Bibliography

Publications of the year

Books and Monographs

[1]

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

[2]

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.

[3]

V. Acuña, G. Didier, A. Maass.
Centered codes, in: Theor. Comput. Sci., 2006.

[4]

J. Allali, M.-F. Sagot.
A multiple layer model to compare RNA secondary > structures, submitted, 2006.

[5]

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.

[6]

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.

[7]

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.

[8]

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, n^o 7116, p. 171-178.

[9]

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.

[10]

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.

[11]

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.

[12]

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.

[13]

B. Boussau, M. Gouy.
Efficient Likelihood Computations with Nonreversible Models of Evolution, in: Systematic Biology, 2006, vol. 55(5), p. 756-768.

[14]

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, n^o 1, p. 27-56.

[15]

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.

[16]

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.

[17]

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.

[18]

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.

[19]

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.

[20]

G. Decelier, Y. Letrillard, S. Charles, C. Biémont.
TESD: A population genomics simulation environment for transposable element dynamics, in: Bioinformatics, in press, 2006.

[21]

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.

[22]

H. de Jong, C. Chaouiya, D. Thieffry.
Dynamical modeling of biological regulatory networks, in: BioSystems, 2006, vol. 84, n^o 2, p. 77-80.

[23]

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.

[24]

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.

[25]

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.

[26]

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.

[27]

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.

[28]

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.

[29]

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.

[30]

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.

[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, n^o 5780, p. 1653-1655.

[32]

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, n^o 6, p. 803-806.

[33]

L. Duret, A. Eyre-Walker, N. Galtier.
A new perspective on isochore evolution, in: Gene, in Press, 2006.

[34]

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.

[35]

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.

[36]

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.

[37]

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.

[38]

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.

[39]

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.

[40]

HoneyBee Genome Sequencing Consortium.
Insights into social insects from the genome of the honeybee Apis mellifera , in: Nature, 2006, vol. 443, n^o 7114, p. 931-949.

[41]

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, n^o 6, p. 745-752.

[42]

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.

[43]

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.

[44]

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.

[45]

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.

[46]

C. Lemaitre, M.-F. Sagot.
A Small Trip in the Untranquil World of Genomes, in: Theoretical Computer Science, accepted with minor revisions, 2006.

[47]

J. R. Lobry, A. Necsulea.
Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes, in: Gene, in press, 2006.

[48]

C. Melodelima, L. Guéguen, D. Piau, C. Gautier.
A computational prediction of isochores based on hidden Markov models, in: Gene, in press, 2006.

[49]

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.

[50]

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.

[51]

F. Rechenmann.
Dessine-moi un génome, in: La Recherche, 2006, vol. 402, p. 82-83.

[52]

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.

[53]

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, n^o 2, p. 124-152.

[54]

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.

[55]

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.

[56]

M. Sémon, L. Duret.
Evolutionary origin and maintenance of coexpressed gene clusters in mammals, in: Mol Biol Evol, 2006, vol. 23, n^o 9, p. 1715-1723.

[57]

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, n^o 3, p. 523-529.

[58]

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.

[59]

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.

[60]

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, n^o 4, p. 472-506.

[61]

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

[62]

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.

[63]

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.

[64]

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.

[65]

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.

[66]

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.

[67]

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.

[68]

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.

[69]

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.

[70]

C. Melodelima, L. Guéguen, C. Gautier, D. Piau.
A Markovian Approach for the Analysis of the Gene Structure, in: PSC'06, 2006.

[71]

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.

[72]

P. Peterlongo, J. Allali, M.-F. Sagot.
The Gapped-Factor Tree, in: PSC'06, 2006.

[73]

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.

[74]

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

[75]

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.