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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, no 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, no 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, no 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, no 24, pp. 3317-3318.
Publications of the year

Doctoral Dissertations and Habilitation Theses

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 2015, vol. 17, no 1, 35 p.

    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, 2015, 38 p. [ DOI : 10.1017/etds.2014.141 ]

    https://hal.inria.fr/hal-01196326
  • 15C. Bettembourg, C. Diot, O. Dameron.

    Optimal threshold determination for interpreting semantic similarity and particularity, in: PLoS ONE, 2015, vol. 10, no 7, e0133579. [ DOI : 10.1371/journal.pone.0133579 ]

    https://hal.archives-ouvertes.fr/hal-01207763
  • 16C. 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
  • 17P. Bordron, M. Latorre, M.-P. Cortes, M. Gonzales, S. Thiele, A. Siegel, A. Maass, D. Eveillard.

    Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach, in: MicrobiologyOpen, 2015. [ DOI : 10.1002/mbo3.315 ]

    https://hal.inria.fr/hal-01246173
  • 18C. Galiez, M. Christophe, F. Coste, P. Baldi.

    VIRALpro: a tool to identify viral capsid and tail sequences, in: Bioinformatics, December 2015.

    https://hal.archives-ouvertes.fr/hal-01242251
  • 19C. Galiez, F. Coste.

    Amplitude spectrum distance: measuring the global shape divergence of protein fragments, in: BMC Bioinformatics, August 2015, vol. 16, no 1, 16 p. [ DOI : 10.1186/s12859-015-0693-y ]

    https://hal.inria.fr/hal-01214482
  • 20V. Picard, A. Siegel, J. Bourdon.

    Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications, in: Electronic Notes in Theoretical Computer Science, 2015, vol. 316C, pp. 67-82. [ DOI : 10.1016/j.entcs.2015.06.011 ]

    https://hal.inria.fr/hal-01196533
  • 21S. 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
  • 22S. 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, no 599, pp. 79–101. [ DOI : 10.1016/j.tcs.2014.06.022 ]

    https://hal.inria.fr/hal-01058610
  • 23S. 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

Invited Conferences

  • 24F. Gondret, I. Louveau, M. Houee, D. Causeur, A. Siegel.

    Data integration, in: Meeting INRA-ISU, Ames, United States, March 2015, 11 diapositives.

    https://hal.archives-ouvertes.fr/hal-01210940
  • 25T. Jolivet, A. Siegel.

    Decidability Problems for Self-induced Systems Generated by a Substitution, in: MCU 2015 : Machines, Computation and Universality (7th conference), Famagusta, Cyprus, Springer, 2015, vol. Lecture Notes in Computer Science 9288. [ DOI : 10.1007/978-3-319-23111-2 ]

    https://hal.inria.fr/hal-01196152

International Conferences with Proceedings

  • 26C. Galiez, F. Coste.

    Structural conservation of remote homologues: better and further in contact fragments, in: 3DSIG: Structural Bioinformatics and Computational Biophysics, Dublin, France, July 2015, 1 p.

    https://hal.inria.fr/hal-01214506
  • 27L. Miclet, J. Nicolas.

    From formal concepts to analogical complexes, in: CLA 2015, Clermont-Ferrand, France, LIMOS, CNRS et Université Blaise Pascal, October 2015, 12 p.

    https://hal.inria.fr/hal-01198943
  • 28V. Picard, A. Siegel, J. Bourdon.

    A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks, in: IJCAI workshop BAI: Bioinformatics and Artificial Intelligence, Buenos Aeres, Argentina, CEUR-WS, 2015.

    https://hal.inria.fr/hal-01196598

Conferences without Proceedings

  • 29A. Antoine-Lorquin, S. Lagarrigue, F. Lecerf, J. Nicolas, C. Belleannée.

    Comparison of the targets obtained by a scoring matrix and by a regular expression. Application to the search for LXR binding sites, in: JOBIM 2015- 16e Journées Ouvertes en Biologie, Informatique et Mathématiques, Clermont-Ferrand, France, July 2015.

    https://hal.inria.fr/hal-01197050
  • 30C. Bettembourg, O. Dameron, A. Bretaudeau, F. Legeai.

    AskOmics : Intégration et interrogation de réseaux de régulation génomique et post-génomique, in: IN OVIVE (INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement), Rennes, France, June 2015, 7 p.

    https://hal.inria.fr/hal-01184903
  • 31M. Ostrowski, L. Paulevé, T. Schaub, A. Siegel, C. Guziolowski.

