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Bibliography

Major publications by the team in recent years
  • 1J. Bourdon, D. Eveillard, A. Siegel.

    Integrating quantitative knowledge into a qualitative gene regulatory network, in: PLoS Computational Biology, September 2011, vol. 7, no 9. [ DOI : 10.1371/journal.pcbi.1002157 ]

    http://hal.archives-ouvertes.fr/hal-00626708
  • 2A. Bretaudeau, F. Coste, F. Humily, L. Garczarek, G. Le Corguillé, C. Six, M. Ratin, O. Collin, W. M. Schluchter, F. Partensky.

    CyanoLyase: a database of phycobilin lyase sequences, motifs and functions, in: Nucleic Acids Research, November 2012, vol. 41. [ DOI : 10.1093/nar/gks1091 ]

    http://hal.inria.fr/hal-00760946
  • 3F. Coste, G. Kerbellec.

    A Similar Fragments Merging Approach to Learn Automata on Proteins, in: ECML:Machine Learning: ECML 2005, 16th European Conference on Machine Learning, Porto, Portugal, October 3-7, 2005, Proceedings, J. Gama, R. Camacho, P. Brazdil, A. Jorge, L. Torgo (editors), Lecture Notes in Computer Science, Springer, 2005, vol. 3720, pp. 522-529.
  • 4M. Gebser, C. Guziolowski, M. Ivanchev, T. Schaub, A. Siegel, P. Veber, S. Thiele.

    Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming, in: Principles of Knowledge Representation and Reasoning, AAAI Press, 2010.
  • 5C. Guziolowski, A. Bourdé, F. Moreews, A. Siegel.

    BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks, in: Bmc Genomics, 2009, vol. 26, no 10, 244 p. [ DOI : 10.1186/1471-2164-10-244 ]

    http://hal.inria.fr/inria-00429804
  • 6C. Guziolowski, S. Videla, F. Eduati, S. Thiele, T. Cokelaer, A. Siegel, J. Saez-Rodriguez.

    Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming, in: Bioinformatics, August 2013, vol. 29, no 18, pp. 2320-2326. [ DOI : 10.1093/bioinformatics/btt393 ]

    http://hal.inria.fr/hal-00853704
  • 7J. Nicolas, P. Durand, G. Ranchy, S. Tempel, A.-S. Valin.

    Suffix-Tree Analyser (STAN): looking for nucleotidic and peptidic patterns in genomes, in: Bioinformatics (Oxford, England), 2005, vol. 21, pp. 4408-4410.

    http://hal.archives-ouvertes.fr/hal-00015234
  • 8S. Prigent, G. Collet, S. M. Dittami, L. Delage, F. Ethis de Corny, O. Dameron, D. Eveillard, S. Thiele, J. Cambefort, C. Boyen, A. Siegel, T. Tonon.

    The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond., in: Plant Journal, September 2014, pp. 367-81. [ DOI : 10.1111/tpj.12627 ]

    https://hal.archives-ouvertes.fr/hal-01057153
  • 9C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas.

    CRISPI: a CRISPR interactive database, in: Bioinformatics, 2009, vol. 25, no 24, pp. 3317-3318.
Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 10G. Garet.

    Classification and characterization of enzymatic families with formal methods, Université de Rennes 1, December 2014.

    https://hal.inria.fr/tel-01096916
  • 11S. Prigent.

    Combinatorial completion for the reconstruction of metabolic networks, and application to the brown alga model Ectocarpus siliculosus, Université de Rennes 1, November 2014.

    https://hal.inria.fr/tel-01093287
  • 12S. Videla.

    Reasoning on the response of logical signaling networks with answer set programming, Université Rennes 1 ; Universität Postdam‎ (Allemagne), July 2014.

    https://tel.archives-ouvertes.fr/tel-01070436
  • 13V. Wucher.

    Modeling of a gene network between mRNAs and miRNAs to predict gene functions involved in phenotypic plasticity in the pea aphid, Universite Rennes 1, November 2014.

    https://hal.archives-ouvertes.fr/tel-01095967

Articles in International Peer-Reviewed Journals

  • 14O. Abdou-Arbi, S. Lemosquet, V. Milgen, A. Siegel, J. Bourdon.

    Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs, in: BMC Systems Biology, 2014, vol. 8, no 1, 8 p. [ DOI : 10.1186/1752-0509-8-8 ]

    https://hal.inria.fr/hal-00947219
  • 15G. Andrieux, M. Le Borgne, N. Théret.

