Overall Objectives
Scientific Foundations
Application Domains
New Results
Contracts and Grants with Industry
Other Grants and Activities


Publications of the year

Books and Monographs

J.-P. Dumas, J.-L. Roch, E. Tannier, S. Varette.
Théorie des codes, sciences sup, To appear, Dunod, 2007.

Articles in refereed journals and book chapters

G. Achaz, F. Boyer, E. Rocha, A. Viari, E. Coissac.
Repseek, a tool to retrieve approximate repeats from large DNA sequences., in: Bioinformatics, 2006, vol. in press.
V. Acuña, G. Didier, A. Maass.
Centered codes, in: Theor. Comput. Sci., 2006.
J. Allali, M.-F. Sagot.
A multiple layer model to compare RNA secondary > structures, submitted, 2006.
A. Aouacheria, C. Geourjon, N. Aghajari, V. Navratil, G. Deleage, C. Lethias, J. Y. Exposito.
Insights into Early Extracellular Matrix Evolution: Spongin Short Chain Collagen-related Proteins are Homologous to Basement Membrane Type IV Collagens and Form a Novel Family Widely Distributed in Invertebrates, in: Mol Biol Evol, 2006.
A. Aouacheria, V. Navratil, A. Barthelaix, D. Mouchiroud, C. Gautier.
Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues, in: BMC Genomics, 2006, vol. 7, 94 p.
A.-M. Arigon, G. Perrière, M. Gouy.
HoSeqI: automated homologous sequence identification in gene family databases, in: Bioinformatics, 2006, vol. 22(14), p. 1786-1787.
J. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin, B. Porcel, B. Segurens, V. Daubin, V. Anthouard, N. Aiach, O. Arnaiz, A. Billaut, J. Beisson, I. Blanc, K. Bouhouche, F. Camara, S. Duharcourt, R. Guigo, D. Gogendeau, M. Katinka, A. Keller, R. Kissmehl, C. Klotz, F. Koll, A. Le Mouel, G. Lepere, S. Malinsky, M. Nowacki, J. Nowak, H. Plattner, J. Poulain, F. Ruiz, V. Serrano, M. Zagulski, P. Dessen, M. Betermier, J. Weissenbach, C. Scarpelli, V. Schachter, L. Sperling, E. Meyer, J. Cohen, P. Wincker.
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia , in: Nature, 2006, vol. 444, no 7116, p. 171-178.
G. Batt, R. Casey, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider.
Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux, in: Technique et Science Informatiques, 2006.
G. Batt, R. Casey, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider.
Qualitative analysis of the dynamics of genetic regulatory networks using piecewise-linear models, in: Mathematical and Computational Methods in Biology, Paris, E. Pecou, S. Martinez, A. Maass (editors), Editions Hermann, 2006, p. 206-239.
E. Billoir, A. Péry, S. Charles.
Integration of both lethal and sublethal effects of toxic compounds in population dynamics of Daphnia magna : a combination of DEBtox models and matrix population models, in: Ecological Modelling, in press, 2006.
R. Bourqui, L. Cottret, V. Lacroix, D. Auber, P. Mary, M.-F. Sagot, F. Jourdan.
Metabolic network visualization using a constraint planar graph drawing algorithm, in: BMC Bioinformatics, submitted, 2006.
B. Boussau, M. Gouy.
Efficient Likelihood Computations with Nonreversible Models of Evolution, in: Systematic Biology, 2006, vol. 55(5), p. 756-768.
R. Casey, H. de Jong, J.-L. Gouzé.
Piecewise-linear models of genetic regulatory networks: Equilibria and their stability, in: Journal of Mathematical Biology, 2006, vol. 52, no 1, p. 27-56.
S. Charles, H. Persat, J.-P. Mallet.
Population dynamics of grayling: Modelling temperature and discharge effects, in: Mathematical Modelling of Natural Phenomena, in press, 2006.
J. Charlet, B. Cremilleux, M. De Carvalho, C. Garbay, J. Jabre, D. Janas, A. Labarre-Vila, V. Luengo, V. Rialle, D. Ziébelin.
Traitement de l'information en médecine et ENMG, in: Revue de Neurophysiologie clinique, 2006.
A. Chaumot, N. Milioni, A. Abdoli, D. Pont, S. Charles.
First step of a modeling approach to evaluate spatial heterogeneity in a fish (Cottus gobio) population dynamics, in: Ecological Modelling, 2006, vol. 197(3-4), p. 263-273.
Y. Clément, R. Tavares, G. Marais.
Does lack of recombination enhance asymmetric evolution among duplicate genes? Insights from the Drosophila melanogaster genome, in: Gene, in press, 2006.
M. Crochemore, C. Iliopoulos, M. Mohamed, M.-F. Sagot.
Longest Repeats with a Block of k Don't Cares, in: Theor Comput Sci, in press, 2006.
