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VirHunter: a deep learning-based method for detection of novel viruses in plant sequencing data

Grigorii Sukhorukov , Macha Nikolski
PlantGen 2021, Jun 2021, Novosibirsk, Russia
Conference poster hal-03271424v1
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Approximation Hardness of the Cross-Species Conserved Active Modules Detection Problem

Thomas Hume , Hayssam Soueidan , Macha Nikolski , Guillaume Blin
41st International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM'15), Jan 2015, Pec pod Sněžkou, Czech Republic. pp. 242-253
Conference papers hal-01056406v1

An introduction to metabolic networks and their structural analysis.

Vincent Lacroix , Ludovic Cottret , Patricia Thebault , Marie-France Sagot
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008, 5 (4), pp.594-617. ⟨10.1109/TCBB.2008.79⟩
Journal articles hal-00355497v1

Microbiomes and Holobionts

Derek Skillings , Katarzyna B Hooks
Reference Module in Earth Systems and Environmental Sciences, 2018
Book sections hal-01893113v1
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Genome-Wide Reconstitution of Chromatin Transactions: RSC Preferentially disrupts H2A.Z-Containing Nucleosomes

Aylin Cakiroglu , Cédric Clapier , Andreas H Ehrensberger , Elodie Darbo , Bradley R Cairns , et al.
2018
Preprints, Working Papers, ... hal-01884309v1
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Emergence of Atypical Mycoplasma agalactiae Strains Harboring a New Prophage and Associated with an Alpine Wild Ungulate Mortality Episode

Florence Tardy , Eric Baranowski , Laurent-Xavier Nouvel , Virginie Mick , Lucia Manso-Silvan , et al.
Applied and Environmental Microbiology, 2012, 78 (13), pp.4659-4668. ⟨10.1128/AEM.00332-12⟩
Journal articles hal-00939842v1

Further Steps in TANGO: improved taxonomic assignment in metagenomics

Macha Nikolski , Daniel Alonso-Alemany , Aurélien Barré , Stefano Beretta , Paola Bonizzoni , et al.
Bioinformatics, 2013, pp.10.1093/bioinformatics/btt256. ⟨10.1093/bioinformatics/btt256⟩
Journal articles hal-00848263v1

MolliGen 3.0, evolution of a database dedicated to the comparative genomics of mollicutes

Aurélien Barré , Claire Lemaitre , Patricia Thebault , Antoine de Daruvar , Alain Blanchard , et al.
Congress of the International Organization for Mycoplasmology ; 2010/07/11-16 ; Chianciano Terme (ITA). IOM congress 2010., 2010, Italy
Conference papers hal-00649151v1
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Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study

Thomas Bazin , Katarzyna B Hooks , Thomas Barnetche , Marie-Elise Truchetet , Raphaël Enaud , et al.
Scientific Reports, 2018, 8 (1), pp.5446. ⟨10.1038/s41598-018-23571-4⟩
Journal articles hal-01760163v1

CBIB/MaBioVis : noeud Bordelais de GRISBI

Tiphaine Martin
BIOinformatique à GRAnde échelLE - BIOGRALE 2008, Christophe CARON and Olivier COLLIN and Antoine de DARUVAR and Gael EVEN and Hugues LEROY and Tiphaine MARTIN and Claudine MEDIGUE and Frédéric PLEWNIAK and Bruno SPATARO and Christophe BLANCHET, Nov 2008, Lyon, France
Conference papers inria-00614465v1
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A community effort to create standards for evaluating tumor subclonal reconstruction

Adriana Salcedo , Maxime Tarabichi , Shadrielle Melijah G. Espiritu , Amit Deshwar , Matei David , et al.
Nature Biotechnology, 2020, 38 (1), pp.97-107. ⟨10.1038/s41587-019-0364-z⟩
Journal articles hal-02438695v1
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Genome Sequences of Two Tunisian Field Strains of Avian Mycoplasma, M. meleagridis and M. gallinarum

Elhem Yacoub , Pascal Sirand-Pugnet , Aurélien Barré , Alain Blanchard , Christophe Hubert , et al.
Genome Announcements, 2016, 4 (3), pp.e00558-16. ⟨10.1128/genomeA.00558-16⟩
Journal articles pasteur-02015202v1

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model

Mohammed El-Kebir , Hayssam Soueidan , Thomas Hume , Daniela Beisser , Marcus Dittrich , et al.
Bioinformatics, 2015, 31 (19), ⟨10.1093/bioinformatics/btv316⟩
Journal articles hal-01248545v1

Insights into genome plasticity of the wine-making bacterium Oenococcus oeni strain ATCC BAA-1163 by decryption of its whole genome.