    An integrative modeling framework reveals plasticity of TGF-β signaling, in: BMC Systems Biology, 2014, vol. 8, no 1, 30 p. [ DOI : 10.1186/1752-0509-8-30 ]

    http://www.hal.inserm.fr/inserm-00978313
  • 16V. Berthé, T. Jolivet, A. Siegel.

    Connectedness of fractals associated with Arnoux–Rauzy substitutions, in: RAIRO: Informatique Théorique et Applications / RAIRO: Theoretical Informatics and Applications, 2014, vol. 48, no 3, pp. 249-266. [ DOI : 10.1051/ita/2014008 ]

    https://hal.inria.fr/hal-01079727
  • 17C. Bettembourg, C. Diot, O. Dameron.

    Semantic particularity measure for functional characterization of gene sets using gene ontology, in: PLoS ONE, 2014, vol. 9, no 1, e86525. [ DOI : 10.1371/journal.pone.0086525 ]

    https://hal.inria.fr/hal-00941850
  • 18P. Blavy, F. Gondret, S. Lagarrigue, J. Van Milgen, A. Siegel.

    Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism, in: BMC Systems Biology, 2014, vol. 8, no 1, 32 p. [ DOI : 10.1186/1752-0509-8-32 ]

    https://hal.inria.fr/hal-00980499
  • 19S. M. Dittami, T. Barbeyron, C. Boyen, J. Cambefort, G. Collet, L. Delage, A. Gobet, A. Groisillier, C. Leblanc, G. Michel, D. Scornet, A. Siegel, J. E. Tapia, T. Tonon.

    Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae, in: Frontiers in Genetics, 2014, vol. 5, 241 p. [ DOI : 10.3389/fgene.2014.00241 ]

    https://hal.inria.fr/hal-01079739
  • 20F. Herault, A. Vincent, O. Dameron, P. Le Roy, P. Cherel, M. Damon.

    The longissimus and semimembranosus muscles display marked differences in their gene expression profiles in pig, in: PLoS ONE, 2014, vol. 9, no 5, e96491. [ DOI : 10.1371/journal.pone.0096491 ]

    https://hal.inria.fr/hal-00989635
  • 21S. Laurent, A. Richard, O. Mulner-Lorillon, J. Morales, D. Flament, V. Glippa, J. Bourdon, P. Gosselin, A. Siegel, P. Cormier, R. Bellé.

    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, in: Frontiers in Genetics, 2014, vol. 5, 117 p. [ DOI : 10.3389/fgene.2014.00117 ]

    https://hal.inria.fr/hal-01079758
  • 22S. Prigent, G. Collet, S. M. Dittami, L. Delage, F. Ethis de Corny, O. Dameron, D. Eveillard, S. Thiele, J. Cambefort, C. Boyen, A. Siegel, T. Tonon.

    The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond, in: Plant Journal, September 2014, pp. 367-81. [ DOI : 10.1111/tpj.12627 ]

    https://hal.archives-ouvertes.fr/hal-01057153
  • 23S. Videla, C. Guziolowski, F. Eduati, S. Thiele, M. Gebser, J. Nicolas, J. Saez-Rodriguez, T. Schaub, A. Siegel.

    Learning Boolean logic models of signaling networks with ASP, in: Journal of Theoretical Computer Science (TCS), June 2014. [ DOI : 10.1016/j.tcs.2014.06.022 ]

    https://hal.inria.fr/hal-01058610

Invited Conferences

  • 24A. Siegel, C. Guziolowski, S. Videla, T. Schaub.

    Improving robustness in the study of logical model of signalling networks with answer set programming, in: ECCB 2014 - Workshop on Logical Modelling and Analysis of Cellular Networks, Strasbourg, France, September 2014.

    https://hal.inria.fr/hal-01095607
  • 25A. Siegel.

    Using ASP to integrate large-scale heterogeneous information about the response of a biological system , in: 5th Workshop on Logic and Systems Biology (associated with CSL/LICS 2014), VIenna, Austria, July 2014.

    https://hal.inria.fr/hal-01095609

International Conferences with Proceedings

  • 26V. Acuña, A. Aravena, A. Maass, A. Siegel.

    Modeling parsimonious putative regulatory networks: complexity and heuristic approach, in: 15th conference in Verification, Model Checking, and Abstract Interpretation, San Diego, United States, Springer, 2014, vol. 8318, pp. 322-336. [ DOI : 10.1007/978-3-642-54013-4_18 ]

    https://hal.inria.fr/hal-00926477
  • 27C. Belleannée, O. Sallou, J. Nicolas.

    Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling, in: PRIB - 9th IAPR International Conference on Pattern Recognition in Bioinformatics, Stockholm, Sweden, M. Comin, L. Kall, E. Marchiori, A. Ngom, J. Rajapakse (editors), Springer International Publishing, August 2014, vol. 8626, pp. 34-47. [ DOI : 10.1007/978-3-319-09192-1_4 ]

    https://hal.inria.fr/hal-01059506
  • 28F. Coste, G. Garet, A. Groisillier, J. Nicolas, T. Tonon.

    Automated Enzyme classification by Formal Concept Analysis, in: ICFCA - 12th International Conference on Formal Concept Analysis, Cluj-Napoca, Romania, Springer, June 2014.

    https://hal.inria.fr/hal-01063727
  • 29F. Coste, G. Garet, J. Nicolas.

    A bottom-up efficient algorithm learning substitutable languages from positive examples, in: ICGI (International Conference on Grammatical Inference), Kyoto, Japan, A. Clark, M. Kanazawa, R. Yoshinaka (editors), The 12th International Conference on Grammatical Inference, September 2014, vol. 34, pp. 49-63.

    https://hal.inria.fr/hal-01080249
  • 30F. Legeai, T. Derrien, V. Wucher, D. Audrey, G. Le Trionnaire, D. Tagu.

    Long non-­‐coding RNA in the pea aphid; identification and comparative expression in sexual and asexual embryos, in: Arthropod Genomics Symposium, Urbana, United States, June 2014.

    https://hal.inria.fr/hal-01091304
  • 31N. Maillet, G. Collet, T. Vannier, D. Lavenier, P. Peterlongo.

    COMMET: comparing and combining multiple metagenomic datasets, in: IEEE BIBM 2014, Belfast, United Kingdom, November 2014.

    https://hal.inria.fr/hal-01080050
  • 32L. Miclet, N. Barbot, H. Prade.

    From analogical proportions in lattices to proportional analogies in formal concepts, in: ECAI - 21th European Conference on Artificial Intelligence, Prague, Czech Republic, August 2014.

    https://hal.inria.fr/hal-01000314
  • 33V. Picard, A. Siegel, J. Bourdon.

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

    https://hal.inria.fr/hal-01079768

Conferences without Proceedings

  • 34H. Bazille, J. Nicolas.

    Computational Protein Design: trying an Answer Set Programming approach to solve the problem, in: 10th Workshop on Constraint-Based Methods for Bioinformatics (WCB'14), Lyon, France, Nicos Angelopoulos (Imperial College, UK) , Simon de Givry (MIAT-INRA, France), September 2014.

    https://hal.inria.fr/hal-01063030
  • 35M. Boccara, M. Carpentier, J. Chomilier, F. Coste, C. Galiez, J. Pothier, A. Veluchamy.

    Identifying distant homologous viral sequences in metagenomes using protein structure information, in: ECCB'14 Workshop on Recent Computational Advances in Metagenomics, Strasbourg, France, September 2014.

    https://hal.archives-ouvertes.fr/hal-01090987
  • 36F. Moreews, Y. Le Bras, O. Dameron, C. Monjeaud, O. Collin.

    Integrating GALAXY workflows in a metadata management environment, in: Galaxy Community Conference, Baltimore, United States, July 2014.

    https://hal.inria.fr/hal-01093058

Scientific Books (or Scientific Book chapters)

  • 37L. Miclet, N. Barbot, B. Jeudy.

    Analogical Proportions in a Lattice of Sets of Alignments Built on the Common Subwords in a Finite Language, in: Computational Approaches to Analogical Reasoning: Current Trends, Studies in Computational Intelligence, H. Prade, G. Richard (editors), Springer-Verlag Berlin Heidelberg, 2014, pp. 245-260. [ DOI : 10.1007/978-3-642-54516-0_10 ]

    https://hal.inria.fr/hal-00974656
  • 38T. Schaub, A. Siegel, S. Videla.

    Reasoning on the response of logical signaling networks with Answer Set Programming, in: Logical Modeling of Biological Systems, Wiley Online Librairy, 2014, pp. 49-92. [ DOI : 10.1002/9781119005223.ch2 ]

    https://hal.inria.fr/hal-01079762
  • 39V. Wucher, D. Tagu, J. Nicolas.

    B. Lausen, S. Krolak-Schwerdt, M. Böhmer (editors), Edge Selection in a Noisy Graph by Concept Analysis – Application to a Genomic Network, Data Science, Learning by Latent Structures, and Knowledge Discovery, Springer, 2014, 550 p.

    https://hal.inria.fr/hal-01093337

Scientific Popularization

Other Publications

  • 42H. Bazille.

