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ANR project: Code decision (reference) : ANR-11-INBS-0013
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Genomic characterization of Tenacibaculum maritimum O‐antigen gene cluster and development of a multiplex PCR‐based serotyping scheme

Pierre Lopez , Sébastien Bridel , Denis Saulnier , Rarahu David , Beatriz Magariños et al.
Transboundary and emerging diseases, 2022, 69 (5), ⟨10.1111/tbed.14637⟩
Journal articles hal-04006953v1
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Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge

Damien Courtine , Erwann Vince , Loïs Maignien , Xavier Philippon , Nicolas Gayet et al.
International Journal of Systematic and Evolutionary Microbiology, 2021, 71 (7), ⟨10.1099/ijsem.0.004853⟩
Journal articles hal-03367146v1
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Comparative genomics of Chrysochromulina Ericina Virus (CeV) and other microalgae-infecting large DNA viruses highlight their intricate evolutionary relationship with the established Mimiviridae family.

Lucie Gallot-Lavallee , Guillaume Blanc , Jean-Michel Claverie
Journal of Virology, 2017, 91 (14), pp.230-247
Journal articles hal-01527439v1

Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools

Chris Spronk , Szymon Żerko , Michał Górka , Wiktor Koźmiński , Benjamin Bardiaux et al.
Journal of Biological Inorganic Chemistry, 2018, 23 (8), pp.1309-1330. ⟨10.1007/s00775-018-1616-y⟩
Journal articles pasteur-02329962v1
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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⟩
Journal articles hal-03089210v1

Bioimage analysis workflows: community resources to navigate through a complex ecosystem

Perrine Paul-Gilloteaux , Sébastien Tosi , Jean-Karim Hériché , Alban Gaignard , Hervé Ménager et al.
F1000Research, 2021, 10, pp.320. ⟨10.12688/f1000research.52569.1⟩
Journal articles hal-03208600v1
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Noumeavirus replication relies on a transient remote control of the host nucleus

Elisabeth Fabre , Sandra Jeudy , Sébastien Santini , Matthieu Legendre , Mathieu Trauchessec et al.
Nature Communications, 2017, 8, pp.15087. ⟨10.1038/ncomms15087⟩
Journal articles hal-01534406v1
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RSAT 2018: regulatory sequence analysis tools 20th anniversary

Nga thi thuy Nguyen , Bruno Contreras-Moreira , Jaime Castro-Mondragon , Walter Santana-Garcia , Raul Ossio et al.
Nucleic Acids Research, 2018, 46 (W1), pp.W209 - W214. ⟨10.1093/nar/gky317⟩
Journal articles hal-01874932v1
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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 et al.
médecine/sciences, In press, Août-Septembre 2020, 36, ⟨10.1051/medsci/2020123⟩
Journal articles hal-02891455v8

Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705

Lucrecia Terán , Sergio A. Cuozzo , María C. Aristimuño Ficoseco , Silvina Fadda , Stephane Chaillou et al.
PLoS ONE, 2020, 15 (4), ⟨10.1371/journal.pone.0230857⟩
Journal articles hal-02921909v1

Mesorhizobium ventifaucium sp. nov. and Mesorhizobium escarrei sp. nov., two novel root-nodulating species isolated from Anthyllis vulneraria

Roba Mohamad , Anne Willems , Antoine Le Quéré , Marjorie Pervent , Géraldine Maynaud et al.
Systematic and Applied Microbiology, 2022, 45 (5), ⟨10.1016/j.syapm.2022.126341⟩
Journal articles hal-03811788v1
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Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors

Nga thi thuy Nguyen , Pierre Vincens , Jean François Dufayard , Hugues Roest crollius , Alexandra Louis et al.
Nucleic Acids Research, 2022, 50 (D1), pp.D1025-D1031. ⟨10.1093/nar/gkab1091⟩
Journal articles hal-03438462v1
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NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Frédéric Lemoine , Damien Correia , Vincent Lefort , Olivia Doppelt-Azeroual , Fabien Mareuil et al.
Nucleic Acids Research, 2019, 47 (W1), pp.W260-W265. ⟨10.1093/nar/gkz303⟩
Journal articles hal-02341225v1
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Distributed Caching of Scientific Workflows in Multisite Cloud

Gaëtan Heidsieck , Daniel de Oliveira , Esther Pacitti , Christophe Pradal , Francois Tardieu et al.
DEXA 2020 - 31st International Conference on Database and Expert Systems Applications, Sep 2020, Bratislava, Slovakia. pp.51-65, ⟨10.1007/978-3-030-59051-2_4⟩
Conference papers hal-02962579v1
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The African swine fever modelling challenge: Model comparison and lessons learnt

