CV HAL - Guillaume GAUTREAU

Delineation of integrative conjugative elements in bacterial genomes : Leveraging pangenome and machine learning approaches

Mamadou-Aliou Diallo , Thomas Lacroix , Hélène Chiapello , Guillaume Gautreau

Journées Ouvertes en Biologie, Informatique, et Mathématiques 2026, Jun 2026, Strasbourg, France

Poster de conférence hal-05739811v1

Balancing Open Science and Data Privacy: The Challenge of Human Microbiome Research

Guillaume Gautreau , Aicha El Jai , Nicolas Pons , Claudine Médigue , Hélène Chiapello et al.

Journées ouvertes en biologie, informatique et mathématiques 2026, Jul 2026, Strasbourg, France.

Poster de conférence hal-05673622v1

Could the methylome be a new lever for steering microbial communities? A meta-epigenomics workflow to analyse microbial samples

Benjamin Prehaud , Iacopo Passeri , Joël Doré , Béatrice de Montera , Guillaume Gautreau

Journées Ouvertes en Biologie, Informatique, et Mathématiques 2026, Jun 2026, Strasbourg, France

Poster de conférence hal-05739806v1

Cloud4SAMS: a trusted research environment to handle human gut microbiome data

Pauline Barbet , Eugeni Belda , Audrey Bihouee , Alexandrina Bodrug , Paul Breugnot et al.

JOBIM 2026, Jun 2026, Strasbourg, France

Poster de conférence hal-05673661v1

Few-shot learning strategy for Predicting Meropenem Resistance genes in Escherichia coli

Meriem Youssef , David Vallenet , A. Calteau , Guillaume Gautreau

JOBIM 2026, Jun 2026, Strasbourg, France

Poster de conférence hal-05672694v1

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 2025, Jul 2025, Bordeaux, France. https://jobim2025.labri.fr/JOBIM2025_proceedings_posters.pdf

Poster de conférence hal-05176404v1

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

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. , SAMS

Poster de conférence hal-04634008v1

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

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

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

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

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

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

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

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

Stabilization of cyclin D3 protein by CDKN1A (p21Cip/Waf1) in butyrate-treated cells

Mohammed Ala Ghrib , Guy W Dayhoff , Cherif Chahtour , Carine Rodrigues-Machado , Abdelrahaman Youssef et al.

Cell Communication and Signaling, 2026, 24, ⟨10.1186/s12964-026-02767-6⟩

Article dans une revue hal-05661774v1

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

Jean Mainguy , Téo Lemane , Adelme Bazin , Jérôme Arnoux , Guillaume Gautreau et al.

Nucleic Acids Research, 2026, ⟨10.1093/nar/gkag948⟩

Article dans une revue hal-05779522v1

CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data

Lindsay Goulet , Florian Plaza Oñate , Alexandre Famechon , Benoît Quinquis , Eugeni Belda et al.

Nature Communications, 2026, 17 (1), pp.6258. ⟨10.1038/s41467-026-72637-9⟩

Article dans une revue hal-05698984v1

Rôle de la dysbiose intestinale au cours des spondyloarthrites (SpA) : pathogénie de Ruminococcus gnavus

M. Jacoutot , M. Beaufrère , P. Karpman , E. Frison , V. Robert et al.

Revue du Rhumatisme, 2024, 91 (1), pp.A109. ⟨10.1016/j.rhum.2024.10.407⟩

Article dans une revue hal-05739795v1

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

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

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

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

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

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

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.

MethodsX, 2017, ⟨10.1016/j.ymeth.2017.09.005⟩

Article dans une revue hal-02386051v1

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

From Concept to Perspective: Digital Twins of Microbial Systems

Simon Labarthe , Nicolas Creusot , Clémence Frioux , Guillaume Gautreau , Elie Desmond-Le Quéméner et al.

