DV

David Vallenet

63 %
Libre accès
126
Documents
Affiliation actuelle
  • Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM)
Contact

Domaines de recherche

Génomique, Transcriptomique et Protéomique [q-bio.GN] Bio-Informatique, Biologie Systémique [q-bio.QM] Bactériologie Sciences du Vivant [q-bio]

Publications

Publications

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Complete genome sequence of $Hyphomicrobium/ sp$ . strain 1Nfss2.1 from marine sediments of the Berre lagoon, France

Manon Bartoli , Nathalie Pradel , Stéphanie Fouteau , Zoé Rouy , Corinne Cruaud et al.

Microbiology Resource Announcements, 2025, ⟨10.1128/mra.00254-25⟩

Article dans une revue cea-05163110v1
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Complete genome sequence of Nitratireductor aquimarinus strain MNA2.1 isolated from sediments of the Berre lagoon, France

Nathalie Pradel , Stéphanie Fouteau , Manon Bartoli , Zoé Rouy , Corinne Cruaud et al.

Microbiology Resource Announcements, 2025, 14, ⟨10.1128/mra.00259-25⟩

Article dans une revue hal-05394740v1
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Magnetotactic bacteria affiliated with diverse <i>Pseudomonadota</i> families biomineralize intracellular Ca-carbonate

Camille C Mangin , Karim Benzerara , Marine Bergot , Nicolas Menguy , Béatrice Alonso et al.

The International Society of Microbiologial Ecology Journal, 2025, 19 (1), pp.wrae260. ⟨10.1093/ismejo/wrae260⟩

Article dans une revue hal-04942957v1
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A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening

Eddy Elisée , Laurine Ducrot , Raphaël Méheust , Karine Bastard , Aurélie Fossey-Jouenne et al.

Nature Communications, 2024, 15, pp.4933. ⟨10.1038/s41467-024-49009-2⟩

Article dans une revue hal-04645174v1
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A novel binary pesticidal protein from Chryseobacterium arthrosphaerae controls western corn rootworm by a different mode of action to existing commercial pesticidal proteins

Rania Jabeur , Virginie Guyon , Szabolcs Toth , Adriano E Pereira , Man P Huynh et al.

PLoS ONE, 2023, 18 (2), pp.e0267220. ⟨10.1371/journal.pone.0267220⟩

Article dans une revue cea-04285418v1
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A model industrial workhorse: $Bacillus\ subtilis$ strain 168 and its genome after a quarter of a century

Erhard Bremer , Alexandra Calteau , Antoine Danchin , Colin Harwood , John D Helmann et al.

Microbial Biotechnology, 2023, 16 (6), pp.1203-1231. ⟨10.1111/1751-7915.14257⟩

Article dans une revue cea-04284953v1
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Magnetosome proteins belong to universal protein families involved in many cell processes

Caroline L Monteil , David Vallenet , Dirk Schüler , Christopher T Lefevre

Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (39), ⟨10.1073/pnas.2208648119⟩

Article dans une revue hal-03872975v1
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Complete Genome Sequence of Tepidibacter sp. Strain 8C15b, Isolated from Bank Sediments of Haiphong Bay, Vietnam

Stéphanie Fouteau , Vuong Bui Van , Zoé Rouy , Mélanie Beraud , Corinne Cruaud et al.

Microbiology Resource Announcements, 2022, 11 (7), ⟨10.1128/mra.00132-22⟩

Article dans une revue hal-03778996v1
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A roadmap for the functional annotation of protein families: a community perspective

Valérie De Crecy-Lagard , Rocio Amorin De Hegedus , Cecilia Arighi , Jill Babor , Alex Bateman et al.

Database - The journal of Biological Databases and Curation, 2022, 2022, ⟨10.1093/database/baac062⟩

Article dans une revue hal-04281352v1

Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period

Guilhem Royer , Mélanie Mercier Darty , Olivier Clermont , Bénédicte Condamine , Cédric Laouenan et al.

Genome Medicine, 2021, 13 (1), pp.77. ⟨10.1186/s13073-021-00892-0⟩

Article dans une revue hal-04283547v1

Complete Genome Sequences of Two Pseudomonas Species Isolated from Marine Environments of the Pacific Ocean

Shi-Zhen Wang , Corinne Cruaud , Jean-Marc Aury , David Vallenet , Julie Poulain et al.

