From a biological hypothesis to the construction of a mathematical model

Methods in Molecular Biology

Volumn 1021, Issue , 2013, Pages 107-125

  Cohen, David ^a,b,c   Kuperstein, Inna ^a,b,c   Barillot, Emmanuel ^a,b,c   Zinovyev, Andrei ^a,b,c   Calzone, Laurence ^a,b,c  

^a INSTITUT CURIE   (France)

^b INSERM U900   (France)

^c PSL RESEARCH UNIVERSITY   (France)

Author keywords

Boolean; Formalism; Mathematical model; Network diagram; ODE

Indexed keywords

CYCLIN E; RETINOBLASTOMA PROTEIN;

ARTICLE; BINDING AFFINITY; BIOCHEMISTRY; BIOLOGICAL HYPOTHESIS; CHEMICAL REACTION KINETICS; ENZYME KINETICS; EPITHELIAL MESENCHYMAL TRANSITION; GENETIC CORRELATION; HIGH THROUGHPUT SEQUENCING; HYPOTHESIS; MATHEMATICAL MODEL; MICHAELIS MENTEN KINETICS; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; STEADY STATE; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; WORKFLOW;

EID: 84883254648     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-450-0_6     Document Type: Article

References (48)

1. Hoffmann R, Valencia A (2004) A gene network for navigating the literature. Nat Genet 36:664.
2. Larkin JH, Simon HA (1987) Why a diagram is (sometimes) worth ten thousand words. Cogn Sci 11(1):65-100
3. Le Novère N, Hucka M, Mi H et al (2009) The systems biology graphical notation.Nat Biotechnol 27(8):735-741. doi:10.1038/nbt.1558
4. Wang PI, Marcotte EM (2010) It's the machine that matters: predicting gene function and phenotype from protein networks. J Proteomics 73(11):2277-2289
5. Dixon SJ, Costanzo M, Baryshnikova A et al (2009) Systematic mapping of genetic interaction networks. Annu Rev Genet 43(1):601-625. doi:10.1146/annurev. genet.39.073003.114751
6. Ideker T, Krogan NJ (2012) Differential network biology. Mol Syst Biol 8:565. doi:10.1038/msb.2011.99
7. Przulj N (2011) Protein-protein interactions: making sense of networks via graph-theoretic modeling. Bioessays 33(2):115-123. doi:10.1002/bies. 201000044
8. Schmeier S, Schaefer U, Essack M et al (2011) Network analysis of microRNAs and their regulation in human ovarian cancer. BMC Syst Biol 5:183. doi:10.1186/1752-0509-5-183
9. Pratt CH, Vadigepalli R, Chakravarthula P et al (2008) Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium. Mol Vis 14:1414-1428
10. Cheng C, Yan K-K, Hwang W et al (2011) Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol 7(11): e1002190
11. Calzone L, Gelay A, Zinovyev A et al (2008) A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol 4:174. doi:10.1038/msb.2008.7
12. Caron E, Ghosh S, Matsuoka Y et al (2010) A comprehensive map of the mTOR signaling network. Mol Syst Biol 6:453. doi:10.1038/msb.2010.108
13. Patil S, Pincas H, Seto J et al (2010) Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. BMC Syst Biol 4(1):137
14. Kohn KW (1999) Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell 10(8):2703-2734
15. Joshi-Tope G, Gillespie M,Vastrik I et al (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33(Database issue): D428-D432. doi:10.1093/nar/gki072
16. Kanehisa M (2002) The KEGG database. Novartis Found Symp 247:91-101; discussion 101-103, 119-128, 244-252
17. KitanoH, Funahashi A,Matsuoka Yet al (2005) Using process diagrams for the graphical representation of biological networks.NatBiotechnol 23(8):961-966. doi:10.1038/nbt1111
18. Czauderna T, Klukas C, Schreiber F (2010) Editing, validating and translating of SBGN maps. Bioinformatics 26(18):2340-2341. doi:10.1093/ bioinformatics/btq407
19. Florez LA, Lammers CR, Michna R et al (2010) Cell Publisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways. Bioinformatics 26(23):2997-2999. doi:10.1093/ bioinformatics/btq585
20. Kono N, Arakawa K, Ogawa R et al (2009) Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One 4(11):e7710. doi:10.1371/journal.pone.0007710
21. Smoot ME, Ono K, Ruscheinski J et al (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27(3):431-432. doi:10.1093/bioinformatics/btq675