    Boolean Network Identification from Multiplex Time Series Data, in: CMSB 2015 - 13th conference on Computational Methods for Systems Biology, Nantes, France, O. Roux, J. Bourdon (editors), Lecture Notes in Computer Science, Springer International Publishing, September 2015, vol. 9308, pp. 170-181. [ DOI : 10.1007/978-3-319-23401-4_15 ]

    https://hal.archives-ouvertes.fr/hal-01164751

Scientific Books (or Scientific Book chapters)

  • 32S. Akiyama, M. Barge, V. Berthé, J.-Y. Lee, A. Siegel.

    On the Pisot Substitution Conjecture, in: Mathematics of Aperiodic Order, Progress in mathematics, Springer, 2015, vol. 309, pp. 33-72. [ DOI : 10.1007/978-3-0348-0903-0_2 ]

    https://hal.inria.fr/hal-01196318
  • 33F. Coste.

    Learning the Language of Biological Sequences, in: Topics in Grammatical Inference, J. Heinz, J. M. Sempere (editors), Springer-Verlag Berlin Heidelberg, 2016.

    https://hal.inria.fr/hal-01244770
  • 34D. S. Gonçalves, J. Nicolas, A. Mucherino, C. Lavor.

    Finding Optimal Discretization Orders for Molecular Distance Geometry by Answer Set Programming, in: Studies in Computational Intelligence, S. Fidanova (editor), Recent Advances in Computational Optimization, Springer, July 2015, vol. 610, pp. 1-15.

    https://hal.inria.fr/hal-01196714
  • 35J. Nicolas, P. Peterlongo, S. Tempel.

    Finding and Characterizing Repeats in Plant Genomes, in: Plant Bioinformatics: Methods and Protocols, D. Edwards (editor), Methods in Molecular Biology, Humana Press - Springer Science+Business Media, November 2015, no 1374, 365 p. [ DOI : 10.1007/978-1-4939-3167-5_17 ]

    https://hal.inria.fr/hal-01228488

Other Publications

  • 36J. COQUET, G. Andrieux, J. Nicolas, O. Dameron, N. Théret.

    Topological and semantic Web based method for analyzing TGF-β signaling pathways, December 2015, JOBIM 2015, Poster.

    https://hal.archives-ouvertes.fr/hal-01242893
  • 37F. 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
  • 38M. Jusot.

    Caractérisation en séquence et en structure des protéines virales, UP7 - Université Paris Diderot - Paris 7, June 2015.

    https://hal.inria.fr/hal-01246372
  • 39M. Petera, G. Le Corguille, M. Landi, M. Monsoor, M. TREMBLAY FRANCO, C. Duperier, J.-F. Martin, D. Jacob, Y. Guitton, M. Lefebvre, E. Pujos-Guillot, F. Giacomoni, E. Thévenot, C. Caron.

    Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics, July 2015, JOBIM 2015 (16. édition des Journées Ouvertes en Biologie, Informatique et Mathématiques ), Poster - Paper reference: Giacomoni et al. (2014) Workflow4Metabolomics: A collaborative research infrastructure for com-putational metabolomics. Bioinformatics http://dx.doi.org/10.1093/bioinformatics/btu813.

    https://hal.archives-ouvertes.fr/hal-01214152
References in notes
  • 40O. 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, no 1, 8 p. [ DOI : 10.1186/1752-0509-8-8 ]

    https://hal.inria.fr/hal-00947219
  • 41V. 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
  • 42G. Andrieux, M. Le Borgne, N. Théret.

    An integrative modeling framework reveals plasticity of TGF-Beta 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
  • 43C. Baral.

    Knowledge Representation, Reasoning and Declarative Problem Solving, Cambridge University Press, 2010.
  • 44J. B. L. Bard, S. Y. Rhee.

    Ontologies in biology: design, applications and future challenges, in: Nature reviews. Genetics, 2004, vol. 5, no 3, pp. 213–222.
  • 45T. 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
  • 46R. Bellazzi.

    Big Data and Biomedical Informatics: A Challenging Opportunity, in: Yearbook of medical informatics, 2014, vol. 9, no 1, In press.
  • 47R. 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, no 6, pp. 536–544.
  • 48C. 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
  • 49R. 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.
  • 50R. 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
  • 51C. Bizer, T. Heath, T. Berners Lee.

    Linked Data–The story so far, in: International Journal on Semantic Web and Information Systems, 2009, vol. 5, no 3, pp. 1–22.
  • 52J. A. Blake, C. J. Bult.