Microbiology Resource Announcements, 2021, 10 (16), ⟨10.1128/mra.01062-19⟩

Article dans une revue hal-04178012v1
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From strain characterization to field authorization: highlights on $Bacillus\ velezensis$ strain B25 beneficial properties for plants and its activities on phytopathogenic fungi

Pierre Joly , Alexandra Calteau , Aurélie Wauquier , Rémi Dumas , Mylène Beuvin et al.

Microorganisms, 2021, 9 (9), pp.e1924. ⟨10.3390/microorganisms9091924⟩

Article dans une revue cea-04284767v1
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Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period

Guilhem Royer , Mélanie Mercier Darty , Olivier Clermont , Bénédicte Condamine , Cédric Laouenan et al.

Genome Medicine, 2021, 13 (1), pp.77. ⟨10.1186/s13073-021-00892-0⟩

Article dans une revue hal-04298243v1
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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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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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Construction of a complete set of Neisseria meningitidis mutants and its use for the phenotypic profiling of this human pathogen

A. Muir , I. Gurung , A. Cehovin , A. Bazin , D. Vallenet et al.

Nature Communications, 2020, 11 (1), pp.5541. ⟨10.1038/s41467-020-19347-y⟩

Article dans une revue hal-03512357v1
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Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6

Albane Jouault , Angélique Gobet , Marjolaine Simon , Emilie Portier , Morgan Perennou et al.

Applied and Environmental Microbiology, 2020, 86 (20), pp.e00893-20. ⟨10.1128/AEM.00893-20⟩

Article dans une revue hal-03027967v1

Erratum for Jouault et al., "Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6

Albane Jouault , Angelique Gobet , Marjolaine Simon , Emilie Portier , Morgan Perennou et al.

Applied and Environmental Microbiology, 2020, 86 (23), pp.e02431-20. ⟨10.1128/AEM.02431-20⟩

Article dans une revue hal-05058199v1

Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6

Albane Jouault , Angelique Gobet , Marjolaine Simon , Emilie Portier , Morgan Perennou et al.

Applied and Environmental Microbiology, 2020, 86 (20), pp.e00893-20. ⟨10.1128/AEM.02431-20⟩

Article dans une revue hal-05393165v1
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Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist

Caroline Monteil , David Vallenet , Nicolas Menguy , Karim Benzerara , Valérie Barbe et al.

Nature Microbiology, 2019, 4 (7), pp.1088-1095. ⟨10.1038/s41564-019-0432-7⟩

Article dans une revue cea-02122376v1
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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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GROOLS: reactive graph reasoning for genome annotation through biological processes

Jonathan Mercier , Adrien Josso , Claudine Medigue , David Vallenet

BMC Bioinformatics, 2018, 19, pp.132. ⟨10.1186/s12859-018-2126-1⟩

Article dans une revue cea-04313474v1
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PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level

G. Royer , J. W. Decousser , C. Branger , M. Dubois , C. Medigue et al.

Microbial Genomics, 2018, 4 (9), pp.000211. ⟨10.1099/mgen.0.000211⟩

Article dans une revue cea-02291353v1

The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification

M. Desroches , G. Royer , D. Roche , M. Mercier-Darty , D. Vallenet et al.

MSphere, 2018, 3 (1), ⟨10.1128/mSphere.00553-17⟩

Article dans une revue hal-04283164v1
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Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches

Angélique Gobet , Tristan Barbeyron , Maria Matard-Mann , Ghislaine Magdelenat , David Vallenet et al.

Frontiers in Microbiology, 2018, 9, pp.2740. ⟨10.3389/fmicb.2018.02740⟩

Article dans une revue hal-01944299v1
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Transcriptome Profiles of Nod Factor-independent Symbiosis in the Tropical Legume Aeschynomene evenia

Djamel Gully , Pierre Czernic , Stéphane Cruveiller , Frédéric Mahé , Cyrille Longin et al.

Scientific Reports, 2018, 8 (1), pp.10934. ⟨10.1038/s41598-018-29301-0⟩

Article dans une revue hal-02506906v1
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Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement

Rainer Borriss , Antoine Danchin , Colin R. Harwood , Claudine Médigue , Eduardo P. C. Rocha et al.

Microbial Biotechnology, 2018, 11 (1), pp.3-17. ⟨10.1111/1751-7915.13043⟩

Article dans une revue cea-02291345v1
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MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

David Vallenet , Alexandra Calteau , Stéphane Cruveiller , Mathieu Gachet , Aurélie Lajus et al.

