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Estimating probabilistic context-free grammars for proteins using contact map constraints

Witold Dyrka , Mateusz Pyzik , François Coste , Hugo Talibart
PeerJ, 2019, 7, pp.1-35. ⟨10.7717/peerj.6559⟩
Journal articles hal-02400871v1
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Identifying distant homologous viral sequences in metagenomes using protein structure information

Martine Boccara , Mathilde Carpentier , Jacques Chomilier , François Coste , Clovis Galiez et al.
ECCB'14 Workshop on Recent Computational Advances in Metagenomics, Sep 2014, Strasbourg, France
Conference papers hal-01090987v1

Mise à jour incrémentale de tableau des suffxes en cours de recodage

François Coste , Pierre Peterlongo , Matthias Gallé
Algorithmique, combinatoire du texte et applications en bio-informatique, Sep 2007, Chessy, France
Conference papers inria-00186352v1

A bottom-up efficient algorithm learning substitutable languages from positive examples

François Coste , Gaelle Garet , Jacques Nicolas
ICGI (International Conference on Grammatical Inference), Sep 2014, Kyoto, Japan. pp.49--63
Conference papers hal-01080249v1
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A Similar Fragments Merging Approach to Learn Automata on Proteins

François Coste , Goulven Kerbellec
[Research Report] RR-5672, INRIA. 2005, pp.17
Reports inria-00070340v1
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PPalign: optimal alignment of Potts models representing proteins with direct coupling information

Hugo Talibart , François Coste , Mathilde Carpentier
ISMB 2022 - 30th Conference on Intelligent Systems for Molecular Biology, Jul 2022, Madison, United States. pp.1-1
Poster communications hal-03926272v1
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Using residues coevolution to search for protein homologs through alignment of Potts models

Hugo Talibart , François Coste
CECAM 2019 - workshop on Co-evolutionary methods for the prediction and design of protein structure and interactions, CECAM-HQ-EPFL, Jun 2019, Lausanne, Switzerland. pp.1-2
Conference papers hal-02402646v1

Mutually Compatible and Incompatible Merges for the Search of the Smallest Consistent DFA

François Coste , John Abela , Sandro Spina
ICGI 2004: Grammatical Inference: Algorithms and Applications, 2004, Athens, Greece. pp.28-39, ⟨10.1007/978-3-540-30195-0_4⟩
Conference papers istex hal-03405523v1

Choosing Word Occurrences for the Smallest Grammar Problem

Rafael Carrascosa , François Coste , Matthias Gallé , G. Infante-Lopez
LATA, May 2010, Trier, Germany
Conference papers inria-00476840v1
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Learning Automata on Protein Sequences

François Coste , Goulven Kerbellec
JOBIM, Jul 2006, Bordeaux, France. pp.199--210
Conference papers inria-00180429v1
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Amplitude spectrum distance: measuring the global shape divergence of protein fragments

Clovis Galiez , François Coste
BMC Bioinformatics, 2015, 16 (1), pp.16. ⟨10.1186/s12859-015-0693-y⟩
Journal articles hal-01214482v1
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Functional Motif Prediction in ADAMTS-TSL proteins Based on Module(s) and Phenotype(s) Co-appearance

Olivier Dennler , Samuel Blanquart , François Coste , Catherine Belleannée , Nathalie Théret et al.
ALPHY/AIEM 2022 - Rencontres Génomique évolutive, Bioinformatique, Alignement et Phylogénie, Mar 2022, Rennes, France
Poster communications hal-03870590v1
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CyanoLyase: a database of phycobilin lyase sequences, motifs and functions

Anthony Bretaudeau , François Coste , Florian Humily , Laurence Garczarek , Gildas Le Corguillé et al.
Nucleic Acids Research, 2012, pp.6. ⟨10.1093/nar/gks1091⟩
Journal articles hal-01094087v1

VIRALpro: a tool to identify viral capsid and tail sequences

Clovis Galiez , Magnan Christophe , François Coste , Pierre Baldi
Journal articles hal-01242251v1
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Deep learning languages: a key fundamental shift from probabilities to weights?

