Publications

Publications

This page is updated on an irregular basis… browse HAL for new publications

• Predicting enzymatic function of protein sequences with attention, Nicolas Buton, François Coste, Yann Le Cunff Bioinformatics, 2023
• Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family, Olivier Dennler, Samuel Blanquart, Catherine Belleannée, Nathalie Théret. PLOS Computational Biology, 2023
• PPalign: optimal alignment of Potts models representing proteins with direct coupling information
  Hugo Talibart, François Coste
  BMC Bioinformatics (2021)
• ComPotts: Optimal alignment of coevolutionary models for protein sequences
  Hugo Talibart, François Coste
  JOBIM 2020 (video)
• Extracellular vesicles produced by human and animal Staphylococcus aureus strains share a highly conserved core proteome
  Natayme Rocha Tartaglia, Aurélie Nicolas, Vinícius de Rezende Rodovalho, Brenda Silva Rosa da Luz, Valérie Briard-Bion, Zuzana Krupova, Anne Thierry, François Coste, Agnes Burel, Patrice Martin, Julien Jardin, Vasco Azevedo, Yves Le Loir, Eric Guédon
  Scientific Reports, Nature Publishing Group, 2020
• 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. (also presented as a poster at Jobim 2019)
  slides
• Estimating probabilistic context-free grammars for proteins using contact map constraints
  Witold Dyrka, Mateusz Pyzik, François Coste, Hugo Talibart
  PeerJ, 2019.
• Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction
  François Coste, Jacques Nicolas,
  ICGI 2018. (slides)
• How to measure the topological quality of protein parse trees?
  Mateusz Pyzik, François Coste and Witold Dyrka.
  ICGI 2018.
  Extended version of:  How to measure the topological quality of protein grammars? Witold Dyrka, François Coste, Olgierd Unold, Lukasz Culer, Agnieszka Kaczmarek. ICGI 2016.
• Learning the Language of Biological Sequences,
  François Coste.
  In Topics in Grammatical Inference, editors: J. Heinz, J.M. Sempere,  Springer 2016.
• A refined parsing graph approach to learn smaller contextually substitutable grammars with less data
  François Coste, Mikail Demirdelen
  ICGI 2016.
• VIRALpro: a tool to identify viral capsid and tail sequences
  Clovis Galiez, Magnan Christophe, François Coste, Pierre Baldi
  Bioinformatics, 2015
• Structural conservation of remote homologues: better and further in contact fragments
  Clovis Galiez, François Coste
  poster at ISMB/ECCB 2015 – 3DSIG: Structural Bioinformatics and Computational Biophysics
• Amplitude Spectrum Distance: measuring the global shape divergence of protein fragments
  Clovis Galiez, François Coste
  BMC Bioinformatics 2015, 16:256
                Implementation of ASD and supplementary material are available from Clovis’ page
• A bottom-up efficient algorithm learning substitutable languages from positive examples
  François Coste, Gaëlle Garet, Jacques Nicolas
  ICGI 2014
• Identifying distant homologous viral sequences in metagenomes using protein structure information
  Martine Boccara, Mathilde Carpentier, Jacques Chomilier, François Coste, Clovis Galiez, Joel Pothier, Alaguraj Veluchamy
  ECCB’14 Workshop on Recent Computational Advances in Metagenomics
• Automated Enzyme classification by Formal Concept Analysis
  François Coste, Gaëlle Garet, Agnès Groisillier,  Jacques Nicolas  Thierry Tonon
  ICFCA 2014.
  (slides by Gaelle)
• Le langage des molécules du vivant
  Jacques Nicolas, Catherine Belleannée, François Coste
  Bibliothèque Tangente, Editions Pôle Paris, 2014
• Bioinformatique
  François Coste, Claire Nédellec, Thomas Schiex, Jean-Philippe Vert
  In Panorama actuel de l’intelligence artificielle, volume 3: frontières et  applications, editors: P. Marquis, O. Papini, and H. Prade, Cépaduès.
• Learning Context Free Grammars on Proteins by Local Substitutability
  François Coste, Gaelle Garet, Jacques Nicolas
  preprint 2012, first submission of ReGLiS and definition of prime and composite classes.
  