Nucleic Acids Research, 2017, 45 (D1), pp.D517-D528. ⟨10.1093/nar/gkw1101⟩

Article dans une revue cea-04320303v1

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

Karine Bastard , Alain Perret , Aline Mariage , Thomas Bessonnet , Agnès Pinet-Turpault et al.

Nature Chemical Biology, 2017, 13, pp.858-866. ⟨10.1038/nchembio.2397⟩

Article dans une revue cea-02132779v1
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Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria

Laurence Blanchard , Philippe Guérin , David Roche , Stéphane Cruveiller , David Pignol et al.

MicrobiologyOpen, 2017, 6 (4), pp.477 - 477. ⟨10.1002/mbo3.477⟩

Article dans une revue hal-01713005v1
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Complete genome sequence of Bradyrhizobium sp. ORS285, a photosynthetic strain able to establish Nod factor-dependent or Nod factor-independent symbiosis with aeschynomene legumes

Djamel Gully , Albin Teulet , Nicolas Busset , Nico Nouwen , Joël Fardoux et al.

Genome Announcements, 2017, 5 (30), pp.e00421-17. ⟨10.1128/genomeA.00421-17⟩

Article dans une revue cea-04315748v1
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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle , Rémi Planel , Simon Penel , David Chapulliot , Valérie Barbe et al.

Genome Biology and Evolution, 2017, 9 (12), pp.3413 - 3431. ⟨10.1093/gbe/evx255⟩

Article dans une revue hal-01913841v1
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Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

Elizabeth Ficko-Blean , Aurelie Prechoux , François Thomas , Tatiana Rochat , Robert Larocque et al.

Nature Communications, 2017, 8, pp.1685. ⟨10.1038/s41467-017-01832-6⟩

Article dans une revue hal-01899178v1

Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium

Jonathan Gerbore , Aline Brutel , Arnaud Lemainque , Barbara Mairey , Claudine Medigue et al.

Genome Announcements, 2016, 4 (2), ⟨10.1128/genomeA.00058-16⟩

Article dans une revue cea-04541792v1

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

Eugeni Belda , Ruben G. A. Van Heck , Maria José Lopez-Sanchez , Stéphane Cruveiller , Valérie Barbe et al.

Environmental Microbiology, 2016, 18 (10), pp.3403-3424. ⟨10.1111/1462-2920.13230⟩

Article dans une revue cea-04541789v1
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A new network representation of the metabolism to detect chemical transformation modules

Maria Sorokina , Claudine Medigue , David Vallenet

BMC Bioinformatics, 2015, 16, pp.385. ⟨10.1186/s12859-015-0809-4⟩

Article dans une revue cea-04573300v1
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Profiling the orphan enzymes

Maria Sorokina , Mark Stam , Claudine Médigue , Olivier Lespinet , David Vallenet

Biology Direct, 2014, 9 (1), pp.10. ⟨10.1186/1745-6150-9-10⟩

Article dans une revue (article de synthèse) hal-04011158v1

Large α-aminonitrilase activity screening of nitrilase superfamily members: Access to conversion and enantiospecificity by LC–MS

Franck Bordier , Mark Stam , Ekaterina Darii , Sabine Tricot , Aurélie Fossey et al.

Journal of Molecular Catalysis B: Enzymatic, 2014, 107, pp.79-88. ⟨10.1016/j.molcatb.2014.05.019⟩

Article dans une revue hal-02504052v1

Revealing the hidden functional diversity of an enzyme family

Karine Bastard , Adam Alexander Thil Smith , Carine Vergne-Vaxelaire , Alain Perret , Anne Zaparucha et al.

Nature Chemical Biology, 2014, 10 (1), pp.42-49. ⟨10.1038/nchembio.1387⟩

Article dans une revue hal-02504067v1
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RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium $Deinococcus\ deserti$

Arjan de Groot , David Roche , Bernard Fernandez , Monika Ludanyi , Stéphane Cruveiller et al.

Genome Biology and Evolution, 2014, 6 (4), pp.932-948. ⟨10.1093/gbe/evu069⟩

Article dans une revue hal-02014046v1
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Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

Jérémy Andres , Florence Arsène-Ploetze , Valérie Barbe , Céline Brochier-Armanet , Jessica Cleiss-Arnold et al.

