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Jacques Nicolas



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The genomic basis of the Streptococcus thermophilus health-promoting properties

Emeline Roux , Aurélie Nicolas , Florence Valence , Grégoire Siekaniec , Victoria Chuat
BMC Genomics, 2022, 23, pp.1-23. ⟨10.1186/s12864-022-08459-y⟩
Journal articles hal-03612308v1
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Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

Grégoire Siekaniec , Emeline Roux , Téo Lemane , Eric Guédon , Jacques Nicolas
Microbial Genomics, 2021, 7 (11), pp.1-14. ⟨10.1099/mgen.0.000654⟩
Journal articles hal-03444296v1
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Sequencing DNA with nanopores: Troubles and biases

Clara Delahaye , Jacques Nicolas
PLoS ONE, 2021, 16 (10), pp.e0257521. ⟨10.1371/journal.pone.0257521⟩
Journal articles hal-03362956v1
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Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

Arnaud Belcour , Jean Girard , Méziane Aite , Ludovic Delage , Camille Trottier
iScience, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩
Journal articles hal-01943880v2
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Formalizing and enriching phenotype signatures using Boolean networks

Méline Wery , Olivier Dameron , Jacques Nicolas , Elisabeth Rémy , Anne Siegel
Journal of Theoretical Biology, 2019, 467, pp.66-79. ⟨10.1016/j.jtbi.2019.01.015⟩
Journal articles hal-02018724v1
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De Novo Clustering of Long Reads by Gene from Transcriptomics Data

Camille Marchet , Lolita Lecompte , Corinne da Silva , Corinne Cruaud , Jean-Marc Aury
Nucleic Acids Research, In press, pp.1-12. ⟨10.1093/nar/gky834⟩
Journal articles hal-01643156v2
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Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

Julie Laniau , Clémence Frioux , Jacques Nicolas , Caroline Baroukh , Maria-Paz Cortés
PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩
Journal articles hal-01635688v1
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Learning Boolean logic models of signaling networks with ASP

Santiago Videla , Carito Guziolowski , Federica Eduati , Sven Thiele , Martin Gebser
Theoretical Computer Science, 2015, 599, pp.79-101. ⟨10.1016/j.tcs.2014.06.022⟩
Journal articles hal-01058610v1
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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

An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs

Pierre-François Pluchon , Thomas Fouqueau , Christophe Crezé , Sébastien Laurent , Julien Briffotaux
PLoS ONE, 2013, 8 (11), pp.1-15. ⟨10.1371/journal.pone.0079707⟩
Journal articles hal-00911795v1

ModuleOrganizer: detecting modules in families of transposable elements.

Sebastien Tempel , Christine Rousseau , Fariza Tahi , Jacques Nicolas
BMC Bioinformatics, 2010, 11, pp.474. ⟨10.1186/1471-2105-11-474⟩
Journal articles inria-00536742v1

Décoder le vivant

Jacques Nicolas
Interstices, 2010
Journal articles hal-01350190v1
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Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum.

Fabrice Legeai , Guillaume Rizk , Thomas Walsh , Owain Edwards , Karl Gordon
BMC Genomics, 2010, 11 (1), pp.281. ⟨10.1186/1471-2164-11-281⟩
Journal articles inserm-00482283v1

Introduction Special Theme Computational Biology

Klau Gunnar , Jacques Nicolas
ERCIM News, 2010, Special Theme Computational Biology, 82
Journal articles inria-00537580v1

Décoder le vivant

Jacques Nicolas
DocSciences, 2009, Le numérique et les sciences du vivant, 8, pp.26-33
Journal articles inria-00438517v1
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CRISPI: a CRISPR Interactive database

Christine Rousseau , Mathieu Gonnet , Marc Le Romancer , Jacques Nicolas
Bioinformatics, 2009, 25 (24), pp.3317-3318. ⟨10.1093/bioinformatics/btp586⟩
Journal articles inria-00438512v1

Symbiotic Virus at the Evolutionary Intersection of Three Types of Large DNA Viruses; Iridoviruses, Ascoviruses, and Ichnoviruses

Yves Bigot , Sylvaine Renault , Jacques Nicolas , Corinne Moundras , Marie-Véronique Demattei
PLoS ONE, 2009, 4 (7), pp.e6397. ⟨10.1371/journal.pone.0006397⟩
Journal articles inria-00448730v1
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Model-based Identification of Helitrons Results in a New Classification of Their Families in Arabidopsis thaliana

Sébastien Tempel , Jacques Nicolas , Abdelhak El Amrani , Ivan Couée
Gene, 2007, 403 (1-2), ⟨10.1016/j.gene.2007.06.030⟩
Journal articles inria-00180376v1

Browsing repeats in genomes : Pygram and an application to non-coding region analysis.