    Beyond the data deluge: Data integration and bio-ontologies, in: Journal of Biomedical Informatics, 2006, vol. 39, no 3, pp. 314–320.
  • 53P. 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
  • 54O. Bodenreider, R. Stevens.

    Bio-ontologies: current trends and future directions, in: Briefings in Bioinformatics, 2006, vol. 7, no 3, pp. 256–274.
  • 55P. 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
  • 56N. Cannata, E. Merelli, R. B. Altman.

    Time to Organize the Bioinformatics Resourceome, in: PLoS Computational Biology, 2005, vol. 1, no 7, pp. 0531–0533.
  • 57N. Cannata, M. Schröder, R. Marangoni, P. Romano.

    A Semantic Web for bioinformatics: goals, tools, systems, applications, in: BMC bioinformatics, 2008, vol. 9 Suppl 4, S1 p.
  • 58H. Chen, T. Yu, J. Y. Chen.

    Semantic Web meets Integrative Biology: a survey, in: Briefings in bioinformatics, 2012, vol. 14, no 1, pp. 109–125.
  • 59J. J. Cimino, X. Zhu.

    The practical impact of ontologies on biomedical informatics, in: Methods of information in medicine, 2006.
  • 60G. 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
  • 61F. 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
  • 62S. 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
  • 63O. 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.
  • 64S. 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
  • 65P. Flajolet, R. Sedgewick.

    Analytic Combinatorics, Cambridge University Press, 2009.
  • 66M. 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.
  • 67F. 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
  • 68D. P. Hill, N. Adams, M. Bada, C. Batchelor, T. Z. Berardini, H. Dietze, H. J. Drabkin, M. Ennis, R. E. Foulger, M. A. Harris, J. Hastings, N. S. Kale, P. de Matos, C. J. Mungall, G. Owen, P. Roncaglia, C. Steinbeck, S. Turner, J. Lomax.

    Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology, in: BMC genomics, 2013, vol. 14, 513 p.
  • 69F. 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
  • 70S.-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
  • 71A. Lihonosova, A. Kaminskaya.

    Using Formal Concept Analysis for Finding the Closest Relatives among a Group of Organisms, in: Procedia Computer Science, 2014, vol. 31, no Complete, pp. 860-868.

    http://dx.doi.org/10.1016/j.procs.2014.05.337
  • 72K. 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.
  • 73N. 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
  • 74M. 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
  • 75P.-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
  • 76L. J. G. Post, M. Roos, M. S. Marshall, R. van Driel, T. M. Breit.

    A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data, in: Bioinformatics (Oxford, England), 2007, vol. 23, no 22, pp. 3080–3087.
  • 77S. 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
  • 78M. 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, no 672, pp. 223-234.

    http://hal-lirmm.ccsd.cnrs.fr/lirmm-00531802
  • 79C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas.

    CRISPI: a CRISPR interactive database, in: Bioinformatics, 2009, vol. 25, no 24, pp. 3317-3318.
  • 80L. Royer, M. Reimann, B. Andreopoulos, M. Schroeder.

    Unraveling Protein Networks with Power Graph Analysis, in: PLoS Comput Biol, 07 2008, vol. 4, no 7, e1000108.

    http://dx.plos.org/10.1371%2Fjournal.pcbi.1000108
  • 81A. Ruttenberg, T. Clark, W. Bug, M. Samwald, O. Bodenreider, H. Chen, D. Doherty, K. Forsberg, Y. Gao, V. Kashyap, J. Kinoshita, J. Luciano, M. Scott Marshall, C. Ogbuji, J. Rees, S. Stephens, G. T. Wong, E. Wu, D. Zaccagnini, T. Hongsermeier, E. Neumann, I. Herman, K.-H. Cheung.

    Advancing translational research with the Semantic Web, in: BMC Bioinformatics, 2007, vol. 8, no 3.
  • 82T. Schaub, S. Thiele.

    Metabolic Network Expansion with Answer Set Programming, in: ICLP 2009, LNCS, Springer, 2009, vol. 5649, pp. 312-326.
  • 83S. 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, no 4, pp. 235-242.
  • 84D. Searls.

    The language of genes, in: Nature, 2002, vol. 420, pp. 211-217.
  • 85D. 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.
  • 86Z. 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, no 7, e1002195 p.
  • 87R. Stevens, C. A. Goble, S. Bechhofer.

    Ontology-based Knowledge Representation for Bioinformatics, in: Briefings in bioinformatics, 2000, vol. 1, no 4, pp. 398–416.
  • 88S. 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
  • 89S. 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
  • 90R. 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
  • 91V. 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
  • 92V. 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


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