Genome Biology and Evolution, 2013, 5 (5), pp.934-53. ⟨10.1093/gbe/evt061⟩

Article dans une revue hal-00972245v1
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Sinorhizobium strains comprising five genospecies

Masayuki Sugawara , Brendan Epstein , Brian Badgley , Tatsuya Unno , Lei Xu et al.

Genome Biology, 2013, 14 (2), pp.R17. ⟨10.1186/gb-2013-14-2-r17⟩

Article dans une revue cea-04669820v1

An updated metabolic view of the Bacillus subtilis 168 genome

Eugeni Belda , Agnieszka Sekowska , François Le Fèvre , Anne Morgat , Damien Mornico et al.

Microbiology, 2013, 159 (Pt_4), pp.757-770. ⟨10.1099/mic.0.064691-0⟩

Article dans une revue hal-04578023v1

The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle

A. Zoropogui , P. Pujic , Philippe Normand , Valérie Barbe , Patrick Belli et al.

BMC Genomics, 2013, 14 (1), pp.286. ⟨10.1186/1471-2164-14-286⟩

Article dans une revue hal-02522207v1

Genome Sequence of the Human- and Animal-Pathogenic Strain Nocardia cyriacigeorgica GUH-2

A. Zoropogui , Petar Pujic , Philippe Normand , Valérie Barbe , B. Beaman et al.

Journal of Bacteriology, 2012, 194 (8), pp.2098-2099. ⟨10.1128/JB.00161-12⟩

Article dans une revue hal-02531836v1
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Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

Stefan Engelen , David Vallenet , Claudine Médigue , Antoine Danchin

BMC Genomics, 2012, 13 (1), pp.69. ⟨10.1186/1471-2164-13-69⟩

Article dans une revue hal-04579011v1

The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

Adam Alexander Thil Smith , Eugeni Belda , Alain Viari , Claudine Médigue , David Vallenet

PLoS Computational Biology, 2012, 8 (5), ⟨10.1371/journal.pcbi.1002540⟩

Article dans une revue hal-00763496v1

Genome Sequence of Micromonospora lupini Lupac 08, Isolated from Root Nodules of Lupinus angustifolius

P. Alonso-Vega , Philippe Normand , R. Bacigalupe , Petar Pujic , A. Lajus et al.

Journal of Bacteriology, 2012, 194 (15), pp.4135-4135. ⟨10.1128/JB.00628-12⟩

Article dans une revue hal-02532800v1
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MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

David Vallenet , Eugeni Belda , Alexandra Calteau , Stéphane Cruveiller , Stefan Engelen et al.

Nucleic Acids Research, 2012, 41 (D1), pp.D636 - D647. ⟨10.1093/nar/gks1194⟩

Article dans une revue hal-04578153v1
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Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia

Damien Mornico , Lucie Miche , Gilles Bena , Nico Nouwen , Andre Vermeglio et al.

Genes, 2012, 3 (1), pp.35-61. ⟨10.3390/genes3010035⟩

Article dans une revue hal-01791870v1
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Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics

P.N. Bertin , A. Heinrich-Salmeron , E. Pelletier , F. Goulhen-Chollet , F. Arsène-Ploetze et al.

The International Society of Microbiologial Ecology Journal, 2011, 5 (11), pp.1735-1747. ⟨10.1038/ismej.2011.51⟩

Article dans une revue hal-01631857v1
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A Novel Acyl-CoA Beta-Transaminase Characterized from a Metagenome

Alain Perret , Christophe Lechaplais , Sabine Tricot , Nadia Perchat , Carine Vergne et al.

PLoS ONE, 2011, 6 (8), pp.e22918. ⟨10.1371/journal.pone.0022918⟩

Article dans une revue hal-04579105v1
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Reannotation of the genome sequence of Clostridium difficile strain 630.

Marc Monot , Caroline Boursaux-Eude , Marie Thibonnier , David Vallenet , Ivan Moszer et al.

Journal of Medical Microbiology, 2011, 60 (8), pp.1193-9. ⟨10.1099/jmm.0.030452-0⟩

Article dans une revue pasteur-01370838v1
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Ralstonia syzygii, the Blood Disease Bacterium and Some Asian R. solanacearum Strains Form a Single Genomic Species Despite Divergent Lifestyles

Benoît Remenant , Jean-Charles de Cambiaire , Gilles Cellier , Jonathan M Jacobs , Sophie Mangenot et al.

