Bibliography

Major publications by the team in recent years

• 1C. Belleannée, O. Sallou, J. Nicolas.
  
  Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling, in: PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, 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
• 2J. Bourdon, D. Eveillard, A. Siegel.
  
  Integrating quantitative knowledge into a qualitative gene regulatory network, in: PLoS Computational Biology, September 2011, vol. 7, n^o 9. [ DOI : 10.1371/journal.pcbi.1002157 ]
  
  http://hal.archives-ouvertes.fr/hal-00626708
• 3A. Bretaudeau, F. Coste, F. Humily, L. Garczarek, G. Le Corguille, 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
• 4F. 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.
• 5M. 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.
• 6C. Guziolowski, A. Bourdé, F. Moreews, A. Siegel.
  
  BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks, in: Bmc Genomics, 2009, vol. 26, n^o 10, 244 p. [ DOI : 10.1186/1471-2164-10-244 ]
  
  http://hal.inria.fr/inria-00429804
• 7C. 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, n^o 18, pp. 2320-2326. [ DOI : 10.1093/bioinformatics/btt393 ]
  
  http://hal.inria.fr/hal-00853704
• 8J. 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
• 9S. 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
• 10C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas.
  
  CRISPI: a CRISPR interactive database, in: Bioinformatics, 2009, vol. 25, n^o 24, pp. 3317-3318.

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 11A. Antoine-Lorquin, A. Siegel, C. Belleannée.
  
  Interest of grammatical modelling to achieve pattern matching in genomic sequences, Université de Rennes 1, December 2016.
  
  https://hal.inria.fr/tel-01416734
• 12O. Dameron.
  
  Ontology-based methods for analyzing life science data, Univ. Rennes 1, January 2016, Habilitation à diriger des recherches.
  
  https://hal.inria.fr/tel-01403371

Articles in International Peer-Reviewed Journals

• 13V. Acuña, A. Aravena, C. Guziolowski, D. Eveillard, A. Siegel, A. Maass.
  
  Deciphering transcriptional regulations coordinating the response to environmental changes, in: BMC Bioinformatics, January 2016, vol. 17, n^o 1, pp. 129-42.
  
  https://hal.archives-ouvertes.fr/hal-01260866
• 14V. Berthé, J. Bourdon, T. Jolivet, A. Siegel.
  
  A combinatorial approach to products of Pisot substitutions, in: Ergodic Theory and Dynamical Systems, 2016, vol. 36, n^o 6, pp. 1757-1794. [ DOI : 10.1017/etds.2014.141 ]
  
  https://hal.inria.fr/hal-01196326
• 15P. Bordron, M. Latorre, M.-P. Cortés, M. González, S. Thiele, A. Siegel, A. Maass, D. Eveillard.
  
  Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach, in: MicrobiologyOpen, January 2016, vol. 5, n^o 1, pp. 106-17.
  
  https://hal.archives-ouvertes.fr/hal-01289230
• 16M. Boutet, L. Gauthier, M. Leclerc, G. Gros, V. De Montpreville, N. Théret, E. Donnadieu, F. Mami-Chouaib.
  
  TGF-β signaling intersects with CD103 integrin signaling to promote T lymphocyte accumulation and antitumor activity in the lung tumor microenvironment, in: Cancer Research, 2016, vol. 76, n^o 7, pp. 1757-69. [ DOI : 10.1158/0008-5472.CAN-15-1545 ]
  
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282442
• 17F. J. Cousin, S. Jouan-Lanhouet, N. Théret, C. Brenner, E. Jouan, G. Le Moigne-Muller, M.-T. Dimanche-Boitrel, G. Jan.
  
  The probiotic Propionibacterium freudenreichii as a new adjuvant for TRAIL-based therapy in colorectal cancer, in: Oncotarget, January 2016. [ DOI : 10.18632/oncotarget.6881 ]
  
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259215
• 18P. Finet, B. Gibaud, O. Dameron, R. Lebouquin Jeannes.
  
  Relevance of health level 7 clinical document architecture and integrating the healthcare enterprise cross-enterprise document sharing profile for managing chronic wounds in a telemedicine context, in: Healthcare Technology Letter , 2016, vol. 3, n^o 1, pp. 22-26. [ DOI : 10.1049/htl.2015.0053 ]
  
  https://hal.archives-ouvertes.fr/hal-01301007
• 19C. Galiez, M. Christophe, F. Coste, P. Baldi.
  
