Bibliography

Major publications by the team in recent years

1M. 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, May 2018, vol. 14, n^o 5, e1006146. [ DOI : 10.1371/journal.pcbi.1006146 ]

https://hal-univ-rennes1.archives-ouvertes.fr/hal-01807842
2C. 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
3C. 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
4P. 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
5J. 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
6F. 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
7F. 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
8C. 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
9C. 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
10S. 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
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

12L. Bourneuf.

A search space of graph motifs for graph compression : From Powergraphs to triplet concepts, Université Rennes 1, December 2019.

https://hal.inria.fr/tel-02399641

Articles in International Peer-Reviewed Journals

13S. Blanquart, A.-S. Borowiec, P. Delcourt, M. Figeac, C. A. Emerling, A. S. Meseguer, M. Roudbaraki, N. Prevarskaya, G. Bidaux.

Evolution of the human cold/menthol receptor, TRPM8, in: Molecular Phylogenetics and Evolution, July 2019, vol. 136, pp. 104-118. [ DOI : 10.1016/j.ympev.2019.04.011 ]

https://hal.inria.fr/hal-02284919
14V. 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
15W. Dyrka, M. Pyzik, F. Coste, H. Talibart.

Estimating probabilistic context-free grammars for proteins using contact map constraints, in: PeerJ, March 2019, vol. 7, pp. 1-35. [ DOI : 10.7717/peerj.6559 ]

https://hal.archives-ouvertes.fr/hal-02400871
16M. Folschette, V. Legagneux, A. Poret, L. Chebouba, C. Guziolowski, N. Théret.

A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma, in: BMC Bioinformatics, January 2020. [ DOI : 10.1186/s12859-019-3316-1 ]

https://hal.archives-ouvertes.fr/hal-02095930
17D. Nègre, M. Aite, A. Belcour, C. Frioux, L. Brillet-Guéguen, X. Liu, P. Bordron, O. Godfroy, A. P. Lipinska, C. Leblanc, A. Siegel, S. M. Dittami, E. Corre, G. V. Markov.

Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus, in: Antioxidants, November 2019, vol. 8, n^o 11, 564 p. [ DOI : 10.3390/antiox8110564 ]

https://hal.inria.fr/hal-02395080
18Y. Rivault, O. Dameron, N. Le Meur.

queryMed: Semantic Web functions for linking pharmacological and medical knowledge to data, in: Bioinformatics, January 2019, vol. 35, n^o 17, pp. 3203-3205. [ DOI : 10.1093/bioinformatics/btz034 ]

https://hal.archives-ouvertes.fr/hal-01988699
19K. Straub, M. Linde, C. Kropp, S. Blanquart, P. Babinger, R. Merkl.

Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase, in: Biological Chemistry, February 2019, vol. 400, n^o 3, pp. 367-381. [ DOI : 10.1515/hsz-2018-0344 ]

https://hal.inria.fr/hal-02284913
20M. Wery, O. Dameron, J. Nicolas, E. Rémy, A. Siegel.

Formalizing and enriching phenotype signatures using Boolean networks, in: Journal of Theoretical Biology, 2019, vol. 467, pp. 66-79. [ DOI : 10.1016/j.jtbi.2019.01.015 ]

https://hal.inria.fr/hal-02018724

Invited Conferences

21A. Siegel.

Learning boolean regulations based on prior-knowledge data: a logical-based viewpoint, in: SASB 2019 - 10th International Workshop on Static Analysis for Systems Biology, Porto, Portugal, October 2019.

https://hal.inria.fr/hal-02412421
22A. Siegel.

Using automated reasoning to explore unconventional organisms: a first step to explore host-microbial interactions, in: MPA 2019 - Conference on Metabolic Pathway Analysis, Riga, Latvia, August 2019.

https://hal.inria.fr/hal-02412419

International Conferences with Proceedings

23J. Bakalara, T. Guyet, O. Dameron, E. Oger, A. Happe.

Temporal models of care sequences for the exploration of medico-administrative data, in: 2019 - Workshop IA&Santé, PFIA, Toulouse, France, July 2019, pp. 1-8.

https://hal.archives-ouvertes.fr/hal-02265743
24L. Bourneuf, J. Nicolas.

Concept Lattices as a Search Space for Graph Compression, in: ICFCA 2019 - 15th International Conference on Formal Concept Analysis, Francfort, Germany, D. C. L. B. Sertkaya (editor), ICFCA: International Conference on Formal Concept Analysis, Springer, May 2019, vol. 15th International Conference, n^o 15, pp. 274-289. [ DOI : 10.1007/978-3-030-21462-3_18 ]

https://hal.inria.fr/hal-02399578
25M. Louarn, F. Chatonnet, X. Garnier, T. Fest, A. Siegel, O. Dameron.

Increasing life science resources re-usability using Semantic Web technologies, in: eScience 2019 - 15th International eScience Conference, San Diego, United States, September 2019, pp. 1-9.

https://hal.inria.fr/hal-02274982

Conferences without Proceedings

26L. Bourneuf.

Biseau: An Answer Set Programming Environment for High-Level Specification and Graph Visualization applied to FCA, in: ICFCA 2019 - International Conference on Formal Concept Analysis, Frankfort, Germany, June 2019, pp. 1-6.

https://hal.inria.fr/hal-02399610
27X. Garnier, A. Bretaudeau, F. Legeai, A. Siegel, O. Dameron.

AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resources, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019, 1 p.

https://hal.archives-ouvertes.fr/hal-02401750
28V. J. Henry, G. Bassignana, V. Zujovic, F. De Vico Fallani, O. Dameron, I. Moszer, O. Colliot.