PLoS ONE, 2011, 6 (9), pp.e24356. ⟨10.1371/journal.pone.0024356⟩

Article dans une revue hal-04579060v1

Complete Genome Sequence of Streptomyces cattleya NRRL 8057, a Producer of Antibiotics and Fluorometabolites.

Valérie Barbe , Madeleine Bouzon , Sophie Mangenot , Bernard Badet , Julie Poulain et al.

Journal of Bacteriology, 2011, 193 (18), pp.5055-6. ⟨10.1128/JB.05583-11⟩

Article dans une revue hal-00628567v1

Core and Panmetabolism in Escherichia coli

Gilles Vieira , Victor Sabarly , Pierre-Yves Bourguignon , Maxime Durot , Francois Le Fevre et al.

Journal of Bacteriology, 2011, 193 (6), pp.1461 - 1472. ⟨10.1128/JB.01192-10⟩

Article dans une revue hal-02646830v1

Large-scale transposon mutagenesis of photosynthetic <em>Bradyrhizobium</em> sp. strain ORS278 reveals new genetic loci putatively important for nod-independent symbiosis with <em>Aeschynomene</em> indica

Katia Bonaldi , Benjamin Gourion , Joel Fardoux , Laure Hannibal , Fabienne Cartieaux et al.

Molecular Plant-Microbe Interactions, 2010, 23 (6), pp.760-770. ⟨10.1094/MPMI-23-6-0760⟩

Article dans une revue hal-02662597v1

The Frankia alni Symbiotic Transcriptome

Nicole Alloisio , Clothilde Queiroux , Pascale Fournier , Petar Pujic , Philippe Normand et al.

Molecular Plant-Microbe Interactions, 2010, 23 (5), pp.593-607. ⟨10.1094/MPMI⟩

Article dans une revue hal-00599356v1

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

Valérie Barbe , Stéphane Cruveiller , Frank Kunst , Patricia Lenoble , Guillaume Meurice et al.

Microbiology, 2009, 155 (6), pp.1758-1775. ⟨10.1099/mic.0.027839-0⟩

Article dans une revue hal-04581597v1
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Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Marie Touchon , Claire Hoede , Olivier Tenaillon , Valérie Barbe , Simon Baeriswyl et al.

PLoS Genetics, 2009, 5 (1), pp.e1000344. ⟨10.1371/journal.pgen.1000344⟩

Article dans une revue hal-00390293v1

A Conserved Gene Cluster Rules Anaerobic Oxidative Degradation of L-Ornithine

Nuria Fonknechten , A. Perret , N. Perchat , S. Tricot , C. Lechaplais et al.

Journal of Bacteriology, 2009, 191 (9), pp.3162-3167. ⟨10.1128/JB.01777-08⟩

Article dans une revue hal-02503069v1
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MicroScope: a platform for microbial genome annotation and comparative genomics

David Vallenet , S. Engelen , D. Mornico , S. Cruveiller , L. Fleury et al.

Database - The journal of Biological Databases and Curation, 2009, 2009, bap021. ⟨10.1093/database/bap021⟩

Article dans une revue hal-04581832v1
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NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis

Christophe Rusniok , D. Vallenet , S. Floquet , H. Ewles , C. Mouzé-Soulama et al.

Genome Biology, 2009, 10 (10), pp.R110. ⟨10.1186/gb-2009-10-10-r110⟩

Article dans une revue pasteur-00663857v1
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Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

Stéphane Vuilleumier , Ludmila Chistoserdova , Ming-Chun Lee , Françoise Bringel , Aurélie Lajus et al.

PLoS ONE, 2009, 4 (5), pp.e5584. ⟨10.1371/journal.pone.0005584⟩

Article dans une revue hal-00390607v1

A complete collection of single‐gene deletion mutants of Acinetobacter baylyi ADP1

Véronique de Berardinis , David Vallenet , Vanina Castelli , Marielle Besnard , Agnès Pinet et al.

Molecular Systems Biology, 2008, 4 (1), pp.174. ⟨10.1038/msb.2008.10⟩

Article dans une revue hal-02503013v1

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

Maxime Durot , François Le Fevre , Véronique de Berardinis , Annett Kreimeyer , David Vallenet et al.

