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, e1002157 p. [ DOI : 10.1371/journal.pcbi.1002157 ]

http://hal.archives-ouvertes.fr/hal-00626708
3S. 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, p. 93-115.
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, p. 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
7J. 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, p. 4408-4410.

http://hal.archives-ouvertes.fr/hal-00015234
8A. Siegel, O. Radulescu, M. Le Borgne, P. Veber, J. Ouy, S. Lagarrigue.

Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks, in: Biosystems, 2006, vol. 84, p. 153-174.

http://hal.inria.fr/inria-00178809
9S. 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

Publications of the year

Articles in International Peer-Reviewed Journals

10G. Andrieux, N. Theret, M. Le Borgne, L. Fattet, R. Rimokh.

Dynamic Regulation of Tgf-B Signaling by Tif1 $γ$ : A Computational Approach, in: PLoS ONE, March 2012.

http://hal.inria.fr/hal-00760066
11V. Berthé, T. Jolivet, A. Siegel.

Substitutive Arnoux-Rauzy sequences have pure discrete spectrum, in: Uniform Distribution Theory, 2012, vol. 7, n^o 1, p. 173-197.

http://hal.inria.fr/hal-00750209
12N. J. Bouskill, D. Eveillard, D. Chien, A. Jayakumar, B. B. Ward.

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments., in: Environmental Microbiology, March 2012, vol. 14, n^o 3, p. 714-29. [ DOI : 10.1111/j.1462-2920.2011.02623.x ]

http://hal.inria.fr/hal-00661746
13A. 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, p. D396-D401. [ DOI : 10.1093/nar/gks1091 ]

http://hal.inria.fr/hal-00760946
14R. Carrascosa, F. Coste, M. Gallé, G. Infante-Lopez.

Searching for Smallest Grammars on Large Sequences and Application to DNA, in: Journal of Discrete Algorithms, February 2012, vol. 11, p. 62-72. [ DOI : 10.1016/j.jda.2011.04.006 ]

http://hal.inria.fr/inria-00536633
15R. A. Long, D. Eveillard, S. L. M. Franco, E. Reeves, J. L. Pinckney.

Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats., in: FEMS Microbiology Ecology, August 2012, vol. 83, p. 74-81. [ DOI : 10.1111/j.1574-6941.2012.01457.x ]

http://hal.inria.fr/hal-00752749

International Conferences with Proceedings

16F. Coste, G. Garet, J. Nicolas.

Local Substitutability for Sequence Generalization, in: ICGI 2012, Washington, United States, J. Heinz, C. de la Higuera, T. Oates (editors), JMLR Workshop and Conference Proceedings, MIT Press, September 2012, vol. 21, p. 97-111.

http://hal.inria.fr/hal-00730553
17L. Miclet, N. Barbot, B. Jeudy.

A Lattice of Sets of Alignments Built on the Common Subword in a Finite Language, in: International Conference on Grammatical Inference, United States, 2012, vol. 21, p. 164-176.

http://hal.inria.fr/hal-00726166
18L. Miclet, N. Barbot, B. Jeudy.

Analogical proportions in a lattice of sets of alignments built on the common subwords in a finite language, in: 1st International Workshop on Similarity and Analogy-based methods in AI (SAMAI), Montpellier, France, G. Richard (editor), August 2012, vol. Rapport interne IRIT/RR-2012-20-FR, p. 25-31.

http://hal.inria.fr/hal-00760722

National Conferences with Proceeding

20A. Aravena, C. Guziolowski, A. Siegel, A. Maass.

Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network, in: JOBIM 2012, 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Rennes, France, July 2012, 171 p.

http://hal.inria.fr/hal-00740722
21C. Belleannée, O. Sallou, J. Nicolas.

Expressive Pattern Matching with Logol. Application to the Modelling of -1 Ribosomal Frameshift events, in: JOBIM 2012, 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Rennes, France, July 2012, p. 5-14.

http://hal.inria.fr/hal-00726791
22P. Blavy, F. Gondret, S. Lagarrigue, J. Van Milgen, A. Siegel.

Using large scale knowledge database about reactions and regulations to find key regulators of sets of genes, in: JOBIM 2012, 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Rennes, France, F. Coste, D. Tagu (editors), Inria Rennes Bretagne Atlantique, 2012, p. 123-132.

http://hal.inria.fr/hal-00750512

Conferences without Proceedings

23T. Tonon, P. Bonin, S. Prigent, Z. Shao, A. Groisillier, S. Rousvoal, S. Goulitquer, J. Bourdon, D. Eveillard, C. Boyen, A. Siegel.

Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology, in: Esil 2012: algal post-genomics, Roscoff, France, April 2012.

http://hal.inria.fr/hal-00760640

Scientific Books (or Scientific Book chapters)

24J. Nicolas.

To detect and analyze sequence repeats whatever be their origin, in: Mobile genetic elements: protocols and genomic applications, Y. Bigot (editor), Springer Protocols, Springer, February 2012, vol. 859, p. 69-90. [ DOI : 10.1007/978-1-61779-603-6 ]

http://hal.inria.fr/hal-00730207

Books or Proceedings Editing

25F. Coste, D. Tagu (editors)

JOBIM 2012, 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, 3-6 Juillet 2012, Rennes, Inria Rennes - Bretagne Atlantique, June 2012, 558 p.

http://hal.inria.fr/hal-00740287

Internal Reports

26A. Rocheteau, C. Belleannée.

Recherche d'éléments structurés dans les génomes par modèles logiques, Inria, June 2012, n^o PI-1994, 30 p.

http://hal.inria.fr/hal-00684388

References in notes

27C. Baral.

Knowledge Representation, Reasoning and Declarative Problem Solving, Cambridge University Press, 2010.
28J. Bourdon.

Sources probabilistes: des séquences aux systèmes, Université de Nantes, Nantes, December 2012, 115 pages, Document dH́abilitation à Diriger des Recherches.
29P. Flajolet, R. Sedgewick.

Analytic Combinatorics, Cambridge University Press, 2009.
30M. 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.
31S.-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, p. 226-236. [ DOI : 10.1093/bioinformatics/17.3.226 ]

http://bioinformatics.oxfordjournals.org/content/17/3/226.abstract
32T. Schaub, S. Thiele.

Metabolic Network Expansion with Answer Set Programming, in: ICLP 2009, LNCS, Springer, 2009, vol. 5649, p. 312-326.
33D. Searls.

The language of genes, in: Nature, 2002, vol. 420, p. 211-217.
34D. 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, p. 73-102.

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