Guillaume GAUTREAU

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Documents

Publications

Publications

What can genomics learn from natural language processing?

Guillaume Gautreau

Doctoral. Cité internationale universitaire de Paris, France. 2025

Cours hal-05401386v1
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Bridging Gene-level And Sequence-level Pangenome Graph To Explore Microbial Diversity

Hanin Ali , Bastien Degardins , Charles Paperman , Camille Marchet , Guillaume Gautreau

Journées Ouvertes de Biologie, Informatique et Mathématiques 2024, Jul 2025, Bordeaux, France. https://jobim2025.labri.fr/JOBIM2025_proceedings_posters.pdf

Poster de conférence hal-05176404v1
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To the species level and beyond A rationalized approach to study pangenomes

Emeline Bruyère , Romane Junker , Sandra Dérozier , Hélène Chiapello , Guillaume Gautreau

Journées Ouvertes de Biologie, Informatique et Mathématiques 2024, Jun 2024, Toulouse, France. , Nextcloud, https://nextcloud.inrae.fr/s/An986qpn6CqCQek

Poster de conférence hal-04673896v1
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CroCoDeEL : accurate detection of cross-sample contamination in metagenomic data

Lindsay Goulet , Florian Plaza Oñate , Pauline Barbet , Edi Prifti , Eugeni Belda et al.

10th International Human Microbiome Consortium Congress, Jun 2024, Rome, Italy.

Poster de conférence hal-04634008v1
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Towards a machine learning approach for automated detection of well-to-well contamination in metagenomic data

Lindsay Goulet , Florian Plaza Oñate , Edi Prifti , Eugeni Belda , Emmanuelle Le Chatelier et al.

31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology ( ECCB/ISMB 2023 ), Jul 2023, Lyon, France

Poster de conférence hal-04177345v1
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Towards a machine learning approach for automated detection of well-to-well contamination in metagenomics data

Lindsay Goulet , Florian Plaza Oñate , Edi Prifti , Eugeni Belda , Emmanuelle Le Chatelier et al.

Congrès Junior Pluridisciplinaire 2023, Jun 2023, Gif-sur-Yvette, France

Poster de conférence hal-04179293v1
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Extensive benchmark of machine learning methods for quantitative microbiome data

Sébastien Fromentin , Florian Plaza Oñate , Nicolas Maziers , Samar Berreira Ibraim , Guillaume Gautreau et al.

JOBIM, Jul 2021, Paris, France

Poster de conférence hal-04163473v1

PanGBank: exploring GenBank genomes through a resource of pangenome graphs

Paul Amours , Adelme Bazin , Guillaume Gautreau , Mathieu Dubois , Laura Burlot et al.

JOBIM 2020 Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier (virtual), France

Poster de conférence hal-04360000v1

PanGBank: depicting microbial species diversity via PPanGGOLiN

Guillaume Gautreau , Adelme Bazin , Rémi Planel , Mathieu Gachet , Mathieu Dubois et al.

JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France

Poster de conférence hal-04358380v1
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Comparative microbial pangenomics to explore mobilome dynamics

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , Alexandra Calteau , David Vallenet

JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France

Poster de conférence hal-04358338v1
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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Mylène Beuvin , Laura Burlot et al.

JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France

Poster de conférence hal-04358357v1

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Aurélie Lajus , David Roche et al.

International symposium on environmental and agronomical genomics, Nov 2018, Paris, France

Poster de conférence hal-04357657v1
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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

Claudine Médigue , Alexandra Calteau , Stéphane Cruveiller , Mathieu Gachet , Guillaume Gautreau et al.

JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France

Poster de conférence hal-04356218v1
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SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Guillaume Gautreau , David Pejoski , Roger Le Grand , Antonio Cosma , Anne-Sophie Beignon et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2016, Jun 2016, Lyon, France. ⟨10.7490/f1000research.1112446.1⟩

Poster de conférence hal-04862508v1
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Genome assembly using Nanopore-guided Long and Error-free DNA reads

Guillaume Gautreau , Mohammed‐amin Madoui , Stefan Engelen , Adriana A. Alberti , Caroline Belser et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques 2015, Jul 2015, Clermont-Ferrand, France

Poster de conférence hal-04862540v1

What genomics can learn from Natural Language Processing?

Guillaume Gautreau

iabioscripting : Utilisation des IA génératives comme appui à la programmation et au scripting pour la biologie, Réseau MERIT; l’Institut Français de Bioinformatique (IFB); Université Paris Cité (iPOP-UP et DU omiques), Jun 2025, Paris, France

Communication dans un congrès hal-05119255v1
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Feedback from Evo

Perinelle Naïa , Thomas Lacroix , Hélène Chiapello , Guillaume Kon Kam King , Arnaud Ferré et al.

GT LEGO - Journées du GDR BIMMM, GDR BIMMM, Nov 2025, Nantes, France

Communication dans un congrès hal-05388811v1

Histoire de la pangénomique procaryote

Guillaume Gautreau

Journées BioinfOmics, BioinfOmics, Dec 2024, Toulouse, France

Communication dans un congrès hal-04822722v1
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Integrating complex pangenome graphs

Jérôme Arnoux , Angela Bonifati , A. Calteau , Stefania Dumbrava , Guillaume Gautreau

2024 IEEE 40th International Conference on Data Engineering Workshops (ICDEW), May 2024, Utrecht, New Zealand. pp.350-354, ⟨10.1109/ICDEW61823.2024.00052⟩

Communication dans un congrès hal-04660364v1

CroCoDeEL: accurate detection of cross-sample contaminations in metagenomic data

Lindsay Goulet , Florian Plaza Onate , Edi Prifti , Eugeni Belda , Emmanuelle Le Chatelier et al.

JOBIM2024 : Journées Ouvertes en Biologie, Informatique, et Mathématiques - 2024, Jun 2024, Toulouse, France

Communication dans un congrès hal-04691708v1

From Genomics to Pangenomics: the path to pangenome graphs

Guillaume Gautreau , Adelme Bazin , Jérôme Arnoux

The 20th MicroScope anniversary, Alexandra Calteau; David Vallenet, Sep 2023, Evry-Courcouronnes, France

Communication dans un congrès hal-04371889v1

PPanGGOLiN V2: technical enhancement and new features to analyze thousands of prokaryotic genomes

Jean Mainguy , Jérôme Arnoux , Guillaume Gautreau , Adelme Bazin , David Vallenet et al.

The local pangenome, Oct 2023, Alicante, Spain

Communication dans un congrès hal-04371316v1

panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , David Vallenet , Alexandra Calteau

JOBIM 2021 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2021, Paris (virtual), France

Communication dans un congrès hal-04360257v1

panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , David Vallenet , Alexandra Calteau

the 19th European Conference on Computational Biology, ECCB 2020, Aug 2020, Barcelona (Virtual), Spain

Communication dans un congrès hal-04360043v1

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Mylène Beuvin , Laura Burlot et al.

The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom

Communication dans un congrès hal-04358401v1

Comparative microbial pangenomics to explore mobilome dynamics

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , Alexandra Calteau , David Vallenet

The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom

Communication dans un congrès hal-04359455v1

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel et al.

Genome Informatics 2018, Sep 2018, Hinxton, Cambridge, United Kingdom

Communication dans un congrès hal-04356757v1

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel et al.

JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France

Communication dans un congrès hal-04355945v1

Cybercriminalité en santé : la réponse aux « divulgiciels »

Guillaume Gautreau

Droit, Santé et Société [Journal de médecine légale, droit médical, victimologie, dommage corporel. Série E], 2024, ⟨10.3917/dsso.112.0026⟩

Article dans une revue hal-04812193v1
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COVIDiSTRESS Global Survey dataset on psychological and behavioural consequences of the COVID-19 outbreak

Yuki Yamada , Dominik-Borna Ćepulić , Tao Coll-Martín , Stéphane Debove , Guillaume Gautreau et al.

Scientific Data , 2021, 8 (1), pp.3. ⟨10.1038/s41597-020-00784-9⟩

Article dans une revue (data paper) hal-04329100v1

Stress and worry in the 2020 coronavirus pandemic: relationships to trust and compliance with preventive measures across 48 countries in the COVIDiSTRESS global survey

Andreas Lieberoth , Shiang-Yi Lin , Sabrina Stöckli , Hyemin Han , Marta Kowal et al.

Royal Society Open Science, 2021, 8 (2), ⟨10.1098/rsos.200589⟩

Article dans une revue hal-04329116v1
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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Guillaume Gautreau , Adelme Bazin , Mathieu Gachet , Rémi Planel , Laura Burlot et al.

PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007732⟩

Article dans une revue hal-03089210v1
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panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Adelme Bazin , Guillaume Gautreau , Claudine Médigue , David Vallenet , Alexandra Calteau

Bioinformatics, 2020, 36 (Supplément 2), pp.i651 - i658. ⟨10.1093/bioinformatics/btaa792⟩

Article dans une revue hal-03322363v1
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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

David Vallenet , Alexandra Calteau , Mathieu Dubois , Paul Amours , Adelme Bazin et al.

Nucleic Acids Research, 2019, 48 (D1), pp.D579-D589. ⟨10.1093/nar/gkz926⟩

Article dans une revue hal-02403170v1
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MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

Claudine Médigue , Alexandra Calteau , Stéphane Cruveiller , Mathieu Gachet , Guillaume Gautreau et al.

Briefings in Bioinformatics, 2019, 20 (4), pp.1071-1084. ⟨10.1093/bib/bbx113⟩

Article dans une revue hal-02626039v1
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A computational approach for phenotypic comparisons of cell populations in high-dimensional cytometry data

Ludovic Platon , David Pejoski , Guillaume Gautreau , Brice Targat , Roger Le Grand et al. Article dans une revue hal-02386051v1
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SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Guillaume Gautreau , David Pejoski , Roger Le Grand , Antonio Cosma , Anne-Sophie Beignon et al.

Bioinformatics, 2017, pp.btw708. ⟨10.1093/bioinformatics/btw708⟩

Article dans une revue hal-02385937v1