BMC Systems Biology, 2008, 2 (1), pp.85. ⟨10.1186/1752-0509-2-85⟩

Article dans une revue hal-02503057v1
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Comparative analysis of acinetobacters: three genomes for three lifestyles

David Vallenet , Patrice Nordmann , Valérie Barbe , Laurent Poirel , Sophie Mangenot et al.

PLoS ONE, 2008, 3 (3), pp.e1805. ⟨10.1371/journal.pone.0001805⟩

Article dans une revue cea-04585511v1
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A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

Daniel Muller , Claudine Médigue , Sandrine Koechler , Valérie Barbe , ​mohamed Barakat et al.

PLoS Genetics, 2007, 3 (4), pp.e53. ⟨10.1371/journal.pgen.0030053⟩

Article dans une revue hal-00340034v1

Legumes Symbioses: Absence of Nod Genes in Photosynthetic Bradyrhizobia

Eric Giraud , Lionel Moulin , David Vallenet , Valérie Barbe , Eddie Cytryn et al.

Science, 2007, 316, pp.1307 - 1312. ⟨10.1126/science.1139548⟩

Article dans une revue halsde-00151340v1

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Philippe Normand , Pascal Lapierre , Louis S. Tisa , Johann Peter Gogarten , Nicole Alloisio et al.

Genome Research, 2007, 17, pp.7-15. ⟨10.1101/gr.5798407⟩

Article dans une revue halsde-00140365v1

Identification of the Last Unknown Genes in the Fermentation Pathway of Lysine

Annett Kreimeyer , Alain Perret , Christophe Lechaplais , David Vallenet , Claudine Médigue et al.

Journal of Biological Chemistry, 2007, 282 (10), pp.7191-7197. ⟨10.1074/jbc.M609829200⟩

Article dans une revue hal-02502995v1

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila.

Nicolas Vodovar , David Vallenet , Stéphane Cruveiller , Zoé Rouy , Valérie Barbe et al.

Nat Biotechnol, 2006, 24 (6), pp.673-9. ⟨10.1038/nbt1212⟩

Article dans une revue hal-00133119v1

MaGe: a microbial genome annotation system supported by synteny results

D. Vallenet

Nucleic Acids Research, 2006, 34 (1), pp.53-65. ⟨10.1093/NAR/GKJ406⟩

Article dans une revue hal-02985559v1

Global Comparison of the Membrane Subproteomes between a Multidrug-Resistant Acinetobacter baumannii Strain and a Reference Strain

Axel Siroy , Pascal Cosette , Damien Seyer , Christelle Lemaitre-Guillier , David Vallenet et al.

Journal of Proteome Research, 2006, 5 (12), pp.3385-3398. ⟨10.1021/pr060372s⟩

Article dans une revue hal-02339566v1

Channel Formation by CarO, the Carbapenem Resistance-Associated Outer Membrane Protein of Acinetobacter baumannii

Axel Siroy , Virginie Molle , David Vallenet , Martine Pestel-Caron , Alain Cozzone et al.

Antimicrobial Agents and Chemotherapy, 2005, 49 (12), pp.4876-4883. ⟨10.1128/AAC.49.12.4876-4883.2005⟩

Article dans une revue hal-02282922v1

Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii.

A. Siroy , V. Molle , C. Lemaitre-Guillier , David Vallenet , M. Pestel-Caron et al.

Antimicrob Agents Chemother, 2005, 49, pp.4876-4883

Article dans une revue hal-00313191v1

Expanding the portfolio of native Amine Dehydrogenases by extensive biodiversity screening

Carine Vergne-Vaxelaire , Eddy Elisée , Laurine Ducrot , Raphael Meheust , Mark Stam et al.

BioTrans 2023, Jun 2023, La Rochelle, France

Communication dans un congrès hal-04327737v1

Expanding the portfolio of enzymes for biocatalysis by extensive biodiversity screening

Carine Vergne-Vaxelaire , Eddy Elisée , Laurine Ducrot , Raphael Meheust , Mark Stam et al.

6e Symposium International de l'AFERP, Jul 2023, Orsay - Paris, France

Communication dans un congrès hal-04327790v1

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Jean Mainguy , Laura Bry , Quentin Fernandez De Grado , David Vallenet et al.

