Bérénice Batut

82 %
Libre accès
107
Documents
Affiliations actuelles
  • Institut Français de Bioinformatique (IFB-core)
  • Plateforme Auvergne Bioinformatique (AuBi)
Contact

Publications

Publications

Deposit thumbnail

Establishing the ELIXIR Microbiome Community

Robert D Finn , Bachir Balech , Josephine Burgin , Physilia Chua , Erwan Corre et al.

F1000Research, 2025, 13, pp.50. ⟨10.12688/f1000research.144515.2⟩

Article dans une revue (article de synthèse) hal-04796156v1
Deposit thumbnail

Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology

Coline Royaux , Jean-Baptiste Mihoub , Marie Jossé , Dominique Pelletier , Olivier Norvez et al.

GigaScience, 2025, 14, pp.1-12. ⟨10.1093/gigascience/giae122⟩

Article dans une revue (article de synthèse) hal-05003055v2

PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

Engy Nasr , Anna Henger , Björn Grüning , Paul Zierep , Bérénice Batut

GigaScience, 2025, 14, ⟨10.1093/gigascience/giaf017⟩

Article dans une revue hal-05291561v1
Deposit thumbnail

Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities

Monique Zahn-Zabala , Minna Ahokas , Bérénice Batut , Sebastian Beier , Alexander Botzki et al.

F1000Research, 2025, 14, pp.1422. ⟨10.12688/f1000research.173116.1⟩

Article dans une revue hal-05441563v1
Deposit thumbnail

Clouds influence the functioning of airborne microorganisms

Raphaëlle Péguilhan , Florent Rossi , Muriel Joly , Engy Nasr , Bérénice Batut et al.

Biogeosciences, 2025, 22 (5), pp.1257-1275. ⟨10.5194/bg-22-1257-2025⟩

Article dans une revue hal-05273494v1
Deposit thumbnail

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Linelle Ann L Abueg , Enis Afgan , Olivier Allart , Ahmed Awan , Wendi Bacon et al.

Nucleic Acids Research, 2024, 52 (W1), pp.W83-W94. ⟨10.1093/nar/gkae410⟩

Article dans une revue hal-04645009v1
Deposit thumbnail

Integrative meta-omics in Galaxy and beyond

Valerie C Schiml , Francesco Delogu , Praveen Kumar , Benoit Kunath , Bérénice Batut et al.

Environmental Microbiome, 2023, 18 (1), pp.56. ⟨10.1186/s40793-023-00514-9⟩

Article dans une revue hal-04626370v1
Deposit thumbnail

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Simon Bray , John Chilton , Matthias Bernt , Nicola Soranzo , Marius van den Beek et al.

Genome Research, 2023, 33 (2), pp.261-268. ⟨10.1101/gr.276963.122⟩

Article dans une revue hal-04645001v1
Deposit thumbnail

Galaxy Training: A powerful framework for teaching!

Saskia Hiltemann , Helena Rasche , Simon Gladman , Hans-Rudolf Hotz , Delphine Larivière et al.

PLoS Computational Biology, 2023, 19 (1), pp.e1010752. ⟨10.1371/journal.pcbi.1010752⟩

Article dans une revue hal-04069041v1

An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond

Jason Williams , Rochelle Tractenberg , Bérénice Batut , Erin Becker , Anne Brown et al.

PLoS ONE, 2023, 18 (11), pp.e0293879. ⟨10.1371/journal.pone.0293879⟩

Article dans une revue hal-04644978v1
Deposit thumbnail

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Enis Afgan , Anton Nekrutenko , Bjórn Grüning , Daniel Blankenberg , Jeremy Goecks et al.

Nucleic Acids Research, 2022, 50 (W1), pp.W345-W351. ⟨10.1093/nar/gkac247⟩

Article dans une revue hal-04053853v1

Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine

Omar Mossad , Bérénice Batut , Bahtiyar Yilmaz , Nikolaos Dokalis , Charlotte Mezö et al.