  VIRALpro: a tool to identify viral capsid and tail sequences, in: Bioinformatics, 2016. [ DOI : 10.1093/bioinformatics/btv727 ]
  
  https://hal.archives-ouvertes.fr/hal-01242251
• 20F. Gondret, A. Vincent, M. Houée-Bigot, A. Siegel, S. Lagarrigue, I. Louveau, D. Causeur.
  
  Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location, in: BMC Genomics, December 2016, vol. 17, n^o 1, article number 120. [ DOI : 10.1186/s12864-016-2438-3 ]
  
  https://hal.archives-ouvertes.fr/hal-01286555
• 21M.-A. Laurent, D. Bonnier, N. Théret, P. Tufféry, G. Moroy.
  
  In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1, in: Computational Biology and Chemistry, April 2016, pp. 155-161. [ DOI : 10.1016/j.compbiolchem.2016.01.012 ]
  
  https://hal.inria.fr/hal-01401685
• 22G. Nicolas, D. Wallon, C. Charbonnier, O. Quenez, S. Rousseau, A.-C. Richard, A. Rovelet-Lecrux, S. Coutant, K. Le Guennec, D. Bacq, J.-G. Garnier, R. Olaso, A. Boland, V. MEYER, J.-F. Deleuze, H. M. Munter, G. Bourque, D. Auld, A. Montpetit, M. Lathrop, L. Guyant-Maréchal, O. Martinaud, J. Pariente, A. Rollin-Sillaire, F. Pasquier, I. Le Ber, M. Sarazin, B. Croisile, C. Boutoleau-Bretonnière, C. Thomas-Antérion, C. Paquet, M. Sauvee, O. Moreaud, A. Gabelle, F. Sellal, M. Ceccaldi, L. Chamard, F. Blanc, T. Frebourg, D. Campion, D. Hannequin.
  
  Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons, in: European Journal of Human Genetics, May 2016, vol. 24, n^o 5, pp. 710-716. [ DOI : 10.1038/ejhg.2015.173 ]
  
  https://hal.archives-ouvertes.fr/hal-01431285
• 23M. Ostrowski, L. Paulevé, T. Schaub, A. Siegel, C. Guziolowski.
  
  Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming, in: BioSystems, 2016. [ DOI : 10.1016/j.biosystems.2016.07.009 ]
  
  https://hal.archives-ouvertes.fr/hal-01354075
• 24V. Picard, O. Mulner-Lorillon, J. Bourdon, J. Morales, P. Cormier, A. Siegel, R. Bellé.
  
  Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization, in: Molecular Reproduction and Development, 2016. [ DOI : 10.1002/mrd.22746 ]
  
  http://hal.upmc.fr/hal-01390047
• 25A. Rosier, P. Mabo, L. Temal, P. Van Hille, O. Dameron, L. Deléger, C. Grouin, P. Zweigenbaum, J. Jacques, E. Chazard, L. Laporte, C. Henry, A. Burgun.
  
  Personalized and automated remote monitoring of atrial fibrillation, in: EP-Europace, 2016, vol. 18, n^o 3, pp. 347-352. [ DOI : 10.1093/europace/euv234 ]
  
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01331019
• 26A. Rosier, P. Mabo, L. Temal, P. Van Hille, O. Dameron, L. Deléger, C. Grouin, P. Zweigenbaum, J. Jacques, E. Chazard, L. Laporte, C. Henry, A. Burgun.
  
  Remote Monitoring of Cardiac Implantable Devices: Ontology Driven Classification of the Alerts, in: Studies in Health Technology and Informatics, 2016, vol. 221, pp. 59–63. [ DOI : 10.3233/978-1-61499-633-0-59 ]
  
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01319949
• 27S. Swarup Samal, A. Naldi, D. Grigoriev, A. Weber, N. Théret, O. Radulescu.
  
  Geometric analysis of pathways dynamics: application to versatility of TGF-β receptors, in: BioSystems, July 2016, vol. 149, pp. 3–14. [ DOI : 10.1016/j.biosystems.2016.07.004 ]
  
  https://hal.inria.fr/hal-01379033
• 28S. Videla, J. Saez-Rodriguez, C. Guziolowski, A. Siegel.
  
  caspo: a toolbox for automated reasoning on the response of logical signaling networks families, in: Bioinformatics, 2016. [ DOI : 10.1093/bioinformatics/btw738 ]
  
  https://hal.inria.fr/hal-01426880

International Conferences with Proceedings

• 29T. Guyet, Y. Moinard, J. Nicolas, R. Quiniou.
  