Patrick Durand , Frédéric Mahé , Anne-Sophie Valin , Jacques Nicolas
BMC Bioinformatics, 2006, 7, pp.477. ⟨10.1186/1471-2105-7-477⟩
Journal articles hal-00129773v1

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.

Sébastien Tempel , Mathieu Giraud , Dominique Lavenier , Israël-César C. Lerman , Anne-Sophie Valin
Bioinformatics, 2006, 22(16), pp.1948-1954
Journal articles hal-00090517v1

Suffix-Tree Analyser (STAN): looking for nucleotidic and peptidic patterns in genomes

Jacques Nicolas , Patrick Durand , Grégory Ranchy , Sébastien Tempel , Anne-Sophie Valin
Bioinformatics, 2005, 21(24), pp.4408-4410
Journal articles hal-00015234v1

The dog and rat olfactory receptor repertoires

Pascale Quignon , Mathieu Giraud , Maud Rimbault , Patricia Lavigne , Sandrine Tacher
Genome Biology, 2005, 6 (10), pp.R83. ⟨10.1186/gb-2005-6-10-r83⟩
Journal articles hal-00107100v1
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Twelve numerical, symbolic and hybrid supervised classification methods

Olivier Gascuel , Bernadette Bouchon-Meunier , Gilles Caraux , Patrick Gallinari , Alain Guénoche
International Journal of Pattern Recognition and Artificial Intelligence, 1998, 12 (5), pp.517-572. ⟨10.1142/S0218001498000336⟩
Journal articles hal-01184805v1
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Concept Lattices as a Search Space for Graph Compression

Lucas Bourneuf , Jacques Nicolas
ICFCA 2019 - 15th International Conference on Formal Concept Analysis, Jun 2019, Francfort, Germany. pp.274-289, ⟨10.1007/978-3-030-21462-3_18⟩
Conference papers hal-02399578v1
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Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction

François Coste , Jacques Nicolas
ICGI 2018 - 14th International Conference on Grammatical Inference, Sep 2018, Wrocław, Poland. pp.155 - 168
Conference papers hal-01872266v1
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FCA in a Logical Programming Setting for Visualization-oriented Graph Compression

Lucas Bourneuf , Jacques Nicolas
International Conference on Formal Concept Analysis 2017, Jun 2017, Rennes, France. ⟨10.1007/978-3-319-59271-8_6⟩
Conference papers hal-01558302v1
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Packing graphs with ASP for landscape simulation

Thomas Guyet , Yves Moinard , Jacques Nicolas , René Quiniou
IJCAI 2016 - 25th International joint conference on artificial intelligence , Jul 2016, New-york, United States. pp.8
Conference papers hal-01327368v1
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From formal concepts to analogical complexes

Laurent Miclet , Jacques Nicolas
CLA 2015, LIMOS, CNRS et Université Blaise Pascal, Oct 2015, Clermont-Ferrand, France. pp.12
Conference papers hal-01198943v1
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Comparaison des cibles d’une matrice de score et d’une expression régulière. Application à la recherche de sites de fixation du facteur de transcription LXR

Aymeric Antoine-Lorquin , Sandrine Lagarrigue , Frédéric Lecerf , Jacques Nicolas , Catherine Belleannée
JOBIM 2015- 16e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France
Conference papers hal-01197050v1
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Automated Enzyme classification by Formal Concept Analysis

François Coste , Gaëlle Garet , Agnès Groisillier , Jacques Nicolas , Thierry Tonon
ICFCA - 12th International Conference on Formal Concept Analysis, Jun 2014, Cluj-Napoca, Romania
Conference papers hal-01063727v1

Integration of miRNAs data into a gene network of the pea aphid.