Nature Neuroscience, 2022, 25 (3), pp.295-305. ⟨10.1038/s41593-022-01027-3⟩

Article dans une revue hal-04645004v1

Fostering accessible online education using Galaxy as an e-learning platform

Beatriz Serrano-Solano , Melanie Föll , Cristóbal Gallardo-Alba , Anika Erxleben , Helena Rasche et al.

PLoS Computational Biology, 2021, 17 (5), pp.e1008923. ⟨10.1371/journal.pcbi.1008923⟩

Article dans une revue hal-04645019v1

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

Subina Mehta , Marie Crane , Emma Leith , Bérénice Batut , Saskia Hiltemann et al.

F1000Research, 2021, 10, pp.103. ⟨10.12688/f1000research.28608.2⟩

Article dans une revue hal-04645022v1
Deposit thumbnail

Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes

Gabriel A.B. Marais , Bérénice Batut , Vincent Daubin

Current Biology, 2020, 30 (19), pp.R1083-R1085. ⟨10.1016/j.cub.2020.07.093⟩

Article dans une revue hal-03066151v1
Deposit thumbnail

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg , Bérénice Batut , Peter Belmann , Jochen Blom , Frank Oliver Glöckner et al.

F1000Research, 2020, 8, pp.1877. ⟨10.12688/f1000research.20244.2⟩

Article dans une revue hal-04645046v1

Ten simple rules for making training materials FAIR

Leyla Garcia , Bérénice Batut , Melissa Burke , Mateusz Kuzak , Fotis Psomopoulos et al.

PLoS Computational Biology, 2020, 16 (5), pp.e1007854. ⟨10.1371/journal.pcbi.1007854⟩

Article dans une revue hal-04645027v1
Deposit thumbnail

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Mehmet Tekman , Bérénice Batut , Alexander Ostrovsky , Christophe Antoniewski , Dave Clements et al.

GigaScience, 2020, 9 (10), ⟨10.1093/gigascience/giaa102⟩

Article dans une revue hal-04187533v1

Using the Galaxy Training Network tutorial library for bioinformatics training programs

Dave Clements , Saskia Hiltemann , Bérénice Batut , Helena Rasche , Mohammad Heydarian et al.

Journal of Biomolecular Techniques, 2020, 31 (Suppl), pp.1

Article dans une revue hal-04863936v1

The RNA workbench 2.0: next generation RNA data analysis

Jörg Fallmann , Pavankumar Videm , Andrea Bagnacani , Bérénice Batut , Maria Doyle et al.

Nucleic Acids Research, 2019, 47 (W1), pp.W511-W515. ⟨10.1093/nar/gkz353⟩

Article dans une revue hal-04645055v1
Deposit thumbnail

ASaiM: a Galaxy-based framework to analyze microbiota data

Bérénice Batut , Kevin Gravouil , Clemence Defois , Saskia Hiltemann , Jean-François Brugère et al.

GigaScience, 2018, 7 (6), pp.1-7. ⟨10.1093/gigascience/giy057⟩

Article dans une revue hal-01990448v1
Deposit thumbnail

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan , Dannon Baker , Bérénice Batut , Marius van den Beek , Dave Bouvier et al.

Nucleic Acids Research, 2018, 46 (W1), pp.W537-W544. ⟨10.1093/nar/gky379⟩

Article dans une revue hal-04645092v1

Community-Driven Data Analysis Training for Biology

Bérénice Batut , Saskia Hiltemann , Andrea Bagnacani , Dannon Baker , Vivek Bhardwaj et al.

Cell Systems, 2018, 6 (6), pp.752-758.e1. ⟨10.1016/j.cels.2018.05.012⟩

Article dans une revue hal-04863943v1

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Björn Grüning , Jörg Fallmann , Dilmurat Yusuf , Sebastian Will , Anika Erxleben et al.

Nucleic Acids Research, 2017, 45 (W1), pp.W560-W566. ⟨10.1093/nar/gkx409⟩

Article dans une revue hal-04645102v1

Four simple recommendations to encourage best practices in research software

Rafael Jiménez , Mateusz Kuzak , Monther Alhamdoosh , Michelle Barker , Bérénice Batut et al.