  Packing graphs with ASP for landscape simulation, in: IJCAI 2016 - 25th International joint conference on artificial intelligence, New-york, United States, AAAI, July 2016, 8 p.
  
  https://hal.inria.fr/hal-01327368

National Conferences with Proceedings

• 30Y. Rivault, N. Le Meur, O. Dameron.
  
  Complications post-opératoires et mode de prise en charge en angioplastie : apport du Programme de Médicalisation des Systèmes d'Information (PMSI), in: Congrès Adelf-Epiter 2016, Rennes, France, September 2016.
  
  https://hal.inria.fr/hal-01389688
• 31Y. Rivault, N. Le Meur, O. Dameron.
  
  La gestion de données médico-administratives grâce aux outils du Web sémantique, in: Journées ADELF-EMOIS « Système d’information hospitalier et Epidémiologie », Dijon, France, Revue d'Épidémiologie et de Santé Publique, March 2016, vol. 64, n^o Supplement 1, S15 p. [ DOI : 10.1016/j.respe.2016.01.051 ]
  
  https://hal.archives-ouvertes.fr/hal-01297389

Conferences without Proceedings

• 32A. Antoine-Lorquin, F. Mahé, M. Dunthorn, C. Belleannée.
  
  Impact de la recherche d'amorces mutées sur les résultats d'analyses métagénomiques, in: Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Rennes, France, Jobim-2016, Société Française de Bioinformatique (SFBI), June 2016.
  
  https://hal.archives-ouvertes.fr/hal-01343121
• 33F. Balusson, M.-A. Botrel, O. Dameron, Y. Dauxais, E. Drezen, A. Dupuy, T. Guyet, D. Gross-Amblard, A. Happe, N. Le Meur, B. Le Nautout, E. Leray, E. Nowak, C. Rault, E. Oger, E. Polard.
  
  PEPS: a platform for supporting studies in pharmaco-epidemiology using medico-administrative databases, in: International Congress on e-Health Research, Paris, France, October 2016.
  
  https://hal.inria.fr/hal-01380939
• 34M. Chevallier, M. Aite, J. Got, G. Collet, N. Loira, M.-P. Cortés, C. Frioux, J. Laniau, C. Trottier, A. Maass, A. Siegel.
  
  Handling the heterogeneity of genomic and metabolic networks data within flexible workflows with the PADMet toolbox, in: Jobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Lyon, France, June 2016.
  
  https://hal.inria.fr/hal-01377844
• 35F. Coste, M. Demirdelen.
  
  A refined parsing graph approach to learn smaller contextually substitutable grammars with less data, in: ICGI 2016 - 13th International Conference on Grammatical Inference, Delft, Netherlands, October 2016.
  
  https://hal.inria.fr/hal-01406337
• 36W. Dyrka, F. Coste, O. Unold, L. Culer, A. Kaczmarek.
  
  How to measure the topological quality of protein grammars?, in: ICGI 2016 - 13th International Conference on Grammatical Inference, Delft, Netherlands, October 2016.
  
  https://hal.inria.fr/hal-01406331
• 37F. Legeai, C. Bettembourg, A. Bretaudeau, Y. Chaussin, O. Dameron, D. Tagu.
  
  BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interaction, in: XXVth International Congress of Entomology 2016,, Orlando, Florida, United States, September 2016.
  
  https://hal.inria.fr/hal-01391080
• 38F. Moreews, O. Sallou, O. Collin.
  
  An application suite based on the IFB Container as a Service platform, in: ECCB 2016, Den Haag, Netherlands, ISCB, September 2016.
  
  https://hal.inria.fr/hal-01394295
• 39A. Siegel.
  
  A system biology loop for the identification of boolean networks to model signaling networks. , in: European Conference on Mathematical and Theoretical Biology, Nottingham, France, 2016.
  
  https://hal.inria.fr/hal-01399456

Scientific Books (or Scientific Book chapters)

• 40F. Coste.
  
