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J. Barnat, L. Brim, I. Cerna, S. Drazan, and D. Safranek. Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. In Proceedings of From Biology to Concurrency and Back, ENTCS, Vol. 194/3, Elsevier Science, 2008.
 
P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong. Temporal logic patterns for querying dynamic models of cellular interaction networks.  INRIA Research Report RR-6470, 2008.
 
P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong (2008), Temporal logic patterns for querying dynamic models of cellular interaction networks, Bioinformatics, in press. Special issue ECCB-2008.
 
P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong. Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks. Bioinformatics 24(16), pages 227-233, ECCB 2008 Special Issue, 2008.
 
Blom, S.C.C. and Haverkort, B.R.H.M. and Kuntz, G.W.M. and van de Pol, J.C. (2008) Distributed Markovian Bisimulation Reduction aimed at CSL Model Checking. In: Proceedings of the 7th International Workshop on Parallel and Distributed Methods in verifiCation, 29 Mar 2008, Budapest, Hungary. pp. 35-50. Electronic Notes in Theoretical Computer Science 220 (2). Elsevier. ISSN 1571-0661
 
Stefan Blom and Jaco van de Pol. Symbolic Reachability for Process Algebras with Recursive Data Types. In Theoretical Aspects of Computing - ICTAC 2008, pp 81-95, LNCS 5160, Springer. Available on-line .
 
Radu Mateescu and Emilie Oudot. Improved On-the-Fly Equivalence checking using Boolean Equation Systems. In Proceedings of the 5th International SPIN Workshop on Model Checking of Software SPIN'2008 (Los Angeles, USA), Lecture Notes in Computer Science vol. 5156, pp. 196-213. Springer Verlag, August 2008.
 
Radu Mateescu and Emilie Oudot. Bisimulator 2.0: An On-the-Fly quivalence Checker based on Boolean Equation Systems. In Proceedings of the 6th ACM-IEEE International Conference on Formal Methods and Models for Codesign MEMOCODE'2008, 2008.
 
P.T. Monteiro, H. de Jong, R. Mateescu, A.T. Freitas, H. de Jong (2008), Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks, Proceedings of Eighteenth European Conference on Artifical Intelligence, ECAI-08, M. Ghallab (ed.), IOS Press, Amsterdam, in press.
 
R. Mateescu, P. T. Monteiro, E. Dumas, and H. de Jong. Computation Tree Regular Logic for Genetic Regulatory Networks. In Proceedings of the 6th International Symposium on Automated Technology for Verification and Analysis ATVA'08 (Seoul, South Korea), Lecture Notes in Computer Science vol. 5311, pp. 48-63. Springer Verlag, October 2008.
 
R. Mateescu, P. T. Monteiro, E. Dumas, and H. de Jong. Computation Tree Regular Logic for Genetic Regulatory Networks.
INRIA Research Report RR-6521, May 2008. Available on-line.
 
Hongwu Ma, Guenola Drillon, Igor Goryanin, Integrated Kinetic models of the ammonia regulation in E. coli, International E-coli Alliance (IECA) Conference 2008, Hinxton, Cambridgeshire, 24-28 September 2008
 
Barnat, J. and Chaloupka, J. and van de Pol, J.C. (2008) Improved Distributed Algorithms for SCC Decomposition. In: Proceedings of the 6th International Workshop on Parallel and Distributed Methods in verifiCation, 8 Jul 2007, Berlin. pp. 63-77. Electronic Notes in Theoretical Computer Science 198 (1). Elsevier. ISSN 1571-0661

 
Rodolfo Garcia-Contreras, Frank Bruggeman, Klaas Krab, Fred Boogerd and Hans Westerhoff. Study of the metabolic transitions from rich to poor carbon and nitrogen sources in Escherichia coli. In Proceedings of the International Study Group for Systems Biology (Kongens Lyngby, Denmark), p. 141, August 2008.
 
Rodolfo Garcia-Contreras, Frank Bruggeman, Klaas Krab, Fred Boogerd and Hans Westerhoff. Metabolic transitions from rich to poor carbon and nitrogen sources in Escherichia coli. In Proceedings of the International E. coli Alliance  (Hinxton, United Kingdom), p. P12, September, 2008.
 

D. Ropers, V. Baldazzi, H. de Jong   Model Reduction using Piecewise-linear Approximations Preserve Dynamic Properties of the Carbon Starvation Response in E. coli    IEEE/ACM Transactions on Computational Biology and Bioinformatics  to appear

 
V. Baldazzi, P. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong  Qualitative Analysis of Genetic Regulatory Network in Bacteria,  In Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Biology, W. Dubitzky, J. Southgate and H. Fuss (editors), Springer
 
Bruggeman, F.J., Snoep, J.L. & Westerhoff, H.V. Control, responses and modularity of cellular regulatory networks: a control analysis perspective. IET systems biology 2, 397-410, 2008.
 
van Heeswijk WC, Molenaar D, Hoving S, Westerhoff HV. The pivotal regulator GlnB of Escherichia coli is engaged in subtle and context-dependent control. FEBS Journal 276(12): 3324-40, 2009.
 
