Publications

Chapitres de livre

Bourdon, J. & Eveillard, D., Probabilistic models in systems biology. In book Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications. Elloumi & Zomaya (eds.), Wiley Series in Bioinformatics, 2011. (preprint)

A generic stoichiometric model to analyse the metabolic flexibility of the mammary gland in lactating dairy cows, Lemosquet S; Abdou-Arbi O; Siegel A; Guinard-Flament J; Van Milgen J; Bourdon J, In Modelling nutrient digestion and utilization in farm animals, D. Sauvant, J. Van Milgen, P. Faverdin and N. Friggens eds, Wageningen Academic Publishers, 2010. contrib: modélisation et analyse de réseaux métaboliques

Journaux internationaux

Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. Oumarou Abdou-Arbi, Sophie Lemosquet, Jaap Van Milgen, Anne Siegel, Jérémie Bourdon. BMC Systems Biology, BioMed Central, 2014, 8 (1), pp.8.

Modelization of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive. Sébastien Laurent, Adrien Richard, Odile Mulner-Lorillon, Julia Morales, Didier Flament, Virginie Glippa, Jérémie Bourdon, Pauline Gosselin, Anne Siegel, Patrick Cormier, Robert Bellé. Frontiers in Genetics, 2014, 5, pp.117.

Large deviation properties for patterns, Jérémie Bourdon, Mireille Régnier. Journal of Discrete Algorithms, Elsevier, Volume 24, January 2014, Pages 2–11

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment, Thierry Tonon, Damien Eveillard, Sylvain Prigent, Jérémie Bourdon, Philippe Potin, Catherine Boyen, Anne Siegel, OMICS: A Journal of Integrative Biology, 15(12): 883-892, 2011

Integrating Quantitative Knowledge Into a Qualitative Gene Regulatory Network, Jérémie Bourdon, Damien Eveillard, Anne Siegel, PLOS Computational Biology, PLOS Computational Biology,9(7) : 1-11, 2011

A parallel scheme for comparing transcription factor binding sites matrices, Solenne Carat, Rémi Houlgatte and Jérémie Bourdon, Journal of Bioinformatics and Computational Biology 8(3), (2010). (preprint)

Temporal constraints of a gene regulatory network: Refining a qualitative simulation, Ahmad, J.; Bourdon, J.; Eveillard, D.; Fromentin, J.; Roux, O. & Sinoquet, C., Biosystems 98(3), p. 149-159, (2009) (reprint)

Combinations of cytochrome p450 gene polymorphisms enhancing the risk for sporadic colorectal cancer related to red meat consumption. Sébastien Küry, Bruno Buecher, Sébastien Robiou du Pont, Catherine Scoul, Véronique Sébille, Hélène Colman, Claire Le Houérou, Tanguy Le Neel, Jérémie Bourdon, Roger Faroux, Jean Ollivry, Bernard Lafraise, Louis-Dominique Chupin, and Stéphane Bézieau. Cancer Epidemiology Biomarkers and Prevention, 16:1460–1467, 2007. (reprint)

On the Khintchine constant for centred continued fraction expansions, Jeremie Bourdon, Appl. Math. E-Notes, 7 (2007), 167-174 (reprint)

Dynamical Analysis of a-Euclidean Algorithms, Jérémie Bourdon, Benoît Daireaux, Brigitte Vallée, Journal of algorithms, numéro 44, pp. 246-285, (2002) (reprint)

Size and Path Length of Patricia Tries: Dynamical Sources Context., Jérémie Bourdon, Random Structures and Algorithms, John Wiley and Sons, 19 (3-4), pp. 289--315. (2001) (reprint)

On the Stack-Size of General Tries, Jérémie Bourdon, Markus Nebel, Brigitte Vallée, Theoretical Informatics and Applications, EDP Sciences, 35, pp. 163--185. (2000) (reprint)

Conférences internationales

Multivariate Normal Approximation for the Stochastic Simulation Algorithm: limit theorem and applications. Vincent Picard, Anne Siegel, Jérémie Bourdon. SASB - 5th International Workshop on Static Analysis and Systems Biology, 2014, Munchen, Germany

Generating discrete planes with substitutions. Valerie Berthe, Jérémie Bourdon, Timo Jolivet, Anne Siegel. WORDS - 9th International Conference on Words - 2013, Sep 2013, Turku, Finland

Computing the p-values of selections in huge sets, Jérémie Bourdon, Solenne Carat and Mireille Régnier, Moscow Conference on Computational Molecular Biology (MCCMB'11), Moscow, Russia, July 21–24, 2011.

A statistical method for PWM clustering, Carat, S., Houlgatte, R. and Bourdon, J., In Proceedings of Moscow Conference on Computational Molecular Biology, 89-90 (2009).(reprint)

Statistical Properties of Factor Oracles, Bourdon, J. and Rusu, In proceedings of CPM 2009, LNCS 5577, 326-338, 2009, (reprint) extended version submitted to Journal of Discrete Algorithms.

A Generic Stoichiometric Model to Analyse the Metabolic Flexibility of the Mammary Gland in Lactating Dairy Cows, Lemosquet, S.; Bourdon, J.; Guinard-Flament, J.; Siegel, A. & Milgen, J. V. 7th International Workshop : "Modelling Nutrition Digestion and Utilization in Farm Animals", 2009

Statistical Properties of Similarity Score Functions, Bourdon, J. and Mancheron, A., In Proceedings of the 4th Colloquium on Mathematics and Computer Science. Algorithms, Trees, Combinatorics and Probabilities, Discrete Mathematics and Theoretical Computer Science (DMTCS), pages 129-140, (2006) (reprint)

Pattern Matching Statistics on Correlated sources, Bourdon, J and Vallée, B., Proceedings of LATIN'06, LNCS 3887, pp 224-237. (2006) (reprint)

Generalized Pattern Matching Statistics, Jérémie Bourdon, Brigitte Vallée, Proceedings of colloquium on Mathematics and Computer Science : Algorithms and Trees, Birkhauser, Trends in Mathematics, pp. 249-265 (2002) (reprint)

Conférences nationales avec comité de lecture

La calculette métabolique : une approche de modélisation biochimique pour explorer les contraintes au sein du métabolisme des mammifères, Arbi, O. A.; Bourdon, J.; Siegel, A.; Milgen, J. V. & Lemosquet, S. INRA (ed.) 3èmes Journées d'animation scientifique de Département de Physiologie Animale et Systèmes d'Elevage (PHASE), 2009, p. 132

Using a probabilistic approach for integrating heterogeneous biological knowledges, Bourdon, J., Eveillard, D., Gabillard, S. & Merle, T., In Proceedings of RIAMS 2007.

Distribution des solutions du problème d'affectation multi-objectif et relation avec l'efficacité des algorithmes de résolution, Przybylski, A.; Bourdon, J. & Gandibleux, X. Proc. of ROADEF 2007, Grenoble, France, 2007

Distribution of Solutions of Multi-objective Assignement Problem and Links with the Efficiency of Solving Methods,Przybylski, A.; Bourdon, J. & Gandibleux, X. Proc. of GOR 2007, Saarbrucken, Germany, 2007

Tearing Customers Apart for solving PSP-SOS (2005). Charlotte Truchet, Jérémie Bourdon and Philippe Codognet, IJCAI'05 Constraint Modelling Challenge Entry, Edinburgh, Great Britain.

Habilitation à diriger des recherches

Sources Probabilistes: des séquences aux systèmes. Jérémie Bourdon. Université de Nantes, 2012.

Conférences invitées

Réseaux biologiques semi-quantitatifs : dynamique et propriétés émergentes, Bourdon, J. IV-ème école thématique Rennaise sur les systèmes complexes, Rennes, octobre 2012

_Application des systèmes dynamiques : de l’arithmétique à la bioinformatique, Bourdon, J. Ecole des jeunes chercheurs du GdR Informatique et Mathématiques, Rennes, 2012

Average-case analysis methods dedicated to the study of Biological Networks, Bourdon, J., Moscow Conference on Computational Molecular Biology (MCCMB'11), Moscow, Russia, July 21–24, 2011

Optimisation problems and Graph Theory, Bourdon, J. . International Summer School ``Interfaces between Physics and Computer Science'', H. Meyer-Ortmanns, Bremen, 2007

Dynamical Systems and Analysis of Algorithms. Bourdon, J. Optimization algorithms and quantum disordered systems, L. Cugliandolo, R. Monasson, 2004

Autres publications, notes, posters et preprints

Steady-State Analysis of Reaction Networks. Vincent Picard, Anne Siegel and Bourdon J. Analysis of Algorithms (AofA) 2014, Paris (poster).

A combined approach to identify therapeutic targets involved in Progressive Cardiac Conduction Defect. Audrey Bihouée, Erwan Delage, Sébastien Charneau, Abdelhalim Larlhimi, Audrey Donnart, Damien Eveillard, Bourdon J., Pierre Lindenbaum, Gilles Toumaniantz, Flavien Charpentier, Richard Redon and Géraldine Jean. ECCB 2014, Strasbourg (poster no B40).

MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network. Marko Budinich, Damien Eveillard, Bourdon J., Abdelhalim Larhlimi. ISMB/ECCB 2013, Berlin (poster no O062).

Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology. Thierry Tonon, P. Bonin, Sylvain Prigent, Z. Shao, Agnès Groisillier, Sylvie Rousvoal, Sophie Goulitquer, Bourdon J., Damien Eveillard, Catherine Boyen, Anne Siegel. Esil 2012: algal post-genomics, Apr 2012, Roscoff, France (communication)

Large deviation properties for patterns, Bourdon J., Mireille Regnier. Thierry Lecroq Ed. LSD&LAW 2012, Feb 2012, Londres, United Kingdom (communication)

Integrating qualitative and quantitative knowledge within a probabilistic framework: application to gene regulatory and metabolic networks, Bourdon J., Eveillard & Siegel, Computational Methods in Systems Biology (CMSB) 2012, Londres (poster).

Modeling microbial networks. Eveillard, D., Bourdon, J., Bouskill, N. & Ward, B.B. Jacques Monod Conference series, Integrative Ecological Genomics, Roscoff, France, 2011(communication).

Probabilistic modeling of microbial ecosystems. Eveillard, D., Bourdon, J., Bouskill, N. & Ward, B.B. Ocean Sciences Meeting, San Juan, Puerto Rico, 2011 (communication)

Computing the p-values of selections in genome-wide studies, Jérémie Bourdon, Solenne Carat and Mireille Régnier, Poster accepté à RECOMB 2010 au Portugal en avril 2010.

Complex update strategies for Probabilistic Boolean Networks, Merle, T. and Bourdon, J., WCSB 2010 au Luxembourg en juin 2010.

A p-value computation to assess the significance of huge motif clusters, Bourdon, J., Carat, S. and Régnier, M., Rapport de recherche (preprint)

Pattern Extraction Algorithm using a Gaussian Scoring Scheme. Mancheron, A.; Bourdon, J. Research report, 2008

Toll Based Measures for Dynamical Graphs. Bourdon, J. & Eveillard, D. Research report. arXiv, 2007 (preprint)

POGG: Integrating qualitative and quantitative data of macromolecular networks. A probabilistic toolbox, Giraudet, E.; Docet, E. & Bourdon, J. Rapport interne, 2007, 2p. (preprint)