F1000Research, 2017, 6, pp.876. ⟨10.12688/f1000research.11407.1⟩

Article dans une revue hal-04645108v1
Deposit thumbnail

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota

Clémence Defois , Jérémy Ratel , Sylvain Denis , Bérénice Batut , Réjane Beugnot et al.

Frontiers in Microbiology, 2017, 8, ⟨10.3389/fmicb.2017.01562⟩

Article dans une revue hal-01658582v1

ENASearch: A Python library for interacting with ENA's API

Bérénice Batut , Björn Grüning

Journal of Open Source Software, 2017, 2 (18), pp.418. ⟨10.21105/joss.00418⟩

Article dans une revue hal-04645128v1

Reductive genome evolution at both ends of bacterial population size spectrum

Bérénice Batut , Carole Knibbe , Gabriel Marais , Vincent Daubin

Nature Reviews Microbiology, 2014, 12 (12), pp.841-850. ⟨10.1038/nrmicro3331⟩

Article dans une revue hal-01092392v1
Deposit thumbnail

In silico experimental evolution: a tool to test evolutionary scenarios

Bérénice Batut , David P. Parsons , Stephan Fischer , Guillaume Beslon , Carole Knibbe

BMC Bioinformatics, 2013, 14 (Suppl 15), pp.S11

Article dans une revue hal-00873232v1

MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics Resources

Vivek Ashokan , Clara Emery , Agnès Barnabé , Valentin Loux , Christina Pavloudi et al.

2026

Pré-publication, Document de travail hal-05443844v1

Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)

Wendi Anne Bacon , Sanjay Kumar Srikakulam , Bérénice Batut , Paul Zierep , Anthony Bretaudeau et al.

2025

Pré-publication, Document de travail hal-05249780v1

Community-Curated Galaxy Interfaces with the Galaxy Labs Engine

Cameron Hyde , Anna Syme , Bérénice Batut , Paul Zierep , Winnie Mok et al.

2025

Pré-publication, Document de travail hal-05232706v1

Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities

Clare Garrard , Katharina Heil , Maria Cristina Aspromonte , Bérénice Batut , Magda Chegkazi et al.

2025

Pré-publication, Document de travail hal-05246835v1
Deposit thumbnail

microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data

Engy Nasr , Pierre Amato , Anshu Bhardwaj , Daniel Blankenberg , Daniela Brites et al.

2024

Pré-publication, Document de travail hal-04863955v1
Deposit thumbnail

How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources

Bérénice Batut , Matthias Bernt , Mina Hojat Ansari , Matúš Kalaš , Paul Klemm et al.

2024

Pré-publication, Document de travail hal-04626280v1
Deposit thumbnail

Clouds influence the functioning of airborne microorganisms

Raphaëlle Péguilhan , Florent Rossi , Muriel Joly , Engy Nasr , Bérénice Batut et al.

2024

Pré-publication, Document de travail hal-04863956v1

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

Engy Nasr , Nikos Pechlivanis , Nikolaos Strepis , Pierre Amato , Matthias Bernt et al.

2025

Pré-publication, Document de travail hal-05265009v1
Deposit thumbnail

How to increase the findability, visibility, and impact of Galaxy tools for your scientific community

Paul Zierep , Bérénice Batut , Matúš Kalaš , Tunc Kayikcioglu , Engy Nasr et al.

2024

Pré-publication, Document de travail hal-04626296v1

Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and Beyond

Jason Williams , Rochelle Tractenberg , Bérénice Batut , Erin Becker , Anne Brown et al.

2024

Pré-publication, Document de travail hal-04645151v1
Deposit thumbnail

Clouds, oases for airborne microbes – Differential metagenomics/ metatranscriptomics analyses of cloudy and clear atmospheric situations

Raphaëlle Péguilhan , Florent Rossi , Muriel Joly , Engy Nasr , Bérénice Batut et al.

2024

Pré-publication, Document de travail hal-04626301v1
Deposit thumbnail

Exploring the landscape of the genomic wastewater surveillance ecosystem: a roadmap towards standardization

Fotis Psomopoulos , Konstantinos Kyritsis , Ivan Topolsky , Bérénice Batut , Amy Heather Fitzpatrick et al.

2024

Pré-publication, Document de travail hal-04626360v1

Empowering the community with notebooks for bespoke microbiome analyses

Alexander Rogers , Bérénice Batut , Virginie Grosboillot , Martin Beracochea

2024

Pré-publication, Document de travail hal-04645147v1

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

Simon Bray , Matthias Bernt , Nicola Soranzo , Marius van den Beek , Bérénice Batut et al.

2022

Pré-publication, Document de travail hal-04645155v1

A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

Mehmet Tekman , Bérénice Batut , Alexander Ostrovsky , Christophe Antoniewski , Dave Clements et al.

2020

Pré-publication, Document de travail hal-04863963v1
Deposit thumbnail

Community-Driven Data Analysis Training for Biology

Bérénice Batut , Saskia Hiltemann , Andrea Bagnacani , Dannon Baker , Vivek Bhardwaj et al.

2018

Pré-publication, Document de travail pasteur-02613129v1

ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota

Bérénice Batut , Kévin Gravouil , Clémence Defois , Saskia Hiltemann , Jean-François Brugère et al.

2017

Pré-publication, Document de travail hal-04863972v1
Deposit thumbnail

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Björn Grüning , Ryan Dale , Andreas Sjödin , Brad Chapman , Jillian Rowe et al.

2017

Pré-publication, Document de travail hal-04863967v1
Deposit thumbnail

RNA-Seq Data Analysis in Galaxy

Bérénice Batut , Marius van den Beek , Maria Doyle , Nicola Soranzo

RNA Bioinformatics, 2284, Springer US, pp.367-392, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1307-8_20⟩

Chapitre d'ouvrage hal-04645142v1

The microbiology galaxy lab: The effort of the microGalaxy community to build the first community-driven gateway for reproducible and FAIR analysis of microbial data analysis

Engy Nasr , Nikos Pechlivanis , Nikolaos Strepis , Paul Zierep , Bérénice Batut

European Galaxy Days, Oct 2025, Freiburg, Germany. ⟨10.7490/f1000research.1120314.1⟩

Communication dans un congrès hal-05323230v1

FAIRyMAGS – Optimising Metagenomics Assembled Genomes building: workflow finalisation, training material development, real data evaluation, and resource allocation tool creation

Paul Zierep , Bérénice Batut , Giuseppe Defazio , Bruno Fosso , Martin Beracochea et al.

ELIXIR All Hands Meeting, 2025, Jun 2025, Thessaloniki, Greece. ⟨10.7490/f1000research.1120217.1⟩

Communication dans un congrès hal-05132978v1

ATELIER - Dépôt et curation de données - Communauté Biologie et Santé (plateforme de bioanalyses Galaxy)

Cléa Siguret , Bérénice Batut , Nadia Goué

Printemps de la donnée 2025, Université Clermont-Auvergne, May 2025, Clermont-Ferrand, France

Communication dans un congrès hal-05095680v1

ABRomics : Une plateforme basée sur Galaxy pour la recherche sur la résistance aux antibiotiques et la santé publique

Cléa Siguret , Bérénice Batut , Raphaël Tackx , Julie Lao , Amanda Dieuaide et al.

Journée d’animation annuelle de la plateforme AuBi 2024, Plateforme Auvergne Bioinformatique (AuBi), Dec 2024, Aubière / Clermont-Ferrand, France

Communication dans un congrès hal-05084079v1

Misconceptions about Galaxy debunked by the (French) Galaxy Community

Romane Libouban , Eva Mercier , Thomas Chaussepied , Bérénice Batut , Anthony Bretaudeau et al.

JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024, TOULOUSE, France. pp.1-28

Communication dans un congrès hal-04694551v1
Deposit thumbnail

Galaxy France: an example of a national UseGalaxy server

Clea Siguret , Thomas Chaussepied , Romane Libouban , Eva Mercier , Julien Seiler et al.

GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. pp.1-15, ⟨10.7490/f1000research.1119767.1⟩

Communication dans un congrès hal-04644627v1
Deposit thumbnail

Galaxy CoDex for finding tools, workflows, and training

Bérénice Batut , Wendi Bacon , Paul Zierep , Matthias Bernt , Nicola Soranzo et al.

GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. ⟨10.7490/f1000research.1119764.1⟩

Communication dans un congrès hal-04644966v1
Deposit thumbnail

PathoGFAIR: collection of Galaxy FAIR workflows for pathogen detection and samples comparison

Engy Nasr , Anna Henger , Bjoern Gruening , Paul Zierep , Bérénice Batut

GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. ⟨10.7490/f1000research.1119769.1⟩

Communication dans un congrès hal-04644577v2
Deposit thumbnail

Developing Galaxy as part of an international network

Bérénice Batut

ELIXIR All Hands Meeting 2023, Jun 2023, Dublin (IE), Ireland. ⟨10.7490/f1000research.1119513.1⟩

Communication dans un congrès hal-04761812v1
Deposit thumbnail

Open seeds by OLS: A virtual mentoring & training program for open science ambassadors

Pradeep Eranti , Yochannah Yehudi , Sara El-Gebali , Bérénice Batut

Bioinformatics Open Source Conference, Jul 2024, Lyon, France. ⟨10.7490/f1000research.1119659.1⟩

Communication dans un congrès hal-04760113v1
Deposit thumbnail

ASaiM - From a local project to a global effort to support microbiome data analysis.

Bérénice Batut

Holistic Bioinformatic Approaches used in Microbiome Research - BVCN, Jun 2021, Online, United States

Communication dans un congrès hal-04763640v1
Deposit thumbnail

Empowering usable, and comprehensive bioinformatics training

Bérénice Batut

ISMB 2020 - 28th Intelligent Systems for Molecular Biology Conference, Jul 2020, Montreal (Virtual event), Canada

Communication dans un congrès hal-04763510v1

Single-cell RNA Analysis in Galaxy on 10X Datasets

Mehmet Tekman , Bérénice Batut , Björn Grüning

2019 Galaxy Community Conference (GCC2019), Jul 2019, Freiburg, Germany

Communication dans un congrès hal-04763654v1

Metaproteomics Powered By Metatranscriptomics: Towards a Multi-omic Functional Microbiome Analysis Within Galaxy

Pratik D Jagtap , Subina Mehta , Praveen Kumar , Ray Sajulga , Caleb Easterly et al.

2019 Galaxy Community Conference (GCC2019), Jul 2019, Freiburg, Germany

Communication dans un congrès hal-04763648v1
Deposit thumbnail

Galaxy and training 2019 updates from the Galaxy Training Network

Bérénice Batut , Saskia Hiltemann , Helena Rasche , Subina Mehta , Pratik D Jagtap et al.

GCC2019 - 2019 Galaxy Community Conference, Jul 2019, Freiburg, Germany

Communication dans un congrès hal-04761997v1

Street Science Community: make science tangible & accessible by bringing it to the “street” with open science workshops

Teresa Müller , Bérénice Batut

2019 Galaxy Community Conference (GCC2019), Jul 2019, Freiburg, Germany

Communication dans un congrès hal-04763650v1

Community-driven training for biological data analysis with the Galaxy Training Network

Bérénice Batut

Galaxy Africa conference, Apr 2018, Cape Town, South Africa

Communication dans un congrès hal-04763513v1

A fruitful year for the Galaxy Training materials

Bérénice Batut , Saskia Hiltemann , Björn Grüning

Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference (BOSC2018), Jun 2018, Portland, United States

Communication dans un congrès hal-04763669v1

Building an open, collaborative, online infrastructure for bioinformatics training

Bérénice Batut , Dave Clements , Björn Grüning

Galaxy Community Conference 2017, Jun 2017, Montpellier, France. ⟨10.7490/f1000research.1114447.1⟩

Communication dans un congrès hal-04763025v1

Tool deployment and sustainability in bioinformatics: Fixed!

Bérénice Batut , Jonas Weber , Rolf Backofen , Björn Grüning

Bioinformatics for Human Health and Disease, Nov 2016, Heidelberg, Germany

Communication dans un congrès hal-04764363v1

ASaiM: An intuitive and adjustable pipeline to process metatranscriptomic data from intestinal microbiota

Bérénice Batut , Clémence Defois , Céline Ribière , Cyrielle Gasc , Jean-François Brugère et al.

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

Communication dans un congrès hal-04764365v1

An alife game to teach evolution of antibiotic resistance

Guillaume Beslon , Bérénice Batut , David P. Parsons , Dominique Schneider , Carole Knibbe

ECAL - 12th European Conference on Artificial Life - 2013, Sep 2013, Taormina, Italy. pp.43-50

Communication dans un congrès hal-00849345v1

In silico experimental evolution: a tool to test evolutionary scenarios

Bérénice Batut , David P. Parsons , Stephan Fischer , Guillaume Beslon , Carole Knibbe

11th RECOMB - Comparative Genomics 2013, Oct 2013, Villeurbane, France

Communication dans un congrès hal-04764366v1
Deposit thumbnail

Breaking myths: The reality of Galaxy's capabilities and impact

Gildas Le Corguillé , Anthony Bretaudeau , Björn Grüning , Wendi Bacon , Bérénice Batut

JOBIM 2025 - Journées Ouvertes en bioinformatique et de la biostatistique francophone, Jul 2025, Bordeaux, France. 2025

Poster de conférence hal-05132787v1
Deposit thumbnail

IFB/ELIXIR-FR contributions to the ELIXIR Training Platform Programme

Olivier Sand , Bérénice Batut , Frédéric de Lamotte , Lucie Khamvongsa-Charbonnier , Hélène Chiapello et al.

JOBIM 2025, Jul 2025, Bordeaux, France

Poster de conférence hal-05108322v1
Deposit thumbnail

Contributing to the ELIXIR training life-cycle from the GTN perspective

Helena Rasche , Saskia Hiltemann , Lisanna Paladin , Krzysztof Poterlowicz , Bjoern Gruening et al.

ELIXIR All Hands Meeting 2025, Jun 2025, Thessalonique, Greece. F1000 Research Limited, 2025, ⟨10.7490/f1000research.1120206.1⟩

Poster de conférence hal-05132968v1
Deposit thumbnail

ABRomics-analysis : developing Metagenomic Workflows for National Antibiotic Resistance Surveillance Platform

Hugo Lefeuvre , Audrey Bihouée , Bérénice Batut , Samuel Chaffron , Claudine Médigue et al.

JOBIM, Jul 2025, Bordeaux, France

Poster de conférence hal-05127516v2
Deposit thumbnail

Exploring the Richness of the French Galaxy Ecosystem

Bérénice Batut , Gildas Le Corguillé , Anthony Bretaudeau

JOBIM 2025 - Journées Ouvertes en bioinformatique et de la biostatistique francophone, Jul 2025, Bordeaux, France. 2025

Poster de conférence hal-05132824v1
Deposit thumbnail

Building a standardized database for honey bee microbiome: Addressing metadata and data comparability gaps

Bérénice Batut , Cléa Siguret , Hugo Serville , Geraldine Piot , Ivan Wawrzyniak et al.

JOBIM 2025, Jul 2025, Bordeaux, France.

Poster de conférence hal-05132669v1
Deposit thumbnail

Galaxy training: A powerful framework for teaching!

Helena Rasche , Saskia Hiltemann , Björn Grüning , Bérénice Batut

JOBIM 2025, Jul 2025, Bordeaux, France

Poster de conférence hal-05132944v1
Deposit thumbnail

FAIRing Research Data to Live @AuBi Platform

Francis Ogereau , Mateo Hiriart , Pierre Marin , Bérénice Batut , Cléa Siguret et al.

JOBIM, Jun 2024, Toulouse (FR), France

Poster de conférence hal-04643973v1
Deposit thumbnail

Exploring the richness of the French Galaxy Ecosystem

Bérénice Batut , Gildas Le Corguillé , Yvan Le Bras , Loraine Brillet-Guéguen , Fabien Mareuil et al.

GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. , pp.1-1, 2024, ⟨10.7490/f1000research.1119765.1⟩

Poster de conférence hal-04644779v1
Deposit thumbnail

The ABRomics platform — a One Health Antimicrobial resistance analysis service

Julie Lao , Raphael Tackx , Pierre Marin , Amanda Dieuaide , Thomas Mignon et al.

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

Poster de conférence hal-04618645v1
Deposit thumbnail

microGalaxy SIG: microbial data analysis resources in Galaxy

Paul Zierep , Engy Nasr , Saim Momin , Pratik D Jagtap , Debjyoti Ghosh et al.

GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. ⟨10.7490/f1000research.1119768.1⟩

Poster de conférence hal-04763657v1
Deposit thumbnail

ABRomics: A Galaxy-based one health antimicrobial resistance platform

Pierre Marin , Bérénice Batut , Kenzo-Hugo Hillion , Clea Siguret , Raphael Tackx et al.

GCC 2024 - Galaxy Community Conference 2024, Jun 2024, Brno, Czech Republic. , ⟨10.7490/f1000research.1119762.1⟩

Poster de conférence hal-04619528v1

Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking

Engy Nasr , Anna Henger , Tobias Schindler , Paul Zierep , Björn Grüning et al.

24th Bioinformatics Open Source Conference (BOSC) 2023, Jul 2023, Lyon, France. ⟨10.7490/f1000research.1119510.1⟩

Poster de conférence hal-04765208v1

Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking

Engy Nasr , Anna Henger , Tobias Schindler , Paul Zierep , Björn Grüning et al.

Applied Bioinformatics & Public Health Microbiology, May 2023, Hinxton, United Kingdom. ⟨10.7490/f1000research.1119510.1⟩

Poster de conférence hal-04766230v1
Deposit thumbnail

Open seeds by OLS: A mentoring & training program for open science ambassadors

Mallory Freeberg , Fotis Evangelos Psomopoulos , Diana Pilvar , Bérénice Batut

ELIXIR All Hands 2023, Jun 2023, Dublin, Ireland. ⟨10.7490/f1000research.1119509.1⟩

Poster de conférence hal-04761889v1
Deposit thumbnail

Galaxy Training: A powerful framework for teaching!

Helena Rasche , Saskia Hiltemann , Bérénice Batut

ELIXIR All Hands Meeting 2023, Jun 2023, Dublin, Ireland. ⟨10.7490/f1000research.1119512.1⟩

Poster de conférence hal-04761822v1
Deposit thumbnail

Establishing the ELIXIR microbiome community

Bérénice Batut , Eric Pelletier , Robert D. Finn , Katharina Heil

ELIXIR All Hands 2023, Jun 2023, Dublin, Ireland. ⟨10.7490/f1000research.1119511.1⟩

Poster de conférence hal-04761840v1

Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking

Engy Nasr , Anna Henger , Tobias Schindler , Paul Zierep , Björn Grüning et al.

German Conference on Bioinformatics (GCB) 2023, Sep 2023, Hamburg, Germany. ⟨10.7490/f1000research.1119510.1⟩

Poster de conférence hal-04765295v1
Deposit thumbnail

Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking

Engy Nasr , Anna Henger , Tobias Schindler , Paul Zierep , Björn Grüning et al.

ELIXIR All Hands 2023, Jun 2023, Dublin, Ireland. ⟨10.7490/f1000research.1119510.1⟩

Poster de conférence hal-04761854v1
Deposit thumbnail

Galaxy for long read ONT data analysis and public education

Bérénice Batut , Milad Miladi , Saskia Hiltemann , Willem De Koning , Björn Grüning

German Conference on Bioinformatics (GCB) 2019, Sep 2019, Heidelberg, Germany

Poster de conférence hal-04763036v1

Metaproteomics Powered By Metatranscriptomics:Towards a multi-omic functional microbiome analysis

Pratik D Jagtap , Praveen Kumar , Francesco Delogu , Benoit J Kunath , Sujun Li et al.

