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
3L. Bourneuf, J. Nicolas.

FCA in a Logical Programming Setting for Visualization-oriented Graph Compression, in: International Conference on Formal Concept Analysis 2017, Rennes, France, Lecture Notes in Computer Sciences, June 2017, vol. 10308. [ DOI : 10.1007/978-3-319-59271-8_6 ]

https://hal.archives-ouvertes.fr/hal-01558302
4A. 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
5F. 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.
6M. 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.
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
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
9S. Prigent, C. Frioux, S. M. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, J. Got, D. Eveillard, J. Bourdon, F. Plewniak, T. Tonon, A. Siegel.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, in: PLoS Computational Biology, January 2017, vol. 13, n^o 1, 32 p. [ DOI : 10.1371/journal.pcbi.1005276 ]

https://hal.inria.fr/hal-01449100
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.
11S. Videla, J. Saez-Rodriguez, C. Guziolowski, A. Siegel.

caspo: a toolbox for automated reasoning on the response of logical signaling networks families, in: Bioinformatics, 2017. [ DOI : 10.1093/bioinformatics/btw738 ]

https://hal.inria.fr/hal-01426880

Publications of the year

Doctoral Dissertations and Habilitation Theses

12J. COQUET.

Comprehensive study of large signaling pathways by clustering trajectories and characterization by semantic analysis, Université de Rennes 1, December 2017.

https://hal.inria.fr/tel-01670730
13V. Delannée.

Integrate molecular and cellular scales in the inference of metabolic networks : application to xenobiotics, Université Rennes 1, November 2017.

https://tel.archives-ouvertes.fr/tel-01690005
14V. Delannée.

Integrate molecular and cellular scales in the inference of metabolic networks. Application to xenobiotics, Univ. Rennes 1, November 2017.

https://hal-univ-rennes1.archives-ouvertes.fr/tel-01659375
15J. Laniau.

Biological networks structure : role of internal nodes regarding production of target elements, Inria Rennes - Bretagne Atlantique, October 2017.

https://hal.archives-ouvertes.fr/tel-01656474

Articles in International Peer-Reviewed Journals

16M. P. Cortés, S. N. Mendoza, D. Travisany, A. Gaete, A. Siegel, V. Cambiazo, A. Maass.

Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing, in: Frontiers in Microbiology, December 2017, vol. 8, 15 p. [ DOI : 10.3389/fmicb.2017.02462 ]

https://hal.inria.fr/hal-01661270
17V. Delannée, S. Langouët, N. Théret, A. Siegel.

A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes, in: PeerJ, 2017, vol. 5, e3703 p. [ DOI : 10.7717/peerj.3703 ]

https://hal.inria.fr/hal-01575579
18F. Gondret, A. Vincent, M. Houée-Bigot, A. Siegel, S. Lagarrigue, D. Causeur, H. H. Gilbert, I. Louveau.

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs, in: BMC Genomics, 2017, vol. 18, n^o 1, 244 p. [ DOI : 10.1186/s12864-017-3639-0 ]

https://hal.archives-ouvertes.fr/hal-01494107
19J. Laniau, C. Frioux, J. Nicolas, C. Baroukh, M. P. Cortés, J. Got, C. Trottier, D. Eveillard, A. Siegel.

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks, in: PeerJ, 2017, vol. 5, e3860 p. [ DOI : 10.7717/peerj.3860 ]

https://hal.archives-ouvertes.fr/hal-01635688
20V. Picard, A. Siegel, J. Bourdon.

A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks, in: Journal of computational biology : a journal of computational molecular cell biology, August 2017, vol. 24, n^o 8, pp. 1–12. [ DOI : 10.1089/cmb.2017.0099 ]

https://hal.archives-ouvertes.fr/hal-01552190
21S. Prigent, C. Frioux, S. M. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, J. Got, D. Eveillard, J. Bourdon, F. Plewniak, T. Tonon, A. Siegel.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, in: PLoS Computational Biology, January 2017, vol. 13, n^o 1, 32 p. [ DOI : 10.1371/journal.pcbi.1005276 ]

https://hal.inria.fr/hal-01449100
22S. Videla, J. Saez-Rodriguez, C. Guziolowski, A. Siegel.