  Learning the Language of Biological Sequences, in: Topics in Grammatical Inference, J. Heinz, J. M. Sempere (editors), Springer-Verlag, 2016. [ DOI : 10.1007/978-3-662-48395-4_8 ]
  
  https://hal.inria.fr/hal-01244770

Other Publications

• 41F. Cousin, S. Jouan-Lanhouet, N. Théret, C. Brenner, E. Jouan, G. Le Moigne-Muller, M.-T. Dimanche-Boitrel.
  
  The probiotic [i]Propionibacteriumfreudenreichii[/i] as a new adjuvant for TRAIL-based therapy in colorectal cancer, September 2016, 4 . International Symposium on Propionibacteria and Bibfidobacteria , Poster.
  
  https://hal.archives-ouvertes.fr/hal-01372131
• 42F. Cousin, S. Jouan-Lanhouet, N. Théret, C. Brenner, E. Jouan, G. Le Moigne-Muller, M.-T. Dimanche-Boitrel, G. Jan.
  
  The probiotic [i]Propionibacterium freudenreichii[/i] as a new adjuvant for TRAIL-based therapy in colorectal cancer, June 2016, International Scientific Conference on Probiotics and Prebiotics - IPC2016, Poster.
  
  https://hal.archives-ouvertes.fr/hal-01286497
• 43M. Demirdelen.
  
  Fast parser for biological sequences and a new algorithm for the inference of substitutable languages, Univ. Rennes 1, June 2016.
  
  https://hal.inria.fr/hal-01406352
• 44A. Evrard, C. Bettembourg, O. Dameron, O. Filangi, A. Bretaudeau, F. F. Legeai, R. Delourme, M. Manzanares-Dauleux, M. Jubault.
  
  Comparative genomic analysis of Clubroot resistance in the Brassicaceae family, October 2016, Brassica2016, Poster.
  
  https://hal.inria.fr/hal-01391707
• 45A. Evrard, C. Bettembourg, M. M. Jubault, O. Dameron, O. Filangi, A. Bretaudeau, F. F. Legeai.
  
  Integration and query of biological datasets with Semantic Web technologies: AskOmics, June 2016, Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2016), Poster.
  
  https://hal.inria.fr/hal-01391087
• 46S. Rémy.
  
  Apprentissage profond et acquisition de représentations latentes de séquences peptidiques, ENS Rennes, August 2016.
  
  https://hal.inria.fr/hal-01406368

References in notes

• 47O. Abdou-Arbi, S. Lemosquet, J. Van 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, n^o 1, 8 p. [ DOI : 10.1186/1752-0509-8-8 ]
  
  https://hal.inria.fr/hal-00947219
• 48V. 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
• 49G. Andrieux, M. Le Borgne, N. Théret.
  
  An integrative modeling framework reveals plasticity of TGF-Beta signaling, in: BMC Systems Biology, 2014, vol. 8, n^o 1, 30 p. [ DOI : 10.1186/1752-0509-8-30 ]
  
  http://www.hal.inserm.fr/inserm-00978313
• 50C. Baral.
  
  Knowledge Representation, Reasoning and Declarative Problem Solving, Cambridge University Press, 2010.
• 51T. 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, n^o 1, 146 p. [ DOI : 10.1186/1752-0509-4-146 ]
  
  http://www.hal.inserm.fr/inserm-00984711
• 52R. Bellazzi.
  
  Big Data and Biomedical Informatics: A Challenging Opportunity, in: Yearbook of medical informatics, 2014, vol. 9, n^o 1, In press.
• 53R. Bellazzi, M. Diomidous, I. N. Sarkar, K. Takabayashi, A. Ziegler, A. T. McCray.
  
  Data analysis and data mining: current issues in biomedical informatics, in: Methods of information in medicine, 2011, vol. 50, n^o 6, pp. 536–544.
• 54C. Belleannée, O. Sallou, J. Nicolas.
  
  Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling, in: PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, 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
• 55R. 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, n^o 3, pp. 257-64.
• 56R. Bendaoud, A. Napoli, Y. Toussaint.
  
  Formal Concept Analysis: A Unified Framework for Building and Refining Ontologies, in: Knowledge Engineering: Practice and Patterns, 16th International Conference, EKAW 2008, Acitrezza, Italy, September 29 - October 2, 2008. Proceedings, A. Gangemi, J. Euzenat (editors), Lecture Notes in Computer Science, Springer, 2008, vol. 5268, pp. 156-171.
  
  http://dx.doi.org/10.1007/978-3-540-87696-0_16
• 57C. Bettembourg, C. Diot, O. Dameron.
  
