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.
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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.
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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.
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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. . Electronic Notes in Theoretical Computer
Science 220 ( 2). Elsevier. ISSN 1571-0661
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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 .
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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.
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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.
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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.
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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.
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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.
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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
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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. . Electronic Notes in Theoretical Computer
Science 198 ( 1). Elsevier. ISSN 1571-0661
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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.
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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.
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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
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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 |
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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.
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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.
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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. . Electronic Notes in Theoretical Computer
Science 198 ( 1). Elsevier. ISSN 1571-0661
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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
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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
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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. |
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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
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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
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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.
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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. |
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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
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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. |
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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.
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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. |
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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.
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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.
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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.
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