2026

Pré-publication, Document de travail hal-05613501v1

PPanGGOLiN V2: technical enhancement and extended functionalities for prokaryotic pangenome analysis

Jérôme Arnoux , Jean Mainguy , Adelme Bazin , Guillaume Gautreau , Téo Lemane et al.

2026

Pré-publication, Document de travail hal-05703418v1

Problématiques soulevées par l'analyse et la gestion des données du microbiome humain

Guillaume Gautreau , Eugeni Belda , Christophe Blanchet , Samuel Chaffron , Hélène Chiapello et al.

2026

Pré-publication, Document de travail (working paper) hal-05673743v1

CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data

Lindsay Goulet , Florian Plaza Oñate , Alexandre Famechon , Benoît Quinquis , Eugeni Belda et al.

2025

Pré-publication, Document de travail hal-04902208v1

Un droit unique de la Santé

Guillaume Gautreau

2023

Pré-publication, Document de travail hal-04747042v1

What can genomics learn from natural language processing?

Guillaume Gautreau

Doctoral. Cité internationale universitaire de Paris, France. 2025

Cours hal-05401386v1

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

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

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, Netherlands. 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.

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

Communication dans un congrès hal-04355945v1

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

Conceptualisation et exploitation d’un graphe de pangénome partitionné comme représentation compacte de la diversité du répertoire génique des espèces procaryotes

Guillaume Gautreau

Génomique, Transcriptomique et Protéomique [q-bio.GN]. Université Paris-Saclay, 2020. Français. ⟨NNT : 2020UPASE001⟩

Thèse tel-02933311v1

Guillaume GAUTREAU

Publications

Publications

Delineation of integrative conjugative elements in bacterial genomes : Leveraging pangenome and machine learning approaches

Balancing Open Science and Data Privacy: The Challenge of Human Microbiome Research

Could the methylome be a new lever for steering microbial communities? A meta-epigenomics workflow to analyse microbial samples

Cloud4SAMS: a trusted research environment to handle human gut microbiome data

Few-shot learning strategy for Predicting Meropenem Resistance genes in Escherichia coli

Bridging Gene-level And Sequence-level Pangenome Graph To Explore Microbial Diversity

To the species level and beyond A rationalized approach to study pangenomes

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

Towards a machine learning approach for automated detection of well-to-well contamination in metagenomic data

Towards a machine learning approach for automated detection of well-to-well contamination in metagenomics data

Extensive benchmark of machine learning methods for quantitative microbiome data

PanGBank: exploring GenBank genomes through a resource of pangenome graphs

PanGBank: depicting microbial species diversity via PPanGGOLiN

Comparative microbial pangenomics to explore mobilome dynamics

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

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

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

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Genome assembly using Nanopore-guided Long and Error-free DNA reads

Stabilization of cyclin D3 protein by CDKN1A (p21Cip/Waf1) in butyrate-treated cells

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data

Rôle de la dysbiose intestinale au cours des spondyloarthrites (SpA) : pathogénie de Ruminococcus gnavus

Cybercriminalité en santé : la réponse aux « divulgiciels »

COVIDiSTRESS Global Survey dataset on psychological and behavioural consequences of the COVID-19 outbreak

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

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

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

MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

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

A computational approach for phenotypic comparisons of cell populations in high-dimensional cytometry data

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

From Concept to Perspective: Digital Twins of Microbial Systems

PPanGGOLiN V2: technical enhancement and extended functionalities for prokaryotic pangenome analysis

Problématiques soulevées par l'analyse et la gestion des données du microbiome humain

CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data

Un droit unique de la Santé

What can genomics learn from natural language processing?

What genomics can learn from Natural Language Processing?

Feedback from Evo

Histoire de la pangénomique procaryote

Integrating complex pangenome graphs

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

From Genomics to Pangenomics: the path to pangenome graphs

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

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

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

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

Comparative microbial pangenomics to explore mobilome dynamics

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Conceptualisation et exploitation d’un graphe de pangénome partitionné comme représentation compacte de la diversité du répertoire génique des espèces procaryotes