Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
XML PDF e-pub
PDF e-Pub


Bibliography

Major publications by the team in recent years
[1]
C. 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
[2]
C. 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
[3]
P. 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, no 1, pp. 106-117. [ DOI : 10.1002/mbo3.315 ]
https://hal.inria.fr/hal-01246173
[4]
J. 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, Lecture Notes in Computer Sciences, September 2017, 17 p.
https://hal.archives-ouvertes.fr/hal-01559249
[5]
F. 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
[6]
F. 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
[7]
C. 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, no 17, pp. i934 - i943. [ DOI : 10.1093/bioinformatics/bty588 ]
https://hal.inria.fr/hal-01871600
[8]
C. 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
[9]
S. 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, no 1, 32 p. [ DOI : 10.1371/journal.pcbi.1005276 ]
https://hal.inria.fr/hal-01449100
[10]
S. 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

[11]
C. 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

[12]
M. 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, no 5, e1006146 p. [ DOI : 10.1371/journal.pcbi.1006146 ]
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01807842
[13]
V. 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
[14]
C. 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, no 17, pp. i934 - i943. [ DOI : 10.1093/bioinformatics/bty588 ]
https://hal.inria.fr/hal-01871600
[15]
C. 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
[16]
S. 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, no 9, pp. 1-26. [ DOI : 10.1371/journal.pgen.1007593 ]
https://hal.archives-ouvertes.fr/hal-01871468
[17]
M. 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

[18]
P. Boutillier, F. Camporesi, J. Coquet, J. Feret, K. Q. , 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
[19]
F. 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
[20]
V. 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
[21]
M. 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
[22]
T. 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

[23]
L. 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
[24]
W. 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
[25]
V. 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
[26]
Y. 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
[27]
Y. 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

[28]
C. 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

[29]
A. 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
[30]
N. Guillaudeux.
Prédiction de transcriptome : analyse comparative multi-gènes, orthologues, Univ Rennes ; Inria ; CNRS ; Irisa, June 2018, 42 p.
https://hal.inria.fr/hal-01948461
[31]
C. 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
[32]
J. 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
[33]
G. 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
[34]
T. 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, no 1, pp. 1–130.
[35]
S. 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, no 10, 786 p.
https://doi.org/10.1186/s12864-016-3103-6
[36]
P. 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
[37]
L. 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
[38]
A. 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
[39]
M. 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
[40]
F. 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
[41]
K. Faust, J. Raes.
Microbial interactions: from networks to models, in: Nat. Rev. Microbiol., Jul 2012, vol. 10, no 8, pp. 538–550.
[42]
M. 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, no D1, pp. D1–D5.
[43]
M. 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.
[44]
S. 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
[45]
M. 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, no D1, pp. D372–379.
[46]
D. B. Searls.
String variable grammar: A logic grammar formalism for the biological language of DNA, in: The Journal of Logic Programming, 1995, vol. 24, no 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
[47]
Z. 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.
[48]
R. 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