G. Decelier, Y. Letrillard, S. Charles, C. Biémont.
TESD: A population genomics simulation environment for transposable element dynamics, in: Bioinformatics, in press, 2006.
H. de Jong, D. Ropers.
Strategies for dealing with incomplete information in the modeling of molecular interaction networks, in: Briefings in Bioinformatics, 2006, vol. 7, p. 354-363.
H. de Jong, C. Chaouiya, D. Thieffry.
Dynamical modeling of biological regulatory networks, in: BioSystems, 2006, vol. 84, no 2, p. 77-80.
H. de Jong, D. Ropers.
Qualitative approaches towards the analysis of genetic regulatory networks, in: System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, Cambridge, MA, Z. Szallasi, V. Periwal, J. Stelling (editors), MIT Press, 2006, p. 125-148.
E. de Laplanche, K. Gouget, G. Cléris, F. Dragounoff, J. Demont, A. Morales, L. Bezin, C. Godinot, G. Perrière, D. Mouchiroud, H. Simonnet.
Physiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules, in: Am. J. Physiol. Renal Physiol., 2006, vol. 291, p. 750-760.
S. Descorps-Declere, D. Ziebelin, F. Rechenmann, A. Viari.
Genepi: a blackboard framework for genome annotation, in: BMC Bioinformatics, 2006, vol. 7, p. 450-462.
Y. Diekmann, M.-F. Sagot, E. Tannier.
Evolution under reversals: parsimony and conservation of common intervals, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, 2006.
S. Drulhe, G. Ferrari-Trecate, H. de Jong, A. Viari.
Reconstruction of switching thresholds in piecewise-affine models of genetic regulatory networks, in: Hybrid Systems: Computation and Control (HSCC 2006), Berlin, J. Hespanha, A. Tiwara (editors), Lecture Notes in Computer Science, Springer-Verlag, 2006, vol. 3927, p. 184-199.
R. Duponnois, K. Assigbetsé, H. Ramanankierana, M. Kisa, J. Thioulouse, M. Lepage.
Litter-forager termite mounds enhance the ectomycorrhizal symbiosis between Acacia holosericea A. Cunn. Ex G. Don and Scleroderma dictyosporum isolates, in: FEMS Microbiol Ecol, 2006, vol. 56(2), p. 292-303.
R. Duponnois, M. Kisa, K. Assigbetsé, Y. Prin, J. Thioulouse, M. Issartel, P. Moulin, M. Lepage.
Fluorescent pseudomonads occuring in Macrotermes subhyalinus mound structures decrease Cd toxicity and improve its accumulation in sorghum plants, in: Sci Total Environ, 2006, vol. 370(2-3), p. 391-400.
P. Durand, L. Labarre, A. Meil, J. Divol, Y. Vandenbrouck, A. Viari, J. Wojcik.
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins, in: BMC Bioinformatics, 2006, vol. 7, p. 21-31.
L. Duret, C. Chureau, S. Samain, J. Weissenbach, P. Avner.
The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene, in: Science, 2006, vol. 312, no 5780, p. 1653-1655.
L. Duret.
The GC Content of Primates and Rodents Genomes Is Not at Equilibrium: A Reply to Antezana, in: J Mol Evol, 2006, vol. 62, no 6, p. 803-806.
L. Duret, A. Eyre-Walker, N. Galtier.
A new perspective on isochore evolution, in: Gene, in Press, 2006.
O. Ebenhoh, T. Handorf, D. Kahn.
Evolutionary changes of metabolic networks and their biosynthetic capacities, in: Systems Biology, 2006, vol. 153(5), p. 354-358.
R. Frutos, A. Viari, C. Ferraz, A. Bensaid, A. Morgat, F. Boyer, E. Coissac, N. Vachiery, J. Demaille, D. Martinez.
Comparative Genomics of Three Strains of Ehrlichia ruminantium : A Review, in: Ann N Y Acad Sci., 2006, vol. 1081, p. 417-433.
R. Frutos, A. Viari, C. Ferraz, A. Morgat, S. Eychenie, Y. Kandassamy, I. Chantal, A. Bensaid, E. Coissac, N. Vachiery, J. Demaille, D. Martinez.
Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity, in: J Bacteriol., 2006, vol. 188, p. 2533-2542.
J. Grassot, M. Gouy, G. Perrière, G. Mouchiroud.
Origin and Molecular Evolution of Receptor Tyrosine Kinases with Immunoglobulin-Like Domains, in: Mol. Biol. Evol., 2006, vol. 23(6), p. 1232-1241.
H. Hallay, N. Locker, L. Ayadi, D. Ropers, E. Guittet, C. Branlant.
Biochemical and NMR study on the competition between proteins SC35, SRp40, and heterogeneous nuclear ribonucleoprotein A1 at the HIV-1 Tat Exon 2 splicing site, in: The Journal of Biological Chemistry, 2006, vol. 281, p. 37159-37174.
T. Handorf, O. Ebenhoh, D. Kahn, R. Heinrich.
Hierarchy of metabolic compounds based on their synthesising capacity, in: Systems Biology, 2006, vol. 153(5), p. 359-363.
