus intensity, and temporal regulation of CREB phosphorylation at serine 133. J Neurosci 2005, 25:1137-1148.
    • (2005) J Neurosci , vol.25 , pp. 1137-1148
    • Lee, B.1    Butcher, G.2    Hoyt, K.3    Impey, S.4    Obrietan, K.5
  • 43
    • 65249140538 scopus 로고    scopus 로고
    • CREB in the pathophysiology of cancer: implications for targeting transcription factors for cancer therapy
    • Sakamoto K, Frank D. CREB in the pathophysiology of cancer: implications for targeting transcription factors for cancer therapy. Clin Cancer Res 2009, 15:2583-2587.
    • (2009) Clin Cancer Res , vol.15 , pp. 2583-2587
    • Sakamoto, K.1    Frank, D.2
  • 46
    • 38449088751 scopus 로고    scopus 로고
    • Inferring cellular networks - a review
    • Markowetz F, Spang R. Inferring cellular networks - a review. BMC Bioinf 2007, 8:S5.
    • (2007) BMC Bioinf , vol.8
    • Markowetz, F.1    Spang, R.2
  • 47
    • 74549168922 scopus 로고    scopus 로고
    • Identifying drug effects via pathway alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Datas
    • Mitsos A, Melas IN, Siminelakis P, Chairakaki A, Saez-Rodriguez J, Alexopoulos LG. Identifying drug effects via pathway alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Datas. PLoS Comp Biol 2009, 5(12):e1000591.
    • (2009) PLoS Comp Biol , vol.5 , Issue.12
    • Mitsos, A.1    Melas, I.N.2    Siminelakis, P.3    Chairakaki, A.4    Saez-Rodriguez, J.5    Alexopoulos, L.G.6
  • 48
    • 84860823769 scopus 로고    scopus 로고
    • Reconstructing Boolean Models of Signaling
    • Springer, Berlin, Heidelberg, Chor B
    • Sharan R, Karp RM. Reconstructing Boolean Models of Signaling. Lecture Notes in Computer Science 2012, 261-271. Springer, Berlin, Heidelberg, Chor B.
    • (2012) Lecture Notes in Computer Science , pp. 261-271
    • Sharan, R.1    Karp, R.M.2
  • 50
    • 84866467177 scopus 로고    scopus 로고
    • Integrating literature-constrained and data-driven inference of signalling networks
    • Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J. Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics 2012, 28(18):2311-2317.
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. 2311-2317
    • Eduati, F.1    De Las Rivas, J.2    Di Camillo, B.3    Toffolo, G.4    Saez-Rodriguez, J.5


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