메뉴 건너뛰기




Volumn 21, Issue SUPPL. 1, 2005, Pages

Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BACTERIAL GENETICS; BACTERIAL GROWTH; BIOINFORMATICS; COMPUTER MODEL; COMPUTER SIMULATION; CONTROLLED STUDY; ESCHERICHIA COLI; INFORMATION PROCESSING; NONHUMAN; NUTRITION; PREDICTION; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; STRESS; VALIDATION PROCESS;

EID: 84860513120     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1048     Document Type: Article
Times cited : (147)

References (25)
  • 1
    • 0032716841 scopus 로고    scopus 로고
    • Growth phase-dependent variation in protein composition of the E.coli nucleoid
    • Ali Azam,T., Iwata,A., Nishimura,A., Ueda,S. and Ishihama,A. (1999) Growth phase-dependent variation in protein composition of the E.coli nucleoid. J. Bacteriol., 181, 6361-6370.
    • (1999) J. Bacteriol. , vol.181 , pp. 6361-6370
    • Ali Azam, T.1    Iwata, A.2    Nishimura, A.3    Ueda, S.4    Ishihama, A.5
  • 2
    • 4444326589 scopus 로고    scopus 로고
    • Taming the complexity of biochemical models through bisimulation and collapsing: Theory and practice
    • Antoniotti,M., Piazza,C., Policriti,A., Simeoni,M. and Mishra,B. (2004) Taming the complexity of biochemical models through bisimulation and collapsing: Theory and practice. Theor. Comput. Sci., 325, 45-67.
    • (2004) Theor. Comput. Sci. , vol.325 , pp. 45-67
    • Antoniotti, M.1    Piazza, C.2    Policriti, A.3    Simeoni, M.4    Mishra, B.5
  • 3
    • 0023430342 scopus 로고
    • Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli
    • Balke,V.L. and Gralla,J.D. (1987) Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli. J. Bacteriol., 169, 4499-4506.
    • (1987) J. Bacteriol. , vol.169 , pp. 4499-4506
    • Balke, V.L.1    Gralla, J.D.2
  • 4
    • 24344435117 scopus 로고    scopus 로고
    • Qualitative analysis and verification of hybrid models of genetic regulatory networks
    • Morari,M. and Thiele,L. (eds), Springer, Berlin
    • Batt,G. Ropers,D., de Jong,H., Geiselmann,J., Page,M. and Schneider,D. (2005) Qualitative analysis and verification of hybrid models of genetic regulatory networks. In Morari,M. and Thiele,L. (eds), HSCC' 05, Lecture Notes in Computer Science Vol. 3414, Springer, Berlin, pp. 134-150.
    • (2005) HSCC' 05, Lecture Notes in Computer Science , vol.3414 , pp. 134-150
    • Batt, G.1    Ropers, D.2    de Jong, H.3    Geiselmann, J.4    Page, M.5    Schneider, D.6
  • 5
    • 3042693879 scopus 로고    scopus 로고
    • A fruitful application of formal methods to biological regulatory networks: Extending Thomas' asynchronous logical approach with temporal logic
    • Bernot,G., Comet,J.-P., Richard,A. and Guespin,J. (2004) A fruitful application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. J. Theor. Biol., 229, 339-347.
    • (2004) J. Theor. Biol. , vol.229 , pp. 339-347
    • Bernot, G.1    Comet, J.-P.2    Richard, A.3    Guespin, J.4
  • 8
    • 85034858362 scopus 로고
    • Expressibility results for linear-time and branching-time logics
    • de Bakker,J.W., de Roever,W.P. and Rozenberg,G. (eds), Springer, Berlin
    • Clarke,E.M. and Draghicescu,I.A. (1988) Expressibility results for linear-time and branching-time logics. In de Bakker,J.W., de Roever,W.P. and Rozenberg,G. (eds), REX Workshop, Lecture Notes in Computer Science Vol. 354, Springer, Berlin, pp. 428-437.
