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
• 2C. 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
• 3P. 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
• 4J. Coquet, N. Théret, V. Legagneux, O. Dameron.
  Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-$\beta$ Signaling, in: CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology, Darmstadt, Lecture Notes in Computer Sciences, September 2017, 17 p.
  https://hal.archives-ouvertes.fr/hal-01559249
• 5F. 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
• 6F. Coste, J. Nicolas.
  Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wrocław, Poland, September 2018, vol. 93, pp. 155 - 168.
  https://hal.inria.fr/hal-01872266
• 7C. Frioux, E. Fremy, C. Trottier, A. Siegel.
  Scalable and exhaustive screening of metabolic functions carried out by microbial consortia, in: Bioinformatics, September 2018, vol. 34, n^o 17, pp. i934 - i943. [ DOI : 10.1093/bioinformatics/bty588 ]
  https://hal.inria.fr/hal-01871600
• 8C. Frioux, T. Schaub, S. Schellhorn, A. Siegel, P. Wanko.
  Hybrid Metitebolic Network Completion, in: Theory and Practice of Logic Programming, November 2018, pp. 1-23.
  https://hal.inria.fr/hal-01936778
• 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
• 10S. 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

• 11C. Frioux.
  Investigating host-microbiota cooperation with gap-filling optimization problems, Université de Rennes 1, November 2018.
  https://hal.inria.fr/tel-01945853

Articles in International Peer-Reviewed Journals

• 12M. Aite, M. Chevallier, C. Frioux, C. Trottier, J. Got, M. P. Cortés, S. N. Mendoza, G. Carrier, O. Dameron, N. Guillaudeux, M. Latorre, N. Loira, G. V. Markov, A. Maass, A. Siegel.
  Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models, in: PLoS Computational Biology, 2018, vol. 14, n^o 5, e1006146 p. [ DOI : 10.1371/journal.pcbi.1006146 ]
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01807842
• 13V. Delannée, S. Langouët, A. Siegel, N. Théret.
  In silico prediction of Heterocyclic Aromatic Amines metabolism susceptible to form DNA adducts in humans, in: Toxicology Letters, January 2019, vol. 300, pp. 18-30. [ DOI : 10.1016/j.toxlet.2018.10.011 ]
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01903264
• 14C. Frioux, E. Fremy, C. Trottier, A. Siegel.
  Scalable and exhaustive screening of metabolic functions carried out by microbial consortia, in: Bioinformatics, September 2018, vol. 34, n^o 17, pp. i934 - i943. [ DOI : 10.1093/bioinformatics/bty588 ]
  https://hal.inria.fr/hal-01871600
• 15C. Frioux, T. Schaub, S. Schellhorn, A. Siegel, P. Wanko.
  Hybrid Metabolic Network Completion, in: Theory and Practice of Logic Programming, November 2018, pp. 1-23. [ DOI : 10.1017/S1471068418000455 ]
  https://hal.inria.fr/hal-01936778
• 16S. Gay, J. Bugeon, A. BOUCHAREB, L. Henry, C. DELAHAYE, F. Legeai, J. Montfort, A. Le Cam, A. Siegel, J. Bobe, V. Thermes.
  MiR-202 controls female fecundity by regulating medaka oogenesis, in: PLoS Genetics, September 2018, vol. 14, n^o 9, pp. 1-26. [ DOI : 10.1371/journal.pgen.1007593 ]
  https://hal.archives-ouvertes.fr/hal-01871468
• 17M. Razzaq, L. Paulevé, A. Siegel, J. Saez-Rodriguez, J. Bourdon, C. Guziolowski.
  Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data, in: PLoS Computational Biology, 2018, vol. 14, pp. 1-23. [ DOI : 10.1371/journal.pcbi.1006538 ]
  https://hal.archives-ouvertes.fr/hal-01897020

International Conferences with Proceedings

• 18P. Boutillier, F. Camporesi, J. Coquet, J. Feret, K. Q. Lý, N. Théret, P. Vignet.
  KaSa A Static Analyzer for Kappa, in: CMSB 2018 - 16th International Conference on Computational Methods in Systems Biology, Brno, Czech Republic, M. Češka, D. Šafránek (editors), LNCS, Springer Verlag, September 2018, vol. 11095, pp. 285-291. [ DOI : 10.1007/978-3-319-99429-1_17 ]
  https://hal-univ-rennes1.archives-ouvertes.fr/hal-01888951
• 19F. Coste, J. Nicolas.
  Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wrocław, Poland, September 2018, vol. 93, pp. 155 - 168.
  https://hal.inria.fr/hal-01872266
• 20V. J. Henry, I. Moszer, O. Dameron, M.-C. Potier, M. Hofmann-Apitius, O. Colliot.
  Converting Alzheimer's disease map into a heavyweight ontology: a formal network to integrate data, in: DILS 2018 - 13th International Conference on Data Integration in the Life Sciences, Hannover, Germany, DILS 2018 - 13th International Conference on Data Integration in the Life Sciences, November 2018, pp. 1-9.
  https://hal.archives-ouvertes.fr/hal-01917742
• 21M. Pyzik, F. Coste, W. Dyrka.
  How to measure the topological quality of protein parse trees?, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wroclaw, Poland, September 2018, vol. 93, pp. 118 - 138.
  https://hal.inria.fr/hal-01938608
• 22T. Ribeiro, M. Folschette, M. Magnin, O. Roux, K. Inoue.
  Learning Dynamics with Synchronous, Asynchronous and General Semantics, in: 28th International Conference on Inductive Logic Programming, Ferrara, Italy, Inductive Logic Programming, Springer, Cham, September 2018, vol. LNCS, volume 11105. [ DOI : 10.1007/978-3-319-99960-9_8 ]
  https://hal.archives-ouvertes.fr/hal-01826564

Conferences without Proceedings

• 23L. Bourneuf.
  An Answer Set Programming Environment for High-Level Specification and Visualization of FCA, in: FCA4AI'18 - 6th Workshop «What can FCA do for Artificial Intelligence?», Stockholm, Sweden, July 2018, pp. 1-12.
  https://hal.archives-ouvertes.fr/hal-01945938
• 24W. Dyrka, F. Coste, H. Talibart.
  Where the context-free grammar meets the contact map: a probabilistic model of protein sequences aware of contacts between amino acids, in: ISMB 2018 - 3DSIG: Structural Bioinformatics and Computational Biophysics, Chicago, United States, July 2018.
  https://hal.inria.fr/hal-01939021
• 25V. HENRY, I. Moszer, O. Dameron, M.-C. Potier, M. Hofmann-Apitius, O. Colliot.
  Integrating ontological representation and reasoning into a disease map: application to Alzheimer's disease, in: DMCM 2018 - 3rd Disease Maps Community Meeting, Paris, France, June 2018, pp. 1-2.
  https://hal.archives-ouvertes.fr/hal-01873474
• 26Y. Rivault, O. Dameron, N. Le Meur.
  Ontologies biomédicales et Web Sémantique pour la réutilisation des bases de données médico-administratives en pharmaco-épidémiologie, in: JFO 2018 - 7ème Journées Francophones sur les Ontologies, Hammamet, Tunisia, November 2018, pp. 1-6.
  https://hal.archives-ouvertes.fr/hal-01912046
• 27Y. Rivault, O. Dameron, N. Le Meur.
  queryMed : enrichissement des données de recherche en pharmaco-épidémiologie, in: Septièmes rencontres R, Rennes, France, July 2018, pp. 1-2.
  https://hal.archives-ouvertes.fr/hal-01834137

Scientific Popularization

• 28C. Frioux, E. Fremy, C. Trottier, A. Siegel.
  Scalable and exhaustive screening of metabolic functions carried out by microbial consortia, in: European Conference on Computational Biology, Athènes, Greece, September 2018.
  https://hal.inria.fr/hal-01946860

Other Publications

• 29A. Belcour, J. Girard, M. Aite, L. Delage, C. Trottier, C. Marteau, C. J.-J. Leroux, S. M. Dittami, P. Sauleau, E. Corre, J. Nicolas, C. Boyen, C. Leblanc, J. Collén, A. Siegel, G. V. Markov.
  Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift, December 2018, working paper or preprint.
  https://hal.inria.fr/hal-01943880
• 30N. Guillaudeux.
  Prédiction de transcriptome : analyse comparative multi-gènes, orthologues, Univ Rennes ; Inria ; CNRS ; Irisa, June 2018, 42 p.
  https://hal.inria.fr/hal-01948461
• 31C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.
  CARNAC-LR: De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets, April 2018, pp. 1-2, RECOMB-seq 2018 - Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing, Poster.
  https://hal.archives-ouvertes.fr/hal-01929963
• 32J. Yon, N. Bareille, B. Bed'Hom, X. Berthelot, S. Combes, O. Dameron, G. Foucras, A. Journaux, F. Launay, P.-Y. Le Bail, N. Le Floc'h, M. Martignon, C. Nédellec, M.-H. Pinard - Van Der Laan, E. Quillet, M.-C. Meunier-Salaün.
  Ontologie ATOL : amélioration de l'outil par l'intégration des caractères de santé, April 2018, Journées d'Animation Scientifique du département Phase (JAS Phase 2018), Poster.
  https://hal.archives-ouvertes.fr/hal-01768063

References in notes

• 33G. 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
• 34T. Berners Lee, W. Hall, J. A. Hendler, K. O'Hara, N. Shadbolt, D. J. Weitzner.
  A Framework for Web Science, in: Foundations and Trends in Web Science, 2007, vol. 1, n^o 1, pp. 1–130.
• 35S. Blanquart, J.-S. Varré, P. Guertin, A. Perrin, A. Bergeron, K. M. Swenson.
  Assisted transcriptome reconstruction and splicing orthology, in: BMC Genomics, Nov 2016, vol. 17, n^o 10, 786 p.
  https://doi.org/10.1186/s12864-016-3103-6
• 36P. 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
• 37L. 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
• 38A. 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
• 39M. 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
• 40F. 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), Proceedings of Machine Learning Research, September 2014, vol. 34, pp. 49–63.
  https://hal.inria.fr/hal-01080249
• 41K. Faust, J. Raes.
  Microbial interactions: from networks to models, in: Nat. Rev. Microbiol., Jul 2012, vol. 10, n^o 8, pp. 538–550.
• 42M. Y. Galperin, D. J. Rigden, X. M. Fernández-Suárez.
  The 2015 nucleic acids research database issue and molecular biology database collection, in: Nucleic acids research, 2015, vol. 43, n^o D1, pp. D1–D5.
• 43M. 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.
• 44S. 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
• 45M. H. Saier, V. S. Reddy, B. V. Tsu, M. S. Ahmed, C. Li, G. Moreno-Hagelsieb.
  The Transporter Classification Database (TCDB): recent advances, in: Nucleic Acids Res., Jan 2016, vol. 44, n^o D1, pp. D372–379.
• 46D. B. Searls.
  String variable grammar: A logic grammar formalism for the biological language of DNA, in: The Journal of Logic Programming, 1995, vol. 24, n^o 1, pp. 73 - 102, Computational Linguistics and Logic Programming. [ DOI : 10.1016/0743-1066(95)00034-H ]
  http://www.sciencedirect.com/science/article/pii/074310669500034H
• 47Z. 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.
• 48R. Verborgh, M. Vander Sande, O. Hartig, J. Van Herwegen, L. De Vocht, B. De Meester, G. Haesendonck, P. Colpaert.
  Triple Pattern Fragments: a Low-cost Knowledge Graph Interface for the Web, in: Journal of Web Semantics, March 2016, vol. 37–38, pp. 184–206. [ DOI : doi:10.1016/j.websem.2016.03.003 ]
  http://linkeddatafragments.org/publications/jws2016.pdf