HoneyBee Genome Sequencing Consortium.
Insights into social insects from the genome of the honeybee Apis mellifera , in: Nature, 2006, vol. 443, no 7114, p. 931-949.
A. Khelifi, J. Meunier, L. Duret, D. Mouchiroud.
GC Content Evolution of the Human and Mouse Genomes: Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates, in: J Mol Evol, 2006, vol. 62, no 6, p. 745-752.
V. Lacroix, C. G. Fernandes, M.-F. Sagot.
Motif Search in Graphs: Application to Metabolic Networks, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, 2006.
T. Lefebure, C. J. Douady, M. Gouy, J. Gibert.
Relationship between morphological taxonomy and molecular divergence within Crustacea : Proposal of a molecular threshold to help species delimitation, in: Molecular Phylogenetics and Evolution, 2006, vol. 40(2), p. 435-447.
T. Lefebure, C. J. Douady, M. Gouy, P. Trontelj, J. Briolay, J. Gibert.
Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments, in: Mol. Ecol., 2006, vol. 15(7), p. 1797-1806.
J. Y. Le Hesran, N. Fievet, J. Thioulouse, P. Personne, B. Maubert, S. M'bidias, D. Etye'ale, M. Cot, P. Deloron.
Development of cellular immune responses to Plasmodium falciparum blood stage antigens from birth to 36 months of age in Cameroon, in: Acta Trop, 2006, vol. 98(3), p. 261-269.
C. Lemaitre, M.-F. Sagot.
A Small Trip in the Untranquil World of Genomes, in: Theoretical Computer Science, accepted with minor revisions, 2006.
J. R. Lobry, A. Necsulea.
Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes, in: Gene, in press, 2006.
C. Melodelima, L. Guéguen, D. Piau, C. Gautier.
A computational prediction of isochores based on hidden Markov models, in: Gene, in press, 2006.
A. Necsulea, J. R. Lobry.
Revisiting the directional mutation pressure theory: The analysis of a particular genomic structure in Leishmania major, in: Gene, in press, 2006.
L. Palmeira, L. Guéguen, J. R. Lobry.
UV-targeted dinucleotides are not depleted in light-exposed Prokaryotic genomes, in: Mol Biol Evol, 2006, vol. 23(11), p. 2214-2219.
F. Rechenmann.
Dessine-moi un génome, in: La Recherche, 2006, vol. 402, p. 82-83.
E. M. Rodrigues, M.-F. Sagot, Y. Wakabayashi.
The Maximum Agreement Forest Problem: approximation algorithms and computational experiments, in: Theor Comput Sci, in press, 2006.
D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann.
Qualitative simulation of the carbon starvation response in Escherichia coli , in: BioSystems, 2006, vol. 84, no 2, p. 124-152.
H. Sanguin, B. Remenant, A. Dechesne, J. Thioulouse, T. M. Vogel, X. Nesme, Y. Moenne-Loccoz, G. L. Grundmann.
Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities, in: Appl Environ Microbiol, 2006, vol. 72(6), p. 4302-4312.
A. Sanon, P. Martin, J. Thioulouse, C. Plenchette, R. Spichiger, M. Lepage, R. Duponnois.
Displacement of an herbaceous plant species community by mycorrhizal and non-mycorrhizal Gmelina arborea , an exotic tree, grown in a microcosm experiment, in: Mycorrhiza, 2006, vol. 16(2), p. 125-132.
M. Sémon, L. Duret.
Evolutionary origin and maintenance of coexpressed gene clusters in mammals, in: Mol Biol Evol, 2006, vol. 23, no 9, p. 1715-1723.
M. Sémon, J. R. Lobry, L. Duret.
No evidence for tissue-specific adaptation of synonymous codon usage in humans, in: Mol Biol Evol, 2006, vol. 23, no 3, p. 523-529.
P. Taberlet, E. Coissac, F. Pompanon, L. Gielly, C. Miquel, A. Valentini, T. Vermat, G. Corthier, C. Brochmann, E. Willerslev.
Power and limitations of the chloroplast trnl (uaa) intron for plant dna barcoding, in: Nucleic Acids Res, 2006, vol. in press.
P. Thébault, S. de Givry, T. Schiex, C. Gaspin.
Combining constraint network processing and pattern matching to describe and locate structured motifs in genomic sequences, in: Bioinformatics, 2006, vol. 22(17), p. 2074-2080.
I. Vatcheva, O. Bernard, H. de Jong, N. Mars.
Experiment selection for the discrimination of semi-quantitative models of dynamical systems, in: Artificial Intelligence, 2006, vol. 170, no 4, p. 472-506.
E. Vautrin, S. Charles, S. Genieys, F. Vavre.
Evolution and invasion dynamics of multiple infections with Wolbachia investigated using matrix based models, in: J of Theor Bio, 2006.