Valentin Wucher , Jacques Nicolas , Fabrice F. Legeai , Hervé Seitz , Denis Tagu
7th International Symposium on Molecular Insect Science., 2014, Amsterdam, Netherlands
Conference papers hal-01566284v1
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Computational Protein Design: trying an Answer Set Programming approach to solve the problem

Hugo Bazille , Jacques Nicolas
10th Workshop on Constraint-Based Methods for Bioinformatics (WCB'14), Nicos Angelopoulos (Imperial College, UK) Simon de Givry (MIAT-INRA, France), Sep 2014, Lyon, France
Conference papers hal-01063030v1
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Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling

Catherine Belleannée , Olivier Sallou , Jacques Nicolas
PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Lukas KALL, Aug 2014, Stockholm, Sweden. pp.34-47, ⟨10.1007/978-3-319-09192-1_4⟩
Conference papers hal-01059506v1

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

Edge Selection in a Noisy Graph by Concept Analysis: Application to a Genomic Network

Valentin Wucher , Denis Tagu , Jacques Nicolas
ECDA - European Conference on Data Analysis - 2013, Jul 2013, Luxembourg, Luxembourg
Conference papers hal-00924413v1

Local Substitutability for Sequence Generalization

François Coste , Gaelle Garet , Jacques Nicolas
ICGI 2012, University of Maryland, Sep 2012, Washington, United States. pp.97-111
Conference papers hal-00730553v1
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Recherche d'instances de motifs expressifs avec Logol. Application à la modélisation d'événements de frameshift -1

Catherine Belleannée , Olivier Sallou , Jacques Nicolas
JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.5-14
Conference papers hal-00726791v1
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Identification rapide de familles protéiques par dominance

Mathilde Le Boudic-Jamin , Noël Malod-Dognin , Alexandre Cornu , Jacques Nicolas , Rumen Andonov
12th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF), École Nationale Supérieure des Mines de Saint-Étienne, Mar 2011, Saint-Étienne, France. pp.791-792
Conference papers inria-00611457v1

Prediction and analyzes of non coding RNA sequences in the pea aphid genome

Fabrice Legeai , Guillaume Rizk , T. Walsh , Owain Edwards , Jacques Nicolas
Arthropods Genomics, Jun 2010, Kansas City, United States
Conference papers inria-00537927v1
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SHREC'10 Track: Protein Models

Lazaros Mavridis , Vishwesh Venkatraman , David Ritchie , Naoto Morikawa , Rumen Andonov
Eurographics Workshop on 3D Object Retrieval - 3DOR 2010, May 2010, Norrköping, Sweden
Conference papers inria-00536680v1

Identification and characterization of novel anti-infectious peptides from the male genital tract.

Frédéric Bourgeon , Jacques Nicolas , Nathalie Melaine , Charles Pineau
34th Federation of European Biochemical Societies (FEBS) Congress, Jul 2009, Prague, Czech Republic
Conference papers hal-00667141v1

From AphidBase and Lepido-DB to an Information System for Insect Plant pest genomics studies.

Fabrice Legeai , Jean-Pierre Gauthier , François Cousserans , Emmanuelle d'Alençon , Olivier Collin
1st Workshop on Information System for Insect Pest, Nov 2009, Rennes, France
Conference papers inria-00435823v1
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c-GAMMA: Comparative Genome Analysis of Molecular Markers

Pierre Peterlongo , Jacques Nicolas , Dominique Lavenier , Raoul Vorc'H , Joël Querellou
Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. pp.255-269, ⟨10.1007/978-3-642-04031-3_23⟩
Conference papers inria-00425373v1
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Détection de domaines dans des séquences génomiques : un problème de couverture optimale

Philippe Veber , Sébastien Tempel , Rumen Andonov , Dominique Lavenier , Jacques Nicolas
FRANCORO V/ROADEF 2007, Feb 2007, Grenoble, France
Conference papers hal-00186471v1

Organisation modulaire des séquences d'ADN répétées: application à l'étude des hélitrons non-autonomes dans le génome d'Arabidopsis thaliana

Sébastien Tempel , Mathieu Giraud , Israël-César C. Lerman , Ivan Couée , Abdelhak El Amrani
XIIIe colloque Eléments Transposables, 2005, Orsay, France
Conference papers hal-00015261v1
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The genomic basis of the Streptococcus thermophilus health-promoting properties