• Local Substitutability for Sequence Generalization
  François Coste, Gaelle Garet, Jacques Nicolas
  ICGI 2012, JMLR Workshop and Conference Proceedings vol 21
• CyanoLyase: a database of phycobilin lyase sequences, motifs and functions
  Anthony Bretaudeau, François Coste, Florian Humily, Laurence Garczarek, Gildas Le Corguillé, Christophe Six, Morgane Ratin, Olivier Collin, Wendy M Schluchter, Frédéric Partensky.
  Nucleic Acids Research, Oxford University Press, 2012
• Searching for Smallest Grammars on Large Sequences and Application to DNA
  Rafael Carrascosa, François Coste, Matthias Gallé, Gabriel Infante-Lopez
  Journal of Discrete Algorithms, vol. 11, February 2012, pp 62-72, (paper online).
• The Smallest Grammar Problem as Constituents Choice and Minimal Grammar Parsing
  Rafael Carrascosa, François Coste, Matthias Gallé, Gabrie Infante-Lopez
  Algorithms, 4 (2011) 262-284
• Modelling Biological Sequences by Grammatical Inference
  François Coste
  ICGI 2010 Tutorial Day
  paper, slides
• Choosing word occurrences for the smallest grammar problem
  Rafael Carrascosa, François Coste, Matthias Gallé and Gabriel Infante-Lopez
  LATA 2010
• In place update of suffix array while recoding words
  Matthias Gallé, Pierre Peterlongo and François Coste
  International Journal of Foundation of Computer Science,  vol. 20, Issue 6, 2009, pp. 1025-1045
  abstract, paper
      extended version of paper presented at PSC 2008 (abstract, paper, slides)
      supplementary material (code, data sets, experiments)I
• Proceedings of Grammatical Inference: Algorithms and Applications, 9th International Colloquium (ICGI 2008)
  Editors: Alexander Clark, François Coste, Laurent Miclet
  Lecture Notes in Artificial Intellligence 5278,  Springer 2008
• In place update of suffix array while recoding words
  Matthias Gallé, Pierre Peterlongo and François Coste
  PSC 2008
  abstract, paper, slides, supplementary material (code, data sets, experiments)
• Special issue “IA et Bioinformatique”,
  François Coste and Christine Froidevaux (Eds.),
  Bulletin de l’AFIA, vol. 63, january 2007
• Problème d’optimisation de recherche de cliques pour caractériser des familles de protéines
  François Coste and Goulven Kerbellec
  ROADEF 2007 (.pdf)
• Learning Automata on Protein Sequences
  François Coste and Goulven Kerbellec
  JOBIM 2006.
  abstract, paper, slides (.pdf)
• A Similar Fragments Merging Approach to Learn Automata on Proteins
  
  François Coste and Goulven Kerbellec
  ECML 2005.
  abstract, paper, extended version, data sets
• Progressing the State-of-the art in Grammatical Inference by Competition
  Brad Starkie, François Coste and Menno van Zaanen,
  AI Communications, vol. 18, no. 2, 2005, pp. 93-115. abstract, paper
• The Omphalos Context-free Grammar Learning Competition.
  Brad Starkie, François Coste and Menno van Zaanen.
  Invited Paper, ICGI 2004. abstract, paper, slides (.ppt)
• Introducing Domain and Typing Bias in Automata Inference
  François Coste, Daniel Fredouille, Christopher Kermorvant and Colin de la Higuera
  ICGI 2004. abstract, paper, slides (.ppt, 2.2MB)
• Mutually compatible and incompatible merges for the search of the smallest consistent DFA
  John Abela, François Coste and Sandro Spina
  ICGI 2004. abstract, paper, slides (.ppt)
• Apprentissage d’automates par fusions de paires de fragments significativement similaires et premières expérimentations sur les protéines MIP
  François Coste, Goulven Kerbellec, Boris Idmont, Daniel Fredouille and Christian Delamarche
  JOBIM’04 paper (.pdf), techn. report (.pdf)
• Unambiguous automata inference by means of state-merging methods. François Coste, Daniel Fredouille
  ECML’03
  paper (.ps.gz), complementary experiments (.ps.gz), benchmarks (.tar.gz), slides (.ppt). Parsing ambiguity!
• What is the Search Space for the Inference of Non Deterministic, Unambiguous and Deterministic Automata ?
  François Coste, Daniel Fredouille
  Techn. Report, RR-4907, 2003
• Introduction de connaissances structurelles et langagières pour l’apprentissage d’automates.
  François Coste, Daniel Fredouille
  CAp’03
   .ps.gz, .pdf
• Inférence d’AFNs: restriction de l’espace de recherche aux automates non ambigus
  François Coste, Daniel Fredouille
  CAp’01
    .ps.gz, .pdf  Parsing ambiguity!
  Efficient ambiguity detection in C-NFA, a step toward inference of non deterministic automata 
  François Coste, Daniel Fredouille
  ICGI 2000, Grammatical inference: algorithms and applications, Lisbonne , 25-38 , september , 2000
  paper (ps.gz)  benchmark (.tar.gz). Classification ambiguity!
• De l’inférence régulière à l’apprentissage d’automates classifieurs pour la discrimination de séquences ,
  François Coste,
  CAp 2000, june , 2000. (.ps.gz)
• State merging inference of finite state classifiers
  François Coste,
  technical report 3695, INRIA/IRISA, May 1999
  abstract, paper (.ps.gz)
• How considering incompatible state mergings may reduce the DFA induction search tree
  François Coste, Jacques Nicolas,
  Fourth International Colloquium on Grammatical Inference (ICGI’98), Ames Iowa, USA, 1998
  abstract, paper (.ps.gz)
• Inference of finite automata: reducing the search space with an ordering of pairs of states
  F.Coste, Jacques Nicolas
  10th European Conference on Machine Learning (ECML’98), Chemnitz, Germany, 1998
  abstract, paper (.ps.gz)
• Regular Inference as a graph coloring problem
  François Coste, Jacques Nicolas
  ICML97, Grammatical Inference Workshop, Nashville TN, USA, 1997
  ps, .ps.gz
• L’inférence grammaticale régulière vue comme un problème de coloriage et propagation de contraintes sur un graphe,
  François Coste, Jacques Nicolas,
  IIIèmes Journées Nationales sur la Résolution Pratique de Problèmes NP-Complets, Rennes, France, 1997
  .ps, .ps.gz
• Inférence de grammaires régulières: caractérisation de l’ensemble des solutions canoniques
  François Coste, Jacques Nicolas
  JFA97, Roscoff, France, 1997. (.ps, .ps.gz)
• Coévolution et émergence de stratégies de coopération
  François Coste
  techn. report, 1994 Laboratoire d’Intelligence Artificielle et Systèmes Cognitifs, France Télécom, Brest, France.

Ph.D. Thesis: