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biotoolsSchema: a formalized schema for bioinformatics software description

 Jon Ison , Hans Ienasescu , Emil Rydza , Piotr Chmura , Kristoffer Rapacki , et al.
GigaScience, 2021, 10 (1), pp.giaa157. ⟨10.1093/gigascience/giaa157⟩
Article dans une revue hal-03145289v1
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RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach

 Hermenegildo Taboada-Castro , Jaime Abraham Castro-Mondragón , Alejandro Aguilar-Vera , Alfredo José Hernández-Álvarez , Jacques van Helden , et al.
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.567471⟩
Article dans une revue hal-03141125v1
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Discrimination of Yeast Genes Involved in Methionine and Phosphate Metabolism on the Basis of Upstream Motifs

 Didier Gonze , Sylvie Pinloche , Olivier Gascuel , Jacques van Helden
Bioinformatics, 2005, 21, pp.3490-3500. ⟨10.1093/bioinformatics/bti558⟩
Article dans une revue lirmm-00105316v1
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Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

 Ian Cadby , Matthew Faulkner , Jeanne Chèneby , Justine Long , Jacques van Helden , et al.
Scientific Reports, 2017, 7 (1), ⟨10.1038/s41598-017-16403-4⟩
Article dans une revue hal-01874934v1
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The chromatin environment shapes DNA replication origin organization and defines origin classes

 Christelle Cayrou , Benoit Ballester , Isabelle Peiffer , Romain Fenouil , Philippe Coulombe , et al.
Genome Research, 2015, 25 (12), pp.1873-1885. ⟨10.1101/gr.192799.115⟩
Article dans une revue hal-03101863v1
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In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication

 Franck Touret , Magali Gilles , Karine Barral , Antoine Nougairède , Jacques van Helden , et al.
Scientific Reports, 2020, 10 (1), pp.13093. ⟨10.1038/s41598-020-70143-6⟩
Article dans une revue inserm-02944556v1
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RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

 Walter Santana-Garcia , Maria Rocha-Acevedo , Lucia Ramirez-Navarro , Yvon Mbouamboua , Denis Thieffry , et al.
Computational and Structural Biotechnology Journal, 2019, ⟨10.1016/j.csbj.2019.09.009⟩
Article dans une revue hal-02458940v1
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Transcriptional profiling of midguts prepared from Trypanosoma/T. congolense-positive Glossina palpalis palpalis collected from two distinct Cameroonian foci : coordinated signatures of the midguts’ remodeling as T. congolense-supportive niches

 Jean Tsagmo Ngoune , Flobert Njiokou , Béatrice Loriod , Ginette Kame-Ngasse , Nicolas Fernandez-Nunez , et al.
Frontiers in Immunology, 2017, 8, ⟨10.3389/fimmu.2017.00876⟩
Article dans une revue hal-01874935v1
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COVID-19 epidemiologic surveillance using wastewater

 Virender Sharma , Chetan Jinadatha , Eric Lichtfouse , Etienne Decroly , Jacques van Helden , et al.
Environmental Chemistry Letters, 2021, 19, pp.1911-1915. ⟨10.1007/s10311-021-01188-w⟩
Article dans une revue hal-03125589v1
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Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

 Erwan Sallard , José Halloy , Didier Casane , Etienne Decroly , Jacques van Helden
Environmental Chemistry Letters, 2021, 19 (2), pp.769-785. ⟨10.1007/s10311-020-01151-1⟩
Article dans une revue hal-03243289v1
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Theoretical and empirical quality assessment of transcription factor-binding motifs

 Alejandra Medina-Rivera , Cei Abreu-Goodger , Morgane Thomas-Chollier , Heladia Salgado , Julio Collado-Vides , et al.
Nucleic Acids Research, 2011, 39 (3), pp.808--824. ⟨10.1093/nar/gkq710⟩
Article dans une revue hal-01624287v1
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Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis.

 Elodie Darbo , Carl Herrmann , Thomas Lecuit , Denis Thieffry , Jacques van Helden
BMC Genomics, 2013, 14 (1), pp.226. ⟨10.1186/1471-2164-14-226⟩
Article dans une revue inserm-00842641v1

Correction : Clusters of Conserved Beta Cell Marker Genes for Assessment of Beta Cell Phenotype

 Geert A. Martens , Lei Jiang , Karine H. Hellemans , Geert Stangã© , Harry Heimberg , et al.
PLoS ONE, 2012, 7 (1), ⟨10.1371/annotation/13c6d084-a8fd-4019-a3cf-12a0d8abe309⟩
Article dans une revue hal-01624370v1
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Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns.

 Elisabeth Bon , Serge Casaregola , Gaëlle Blandin , Bertrand Llorente , Cécile Neuvéglise , et al.
Nucleic Acids Research, 2003, 31 (4), pp.1121-35. ⟨10.1093/nar/gkg213⟩
Article dans une revue inria-00339881v1
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Sequanix: a dynamic graphical interface for Snakemake workflows

 Dimitri Desvillechabrol , Rachel Legendre , Claire Rioualen , Christiane Bouchier , Jacques van Helden , et al.
Bioinformatics, 2018, 34 (11), pp.1934 - 1936. ⟨10.1093/bioinformatics/bty034⟩
Article dans une revue hal-01874933v1
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Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example

 Najla Ksouri , Jaime Castro-Mondragón , Francesc Montardit-Tarda , Jacques van Helden , Bruno Contreras-Moreira , et al.
Plant Physiology, 2021, 185 (3), pp.1242-1258. ⟨10.1093/plphys/kiaa091⟩
Article dans une revue hal-03243277v1

Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses.