Blom, S.C.C. and Lisser, B. and van de Pol, J.C. and Weber, M. (2008) A Database Approach to Distributed State Space Generation. In: Proceedings of the 6th International Workshop on Parallel and Distributed Methods in verifiCation, 8 Jul 2007, Berlin. pp. 17-32. Electronic Notes in Theoretical Computer Science 198 (1). Elsevier. ISSN 1571-0661

 
Blom, S.C.C. and van de Pol, J.C. and Weber, M. (2009) Bridging the Gap between Enumerative and Symbolic Model Checkers. Technical Report TR-CTIT-09-30, Centre for Telematics and Information Technology, University of Twente, Enschede. ISSN 1381-3625 (PDF)
 
Blom, S.C.C. and Lisser, B. and van de Pol, J.C. and Weber, M. (2009) A Database Approach to Distributed State-Space Generation. Journal of Logic and Computation, Advance Access published March 5, 2009, doi:10.1093/logcom/exp004. ISSN 0955-792X

 
Barnat, J. and Chaloupka, J. and van de Pol, J.C. (2009) Distributed Algorithms for SCC Decomposition. Journal of Logic and Computation, Advance Access published February 17, 2009, doi:10.1093/logcom/exp003. ISSN 0955-792X

 
Radu Mateescu and Anton Wijs, Efficient On-the-Fly Computation of Weak Tau-Confluence, INRIA Research Report RR-7000, July 2009, http://hal.inria.fr/inria-00407381
 
Radu Mateescu and Anton Wijs, Hierarchical Adaptive State Space Caching Based on Level Sampling, in Proceedings of the 15th International Conference on Tools and Algorithms for the Construction and Analysis of Systems 2009, Stefan Kowalewski and Anna Philippou editors, pringer Lecture Notes in Computer Science 5505, pages 215--229, ISBN 978-3-642-00767-5, http://dx.doi.org/10.1007/978-3-642-00768-2
 
J. Barnat, L. Brim, I. Cerna, S. Drazan, J. Fabrikova, and D. Safranek. On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking. In Theoretical Computer Science 410, pp. 3128-3148, 2009. doi:10.1016/j.tcs.2009.02.017   
 
J. Barnat, L. Brim, I. Cerna, S. Drazan, J. Fabrikova, and D. Safranek. Computational Analysis of Large-Scale Multi-Affine ODE Model.  In Proceedings of High Performance Computational Systems Biology (HiBi 2009), pp. 81-90, IEEE Computer Society, 2009.
 
J. Barnat, L. Brim, I. Cerna, S. Drazan, J. Fabrikova, J. Lanik, D. Safranek, and. H. Ma. BioDiVinE: A Framework for Parallel Analysis of Biological Models.  In Proceedings of 2nd International Workshop on Computational Models for Cell Processes (COMPMOD 2009), pp. 31-45, EPTCS 6, 2009. DOI: 10.4204/EPTCS.6.3
 
Ma, H., Boogerd, F.C. and Goryanin, I. (2009) Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration. Journal of Biotechnology,  Vol. 4, Issue 3, pp. 175-183.  doi:10.1016/j.jbiotec.2009.09.003
 
J. Barnat, L. Brim, and D. Safranek. High-Performance Analysis of Biological Systems Dynamics with the DiVinE Model Checker. Briefings in Bioinformatics, in press, 2010.
 
Blom, S.C.C. and van de Pol, J.C. (2009) Distributed Branching Bisimulation Minimization by Inductive Signatures. Technical Report TR-CTIT-09-37, Centre for Telematics and Information Technology, University of Twente, Enschede. ISSN 1381-3625
 
Blom, S.C.C. and van de Pol, J.C. Distributed Branching Bisimulation Minimization by Inductive Signatures. Proceedings 8th International Workshop on Parallel and Distributed Methods in verification Eindhoven, The Netherlands, November 2009; Lubos Brim and Jaco van de Pol editors; EPTCS 14, 2009, pp. 32-46
 
H. de Jong. Qualitative modeling and simulation of bacterial regulatory networks. In Proceedings of Computational Methods in Systems Biology (CMSB'08), LNCS, vol. 5307, Springer, 2008.
 
D. Ropers and V. Baldazzi  and H. de Jong. Reduction of a kinetic model of the carbon starvation response in Escherichia coli. In Proceedings of the 15th IFAC Symposium on System Identification (SYSID 2009), 2009. http://ibis.inrialpes.fr/article935.html
 
G. Batt, B. Besson, H. de Jong, E. Dumas, J. Geiselmann, P.T. Monteiro, M. Page, and D. Ropers. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks. Chapter in Bacterial molecular networks. Humana Press, 2009. To appear.
 
P.T. Monteiro, E. Dumas, B. Besson, R. Mateescu, M. Page, A.T. Freitas, and H. de Jong. A service-oriented architecture for integrating the modeling and verification of genetic regulatory networks. BMC Bioinformatics, vol. 10, pp. 450, 2009.
 
H. de Jong, D. Ropers, R. Mateescu, and J. Geiselmann. De la cellule a la puce. In La Recherche, Les cahiers de l'INRIA, vol. 419, pages I-II, 2008.
 
L. Brim, J. Barnat, and P. Rockai. DiVinE 2.0: High-Performance Model Checking. In Proceedings of International Workshop on High Performance Computational Systems Biology (HiBi 2009), pages 31-32, IEEE Computer Society, 2009.
 
F. Boyer, B. Besson, G. Baptist, J. Izard, C. Pinel, D. Ropers, J. Geiselmann and H. de Jong, WellReader: A MATLAB Program for the Analysis of Fluorescence and Luminescence Reporter Gene Data To appear in Bioinformatics, 2010.
 
Hidde de Jong, Caroline Ranquet, Delphine Ropers, Corinne Pinel, Johannes Geiselmann. Experimental and Computational Validation of Models Fluorescent and Luminescent Reporter Genes in Bacteria. BMC Systems Biology, in revision.