American Society for Mass Spectrometry 2029, Jun 2019, Atlanta (Georgia), United States

Poster de conférence hal-04761927v1
Deposit thumbnail

Galaxy and Training: 2019 updates from the Galaxy Training Network

Bérénice Batut , Saskia Hiltemann , Helena Rasche , Subina Mehta , Pratik D Jagtap et al.

2019 Galaxy Community Conference (GCC2019), Jul 2019, Freiburg, Germany. ⟨10.7490/f1000research.1117108.1⟩

Poster de conférence hal-04761986v1
Deposit thumbnail

Community-driven training for biological data analysis with the Galaxy training network

Bérénice Batut , Saskia Hiltemann , Björn Grüning

CarpentryCon 2018, May 2018, Dublin, Ireland.

Poster de conférence hal-04763043v1

A fruitful year for the Galaxy Training materials

Bérénice Batut , Saskia Hiltemann , Björn Grüning

Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference (BOSC2018), Jun 2018, Portland, United States

Poster de conférence hal-04864079v1
Deposit thumbnail

Building an open, collaborative, online infrastructure for bioinformatics training

Bérénice Batut , Dave Clements , Björn Grüning

German Conference on Bioinformatics (GCB) 2017, Jul 2017, Tübingen, Germany. ⟨10.7490/f1000research.1114881.1⟩

Poster de conférence hal-04763000v1
Deposit thumbnail

Scaling bioinformatics training: an ELIXIR, GOBLET & Galaxy Training Network collaboration

Bérénice Batut , Björn Grüning , Frederik Coppens , Hans-Rudolf Hotz , Gabriella Rustici et al.

18th Annual Bioinformatics Open Source Conference (BOSC 2017), Jul 2017, Prague, Czech Republic. ⟨10.7490/f1000research.1114489.1⟩

Poster de conférence hal-04763006v1
Deposit thumbnail

A Galaxy-based framework to analyze raw sequencing data from microbiota

Bérénice Batut , Clémence Defois , Kevin Gravouil , Jean-François Brugère , Éric Peyretaillade et al.

Galaxy Community Conference 2017, Jun 2017, Montpellier, France. ⟨10.7490/f1000research.1114448.1⟩

Poster de conférence hal-04763022v1
Deposit thumbnail

How to analyze raw sequencing data from microbiota? Using ASaiM!

Bérénice Batut , Clémence Defois , Kevin Gravouil , Jean-François Brugère , Éric Peyretaillade et al.

German Conference on Bioinformatics (GCB) 2017, Sep 2017, Tubingen, Germany. ⟨10.7490/f1000research.1114882.1⟩

Poster de conférence hal-04762996v1

Stratégies de reconstruction de génomes microbiens à partir de métagenomes

Kevin Gravouil , Corentin Hochart , Bérénice Batut , Clémence Defois , Cyrielle Gasc et al.

JOBIM 2016 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2016, Lyon, France

Poster de conférence hal-04763072v1
Deposit thumbnail

Analyze your microbiota sequencing data using a Galaxy-based framework References

Bérénice Batut , Clémence Defois , Kevin Gravouil , Cyrielle Gasc , Thomas Eymard et al.

JOBIM 2016 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2016, Lyon, France

Poster de conférence hal-04763064v1

Benzo[a]pyrene impacts human gut microbiota volatile metabolome and metatranscriptome

Clémence Defois , Bérénice Batut , Jérémy Ratel , R. Beugnot , Frederic Mercier et al.

10. Joint Symposium INRA-ROWETT, 2016, Clermont Ferrand, France. 2016

Poster de conférence hal-02794365v1

Unexpected genome inflation and streamlining in variable environments

Bérénice Batut , Guillaume Beslon , Carole Knibbe

Journées ouvertes de Biologie Informatique & Mathématiques 2016, Jun 2016, Lyon, France. pp.320-322, 2016

Poster de conférence hal-01375653v1

Simulating evolutionary scenarios to test whether they can induce reductive evolution

Bérénice Batut , Mathilde Dumond , Gabriel Marais , Guillaume Beslon , Carole Knibbe

SMBE 2012 : Society for Molecular Biology and Evolution, Jun 2012, Dublin, Ireland

Poster de conférence hal-00762597v1