 Amira Amrani , Jacques van Helden , Aurélie Bergon , Aicha Aouane , Wajdi Ben Hania , et al.
Environmental Microbiology Reports, 2016, 8 (4), pp.520-6. ⟨10.1111/1758-2229.12427⟩
Article dans une revue istex hal-01410149v1
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The bio.tools registry of software tools and data resources for the life sciences

 Jon Ison , Hans Ienasescu , Piotr Chmura , Emil Rydza , Hervé Ménager , et al.
Genome Biology, 2019, 20 (164), pp.1-4. ⟨10.1186/s13059-019-1772-6⟩
Article dans une revue hal-02408472v1
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IFB/ELIXIR-FR, the french node of ELIXIR

 Anne-Françoise Adam-Blondon , Jacques van Helden , Gildas Le Corguillé , Christophe Blanchet , Hélène Chiapello , et al.
ISMB ECCB 2023, International Society for Computational Biology, Jul 2023, Lyon, France
Communication dans un congrès hal-04503051v1
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An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2

 Jacques van Helden , Colin Butler , Guillaume Achaz , Bruno Canard , Didier Casane , et al.
The Lancet, 2021, 398 (10309), pp.1402-1404. ⟨10.1016/S0140-6736(21)02019-5⟩
Article dans une revue hal-03358748v1
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RSAT 2015: Regulatory Sequence Analysis Tools

 Alejandra Medina-Rivera , Matthieu Defrance , Olivier Sand , Carl Herrmann , Jaime A. Castro-Mondragon , et al.
Nucleic Acids Research, 2015, 43 (W1), pp.W50--W56. ⟨10.1093/nar/gkv362⟩
Article dans une revue hal-01624369v1
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Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks

 Claire Rioualen , Lucie Charbonnier-Khamvongsa , Julio Collado-Vides , Jacques van Helden
Current Protocols in Bioinformatics, 2019, pp.e72. ⟨10.1002/cpbi.72⟩
Article dans une revue hal-02078136v1
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Ancestral state reconstruction of metabolic pathways across pangenome ensembles

 Fotis Psomopoulos , Jacques van Helden , Claudine Médigue , Anastasia Chasapi , Christos Ouzounis
Microbial Genomics, 2020, 6 (11), ⟨10.1099/mgen.0.000429⟩
Article dans une revue hal-03089213v1
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Redefining fundamental concepts of transcription initiation in bacteria

 Citlalli Mejía-Almonte , Stephen Busby , Joseph Wade , Jacques van Helden , Adam Arkin , et al.
Nature Reviews Genetics, 2020, 21 (11), pp.699-714. ⟨10.1038/s41576-020-0254-8⟩
Article dans une revue hal-03139472v1
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Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

 Aurélien Griffon , Quentin Barbier , Jordi Dalino , Jacques van Helden , Salvatore Spicuglia , et al.
Nucleic Acids Research, 2015, 43 (e27), ⟨10.1093/nar/gku1280⟩
Article dans une revue hal-01219379v1
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RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

 Jaime Abraham Castro-Mondragon , Sébastien Jaeger , Denis Thieffry , Morgane Thomas-Chollier , Jacques Van helden
Nucleic Acids Research, 2017, 45 (13), pp.e119--e119. ⟨10.1093/nar/gkx314⟩
Article dans une revue hal-01624366v1
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Clusters of Conserved Beta Cell Marker Genes for Assessment of Beta Cell Phenotype

 Geert A. Martens , Lei Jiang , Karine H. Hellemans , Geert Stange , Harry Heimberg , et al.
PLoS ONE, 2011, 6 (9), ⟨10.1371/journal.pone.0024134⟩
Article dans une revue hal-01624290v1
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An integrated analysis tool reveals intrinsic biases in gene set enrichment

 Nishant Thakur , Nathalie Pujol , Jacques van Helden , Robert H Waterston , Ladeana W. Hillier , et al.
2021
Pré-publication, Document de travail hal-03374674v1

EMERGEN-BioInfo The digital platform for the French SARS-CoV-2 genomic surveillance and research program

 Thomas Denecker , Imane Messak , Anliat Mohamed , Chiara Antoinat , Arthur Le Bars , et al.
Les Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) , 2022, ⟨10.5281/ZENODO.6778707⟩
Article dans une revue hal-04495542v1
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Tracing the origins of SARS-CoV-2 in coronavirus phylogenies

 Erwan Sallard , José Halloy , Didier Casane , Etienne Decroly , Jacques van Helden
Médecine/Sciences, In press, Août-Septembre 2020, 36, ⟨10.1051/medsci/2020123⟩
Article dans une revue hal-02891455v8
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