Hybrid Petri net based modeling for biological pathway simulation

Natural Computing

Volumn 10, Issue 3, 2011, Pages 1099-1120

  Matsuno, Hiroshi ^a   Nagasaki, Masao ^b   Miyano, Satoru ^b  

^a YAMAGUCHI UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Cell Illustrator; Hybrid Petri net; Pathway simulation

Indexed keywords

ANALYTIC METHOD; ARTICLE; BINDING SITE; CELL GROWTH; CIRCADIAN RHYTHM; COMPUTER PROGRAM; CONTROLLED STUDY; GENE SWITCHING; GENETIC TRANSCRIPTION; HYBRID PETRI NET; INFORMATION PROCESSING; LYSOGENIZATION; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; OPERON; PROMOTER REGION; PROTEIN SYNTHESIS; RNA TRANSLATION; ULTRAVIOLET IRRADIATION;

CYANOBACTERIA;

EID: 80055024030     PISSN: 15677818     EISSN: 15729796     Source Type: Journal    
DOI: 10.1007/s11047-009-9164-6     Document Type: Article

References (23)

1. Alla H, David R (1998) Continuous and hybrid Petri nets. J Circuits Syst Comput 8:159-188 (Pubitemid 128540252)
2. Drath R, Engmann U, Schwuchow S (1999) Hybrid aspects of modelling manufacturing systems using modified Petri nets. Proceedings of the 5th workshop on intelligent manufacturing systems, Granado, Brasil
3. Gilbert D, Heiner M (2006) From Petri nets to differential equations-an integrative approach for biochemical network analysis. 27th International conference on application and theory of Petri nets (LNCS4024), pp 181-200 (Pubitemid 44071794)
4. Hardy S, Robillard PN (2008) Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways. Bioinformatics 24(2):209-217
5. Ishiura M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, Tanabe A, Golden SS, Johnson CH, Kondo T (1998) Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281:1519-1523 (Pubitemid 28425578)
6. Iwasaki H, Williams SB, Kitayama Y, Ishiura M, Golden SS, Kondo T (2000) A KaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria. Cell 101: 223-233 (Pubitemid 32004749)
7. Iwasaki H, Nishiwaki T, Kitayama Y, Nakajima M, Kondo T (2002) KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria. Proc Natl Acad Sci USA 99(24):15788-15793 (Pubitemid 35404008)
8. Jeong E, Nagasai M, Saito A, Miyano S (2007a) Cell System Ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol 7:0055
9. Jeong E, Nagasaki M, Miyano S (2007b) Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Inform 18:225-236
10. Kitayama Y, Iwasaki H, Nishiwaki T, Kondo T (2003) KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system. EMBO J 22(9):2127-2134 (Pubitemid 36565537)
11. Koh G, Teong HFC, Clément MV, Hsu D, Thiagarajan PS (2006) A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk. Bioinformatics 22(14):e271-e280 (Pubitemid 44288296)
12. Kojima K, Nagasaki M, Jeong E, Kato M, Miyano S (2007) An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinform 8:76
13. Matsuno H, Doi A, Nagasaki M, Miyano S (2000) Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput 5:338-349. http://www.psb.stanford.edu/psb-online/proceedings/psb00/matsuno.pdf
14. Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, Miyano S (2003a) Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol 3(3):389-404 (Pubitemid 37493057)
15. Matsuno H, Fujita S, Doi A, Nagasaki M, Miyano S (2003b) Towards biopathway modeling and simulation, vol 2679. In: Proceedings of the 24th international conference on applications and theory of Petri nets (ICATPN2003), Lecture Notes in Computer Science, pp 3-22
16. Nagasaki M, Doi A, Matsuno H, Miyano S (2003) Genomic object net: I. A platform for modeling and simulating biopathways. Appl Bioinform 2(3):181-184
17. Nagasaki M, Doi A, Matsuno H, Miyano S (2004) A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Inform 15(1):180-197
18. Nagasaki M, Doi A, Matsuno H, Miyano S (2005) Computational modeling of biological processes with Petri net based architecture. In: Chen YP (ed) Bioinformatics technologies. Springer Press, Berlin, pp 179-243
19. Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T (2006) Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Inform 17(1):46-61
20. Nagasaki M, Saito A, Li C, Jeong E, Miyano S (2008) Systematic reconstruction of TRANSPATH data into cell system markup language. BMC System Biol 2:53
21. Ptashne M (1992) A genetic switch, 2nd edn. Blackwell Science & Cell Press, MA
22. Tasaki S, Nagasaki M, Oyama M, Hata H, Ueno K, Yoshida R, Higuchi T, Sugano S, Miyano S (2006) Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform 17(2):226-228
23. Troncale S, Tahi F, Campard D, Vannier JP, Guespin J (2006) Modeling and simulation with hybrid functional Petri nets of the role of Interleukin-6 in human early haematopoiesis. Pacific Symp Biocomput 11:427-438