François Coste
2019
Preprints, Working Papers, ... hal-02235207v1
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A Similar Fragments Merging Approach to Learn Automata on Proteins

François Coste , Goulven Kerbellec
[Research Report] PI 1735, 2005
Reports inria-00000179v1
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A Similar Fragments Merging Approach to Learn Automata on Proteins

François Coste , Goulven Kerbellec
Machine Learning: ECML 2005, 16th European Conference on Machine Learning, 2005, Porto, Portugal. pp.522-529, ⟨10.1007/11564096_50⟩
Conference papers hal-03405434v1
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Structural conservation of remote homologues: better and further in contact fragments

Clovis Galiez , François Coste
3DSIG: Structural Bioinformatics and Computational Biophysics, Jul 2015, Dublin, France
Conference papers hal-01214506v1

Jobim 2012, 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, 3-6 Juillet 2012, Rennes

François Coste , Denis Tagu
François Coste and Denis Tagu. Inria Rennes - Bretagne Atlantique, pp.558, 2012, 13 978-2-7261-1301-1
Books hal-00740287v1
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ComPotts: Optimal alignment of coevolutionary models for protein sequences

Hugo Talibart , François Coste
JOBIM 2020 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier, France. pp.1-8
Conference papers hal-02862213v1
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Problème d'optimisation de recherche de cliques pour caractériser des familles de protéines

François Coste , Goulven Kerbellec
ROADEF 2007, Universités de Grenoble, Feb 2007, Grenoble, France. pp.157--158
Conference papers inria-00180494v1
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What is the Search Space for the Inference of Non Deterministic, Unambiguous and Deterministic Automata ?

François Coste , Daniel Fredouille
[Research Report] RR-4907, INRIA. 2003
Reports inria-00071673v1

Unambiguous Automata Inference by Means of State-Merging Methods

François Coste , Daniel Fredouille
Machine Learning: ECML 2003, 14th European Conference on Machine Learning, 2003, Cavtat-Dubrovnik, Croatia. pp.60-71, ⟨10.1007/978-3-540-39857-8_8⟩
Conference papers hal-03405541v1
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Inférence d'automates classifieurs par fusions d'état

François Coste
[Rapport de recherche] RR-3695, INRIA. 1999
Reports inria-00072974v1

Introducing Domain and Typing Bias in Automata Inference

François Coste , Daniel Fredouille , Christopher Kermorvant , Colin de La Higuera
ICGI 2004: Grammatical Inference: Algorithms and Applications, 2004, Athens, Greece. pp.115-126, ⟨10.1007/978-3-540-30195-0_11⟩
Conference papers istex hal-03405504v1

Bioinformatique

François Coste , Claire Nédellec , Thomas Schiex , Jean-Philippe Vert
Pierre Marquis and Odile Papini and Henri Prade. Panorama de l'intelligence artificielle Ses bases méthodologiques, ses développements, 3, Cépaduès, 374 p., 2014, 9782364930438
Book sections hal-00857379v1
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Le langage des molécules du vivant

Jacques Nicolas , Catherine Belleannée , François Coste
Bibliothèque Tangente, 2014, 52, pp.8
Journal articles hal-01100051v1
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In-place Update of Suffix Array while Recoding Words

Matthias Gallé , Pierre Peterlongo , François Coste
Prague Stringology Conference 2008, Sep 2008, Prague, Czech Republic. pp.54--67
Conference papers inria-00327582v1
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A refined parsing graph approach to learn smaller contextually substitutable grammars with less data

François Coste , Mikail Demirdelen
ICGI 2016 - 13th International Conference on Grammatical Inference, Oct 2016, Delft, Netherlands
Conference papers hal-01406337v1
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How to measure the topological quality of protein grammars?

Witold Dyrka , François Coste , Olgierd Unold , Lukasz Culer , Agnieszka Kaczmarek et al.
ICGI 2016 - 13th International Conference on Grammatical Inference, Oct 2016, Delft, Netherlands
Conference papers hal-01406331v1