22. Zinovyev A, Viara E, Calzone L et al (2008) BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 24(6):876-877. doi:10.1093/bioinformatics/btm553
23. Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A (2013) BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst Biol 7:18
24. Bachmann J, Raue A, Schilling M et al (2012) Predictive mathematicalmodels of cancer signalling pathways. J Intern Med 271(2):155-165
25. Ay A, Arnosti DN (2011) Mathematical modeling of gene expression: a guide for the perplexed biologist. Crit Rev Biochem Mol Biol 46 (2):137-151. doi:10.3109/10409238.2011. 556597
26. Morris MK, Saez-Rodriguez J, Sorger PK et al (2010) Logic-based models for the analysis of cell signaling networks. Biochemistry 49 (15):3216-3224
27. Karlebach G, Shamir R (2008) Modeling and analysis of regulatory networks. Nat Rev Mol Cell Biol 9:771-780. doi:10.1038/nrm2503
28. Calzone L, Tournier L, Fourquet S et al (2010) Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol 6(3):e1000702
29. Philippi N, Walter D, Schlatter R et al (2009) Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection. BMC Syst Biol 3:97. doi:10.1186/1752-0509-3-97
30. Saez-Rodriguez J, Alexopoulos LG, Zhang M et al (2011) Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res 71(16):5400-5411. doi:10.1158/0008-5472.CAN-10-4453
31. Schlatter R, Schmich K, Avalos Vizcarra I et al (2009)ON/OFF and beyond-a Boolean model of apoptosis. PLoS Comput Biol 5(12): e1000595. doi:10.1371/journal.pcbi.1000595
32. BrittonNF (1986)Reaction-diffusion equations and their applications to biology. Academic, London
33. Hegland M, Burden C, Santoso L et al (2007) A solver for the stochastic master equation applied to gene regulatory networks. J Comput Appl Math 205(2):708-724. doi:10.1016/j. cam.2006.02.053
34. Sherr CJ,McCormick F (2002) TheRBand p53 pathways in cancer. Cancer Cell 2(2):103-112. doi:10.1016/S1535-6108(02)00102-2
35. Polager S, Ginsberg D (2008) E2F at the crossroads of life and death. Trends Cell Biol 18 (11):528-535. doi:10.1016/j.tcb.2008.08.003
36. Calzone L, Fages F, Soliman S (2006) BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22(14):1805-1807. doi:10.1093/bioinformatics/btl172
37. Vass M, Allen N, Shaffer CA, Ramakrishnan N, Watson LT, Tyson JJ (2004) The JigCell model builder and run manager. Bioinformatics 20(18):3680-3681
38. Funahashi A, Matsuoka Y, Jouraku A et al (2008) Cell Designer 3.5: a versatile modeling tool for biochemical networks. Proc IEEE 96 (8):1254-1265
39. Schmidt H, Jirstrand M (2006) Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics 22(4):514-515. doi:10.1093/bioinformatics/bti799
40. Aguda BD, Tang Y (1999) The kinetic origins of the restriction point in the mammalian cell cycle. Cell Prolif 32(5):321-335
41. Qu Z, Weiss JN, MacLellan WR (2003) Regulation of the mammalian cell cycle: a model of the G1-to-S transition. Am J Physiol Cell Physiol 284(2):C349-C364. doi:10.1152/ajpcell.00066.2002
42. Novak B, Tyson JJ (2004) A model for restriction point control of the mammalian cell cycle. J Theor Biol 230(4):563-579. doi:10.1016/j. jtbi.2004.04.039
43. Gonzalez AG, Naldi A, Sanchez L et al (2006) GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems 84(2):91-100. doi:10.1016/j.biosystems.2005.10.003
44. Mussel C, Hopfensitz M, Kestler HA (2010) BoolNet-an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 26(10):1378-1380. doi:10.1093/bioinformatics/btq124
45. Klamt S, Saez-Rodriguez J, Gilles E (2007) Structural and functional analysis of cellular networks with Cell NetAnalyzer. BMC Syst Biol 1(1):2
46. Stoll G, Viara E, Barillot E et al (2012) Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm. BMC Syst Biol 6:116. doi:10.1186/1752-0509-6-116
47. Faure A, Naldi A, Chaouiya C et al (2006) Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22(14):e124-e131. doi:10.1093/bioinformatics/btl210
48. Barillot E, Calzone L, Hupe P, Vert J-P, Zinovyev A (2012) Computational systems biology of cancer. Chapman & Hall, CRC Mathematical & Computational Biology 452 p.