  Optimal threshold determination for interpreting semantic similarity and particularity, in: PLoS ONE, 2015, vol. 10, n^o 7, e0133579. [ DOI : 10.1371/journal.pone.0133579 ]
  
  https://hal.archives-ouvertes.fr/hal-01207763
• 58C. Bettembourg, C. Diot, O. Dameron.
  
  Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI, in: PLoS ONE, 2015, 30 p. [ DOI : 10.1371/journal.pone.0133579 ]
  
  https://hal.inria.fr/hal-01184934
• 59C. Bizer, T. Heath, T. Berners Lee.
  
  Linked Data–The story so far, in: International Journal on Semantic Web and Information Systems, 2009, vol. 5, n^o 3, pp. 1–22.
• 60J. A. Blake, C. J. Bult.
  
  Beyond the data deluge: Data integration and bio-ontologies, in: Journal of Biomedical Informatics, 2006, vol. 39, n^o 3, pp. 314–320.
• 61P. 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, n^o 1, 32 p. [ DOI : 10.1186/1752-0509-8-32 ]
  
  https://hal.inria.fr/hal-00980499
• 62P. 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
• 63H. Chen, T. Yu, J. Y. Chen.
  
  Semantic Web meets Integrative Biology: a survey, in: Briefings in bioinformatics, 2012, vol. 14, n^o 1, pp. 109–125.
• 64G. 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
• 65F. 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
• 66S. Daminelli, V. J. Haupt, M. Reimann, M. Schroeder.
  
  Drug repositioning through incomplete bi-cliques in an integrated drug-target-disease network, in: Integr. Biol., 2012, vol. 4, pp. 778-788.
  
  http://dx.doi.org/10.1039/C2IB00154C
• 67O. Demeure, F. Lecerf, C. Duby, C. Desert, S. Ducheix, H. Guillou, S. Lagarrigue.
  
  Regulation of LPCAT3 by LXR, in: Gene, Jan 2011, vol. 470, n^o 1-2, pp. 7–11.
• 68S. 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
• 69M. 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.
• 70F. Gondret, I. Louveau, M. Houee, D. Causeur, A. Siegel.
  
  Data integration, in: Meeting INRA-ISU, Ames, United States, March 2015, 11 p.
  
  https://hal.archives-ouvertes.fr/hal-01210940
• 71F. Gondret, A. Vincent, M. Houee, S. Lagarrigue, A. Siegel, D. Causeur, I. Louveau.
  
  Integrative responses of pig adipose tissues to high-fat high-fiber diet: towards key regulators of energy flexibility, March 2015, ASAS/ADSA midwest meeting, Poster.
  
  https://hal.archives-ouvertes.fr/hal-01210925
• 72F. 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, n^o 5, e96491. [ DOI : 10.1371/journal.pone.0096491 ]
  
  https://hal.inria.fr/hal-00989635
• 73R. Kaminski, A. Siegel, T. Schaub, S. Videla.
  
  Minimal Intervention Strategies in Logical Signaling Networks with ASP, in: Theory and Practice of Logic Programming, September 2013, vol. 13, n^o Special issue 4-5, pp. 675-690. [ DOI : 10.1017/S1471068413000422 ]
  
  http://hal.inria.fr/hal-00853747
• 74S. 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
• 75F. 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
• 76S.-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, n^o 3, pp. 226-236. [ DOI : 10.1093/bioinformatics/17.3.226 ]
  
  http://bioinformatics.oxfordjournals.org/content/17/3/226.abstract
• 77A. Lihonosova, A. Kaminskaya.
  
  Using Formal Concept Analysis for Finding the Closest Relatives among a Group of Organisms, in: Procedia Computer Science, 2014, vol. 31, n^o Complete, pp. 860-868.
  
  http://dx.doi.org/10.1016/j.procs.2014.05.337
• 78K. M. Livingston, M. Bada, W. A. Baumgartner, L. E. Hunter.
  
  KaBOB: ontology-based semantic integration of biomedical databases, in: BMC bioinformatics, 2015, vol. 16, 126 p.
• 79N. Messai, M.-D. Devignes, A. Napoli, M. Smail-Tabbone.
  
