Bibliography

Major publications by the team in recent years

1T. 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://hal.inria.fr/inria-00538133
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
3A. 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
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, n^o 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, n^o 18, pp. 2320-2326. [ DOI : 10.1093/bioinformatics/btt393 ]

http://hal.inria.fr/hal-00853704
8R. 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
9J. 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
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.

Publications of the year

Doctoral Dissertations and Habilitation Theses

11O. Abdou-Arbi.

Etude de la variabilité des contributions de nutriments à un réseau métabolique : modélisation, optimisation et application en nutrition, Université Rennes 1, September 2013.

http://hal.inria.fr/tel-00924200
12G. Andrieux.

Modélisation dynamique de la signalisation cellulaire : aspects différentiels et discrets; application à la signalisation du facteur de croissance TGF-beta dans le cancer, Université Rennes 1, July 2013.

http://hal.inria.fr/tel-00926487
13A. Aravena.

Probabilistic and constraint based modelling to determine regulation events from heterogeneous biological data, Université Rennes 1, December 2013.

http://hal.inria.fr/tel-00922346
14C. Bettembourg.

Méthodes sémantiques pour la comparaison inter-espèces de voies métaboliques : application au métabolisme des lipides chez l'humain, la souris et la poule, Université Rennes 1, December 2013.

http://hal.inria.fr/tel-00926498

Articles in International Peer-Reviewed Journals

15O. Abdou-Arbi, S. Lemosquet, 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, 8 p. [ DOI : 10.1186/1752-0509-8-8 ]

http://hal.inria.fr/hal-00924253
16C. 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. [ DOI : 10.1371/journal.pone.0086525 ]

http://hal.inria.fr/hal-00941850
17O. Dameron, C. Bettembourg, N. Le Meur.

Measuring the evolution of ontology complexity: the gene ontology case study, in: PLoS ONE, 2013, vol. 8, n^o 10. [ DOI : 10.1371/journal.pone.0075993 ]

http://hal.inria.fr/hal-00877378
18C. 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
19R. 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
20P.-F. Pluchon, T. Fouqueau, C. Crezé, 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, n^o 11. [ DOI : 10.1371/journal.pone.0079707 ]

http://hal.inria.fr/hal-00911795
21E. Quillery, O. Quenez, P. Peterlongo, O. Plantard.

Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms, in: Molecular Ecology Ressources, October 2013, epub ahead of print. [ DOI : 10.1111/1755-0998.12179 ]

http://hal.inria.fr/hal-00880072

Invited Conferences

22A. Siegel.

Extracting robust information from knowledge and observations on a biological system: a formal system framework, in: PRIB - Eighth IAPR International Conference on Pattern Recognition in Bioinformatics - 2013, Nice, France, June 2013.

http://hal.inria.fr/hal-00853839

International Conferences with Proceedings

23V. 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, Lecture Notes in Computer Science, Springer, 2014, vol. 8318, pp. 322-336. [ DOI : 10.1007/978-3-642-54013-4_18 ]

http://hal.inria.fr/hal-00926477
24N. Barbot, L. Miclet, H. Prade.

Analogical proportions and the factorization of information in distributive lattices, in: 10th International Conference on Concept Lattices and Their Applications (CLA), La Rochelle, France, October 2013.

http://hal.inria.fr/hal-00908005
25V. Berthe, J. Bourdon, T. Jolivet, A. Siegel.

Generating discrete planes with substitutions, in: WORDS - 9th International Conference on Words - 2013, Turku, Finland, September 2013.

http://hal.inria.fr/hal-00853758
26P. 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
27G. 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
28L. Paulevé, G. Andrieux, H. Koeppl.

Under-approximating Cut Sets for Reachability in Large Scale Automata Networks, in: 25th International Conference, CAV 2013, Proceedings, Saint Petersburg, Russian Federation, Lecture Notes in Computer Science, July 2013, vol. 8044, pp. 69-84. [ DOI : 10.1007/978-3-642-39799-8_4 ]

http://hal.inria.fr/hal-00769447

National Conferences with Proceedings

29N. Barbot, L. Miclet, H. Prade.

Proportions analogiques et factorisation de l'information dans les treillis distributifs, in: Journées d'Intelligence Artificielle Fondamentale (JIAF), Aix en Provence, France, June 2013.

http://hal.inria.fr/hal-00908020
30A. Bretaudeau, O. Dameron, F. Legeai, Y. Rahbé.

AphidAtlas : avancées récentes, in: Proceedings of BAPOA 2013 MOP. INRA, CIRAD Lavalette Campus Montpellier, France, Montpellier, France, M. Uzest (editor), 2013, [In French].

http://hal.inria.fr/hal-00913155
31A. Rollet, G. Defossez, O. Dameron, CoRIM, Poitou-Charentes, CRISAP, Poitou-Charentes, P. Ingrand.

Développement et évaluation d'un algorithme de représentation des parcours de soins de patientes atteintes d'un cancer du sein à partir des données d'un système d'information régional, in: Proceedings of the conference Évaluation Management Organisation Information Santé (EMOIS2013), Nancy, France, 2013, [In French, short abstract].

http://hal.inria.fr/hal-00913172

Conferences without Proceedings

32V. Wucher, D. Tagu, J. Nicolas.

Edge Selection in a Noisy Graph by Concept Analysis: Application to a Genomic Network, in: ECDA - European Conference on Data Analysis - 2013, Luxembourg, Luxembourg, July 2013.

http://hal.inria.fr/hal-00924413

Scientific Books (or Scientific Book chapters)

33F. Coste, C. Nédellec, T. Schiex, J.-P. Vert.

Bioinformatique, in: Panorama de l'intelligence artificielle Ses bases méthodologiques, ses développements, P. Marquis, O. Papini, H. Prade (editors), Cépaduès, June 2013, vol. 3.

http://hal.inria.fr/hal-00857379

Other Publications

34G. Collet, G. Rizk, R. Chikhi, D. Lavenier.

MINIA on a Raspberry Pi, Assembling a 100 Mbp Genome on a Credit Card Sized Computer, in: JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Toulouse, France, July 2013.

http://hal.inria.fr/hal-00842027

References in notes

35G. Andrieux, L. Fattet, M. Le Borgne, R. Rimokh, N. Théret.

Dynamic regulation of Tgf-B signaling by Tif1 $γ$ : a computational approach, in: PLoS ONE, 2012, vol. 7, n^o 3. [ DOI : 10.1371/journal.pone.0033761 ]

http://hal.inria.fr/hal-00851483
36C. Baral.

Knowledge Representation, Reasoning and Declarative Problem Solving, Cambridge University Press, 2010.
37R. 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.
38S. Bradford, F. Coste, M. Van Zaanen.

Progressing the state-of-the-art in grammatical inference by competition, in: AI Communications, 2005, vol. 18, n^o 2, pp. 93-115.
39O. Demeure, F. Lecerf, C. Duby, C. Desert, S. Ducheix, H. Guillou, S. Lagarrigue.

Regulation of LPCAT3 by LXR, in: Gene, Jan 2011, vol. 470, n^o 1-2, pp. 7–11.
40P. Flajolet, R. Sedgewick.

Analytic Combinatorics, Cambridge University Press, 2009.
41M. 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.
42S.-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, n^o 3, pp. 226-236. [ DOI : 10.1093/bioinformatics/17.3.226 ]

http://bioinformatics.oxfordjournals.org/content/17/3/226.abstract
43C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas.

CRISPI: a CRISPR interactive database, in: Bioinformatics, 2009, vol. 25, n^o 24, pp. 3317-3318.
44T. Schaub, S. Thiele.

Metabolic Network Expansion with Answer Set Programming, in: ICLP 2009, LNCS, Springer, 2009, vol. 5649, pp. 312-326.
45D. Searls.

The language of genes, in: Nature, 2002, vol. 420, pp. 211-217.
46D. Searls.

String Variable Grammar: A Logic Grammar Formalism for the Biological Language of DNA, in: Journal of Logic Programming, 1995, vol. 24, n^o 1&2, pp. 73-102.
47S. 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
48T. Tonon, D. Eveillard, S. Prigent, J. Bourdon, P. Potin, C. Boyen, A. Siegel.

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment, in: Omics : a journal of integrative biology, 2011, vol. 15, n^o 12, pp. 883–892.

Previous |

Home