The local pangenome, Oct 2023, Alicante, Spain

Communication dans un congrès hal-04371302v1

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Laura Bry , Quentin Fernandez De Grado , David Vallenet , Alexandra Calteau

ISMB/ECCB 2023, ISCB ECCB, Jul 2023, Lyon, France

Communication dans un congrès hal-04371284v1

The MicroScope platform: 20 years of expertise in microbial genomics

Claudine Médigue , Alexandra Calteau , David Vallenet

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

Communication dans un congrès hal-04370626v1

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

Diverse Amine dehydrogenases for the biocatalytic synthesis of amines

Carine Vergne-Vaxelaire , Eddy Elisée , Laurine Ducrot , Ombeline Mayol , Raphael Meheust et al.

ENZYNOV'2, Oct 2023, Paris-Romainville, France

Communication dans un congrès hal-04327765v1

Expanding the portfolio of native Amine Dehydrogenases by extensive biodiversity screening

Carine Vergne-Vaxelaire , Eddy Elisée , Laurine Ducrot , Raphael Meheust , Mark Stam et al.

Amine BioCat 5.0, Nov 2022, Groningen, Netherlands

Communication dans un congrès hal-04328280v1

Metagenomic expansion and active site analysis of the Amine Dehydrogenase family

Elisée Eddy , Laurine Ducrot , Raphaël Méheust , Mark Stam , Pelletier Eric et al.

International Congress on Biocatalysis 2022, Aug 2022, Hamburg, Germany

Communication dans un congrès hal-04360123v1

Des pangénomes des microorganismes aux microbiotes

David Vallenet

Les pangénomes, mise à jour et exploitation en agriculture, Académie d'Agriculture de France, Apr 2022, Paris, France

Communication dans un congrès hal-04360283v1

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

MODAMDH: identification of diverse Amine Dehydrogenases by screening biodiversity using innovative in silico approaches

Eddy Elisée , Raphael Meheust , Laurine Ducrot , Mark Stam , Eric Pelletier et al.

International Symposium on High-Throughput Catalyst Design, Jun 2021, Lille (Virtual), France

Communication dans un congrès hal-04328578v1

Large scale exploration of the biocatalytic capability of biodiversity for biocatalysis & synthetic biology applications

Véronique de Berardinis , Jean-Louis Petit , Carine Vergne-Vaxelaire , David Vallenet , Anne Zaparucha

First International symposium on High-Throughput Catalysts Design, Jun 2021, Virtual conference (Lille), France

Communication dans un congrès hal-04315412v1

MODAMDH: identification of diverse Amine Dehydrogenases by screening biodiversity using sequence and structure-based approaches

Elisée Eddy , Laurine Ducrot , Raphaël Méheust , Karine Bastard , Aurélie Fossey-Jouenne et al.

29th Conference on Intelligent Systems for Molecular Biology (ISMB) - 20th European Conference on Computational Biology (ECCB), Jul 2021, Virtual conference, United States

Communication dans un congrès hal-04359840v1

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

Exploring biodiversity for biocatalyst discovery: applications to synthetic chemistry and synthetic biology

Véronique de Berardinis , Anne Zaparucha , David Vallenet , Carine Vergne , Jean-Louis Petit et al.

GMGM Open Scientific day & IPCB Inauguration, May 2019, Strabourg, France

Communication dans un congrès hal-04315453v1

Depicting microbial species diversity via a partitioned pangenome graph

David Vallenet

Animation Thématique "Pan-génomique végétale", GIS Biotechnologies Vertes, Jul 2019, Paris, France

Communication dans un congrès hal-04359803v1

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

Genome Mining for Enzyme Discovery: the role of bioinformatics

David Vallenet

20 ans Protéus, Sep 2018, Nîmes (France), France

Communication dans un congrès hal-04356328v1

Exploration of Acinetobacter baylyi ADP1 sulfur metabolism

Véronique de Berardinis , Alain Perret , Karine Bastard , David Vallenet , Jean-Louis Petit et al.

MicroScope Open Days (MOD), Laboratory of Bioinformatics Analyses for Genomics and Metabolism, May 2018, Paris, France

Communication dans un congrès hal-04315489v1
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PanGBank: a database of pangenome graphs for comparative microbial genomics

Jean Mainguy , Téo Lemane , Claudine Médigue , Alexandra Calteau , David Vallenet

EAGS 2026 - International Environmental and Agronomical Genomics symposium, Feb 2026, Paris, France.