Publications in Conferences and Workshops

S. Abby, M. Gouy, V. Daubin.
Des milliers d'arbres de gènes pour reconstruire l'histoire du vivant, in: Journées Ouvertes : Biologie Informatique et Mathématiques (JOBIM), 2006.
J. Allali, Y. d'Aubenton-Carafa, C. Thermes, M.-F. Sagot.
MiGaL: an efficient tool for RNA secondary structures comparison, in: Journées Ouvertes : Biologie Informatique et Mathématiques (JOBIM), short talk, 2006.
R. Bourqui, D. Auber, V. Lacroix, F. Jourdan.
Metabolic network visualization using a constraint planar graph drawing, in: 10th conf. on Information Visualization, 2006, p. 489-496.
A. Chaumot, S. Charles.
Pollution, stochasticity and spatial heterogeneity in the dynamics of an age-structured population of brown trout living in a river network, in: Population-level Ecotoxicological Risk Assessment: Case Studies, R. Akcakaya (editor), 2006.
J.-J. Daudin, V. Lacroix, F. Picard, S. Robin, M.-F. Sagot.
Uncovering structure in biological networks, in: Journées Ouvertes : Biologie Informatique et Mathématiques (JOBIM), 2006.
H. de Jong.
Qualitative modeling and simulation of genetic regulatory networks: From piecewise-affine differential equations to reporter gene data (and back), in: Proceedings of the Twentieth International Workshop on Qualitative Reasoning, QR-06, Dartmouth,, C. Bailey-Kellogg, B. Kuipers (editors), 2006.
J. Gensel, C. Capponi, P. Genoud, D. Ziébelin.
Vers une intégration des relations Partie-Tout en AROM, in: Langages et Modèles à Objets (LMO'06), 2006.
M. Mariadrissou, J.-J. Daudin, V. Lacroix, V. Miele, F. Picard, S. Robin, M.-F. Sagot.
Uncovering structure in biological networks, in: RIAMS'06, papers accepted to this conference will be submitted a posteriori to Journal of Biological Physics and Chemistry, 2006.
C. Melodelima, L. Guéguen, C. Gautier, D. Piau.
A Markovian Approach for the Analysis of the Gene Structure, in: PSC'06, 2006.
B. Moisuc, P. Genoud, D. Ziébelin, J. Gensel, C. Capponi.
Apports de la modélisation algébrique pour la représentation de connaissances par objets : illustration en AROM, in: Langages et Modèles à Objets (LMO'06), 2006.
P. Peterlongo, J. Allali, M.-F. Sagot.
The Gapped-Factor Tree, in: PSC'06, 2006.
P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot.
Ed'Nimbus: A Lossless Filter for Long Multiple Repetitions with Edit Distance, in: Journées Ouvertes : Biologie Informatique et Mathématiques (JOBIM), short talk, 2006.
N. Pisanti, A. Carvalho, L. Marsan, M.-F. Sagot.
RISOTTO: Fast extraction of motifs with mismatches, in: LATIN'06, J. R. Correa, A. Hevia, M. Kiwi (editors), Lecture Notes in Computer Science, Springer-Verlag, 2006, vol. 3887, p. 757-768.

References in notes

F. Baty, M. P. Bihl, A. C. Culhane, M. Brutsche, G. Perrière.
Optimization of Between Group Analysis of gene expression disease class prediction, in: Proceedings of the 2nd International Symposium on Mathematical and Computational Biology, R. P. Mondaini, R. Dilão (editors), World Scientific Publishing, 2005, p. 351-366.