caspo: a toolbox for automated reasoning on the response of logical signaling networks families, in: Bioinformatics, 2017. [ DOI : 10.1093/bioinformatics/btw738 ]

https://hal.inria.fr/hal-01426880

Invited Conferences

23V. Wucher, F. Legeai, L. Bourneuf, T. Derrien, A. Gallot, S. Hudaverdian, S. Jaubert-Possamai, N. Leterme-Prunier, J. Nicolas, H. Seitz, A. Siegel, S. TANGUY, G. Le Trionnaire, D. Tagu.

Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid, in: 10th Arthropod Genomics Symposium, Notre Dame, United States, June 2017.

https://hal.inria.fr/hal-01566438

International Conferences with Proceedings

25J. Coquet, N. Théret, V. Legagneux, O. Dameron.

Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-β Signaling, in: CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology, Darmstadt, France, Lecture Notes in Computer Sciences, September 2017, 17 p.

https://hal.archives-ouvertes.fr/hal-01559249

National Conferences with Proceedings

27P. FINET, B. Gibaud, O. Dameron, R. Le Bouquin Jeannes.

Interoperable infrastructure and implementation of a health data model for remote monitoring of chronic diseases with comorbidities, in: Journées d'Etude sur la TéléSANté, 6ème edition, Bourges, France, Pôle Capteurs, Université d'Orléans, May 2017.

https://hal.archives-ouvertes.fr/hal-01565009

Conferences without Proceedings

28X. Garnier, A. Bretaudeau, O. Filangi, F. Legeai, A. Siegel, O. Dameron.

AskOmics, a web tool to integrate and query biological data using semantic web technologies, in: JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Lille, France, July 2017, 1 p.

https://hal.inria.fr/hal-01577425
29X. Garnier, O. Dameron, O. Filangi, F. Legeai, A. Bretaudeau.

Integration of Linked Data into Galaxy using Askomics , in: Galaxy Community Conference, Montpellier, France, June 2017.

https://hal.inria.fr/hal-01576870
30C. Lippold, C. Trottier, C. Frioux, M. Chevallier, S. M. Dittami, A. Siegel.

Toward the study of metabolic functions in algal holobionts, in: 4ème Colloque de Génomique Environnementale, Marseille, France, September 2017.

https://hal.inria.fr/hal-01576484
31V. Potdevin, M. Chevallier, R. Garrido Oter, A. Siegel, S. Hacquard, D. Eveillard, P. Vandenkoornhuyse.

Toward a better understanding of the plant microbiota, in: 4ème colloque de Génomique Environnementale, Marseille, France, GDR Génomique Environnementale, September 2017.

https://hal.inria.fr/hal-01576743

Scientific Books (or Scientific Book chapters)

32D. Eveillard, A. Siegel, P. Vandenkoornhuyse.

L'écologie des systèmes, in: Les Big Data à Découvert, M. Bouzeghoub, R. Mosseri (editors), CNRS éditions, 2017.

https://hal.inria.fr/hal-01575603

Other Publications

33A. Antoine-Lorquin, A. Arnaoty, S. Asgari, M. Batailler, L. Beauclair, C. Belleannée, S. Bire, N. Buisine, V. Coustham, A. Girault, S. Guyetant, T. Lecomte, B. Piégu, B. Pitard, I. Stévant, Y. Bigot.

First landscape of binding to chromosomes for a domesticated mariner transposase in the human genome: diversity of genomic targets of SETMAR isoforms in two colorectal cell lines, July 2017, working paper or preprint. [ DOI : 10.1101/115030 ]

https://hal.archives-ouvertes.fr/hal-01558001
34A. Antoine-Lorquin, F. Mahé, M. Dunthorn, C. Belleannée.

Detection of mutated primers and impact on targeted metagenomics results, July 2017, working paper or preprint.

https://hal.archives-ouvertes.fr/hal-01564093
35C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.

De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets, November 2017, working paper or preprint. [ DOI : 10.1101/170035 ]

https://hal.archives-ouvertes.fr/hal-01643156
36M. Ruffini.