Pauline Ezanno , Sébastien Picault , Servane Bareille , Gaël Beaunée , Gert Jan Boender et al.
Epidemics, 2022, 40, pp.100615. ⟨10.1016/j.epidem.2022.100615⟩
Journal articles hal-03765381v1
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Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes

Jean-Michel Claverie , Chantal Abergel
Viruses, 2018, 10 (9), pp.506. ⟨10.3390/v10090506⟩
Journal articles hal-01887346v1
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Accounting for ambiguity in ancestral sequence reconstruction

Adrien Oliva , Sylvain Pulicani , Vincent Lefort , Laurent Brehelin , Olivier Gascuel et al.
Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩
Journal articles pasteur-02404399v1

Reinforcement learning for bioretrosynthesis

Mathilde Koch , Thomas Duigou , Jean-Loup Faulon
ACS Synthetic Biology, 2019, 9 (1), pp.157-168. ⟨10.1021/acssynbio.9b00447⟩
Journal articles hal-02905157v1
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Adaptive Caching for Data-Intensive Scientific Workflows in the Cloud

Gaëtan Heidsieck , Daniel de Oliveira , Esther Pacitti , Christophe Pradal , Francois Tardieu et al.
DEXA 2019 - 30th International Conference on Database and Expert Systems Applications, Aug 2019, Linz, Austria. pp.452-466, ⟨10.1007/978-3-030-27618-8_33⟩
Conference papers hal-02174445v1
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Characterization of accessory genes in coronavirus genomes

Christian Jean Michel , Claudine Mayer , Olivier Poch , Julie D. Thompson
Virology Journal, 2020, 17 (1), pp.131. ⟨10.1186/s12985-020-01402-1⟩
Journal articles hal-03464220v1
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Biogenesis and structure of a type VI secretion baseplate

Yassine Cherrak , Chiara Rapisarda , Riccardo Pellarin , Guillaume Bouvier , Benjamin Bardiaux et al.
Nature Microbiology, 2018, 3 (12), pp.1404-1416. ⟨10.1038/s41564-018-0260-1⟩
Journal articles hal-02342924v1
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Sarah Cohen-Boulakia , Khalid Belhajjame , Olivier Collin , Jérôme Chopard , Christine Froidevaux et al.
Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩
Journal articles hal-01516082v1

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Jeanne Laurentie , Valentin Loux , Christelle Hennequet-Antier , Emilie Chambellon , Julien Deschamps et al.
Journal articles hal-04004063v1
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Genome analysis of Crassaminicella sp. SY095, an anaerobic mesophilic marine bacterium isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge

Xue-Gong Li , Wei-Jia Zhang , Xiao-Qing Qi , Long Fei Wu
Marine Genomics, 2019, pp.100733. ⟨10.1016/j.margen.2019.100733⟩
Journal articles hal-02473056v1
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Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world

Sandra Jeudy , Lionel Bertaux , Jean-Marie Alempic , Audrey Lartigue , Matthieu Legendre et al.
Journal articles hal-02409597v1
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Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes

Matthieu Legendre , Jean-Marie Alempic , Nadège Philippe , Audrey Lartigue , Sandra Jeudy et al.
Frontiers in Microbiology, 2019, 10, pp.430. ⟨10.3389/fmicb.2019.00430⟩
Journal articles hal-02135607v1
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SulfAtlas, the sulfatase database: state of the art and new developments

Mark Stam , Pernelle Lelièvre , Mark Hoebeke , Erwan Corre , Tristan Barbeyron et al.
Nucleic Acids Research, 2023, 51 (D1), pp.D647-D653. ⟨10.1093/nar/gkac977⟩
Journal articles hal-03948623v1
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Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics

Mélanie Pétéra , Gildas Le Corguille , Marion Landi , Misharl Monsoor , Marie A Tremblay-Franco et al.
JOBIM 2015 (16e édition des Journées Ouvertes en Biologie, Informatique et Mathématiques ), Jul 2015, Clermont-Ferrand, France. , 2015, JOBIM (16e édition des Journées Ouvertes en Biologie, Informatique et Mathématiques ). ⟨10.1093/bioinformatics/btu813⟩
Conference poster hal-01214152v1
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IFB-Biosphère : Services cloud pour l'analyse des données des sciences de la vie

Christophe Blanchet , Olivier Collin , Matéo Boudet , Stéphane Delmotte , Hervé Gilquin et al.
Journées RESeaux - JRES 2019, Dec 2019, Dijon, France
Conference papers hal-03297018v1
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ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis

Alyssa Imbert , Magali Rompais , Mohammed Selloum , Florence Castelli , Emmanuelle Mouton-Barbosa et al.
Scientific Data , 2021, 8 (1), pp.311. ⟨10.1038/s41597-021-01095-3⟩
Journal articles pasteur-03453736v1