Emeline Roux , Aurélie Nicolas , Florence Valence , Grégoire Siekaniec , Victoria Chuat
JOBIM 2022 - Les journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. , pp.1-1, 2022
Conference poster hal-03717986v1
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Storing the declaration of human rights on one data DNA molecule

Gouenou Coatrieux , Chloé Berton , Elsa Dupraz , Belaid Hamoum , Thomas Derrien
CominLabs day 2022, Oct 2022, Rennes, France. pp.1-1
Conference poster hal-03817852v1

Identification of bacterial strains using ORI (Oxford nanopore Reads Identification)

Grégoire Siekaniec , Rania Ouazahrou , Gaëlle Boudry , Eric Guédon , Emeline Roux
Microbes 2021 - Société Française de Microbiologie, Sep 2021, Nantes, France
Conference poster hal-03374572v1
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Bacterial strains identification using Oxford Nanopore sequencing

Grégoire Siekaniec , Emeline Roux , Eric Guédon , Jacques Nicolas
JOBIM2020, Jun 2020, Montpellier, France
Conference poster hal-03121440v1
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Topological and semantic Web based method for analyzing TGF-β signaling pathways

Jean Coquet , Geoffroy Andrieux , Jacques Nicolas , Olivier Dameron , Nathalie Théret
JOBIM 2015, Dec 2015, Clermont-Ferrand, France. JOBIM : Journées Ouvertes en Biologie, Informatique & Mathématiques, 2015
Conference poster hal-01242893v1

Searching for Optimal Orders for Discretized Distance Geometry

Douglas Gonçalves , Jacques Nicolas , Antonio Mucherino
Proceedings of Many Faces of Distances (MDF14), Oct 2014, Campinas, São Paulo, Brazil. 2014
Conference poster hal-01093072v1
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IA et bioinformatique

Jacques Nicolas
Sébastien Konieczny; Henri Prade. L’intelligence artificielle: De quoi s’agit-il vraiment ?, Cépaduès, pp.101, 2020, 9782364938502
Book sections hal-03127545v1
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Artificial Intelligence and Bioinformatics

Jacques Nicolas
Marquis, P., Papini, O., Prade, H. A Guided Tour of Artificial Intelligence Research, III, Springer, pp.575, 2020, Interfaces and Applications of Artificial Intelligence, 978-3-030-06169-2
Book sections hal-01850570v2
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Finding and Characterizing Repeats in Plant Genomes

Jacques Nicolas , Pierre Peterlongo , Sébastien Tempel
David Edwards. Plant Bioinformatics: Methods and Protocols, 1374, Humana Press - Springer Science+Business Media, pp.365, 2015, Methods in Molecular Biology, 978-1-4939-3166-8. ⟨10.1007/978-1-4939-3167-5_17⟩
Book sections hal-01228488v1

Finding Optimal Discretization Orders for Molecular Distance Geometry by Answer Set Programming

Douglas S. Gonçalves , Jacques Nicolas , Antonio Mucherino , Carlile Lavor
S. Fidanova. Studies in Computational Intelligence, 610, Springer, pp.1-15, 2015, Recent Advances in Computational Optimization
Book sections hal-01196714v1

Edge Selection in a Noisy Graph by Concept Analysis – Application to a Genomic Network

Valentin Wucher , Denis Tagu , Jacques Nicolas
Lausen, Berthold; Krolak-Schwerdt, Sabine; Böhmer, Matthias. Data Science, Learning by Latent Structures, and Knowledge Discovery, Springer, pp.550, 2014, Data Science, Learning by Latent Structures, and Knowledge Discovery, 978-3-662-44982-0. ⟨10.1007/978-3-662-44983-7_31⟩
Book sections hal-01093337v1
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To detect and analyze sequence repeats whatever be their origin

Jacques Nicolas
Yves Bigot. Mobile genetic elements : protocols and genomic applications, 859, Springer, pp.69-90, 2012, Springer Protocols, 978-1-61779-602-9. ⟨10.1007/978-1-61779-603-6⟩
Book sections hal-00730207v1
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Syntaxe, raisonnement et génomes

Jacques Nicolas
Sciences du Vivant [q-bio]. Université Rennes 1, 2008
Habilitation à diriger des recherches tel-00355156v1