    Protein design: a NP-hard problem in bioinformatics, IRISA-Inria, Campus de Beaulieu, 35042 Rennes cedex, 2014, 42 p.

    http://dumas.ccsd.cnrs.fr/dumas-01088787
  • 43D. Gonçalves, J. Nicolas, A. Mucherino.

    Searching for Optimal Orders for Discretized Distance Geometry, October 2014, Proceedings of Many Faces of Distances (MDF14).

    https://hal.inria.fr/hal-01093072
  • 44Y. Le Bras, A. Roult, C. Monjeaud, B. Mathieu, O. Quenez, H. Claudia, O. Sallou, A. Bretaudeau, O. Collin.

    e-Science in France, a Life science Western story, June 2014, Galaxy Community Conference (GCC2014).

    https://hal.inria.fr/hal-01102432
References in notes
  • 45C. Baral.

    Knowledge Representation, Reasoning and Declarative Problem Solving, Cambridge University Press, 2010.
  • 46T. Baumuratova, D. Surdez, B. Delyon, G. Stoll, O. Delattre, O. Radulescu, A. Siegel.

    Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network., in: BMC Systems Biology, 2010, vol. 4, no 1, 146 p. [ DOI : 10.1186/1752-0509-4-146 ]

    http://www.hal.inserm.fr/inserm-00984711
  • 47R. Bellé, S. Prigent, A. Siegel, P. Cormier.

    Model of cap-dependent translation initiation in sea urchin: a step towards the eukaryotic translation regulation network, in: Molecular Reproduction and Development, 2010, vol. 77, no 3, pp. 257-64.
  • 48P. Bordron, D. Eveillard, A. Maass, A. Siegel.

    An ASP application in integrative biology: identification of functional gene units, in: LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Corunna, Spain, September 2013.

    http://hal.inria.fr/hal-00853762
  • 49S. Bradford, F. Coste, M. Van Zaanen.

    Progressing the state-of-the-art in grammatical inference by competition, in: AI Communications, 2005, vol. 18, no 2, pp. 93-115.
  • 50G. Collet, D. Eveillard, M. Gebser, S. Prigent, T. Schaub, A. Siegel, S. Thiele.

    Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming, in: LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Corunna, Spain, September 2013.

    http://hal.inria.fr/hal-00853752
  • 51O. Demeure, F. Lecerf, C. Duby, C. Desert, S. Ducheix, H. Guillou, S. Lagarrigue.

    Regulation of LPCAT3 by LXR, in: Gene, Jan 2011, vol. 470, no 1-2, pp. 7–11.
  • 52P. Flajolet, R. Sedgewick.

    Analytic Combinatorics, Cambridge University Press, 2009.
  • 53M. Gebser, R. Kaminski, B. Kaufmann, T. Schaub.

    Answer Set Solving in Practice, Synthesis Lectures on Artificial Intelligence and Machine Learning, Morgan and Claypool Publishers, 2012.
  • 54S.-w. Leung, C. Mellish, D. Robertson.

    Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences, in: Bioinformatics, 2001, vol. 17, no 3, pp. 226-236. [ DOI : 10.1093/bioinformatics/17.3.226 ]

    http://bioinformatics.oxfordjournals.org/content/17/3/226.abstract
  • 55P.-F. Pluchon, T. Fouqueau, C. Creze, S. Laurent, J. Briffotaux, G. Hogrel, A. Palud, G. Henneke, A. Godfroy, W. Hausner, M. Thomm, J. Nicolas, D. Flament.

    An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs, in: PLoS ONE, 2013, vol. 8, no 11, e79707. [ DOI : 10.1371/journal.pone.0079707 ]

    http://hal.inria.fr/hal-00911795
  • 56C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas.

    CRISPI: a CRISPR interactive database, in: Bioinformatics, 2009, vol. 25, no 24, pp. 3317-3318.
  • 57T. Schaub, S. Thiele.

    Metabolic Network Expansion with Answer Set Programming, in: ICLP 2009, LNCS, Springer, 2009, vol. 5649, pp. 312-326.
  • 58D. Searls.

    The language of genes, in: Nature, 2002, vol. 420, pp. 211-217.
  • 59D. Searls.

    String Variable Grammar: A Logic Grammar Formalism for the Biological Language of DNA, in: Journal of Logic Programming, 1995, vol. 24, no 1&2, pp. 73-102.
  • 60S. Tempel, C. Rousseau, F. Tahi, J. Nicolas.

    ModuleOrganizer: detecting modules in families of transposable elements, in: BMC Bioinformatics, 2010, vol. 11, 474 p. [ DOI : 10.1186/1471-2105-11-474 ]

    http://hal.inria.fr/inria-00536742


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