Elisabeth Bon , Cosette Granvalet , Fabienne Remize , Diliana Dimova , Patrick Lucas , et al.
9th Symposium on Lactic Acid Bacteria, Sep 2008, Egmond aan Zee, Netherlands. pp.A047
Conference papers inria-00340073v1
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Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi , Shuo Liu , A. Cornille , David Tricon , Quynh Trang Bui , et al.
Nature Communications, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩
Journal articles hal-03282504v1

Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Reza Salek , Steffen Neumann , Daniel Schober , Jan Hummel , Kenny Billiau , et al.
Metabolomics, 2015, 11 (6), pp.1598-1599. ⟨10.1007/s11306-015-0822-7⟩
Journal articles hal-02630736v1

Complete genome sequence of Mycoplasma mycoides subsp. mycoides T1/44, vaccine strain against contagious bovine pleuropneumonia

Géraldine Gourgues , Aurélien Barré , Emmanuel Beaudoing , Johann Weber , Ghislaine Magdelenat , et al.
IOM 2016 - 21. Congress of the International Organization for Mycoplasmology, Jul 2016, Brisbane, Australia. 2016
Conference poster hal-02743313v1
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Développement d'outils informatiques pour le traitement et l'analyse des données en RMN-1H, dans un contexte d'expériences métabolomiques

Daniel Jacob , Catherine C. Deborde , Stéphane Bernillon , Annick Moing
5. Journées scientifiques du Réseau Français de Métabolomique et Fluxomique, Labo/service de l'auteur, Ville service., May 2011, Paris, France
Conference papers hal-02747402v1

Changing paradigm on the evolution of Mycoplasmas by exploring their pan-genome.

Christine Citti , Xavier X. Nouvel , Emilie Dordet-Frisoni , Marc Serge Marenda , Florence Tardy , et al.
112th General meeting of American society for Microbiology (ASM), Jun 2012, San Franscisco, United States
Conference papers hal-02933364v1

Proteomic analysis during ontogenesis of secondary xylem in maritime pine

Marcelo Arnoldo Garces , Grégoire G. Le Provost , Céline C. Lalanne , Stéphane Claverol , Aurélien Barré , et al.
Tree Physiology, 2014, 34 (11), pp.1263-1277. ⟨10.1093/treephys/tpt117⟩
Journal articles hal-02632854v1
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Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats

Virginie Dupuy , Pascal Sirand-Pugnet , Eric Baranowski , Aurélien Barré , Marc Breton , et al.
Genome Announcements, 2013, 1 (3), pp.e00354-13. ⟨10.1128/genomeA.00354-13⟩
Journal articles hal-00907450v1
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Bioinformatics methods for analyzing anti-hormonal treatment resistance in breast cancer

Justine Rudewicz , Hayssam Soueidan , Audrey Gros , Gaetan Macgrogan , Hervé Bonnefoi , et al.
BCBB 2014 (Bordeaux Computational Biology and Bioinformatics), Nov 2014, Bordeaux, France
Conference poster hal-01120049v1
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A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships

Claire Lemaitre , Aurélien Barré , Christine Citti , Florence Tardy , François Thiaucourt , et al.
BMC Bioinformatics, 2011, 12 (1), pp.457. ⟨10.1186/1471-2105-12-457⟩
Journal articles hal-00784414v1
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VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data

Grigorii Sukhorukov , Maryam Khalili , Olivier Gascuel , Thierry Candresse , Armelle Marais , et al.
Frontiers in Bioinformatics, 2022, 2, pp.867111. ⟨10.3389/fbinf.2022.867111⟩
Journal articles hal-03671482v1

OENOCOCCUS OENI (alias Leuconostoc oenos) UNE BACTERIE LACTIQUE DU VIN. QUE NOUS APPORTE LE SEQUENCAGE DE SON GENOME?

Elisabeth Bon , Patrick Lucas , Antoine de Daruvar , Aline Lonvaud-Funel
Rencontres Annuelles de l'ISVV, Institut des Sciences de la Vigne et du Vin (ISVV). Villenave d'Ornon, FRA., Jun 2008, Bordeaux, France
Conference papers inria-00407904v1

Genetic markers for characterisation of the adaptability of oenococcus to wine

Arnaud Delaherche , Emmanuel Gindreau , Elisabeth Bon , Aline Lonvaud-Funel
8th International Symposium on Lactic Acid Bacteria (LAB8), Aug 2005, Egmond aan Zee, Netherlands
Conference papers inria-00395779v1

Présentation des Centres Bioinformatiques Régionaux : RENABI-GO

Tiphaine Martin , Christophe C. Caron , Olivier Collin
Journées GRISBI 2011 : scientifiques et technologique, Christophe Blanchet and Christophe Caron and Olivier Collin and Stéphane Delmotte and Clément Gauthey and Tiphaine Martin and Franck Samson and Bruno Spataro, May 2011, Lyon, France
Conference papers inria-00614475v1

MICADo - Looking for mutations in targeted PacBio cancer data: an alignment-free method

Justine Rudewicz , Hayssam Soueidan , Raluca Uricaru , Hervé Bonnefoi , Richard Iggo , et al.
Frontiers in Genetics, 2016, ⟨10.3389/fgene.2016.00214⟩
Journal articles hal-01409750v1
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Dysbiosis and Its Discontents

Katarzyna B Hooks , Maureen A O'Malley
mBio, 2017, 8 (5), pp. e01492-17. ⟨10.1128/mBio.01492-17⟩
Journal articles hal-01677295v1

Using transcriptome analysis to identify osmotic stress candidate genes in maritime pine (Pinus pinaster Ait.)

Jean-Marc Frigerio , Christian Dubos , Philippe Chaumeil , Franck F. Salin , V. Garcia , et al.
Sustainable Forestry, Wood products and Biotechnology, BIOFOR 02, Nov 2002, Vitoria-Gasteiz, Spain
Conference papers hal-02764394v1