A new dichotomic algorithm for the uniform random generation of words in regular languages16 August 2012Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Theoretical Computer Science (2012), DOI 10.1016/j.tcs.2012.07.025
A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency25 March 2008By Patrick Amar et Al.
BMC Systems Biology 2008, 2:27
Automated motif extraction and classification in RNA tertiary structures29 November 2008Mahassine Djelloul and Alain Denise. RNA December 2008 14:2489-2497.
Automated prediction of three-way junction topological families in RNA secondary structures11 February 2012Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, Éric Westhof.
Computational Biology and Chemistry 37 (2012) 1–5
Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm1 June 2010Claire Herrbach, Alain Denise and Serge Dulucq. Theoretical Computer Science 411 (2010) 2423-2432.
Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis9 February 2016D. Ellison, A. Mugler, M.D. Brennan, S.H. Lee, R.J. Huebner,
E.R. Shamir, L.A. Woo, J. Kim, P. Amar, I. Nemenman,
A.J. Ewald and A. Levchenko
Chromosome Replication in Escherichia coli: Life on the Scales. Vic NORRIS and Patrick AMAR29 October 2012Life 2012, 2(4), 286-312; doi:10.3390/life2040286
Computer‐aided biochemical programming of synthetic microreactors as diagnostic devices27 April 2018Alexis Courbet, Patrick Amar, Francois Fages, Eric Renard, Franck Molina
Mol Syst Biol. (2018) 14: e7845
DOI 10.15252/msb.20177845
Computing with Synthetic Protocells13 May 2015Alexis Courbet, Franck Molina and Patrick Amar
Coverage-biased random explo-ration of large models and application to testing27 March 2011A. Denise, M.-C. Gaudel, S.-D. Gouraud, R. Lassaigne, J. Oudinet S. Peyronnet, STTT: Int. Jal on SOFTWARE TOOLS FOR TECHNOLOGY TRANSFER, DOI: 10.1007/s10009-011-0190-1
GenoQuery: a new querying module for functional annotation in a genomic warehouse1 July 2008Novel insights regarding the sigmoidal pattern of resistance to neomycin conferred by the aphII gene in Streptomyces lividans.2 May 2013Nicolas Seghezzi, Marie-Joelle Virolle and Patrick Amar
Sensor potency of the moonlighting enzyme-decorated cytoskeleton: the cytoskeleton as a metabolic sensor26 February 2013Vic Norris, Patrick Amar, Guillaume Legent, Camille Ripoll, Michel Thellier and Judit Ovádi
The Average Complexity of Tree Alignment28 January 2008We have proved that the average complexity of the pairwise ordered tree alignment algorithm of Jiang, Wang and Zhang is in O(nm), where n and m stand for the sizes of the two trees, respectively.
The Mimic Chain Reaction. V. Norris, A. Thierry, P. Amar, B. Holland, F. Molina5 December 2012J Mol Microbiol Biotechnol 2012;22:335-343 (doi: 10.1159/000345328)
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots7 August 2012Philippe Rinaudo, Yann Ponty, Dominique Barth, and Alain Denise. WABI 2012.
Uniform trace sampling in very large models6 November 2007A new algorithm makes it possible to draw traces uniformly at random in very large models of concurrent systems.
VARNA software distinguished15 July 2011VARNA distinguished in the 2010 CNRS scientific report.