  Many-Valued Concept Lattices for Conceptual Clustering and Information Retrieval, in: Proceedings of the 2008 Conference on ECAI 2008: 18th European Conference on Artificial Intelligence, Amsterdam, The Netherlands, The Netherlands, IOS Press, 2008, pp. 127–131.
  
  http://dl.acm.org/citation.cfm?id=1567281.1567313
• 80M. Obitko, V. Snásel, J. Smid.
  
  Ontology Design with Formal Concept Analysis, in: Proceedings of the CLA 2004 International Workshop on Concept Lattices and their Applications, Ostrava, Czech Republic, September 23-24, 2004, V. Snásel, R. Belohlávek (editors), CEUR Workshop Proceedings, CEUR-WS.org, 2004, vol. 110.
  
  http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-110/paper12.pdf
• 81P.-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, n^o 11, e79707. [ DOI : 10.1371/journal.pone.0079707 ]
  
  http://hal.inria.fr/hal-00911795
• 82S. 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
• 83M. Rouane-Hacene, M. Huchard, A. Napoli, P. Valtchev.
  
  Using Formal Concept Analysis for Discovering Knowledge Patterns, in: CLA'10: 7th International Conference on Concept Lattices and Their Applications, Sevilla, Spain, S. O. Marzena Kryszkiewicz (editor), CEUR, University of Sevilla, October 2010, n^o 672, pp. 223-234.
  
  http://hal-lirmm.ccsd.cnrs.fr/lirmm-00531802
• 84C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas.
  
  CRISPI: a CRISPR interactive database, in: Bioinformatics, 2009, vol. 25, n^o 24, pp. 3317-3318.
• 85L. Royer, M. Reimann, B. Andreopoulos, M. Schroeder.
  
  Unraveling Protein Networks with Power Graph Analysis, in: PLoS Comput Biol, 07 2008, vol. 4, n^o 7, e1000108.
  
  http://dx.plos.org/10.1371%2Fjournal.pcbi.1000108
• 86T. 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
• 87T. Schaub, S. Thiele.
  
  Metabolic Network Expansion with Answer Set Programming, in: ICLP 2009, LNCS, Springer, 2009, vol. 5649, pp. 312-326.
• 88S. Schulz, L. Balkanyi, R. Cornet, O. Bodenreider.
  
  From Concept Representations to Ontologies: A Paradigm Shift in Health Informatics?, in: Healthcare informatics research, 2013, vol. 19, n^o 4, pp. 235-242.
• 89D. Searls.
  
  The language of genes, in: Nature, 2002, vol. 420, pp. 211-217.
• 90D. Searls.
  
  String Variable Grammar: A Logic Grammar Formalism for the Biological Language of DNA, in: Journal of Logic Programming, 1995, vol. 24, n^o 1&2, pp. 73-102.
• 91Z. D. Stephens, S. Y. Lee, F. Faghri, R. H. Campbell, C. Zhai, M. J. Efron, R. Iyer, M. C. Schatz, S. Sinha, G. E. Robinson.
  
  Big Data: Astronomical or Genomical?, in: PLoS biology, 2015, vol. 13, n^o 7, e1002195 p.
• 92S. 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
• 93S. Thiele, J. Saez-Rodriguez, L. Cerone, A. Siegel, C. Guziolowski, S. Klamt.
  
  Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies, in: BMC Bioinformatics, 2015, vol. 16, 345 p. [ DOI : 10.1186/s12859-015-0733-7 ]
  
  https://hal.inria.fr/hal-01225228
• 94S. 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), September 2015, n^o 599, pp. 79-101. [ DOI : 10.1016/j.tcs.2014.06.022 ]
  
  https://hal.inria.fr/hal-01058610
• 95S. Videla, I. Konokotina, L. Alexopoulos, J. Saez-Rodriguez, T. Schaub, A. Siegel, C. Guziolowski.
  
  Designing experiments to discriminate families of logic models, in: Frontiers in Bioengineering and Biotechnology, September 2015, 9 p. [ DOI : 10.3389/fbioe.2015.00131 ]
  
  https://hal.inria.fr/hal-01196178
• 96R. Wille.
  
  restructuring lattice theory: an approach based on hierarchies of concepts, in: Proceedings of the 7th International Conference on Formal Concept Analysis, Berlin, Heidelberg, ICFCA '09, Springer-Verlag, 2009, pp. 314–339.
  
  http://dx.doi.org/10.1007/978-3-642-01815-2_23
• 97V. 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
• 98V. 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