Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Mitsos, Alexander ^a   Melas, Ioannis N ^b   Morris, Melody K ^a,c   Saez Rodriguez, Julio ^d   Lauffenburger, Douglas A ^a,c   Alexopoulos, Leonidas G ^b  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FUZZY LOGIC; GENETIC ALGORITHM; INFORMATION SCIENCE; LIVER CELL; MATHEMATICAL MODEL; PROCESS OPTIMIZATION; PROTEOMICS; QUANTITATIVE ANALYSIS; SIGNAL PROCESSING; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; FUZZY LOGIC; HEPATOCYTES; HUMANS; INFORMATION THEORY; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS; PHOSPHOPROTEINS; PRIMARY CELL CULTURE; PROTEIN INTERACTION MAPPING; PROTEOME; SIGNAL TRANSDUCTION;

EID: 84870577280     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050085     Document Type: Article

References (53)

1. Downward J, (2001) The ins and outs of signalling. Nature 411: 759-762.
2. Pandey A, Mann M, (2000) Proteomics to study genes and genomes. Nature 405: 837-846.
3. de Hoog CL, Mann M, (2004) Proteomics. Annual Review of Genomics and Human Genetics 5: 267-293.
4. Souchelnytskyi S, (2005) Bridging proteomics and systems biology: What are the roads to be traveled? Proteomics 5: 4123-4137.
5. Melas I, Mitsos A, Messinis D, Weiss T, Alexopoulos L, (2011) Combined logical and data-driven models for linking signalling pathways to cellular response. Bmc Systems Biology 5: 107.
6. Ewing RM, Chu P, Elisma F, Li H, Taylor P, et al. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology 3: 89.
7. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
8. Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 28: 27-30.
9. Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Research 33: D428-D432.
10. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, et al. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Research 39: D685-D690.
11. Hughey JJ, Lee TK, Covert MW, (2010) Computational modeling of mammalian signaling networks. Wiley Interdiscip Rev Syst Biol Med 2: 194-209.
12. Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK, (2006) Physicochemical modelling of cell signalling pathways. Nature Cell Biology 8: 1195-1203.
13. Barabasi AL, Oltvai ZN, (2004) Network biology: Understanding the cell's functional organization. Nature Reviews Genetics 5: 101-U115.
14. Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang DU, (2006) Complex networks: Structure and dynamics. Physics Reports-Review Section of Physics Letters 424: 175-308.
15. Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED, (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193.
16. Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA, (2009) Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. Plos Computational Biology 5 (4): e1000340.
17. Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA, (2010) Logic-based models for the analysis of cell signaling networks. Biochemistry 49: 3216-3224.
18. Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S, (2009) The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. Plos Computational Biology 5(8): e1000438.
19. Klamt S, Saez-Rodriguez J, Gilles ED, (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. Bmc Systems Biology Jan 8 1: 2.
20. Bosl WJ, (2007) Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery. Bmc Systems Biology Feb 15 1: 13.
21. Mahdavi A, Davey RE, Bhola P, Yin T, Zandstra PW, (2007) Sensitivity analysis of intracellular signaling pathway kinetics predicts targets for stem cell fate control. Plos Computational Biology 3: e130.
22. Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G, (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nature Biotechnology 20: 370-375.
23. Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, et al. (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics 15: 72-84.
24. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, et al. (2006) Copasi- a Complex Pathway Simulator. Bioinformatics 22: 3067-3074.
25. Yue H, Brown M, Knowles J, Wang H, Broomhead DS, et al. (2006) Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-κB signalling pathway. Molecular BioSystems 2: 640-649.
26. Quach M, Brunel N, d'Alche-Buc F, (2007) Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference. Bioinformatics 23: 3209-3216.
27. Hinze T, Hayat S, Lenser T, Matsumaru N, Dittrich P (2007) Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo. 8th Workshop on Membrane Computing: 363-382.
28. Qiu P, Plevritis SK, (2011) Reconstructing directed signed gene regulatory network from microarray data. IEEE Trans Biomed Eng 58: 3518-3521.
29. Salwinski L, Eisenberg D, (2004) In silico simulation of biological network dynamics. Nature Biotechnology 22: 1017-1019.
30. Kholodenko BN, Demin OV, Moehren G, Hoek JB, (1999) Quantification of short term signaling by the epidermal growth factor receptor. Journal of Biological Chemistry 274: 30169-30181.
31. Orton RJ, Sturm OE, V V, Calder M, Gilbert DR, et al. (2005) Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. Biochemical Journal 392: 249-261.
32. Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, et al. (2009) Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular Systems Biology 5: 331.
33. Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA, (2011) Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli. Plos Computational Biology 7: e1001099.
34. Lipniacki T, Paszek P, Brasier AR, Luxon B, Kimmel M, (2004) Mathematical model of NF-kappa B regulatory module. Journal of Theoretical Biology 228: 195-215.
35. Chu Y, Jayaraman A, Hahn J, (2007) Parameter sensitivity analysis of IL-6 signalling pathways. IET Syst Biol 1: 342-352.
36. Zhang Y, Rundell A, (2006) Comparative study of parameter sensitivity analyses of the TCR-activated Erk-MAPK signalling pathway. Syst Biol (Stevenage) 153: 201-211.
37. Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK, (2010) Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes. Molecular & Cellular Proteomics 9: 1849-1865.
38. Chou IC, Voit EO, (2009) Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math Biosci 219: 57-83.
39. Kauffman SA, (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 22: 437-467.
40. Thakar J, Pilione M, Kirimanjeswara G, Harvill ET, Albert R, (2007) Modeling systems-level regulation of host immune responses. Plos Computational Biology 3: e109.
41. Helikar T, Konvalina J, Heidel J, Rogers JA, (2008) Emergent decision-making in biological signal transduction networks. Proc Natl Acad Sci U S A 105: 1913-1918.
42. Bornholdt S, (2008) Boolean network models of cellular regulation: prospects and limitations. J R Soc Interface 5Suppl 1: S85-94.
43. Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, et al. (2010) Mathematical modelling of cell-fate decision in response to death receptor engagement. Plos Computational Biology 6: e1000702.
44. Chaouiya C, Naldi A, Thieffry D, (2012) Logical modelling of gene regulatory networks with GINsim. Methods Mol Biol 804: 463-479.
45. Mendoza L, Xenarios I, (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor Biol Med Model 3: 13.
46. Watterson S, Marshall S, Ghazal P, (2008) Logic models of pathway biology. Drug Discov Today 13: 447-456.
47. Mitsos A, Melas IN, Siminelakis P, Chairakaki AD, Saez-Rodriguez J, et al. (2009) Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data. Plos Computational Biology 5(12): e1000591.
48. Melas IN, Mitsos A, Messinis D, Weiss T, Saez-Rodriguez J, et al. (2012) Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data. Molecular Biosystems 8(5): 1571-84.
49. Wachter A, Biegler LT, (2006) On the Implementation of an Interior-Point Filter Line-Search Algorithm for Large-Scale Nonlinear Programming. Mathematical Programming 106: 25-57.
50. Beck JV, Kenneth JA (1977) Parameter estimation in engineering and science.
51. Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J (2012) Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics [Epub ahead of print].
52. Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, et al. (2008) Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics 24: 840-847.
53. MacNamara A, Terfve C, Henriques D, Bernab BP, Saez-Rodriguez J, (2012) State-time spectrum of signal transduction logic models. Physical Biology 9 (4):: 045003.