Conciliation of process description and molecular interaction networks using logical properties of ontology, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019.

https://hal.archives-ouvertes.fr/hal-02301702
29N. Le Meur, Y. Rivault, O. Dameron.

Linking pharmacological and medical knowledge using semantic Web technologies, in: useR! 2019 - Conférence internationale des utilisateurs de R, Toulouse, France, July 2019.

https://hal.archives-ouvertes.fr/hal-02294364
30H. Talibart, F. Coste.

Using residues coevolution to search for protein homologs through alignment of Potts models, in: CECAM 2019 - workshop on Co-evolutionary methods for the prediction and design of protein structure and interactions, Lausanne, Switzerland, CECAM-HQ-EPFL, June 2019, pp. 1-2.

https://hal.inria.fr/hal-02402646

Other Publications

31A. Abel.

Faster SPARQL Federated Queries, Université Rennes1, June 2019.

https://hal.inria.fr/hal-02269417
32P. Beaudier.

Evaluation of the public databases' relevance as comprehensive tools for pharmacological mechanisms, Université de Rennes 1, June 2019.

https://hal.inria.fr/hal-02191210
33A. Belcour, C. Frioux, M. Aite, A. Bretaudeau, A. Siegel.

Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species, December 2019, working paper or preprint. [ DOI : 10.1101/803056 ]

https://hal.inria.fr/hal-02395024
34B. Burgunter-Delamare, H. Kleinjan, C. Frioux, E. Fremy, M. Wagner, E. Corre, A. Le Salver, C. Leroux, C. Leblanc, A. Siegel, S. M. Dittami.

Metabolic complementarity between a brown alga and associated 1 cultivable bacteria provide indications of beneficial interactions, October 2019, working paper or preprint. [ DOI : 10.1101/813683 ]

https://hal.sorbonne-universite.fr/hal-02333039
35F. Casse Encadrée.

Regulation of genes regulating fecondity and early embryonic development by miRNAs in the Medaka fish, Univ Rennes, Inria, CNRS, IRISA, June 2019.

https://hal.inria.fr/hal-02192476
36F. Coste.

Deep learning languages: a key fundamental shift from probabilities to weights?, August 2019, https://arxiv.org/abs/1908.00785 - working paper or preprint.

https://hal.inria.fr/hal-02235207
37O. Dennler.

Caractérisation en modules fonctionnels de la famille de protéines ADAMTS / ADAMTSL, Univ Rennes, June 2019.

https://hal.inria.fr/hal-02403084
38S. M. Dittami, E. Corre, L. Brillet-Guéguen, A. P. Lipinska, M. Aite, K. Avia, C. Caron, C. H. Cho, J. Collen, A. Cormier, L. Delage, S. Doubleau, C. Frioux, A. Gobet, I. González-Navarrete, A. Groisillier, C. Hervé, D. Jollivet, H. Kleinjan, C. Leblanc, X. Liu, D. Marie, G. V. Markov, A. E. Minoche, P. Pericard, M.-M. Perrineau, A. F. Peters, A. Siegel, C. Trottier, H. S. Yoon, H. Himmelbauer, C. Boyen, T. Tonon.

The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga, October 2019, working paper or preprint. [ DOI : 10.1101/307165 ]

https://hal.sorbonne-universite.fr/hal-02333021
39N. Guillaudeux, C. Belleannée, S. Blanquart, J.-S. Varré.

Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?, July 2019, vol. 8, 1 p, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster présenté à JOBIM 2019 (https://jobim2019.sciencesconf.org/) qui s'est déroulé du 2 au 5 juillet 2019 et à ISMB/ECCB 2019 (https://www.iscb.org/ismbeccb2019) qui s'est déroulé du 21 au 25 juillet 2019. [ DOI : 10.7490/f1000research.1117311.1 ]

https://hal.inria.fr/hal-02267357
40H. Talibart, F. Coste.

Using residues coevolution to search for protein homologs through alignment of Potts models, July 2019, 1 p, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.

https://hal.inria.fr/hal-02402687
41K. Thuillier.

Linear programming for metabolic network completion, Inria Rennes - Bretagne Atlantique and University of Rennes 1, France, December 2019.

https://hal.inria.fr/hal-02408003
42M. Wery, E. Becker, F. Auge, C. Bettembourg, O. Dameron, A. Siegel.

Identification of causal signature using omics data integration and network reasoning-based analysis, July 2019, 1 p, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.

https://hal.inria.fr/hal-02193860

References in notes

43G. 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
44T. 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.
45C. 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
46S. 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
47P. 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
48P. 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
49M. 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
50A. 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
51J. 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
52M.-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
53F. 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
54V. 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
55S. 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
56K. Faust, J. Raes.

Microbial interactions: from networks to models, in: Nat. Rev. Microbiol., Jul 2012, vol. 10, n^o 8, pp. 538–550.
57M. 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.
58M. 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.
59F. 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
60F. 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
61M.-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, vol. 61, pp. 155-161. [ DOI : 10.1016/j.compbiolchem.2016.01.012 ]

https://hal.archives-ouvertes.fr/hal-02394687
62S. 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
63S. 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
64Y. Rivault.

Care trajectory analysis using medico-administrative data : contribution of a knowledge-based enrichment from the Linked Data, Université Rennes 1, January 2019.

https://tel.archives-ouvertes.fr/tel-02137442
65M. 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.
66D. B. Searls.

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67Z. 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.

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68R. 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

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