Poster de conférence hal-05523557v1
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PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Laura Bry , Quentin Fernandez De Grado , David Vallenet , Alexandra Calteau

ISMB/ECCB 2023, Jul 2023, Lyon, France

Poster de conférence hal-04358457v1

An integrative bioinformatics approach to explore the biodiversity of enzyme families

Elisée Eddy , Mark Stam , Raphaël Méheust , Carine Vergne-Vaxelaire , David Vallenet

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, Jul 2022, Rennes, France

Poster de conférence hal-04360074v1

Metagenomic expansion and active site analysis of the Amine Dehydrogenase family

Elisée Eddy , Laurine Ducrot , Raphaël Méheust , Mark Stam , Pelletier Eric et al.

International Congress on Biocatalysis 2022, Aug 2022, Hamburg, Germany

Poster de conférence hal-04360138v1

MicroScope: a web platform for microbial genome annotation through pangenomic and metabolic analysis

Alexandra Calteau , Mathieu Dubois , Jérôme Arnoux , Adelme Bazin , Mylène Beuvin et al.

The 2nd FEMS Conference on Microbiology, Jun 2022, Belgrade, Serbia

Poster de conférence hal-04371191v1
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PANORAMA : comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Alexandra Calteau , David Vallenet

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, Jul 2022, Rennes, France

Poster de conférence hal-04371243v1

MicroScope: a web platform for microbial genome annotation through pangenomic and metabolic analysis

Alexandra Calteau , Mathieu Dubois , Jérôme Arnoux , Lucie Coffion , Stéphanie Fouteau et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, Jul 2022, Rennes, France

Poster de conférence hal-04360324v1

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Jérôme Arnoux , Alexandra Calteau , David Vallenet

The 2nd FEMS Conference on Microbiology, Jun 2022, Belgrade, Serbia

Poster de conférence hal-04371199v1

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

Alexandra Calteau , Mathieu Dubois , Jérôme Arnoux , Adelme Bazin , Mylène Beuvin et al.

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

Poster de conférence hal-04360241v1

MicroScope: an Integrated Platform for the Annotation and Exploration of Microbial Gene Functions through Genomic, Pangenomic and Metabolic Comparative Analysis

Alexandra Calteau , Mathieu Dubois , Adelme Bazin , Mylène Beuvin , Stéphanie Fouteau et al.

World Microbe Forum 2021, Jun 2021, Virtual, United States

Poster de conférence hal-04360076v1

MODAMDH: identification of diverse Amine Dehydrogenases by screening biodiversity using sequence and structure-based approaches

Elisée Eddy , Laurine Ducrot , Raphaël Méheust , Karine Bastard , Aurélie Fossey-Jouenne et al.

BioTrans 2021, Jul 2021, Graz (Virtual Conference), Austria

Poster de conférence hal-04360034v1

MODAMDH: identification of diverse Amine Dehydrogenases by screening biodiversity using sequence and structure-based approaches

Elisée Eddy , Laurine Ducrot , Raphaël Méheust , Karine Bastard , Aurélie Fossey-Jouenne et al.

29th Conference on Intelligent Systems for Molecular Biology (ISMB) - 20th European Conference on Computational Biology (ECCB), Jul 2021, Virtual conference, United States

Poster de conférence hal-04359878v1

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

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

David Vallenet , Alexandra Calteau , Paul Amours , Jérôme Arnoux , Adelme Bazin et al.

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

Poster de conférence hal-04359963v1

PanFam: a pangenomic workflow for the iterative construction of gene families on thousands of genomes

Jérôme Arnoux , Mylène Beuvin , Adelme Bazin , Alexandra Calteau , David Vallenet

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

Poster de conférence hal-04360011v1

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

Analyzing prokaryotic transcriptomics in the light of genome data with the MicroScope platform

David Roche , Alexandra Calteau , David Vallenet

Francis Martin; Stephane Uroz. Microbial Environmental Genomics (MEG), 2605, Springer US, pp.241-270, 2022, Methods in Molecular Biology, 978-1-0716-2871-3. ⟨10.1007/978-1-0716-2871-3_13⟩

Chapitre d'ouvrage cea-04286744v1
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Des génomes au métabolisme des microorganismes

David Vallenet

Bio-Informatique, Biologie Systémique [q-bio.QM]. Université d'Évry-Val-d'Essonne, 2020

HDR tel-04355465v1