Better scoring schemes for the recognition of functional proteins by protomata, Rennes 1, June 2017.

https://hal.inria.fr/hal-01557941

References in notes

37O. 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
38V. 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
39V. 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
40G. 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
41A. Antoine-Lorquin, F. Mahé, M. Dunthorn, C. Belleannée.

Detection of mutated primers and impact on targeted metagenomics results, in: RCAM'16 ”Recent Computational Advances in Metagenomics”, The Hague, Netherlands, September 2016.

https://hal.inria.fr/hal-01576304
42A. 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
43T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant, L. Clementi, J. Ren, W. W. Li, W. S. Noble.

MEME Suite: tools for motif discovery and searching, in: Nucleic Acids Research, 2009, vol. 37, n^o suppl_2, W202 p.

http://dx.doi.org/10.1093/nar/gkp335
44T. L. Bailey, J. Johnson, C. E. Grant, W. S. Noble.

The MEME Suite, in: Nucleic Acids Research, 2015, vol. 43, n^o W1, pp. W39-W49.

http://dx.doi.org/10.1093/nar/gkv416
45F. 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
46C. Baral.

Knowledge Representation, Reasoning and Declarative Problem Solving, Cambridge University Press, 2010.
47T. 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
48R. Bellazzi.

Big Data and Biomedical Informatics: A Challenging Opportunity, in: Yearbook of medical informatics, 2014, vol. 9, n^o 1, In press.
49R. 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.
50C. 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
51R. 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.
52R. 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
53C. Bettembourg, O. Dameron, A. Bretaudeau, F. Legeai.

AskOmics : IntÃ©gration et interrogation de rÃ©seaux de rÃ©gulation gÃ©nomique et post-gÃ©nomique, in: IN OVIVE (INtÃ©gration de sources/masses de donnÃ©es hÃ©tÃ©rogÃ¨nes et Ontologies, dans le domaine des sciences du VIVant et de lâEnvironnement), Rennes, France, June 2015, 7 p.

https://hal.inria.fr/hal-01184903
54C. Bettembourg, C. Diot, O. Dameron.

Semantic particularity measure for functional characterization of gene sets using gene ontology, in: PLoS ONE, 2014, vol. 9, n^o 1, e86525. [ DOI : 10.1371/journal.pone.0086525 ]

https://hal.inria.fr/hal-00941850
55C. 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
56C. 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
57C. 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.
58J. 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.
59P. 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
60P. 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
61P. Bordron, M. Latorre, M. P. Cortés, 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, vol. 5, n^o 1, pp. 106-117. [ DOI : 10.1002/mbo3.315 ]

https://hal.inria.fr/hal-01246173
62A. 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, 6 p. [ DOI : 10.1093/nar/gks1091 ]

https://hal.inria.fr/hal-01094087
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.
64M. 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
65G. 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
66F. 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
67F. 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
68S. 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
69S. 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
70A. Evrard, C. Bettembourg, 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
71R. D. Finn, J. Clements, W. Arndt, B. L. Miller, T. J. Wheeler, F. Schreiber, A. Bateman, S. R. Eddy.

HMMER web server: 2015 update, in: Nucleic Acids Research, 2015, vol. 43, n^o W1, W30 p.

http://dx.doi.org/10.1093/nar/gkv397
72C. 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
73M. 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.
74F. 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
75F. 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
76F. 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, 120 p, article number 120. [ DOI : 10.1186/s12864-016-2438-3 ]

https://hal.archives-ouvertes.fr/hal-01286555
77C. 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
78C. Guziolowski, S. Videla, F. Eduati, S. Thiele, T. Cokelaer, A. S. Siegel, J. Saez-Rodriguez.

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming, in: Bioinformatics, 2013, vol. 29, pp. 2320-2326. [ DOI : 10.1093/bioinformatics/btt393 ]

https://hal.inria.fr/hal-00853704v1
79F. 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
80R. 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
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PyBoolNet: a python package for the generation, analysis and visualization of boolean networks, in: Bioinformatics, 2017, vol. 33, n^o 5, pp. 770-772.

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