PATHLOGIC-S: A scalable boolean framework for modelling cellular signalling

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Fearnley, Liam G ^a   Nielsen, Lars K ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL REACTION KINETICS; COMPUTER PROGRAM; COMPUTER SYSTEM; CONCEPTUAL FRAMEWORK; DYNAMICS; FACTUAL DATABASE; INFORMATION PROCESSING; INTRACELLULAR SIGNALING; MATHEMATICAL COMPUTING; NUCLEOTIDE SEQUENCE; PROCESS DEVELOPMENT; PROCESS MODEL; REGULATORY MECHANISM; VALIDATION PROCESS;

CELLS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY;

EID: 84864667424     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041977     Document Type: Article

References (38)

1. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, et al. (2008) Reactome knowledgebase of biological pathways and processes. Nucleic Acids Research 37: D619-22.
2. Matthews L, D'Eustachio P, Gillespie M, Croft D, de Bono B, et al. (2007) An introduction to the Reactome knowledgebase of human biological pathways and processes. Bioinformatics Primer, NCI/Nature Pathway Interaction Database. doi:10.1038/pid.2007.3.
3. Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, et al. (2007) Reactome: A knowledge base of biologic pathways and processes. Genome Biology 8: R39.
4. Joshi-Tope G, Vastrik I, Gopinath G, Matthews L, Schmidt E, et al. (2003) The Genome Knowledgebase: A resource for biologists and bioinformaticists. Cold Spring Harbour Symposia on Quantitative Biology 68: 237-244.
5. Thomas P, Kejariwal A, Campbell M, Mi H, Diemer K, et al. (2003) Panther: A browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Research 31: 334-341.
6. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, et al. (2009) PID: the Pathway Interaction Database. Nucleic Acids Research 37: D674-D679.
7. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, et al. (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences 104: 1777-1782.
8. Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, et al. (2007) A logical model provides insights into T cell receptor signaling. PLoS Computational Biology 3: e163.
9. Dasika M, Burgard A, Maranas C, (2006) A computational framework for the topological analysis and targeted disruption of signal transduction networks. Biophysical Journal 91: 382-398.
10. Haus UU, Niermann K, Truemper K, Weismantel R, (2009) Logic integer programming models for signaling networks. Journal of Computational Biology 16: 725-743.
11. Chen WW, Niepel M, Sorger PK, (2010) Classic and contemporary approaches to modeling biochemical reactions. Genes & Development 24: 1861-1875.
12. Moles CG, Mendes P, Banga JR, (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Research 13: 2467-2474.
13. Becker SA, Feist AM, Mo ML, Hannum G, Palsson B, et al. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox. Nature Protocols 2: 727-738.
14. Hyduke DR, Palsson BO, (2010) Towards genome-scale signalling network reconstructions. Nature Reviews Genetics 11: 297-307.
15. Palsson BO, (2006) Systems biology: properties of reconstructed networks. Cambridge University Press.
16. Nielsen LK, (2011) Metabolic engineering: from retrofitting to green field. Nature Chemical Biology 7: 408-409.
17. Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED, (2006) A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7: 56.
18. Klamt S, Saez-Rodriguez J, Gilles ED, (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 1: 2.
19. Handorf T, Klipp E, (2012) Modeling mechanistic biological networks: an advanced boolean approach. Bioinformatics 28: 557-563.
20. Haus UU, Niermann K, Truemper K, Weismantel R, (2008) Linear satisfiability algorithm for 3CNF formulas of certain signaling networks. Journal on Satisfiability, Boolean Modeling and Computation 6: 13-32.
21. Graves JD, Craxton A, Clark EA, (2004) Modulation and function of caspase pathways in B lymphocytes. Immunol Rev 197: 129-146.
22. Su B, Jacinto E, Hibi M, Kallunki T, Karin M, et al. (1994) JNK is involved in signal integration during costimulation of T lymphocytes. Cell 77: 727-736.
23. Harlin H, Podack E, Boothby M, Alegre ML, (2002) TCR-independent CD30 signaling selectively induces IL-13 production via a TNF receptor-associated factor/p38 mitogen-activated protein kinase-dependent mechanism. J Immunol 169: 2451-2459.
24. Acuto O, Michel F, (2003) CD28-mediated co-stimulation: a quantitative support for TCR signalling. Nat Rev Immunol 3: 939-951.
25. Rivas FV, O'Herrin S, Gajewski TF, (2001) CD28 is not required for c-Jun N-terminal kinase activation in T cells. J Immunol 167: 3123-3128.
26. Healy JI, Dolmetsch RE, Timmerman LA, Cyster JG, Thomas ML, et al. (1997) Different nuclear signals are activated by the B cell receptor during positive versus negative signaling. Immunity 6: 419-428.
27. Bertsimas D, Weismantel R, (2005) Optimization over integers. Athena Scientific, I-X, pp 1-602.
28. Shannon P, Markiel A, Ozier O, Baliga N, Wang J, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498-2504.
29. Gansner ER, North SC, (2000) An open graph visualization system and its applications to software engineering. Software - Practice and Experience 30: 1203-1233.
30. Tarjan R, (1971) Depth-first search and linear graph algorithms. In: Proceedings of the Annual Symposium on Switching and Automata Theory. pp. 114-121 doi:10.1109/SWAT.1971.10.
31. Gosling J, Joy B, Steele G, Bracha G, (2005) The JavaTMLanguage Specification. Addison-Wesley. Available online at http://java.sun.com/docs/books/jls/. Retrieved March 2012.
32. BioPAX: Biological pathways exchange. BioPAX Consortium. Available: http://www.biopax.org. Accessed 2011 Jun.
33. Berkelaar M, Eikland K, Notebaert P (2010) lp solve version 5.5.2.0. Available: http://sourceforge.net/projects/lpsolve/. Accessed 2012 Mar.
34. Himsolt M (1996) GML: A portable graph file format. Technical report, University of Passau. Available: http://www.fim.uni-passau.de/fileadmin/files/lehrstuhl/brandenburg/projekte/gml/gml-technical-re.
35. Chang CS, Kokontis J, Liao ST, (1988) Molecular cloning of human and rat complementary dna encoding androgen receptors. Science 240: 324-326.
36. Fliss AE, Rao J, Melville MW, Cheetham ME, Caplan AJ, (1999) Domain requirements of DnaJ-like (Hsp40) molecular chaperones in the activation of a steroid hormone receptor. Journal of Biological Chemistry 274: 34045-34052.
37. Simental JA, Sar M, Lane MV, French FS, Wilson EM, (1991) Transcriptional activation and nuclear targeting signals of the human androgen receptor. Journal of Biological Chemistry 266: 510-518.
38. Zhang Y, Yang Y, Yeh S, Chang C, (2004) Ara67/pat1 functions as a repressor to suppress androgen receptor transactivation. Molecular Cell Biology 24: 1044-1057.