Bibliography

Publications of the year

Articles in International Peer-Reviewed Journal

[1]

V. Baldazzi, P. Paci, M. Bernaschi, F. Castiglione.
Modeling lymphocyte homing and encounters in lymph nodes, in: BMC Bioinformatics, 2009, vol. 10, 387 p.

[2]

F. Boyer, B. Besson, G. Baptist, J. Izard, C. Pinel, D. Ropers, J. Geiselmann, H. de Jong.
A MATLAB program for the analysis of fluorescence and luminescence reporter gene data, in: Bioinformatics, 2010, In press.

[3]

F. Corblin, S. Tripodi, E. Fanchon, D. Ropers, L. Trilling.
A declarative constraint-based method for analyzing discrete genetic regulatory networks, in: Biosystems, 2009, vol. 98, n^o 2, p. 91-104.

[4]

G. Khoury, L. Ayadi, J.-M. Saliou, S. Sanglier, D. Ropers, C. Branlant.
New actors in regulation of HIV-1 tat mRNA production, in: Retrovirology, 2009, vol. 6, n^o Suppl 2, P46 p.

[5]

P. Monteiro, E. Dumas, B. Besson, R. Mateescu, M. Page, A. Freitas, H. de Jong.
A service-oriented architecture for integrating the modeling and verification of genetic regulatory networks, in: BMC Bioinformatics, 2009, vol. 10, 450 p.

[6]

D. Ropers, V. Baldazzi, H. de Jong.
Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli , in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, In press.

[7]

J.-M. Saliou, C. Bourgeois, L. A.-B. Mena, D. Ropers, S. Jacquenet, V. Marchand, J. Stévenin, C. Branlant.
Role of RNA structure and protein factors in the control of HIV-1 splicing, in: Frontiers in Bioscience, 2009, vol. 14, p. 2714-2729.

International Peer-Reviewed Conference/Proceedings

[8]

R. Porreca, S. Drulhe, H. de Jong, G. Ferrari-Trecate.
Identification of parameters and structure of piecewise affine models of genetic networks, in: Proceedings of the 15th IFAC Symposium on System Identification, SYSID 2009, Saint Malo, France, 2009.

[9]

R. Porreca, S. Drulhe, H. de Jong, G. Ferrari-Trecate.
Inferring structure and parameters of genetic regulatory networks: an approach based on hybrid systems, in: Workshop on Classification and Forecasting Models, ECOBIOSYS 2009, Milano, Italy, 2009.

[10]

D. Ropers, V. Baldazzi, 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, Saint Malo, France, 2009.

National Peer-Reviewed Conference/Proceedings

[11]

P. Monteiro, P. Dias, D. Ropers, A. Oliveira, A. Freitas, I. Sa-Correia, M. Teixeira.
The regulatory network underlying the transcriptional up-regulation of the FRL1 gene in mancozeb stressed yeast cells: qualitative modeling and simulation, in: Proceedings of the Congresso Nacional MicroBiotec'09, Vilamoura, Portugal, 2009.

Scientific Books (or Scientific Book chapters)

[12]

V. Baldazzi, P. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong.
Qualitative analysis of genetic regulatory networks in bacteria, in: Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, W. Dubitzky, J. Southgate and H. Fuss, 2009, In press.

[13]

G. Batt, B. Besson, H. de Jong, E. Dumas, J. Geiselmann, P. Monteiro, M. Page, D. Ropers.
Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks, in: Bacterial molecular networks, J. van Helden, A. Toussaint and D. Thiefry, 2009, To appear.

Scientific Popularization

[14]

H. de Jong.
Vers la cellule virtuelle, in: DocSciences, 2009, vol. 8, p. 20-25.

[15]

F. Rechenmann.
Le génome, moteur de la bio-informatique, in: Dossiers de La Recherche : Le pouvoir des mathématiques, 2009, vol. 37, p. 36-37.