    • (1988) REX Workshop, Lecture Notes in Computer Science , vol.354 , pp. 428-437
    • Clarke, E.M.1    Draghicescu, I.A.2
  • 10
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong,H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol., 9, 69-105.
    • (2002) J. Comput. Biol. , vol.9 , pp. 69-105
    • de Jong, H.1
  • 11
    • 0345269975 scopus 로고    scopus 로고
    • Genetic Network Analyzer: Qualitative simulation of genetic regulatory networks
    • de Jong,H., Geiselmann,J., Hernandez,C. and Page,M. (2003) Genetic Network Analyzer: Qualitative simulation of genetic regulatory networks. Bioinformatics, 19, 336-344.
    • (2003) Bioinformatics , vol.19 , pp. 336-344
    • de Jong, H.1    Geiselmann, J.2    Hernandez, C.3    Page, M.4
  • 13
    • 0025250502 scopus 로고
    • Bacterial topoisomerases and the control of DNA supercoiling
    • Drlica,K. (1990) Bacterial topoisomerases and the control of DNA supercoiling. Trends Genet., 6, 433-437.
    • (1990) Trends Genet. , vol.6 , pp. 433-437
    • Drlica, K.1
  • 14
    • 0036364829 scopus 로고    scopus 로고
    • Pathway logic: Symbolic analysis of biological signaling
    • Altman,R.B., Dunker,A.K., Hunter,L., Jung,T., and Klein,T.C. (eds), World Scientific Publishing Singapore
    • Eker,S., Knapp,M., Laderoute,K., Lincoln,P., Meseguer,J. and Sönmez,M.K. (2002) Pathway logic: Symbolic analysis of biological signaling. In Altman,R.B., Dunker,A.K., Hunter,L., Jung,T., and Klein,T.C. (eds), PSB'02, World Scientific Publishing, Singapore, pp. 400-412.
    • (2002) PSB'02 , pp. 400-412
    • Eker, S.1    Knapp, M.2    Laderoute, K.3    Lincoln, P.4    Meseguer, J.5    Sönmez, M.K.6
  • 15
    • 35248832573 scopus 로고    scopus 로고
    • Automated symbolic reachability analysis, with application to Delta-Notch signaling automata
    • Maler,O. and Pnueli,A. (eds), Springer, Berlin
    • Ghosh,R., Tiwari,A. and Tomlin,C.J. (2003) Automated symbolic reachability analysis, with application to Delta-Notch signaling automata. In Maler,O. and Pnueli,A. (eds), HSCC' 03, Lecture Notes in Computer Science Vol. 2623, Springer, Berlin, pp. 233-248.
    • (2003) HSCC' 03, Lecture Notes in Computer Science , vol.2623 , pp. 233-248
    • Ghosh, R.1    Tiwari, A.2    Tomlin, C.J.3
  • 16
    • 0015609281 scopus 로고
    • The logical analysis of continuous non-linear biochemical control networks
    • Glass,L. and Kauffman,S.A. (1973) The logical analysis of continuous non-linear biochemical control networks. J. Theor. Biol., 39, 103-129.
    • (1973) J. Theor. Biol. , vol.39 , pp. 103-129
    • Glass, L.1    Kauffman, S.A.2
  • 17
    • 0036938728 scopus 로고    scopus 로고
    • A class of piecewise-linear differential equations arising in biological models
    • Gouzé,J.-L. and Sari,T. (2002) A class of piecewise-linear differential equations arising in biological models. Dyn. Syst., 17, 299-316.
    • (2002) Dyn. Syst. , vol.17 , pp. 299-316
    • Gouzé, J.-L.1    Sari, T.2
  • 18
    • 0000291637 scopus 로고    scopus 로고
    • The general stress response in E.coli
    • Storz,G. and Hengge-Aronis,R. (eds), ASM Press, Washington, DC
    • Hengge-Aronis,R. (2000) The general stress response in E.coli. In Storz,G. and Hengge-Aronis,R. (eds), Bacterial Stress Responses. ASM Press, Washington, DC, pp. 161-177.
    • (2000) Bacterial Stress Responses , pp. 161-177
    • Hengge-Aronis, R.1
  • 19
    • 0001175140 scopus 로고    scopus 로고
    • Morphological and physiological changes during stationary phase
    • Neidhardt,F.C., Curtiss III,R., Ingraham,J.L., Lin,E.C.C., Low,K.B., Magasanik,B., Reznikoff,W.S., Riley,M., Schaechter,M. and Umbarger,H.E. (eds), ASM Press, Washington, DC
    • Huisman,G.W., Siegele,D.A., Zambrano,M.M. and Kolter,R. (1996) Morphological and physiological changes during stationary phase. In Neidhardt,F.C., Curtiss III,R., Ingraham,J.L., Lin,E.C.C., Low,K.B., Magasanik,B., Reznikoff,W.S., Riley,M., Schaechter,M. and Umbarger,H.E. (eds), Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC, pp. 1672-1682.
    • (1996) Escherichia Coli and Salmonella: Cellular and Molecular Biology , pp. 1672-1682
    • Huisman, G.W.1    Siegele, D.A.2    Zambrano, M.M.3    Kolter, R.4
  • 20
    • 16344381707 scopus 로고    scopus 로고
    • Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
    • Koch,I., Junker,B.H. and Heiner,M. (2005) Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21, 1219-1226.
    • (2005) Bioinformatics , vol.21 , pp. 1219-1226
    • Koch, I.1    Junker, B.H.2    Heiner, M.3
  • 21
    • 0037332768 scopus 로고    scopus 로고
    • Efficient on-the-fly model-checking for regular alternation-free mu-calculus
    • Mateescu,R. and Sighireanu,M. (2003) Efficient on-the-fly model-checking for regular alternation-free mu-calculus. Sci. Comput. Program., 46, 255-281.
    • (2003) Sci. Comput. Program. , vol.46 , pp. 255-281
    • Mateescu, R.1    Sighireanu, M.2
  • 22
    • 29144514336 scopus 로고    scopus 로고
    • XTL: A meta-language and tool for temporal logic model-checking
    • Margaria,T. and Steffen,B. (eds) Brics,. Aalborg
    • Mateescu,R. and Garavel,H. (1998) XTL: A meta-language and tool for temporal logic model-checking. In Margaria,T. and Steffen,B. (eds) STTT'98. Brics, Aalborg, pp. 33-42.
    • (1998) STTT'98 , pp. 33-42
    • Mateescu, R.1    Garavel, H.2
  • 23
    • 0035235039 scopus 로고    scopus 로고
    • Representation and simulation of biochemical processes using the pi-calculus process algebra
    • Altman,R.B., Dunker,A.K., Hunter,L. and Klein,T.E. (eds), World Scientific Publishing, Singapore
    • Regev,A., Silverman,W. and Shapiro,E. (2001) Representation and simulation of biochemical processes using the pi-calculus process algebra. In Altman,R.B., Dunker,A.K., Hunter,L. and Klein,T.E. (eds), PSB'01.World Scientific Publishing, Singapore, pp. 459-470.
    • (2001) PSB'01 , pp. 459-470
    • Regev, A.1    Silverman, W.2    Shapiro, E.3
  • 24
    • 29144503020 scopus 로고    scopus 로고
    • Qualitative simulation of nutritional stress response in Escherichia coli
    • Technical Report INRIA RR-5412
    • Ropers,D., de Jong,H., Page,M., Schneider,D. and Geiselmann,J. (2004) Qualitative simulation of nutritional stress response in Escherichia coli. Technical Report INRIA RR-5412.
    • (2004)
    • Ropers, D.1    de Jong, H.2    Page, M.3    Schneider, D.4    Geiselmann, J.5
  • 25
    • 0031144307 scopus 로고    scopus 로고
    • Proving properties of continuous systems: Qualitative simulation and temporal logic
    • Shults,B. and Kuipers,B.J. (1997) Proving properties of continuous systems: Qualitative simulation and temporal logic. Artif. Intell., 92, 91-130.
    • (1997) Artif. Intell. , vol.92 , pp. 91-130
    • Shults, B.1    Kuipers, B.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.