DV

David Vallenet

62%
Libre accès
122
Documents
Affiliation actuelle
  • Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM)
Contact

Présentation

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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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-04942957 v1
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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-04645174 v1
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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-04285418 v1
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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-04284953 v1
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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-03872975 v1
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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-03778996 v1
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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-04281352 v1

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-04283547 v1

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-04298243 v1

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-04178012 v1
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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-04284767 v1
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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-03089210 v1
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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-03512357 v1
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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-03027967 v1
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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-03322363 v1
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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-02122376 v1
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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-02626039 v1
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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-02403170 v1
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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-02291345 v1
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Evolutionary evidence of algal polysaccharide degradation acquisition by pseudoalteromonas carrageenovora 9(t) to adapt to macroalgal niches

Angélique Gobet , Tristan Barbeyron , Maria Matard-Mann , Ghislaine Magdelenat , David Vallenet et al.
Frontiers in Microbiology, 2018, 9, ⟨10.3389/fmicb.2018.02740⟩
Article dans une revue hal-02625316 v1
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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-02291353 v1
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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-04313474 v1

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-04283164 v1
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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
Article dans une revue hal-01944299 v1
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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-02506906 v1

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-02132779 v1
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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-04315748 v1
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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-01713005 v1
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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-04320303 v1
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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-01913841 v1
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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-01899178 v1

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-04541792 v1

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-04541789 v1
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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-04573300 v1

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-02504052 v1
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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-04011158 v1

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-02504067 v1
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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-02014046 v1
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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-00972245 v1
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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-04669820 v1

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-04578023 v1

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-02522207 v1
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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-04579011 v1

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-00763496 v1

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-02532800 v1

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-02531836 v1
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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-04578153 v1
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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-01791870 v1

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-02646830 v1
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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-01631857 v1
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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-04579105 v1
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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-01370838 v1
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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-04579060 v1

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-00628567 v1

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-02662597 v1

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-00599356 v1

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-02503069 v1
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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-00390293 v1

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-04581597 v1
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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-00663857 v1
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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-04581832 v1
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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-00390607 v1

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-02503013 v1

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-02503057 v1
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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-04585511 v1
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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-00340034 v1

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-00151340 v1

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-00140365 v1

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-02502995 v1

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-02339566 v1

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-00133119 v1

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-02985559 v1

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-00313191 v1

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-02282922 v1

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-04327765 v1

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-04327737 v1

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-04327790 v1

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-04371302 v1

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-04371284 v1

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-04370626 v1

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-04371316 v1

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-04328280 v1

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-04360283 v1

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-04360123 v1

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-04315412 v1

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-04328578 v1

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-04360257 v1

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-04359840 v1

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-04360043 v1

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-04359803 v1

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-04315453 v1

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-04358401 v1

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-04359455 v1

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-04356757 v1

Genome Mining for Enzyme Discovery: the role of bioinformatics

David Vallenet
20 ans Protéus, Sep 2018, Nîmes (France), France
Communication dans un congrès hal-04356328 v1

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-04355945 v1

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-04315489 v1
Image document

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-04358457 v1

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-04371199 v1

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-04360074 v1

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-04360138 v1

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-04371191 v1
Image document

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-04371243 v1

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-04360324 v1

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-04360241 v1

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-04359878 v1

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-04360076 v1

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-04360034 v1

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-04360000 v1

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-04359963 v1

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-04360011 v1

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-04358380 v1
Image document

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-04358338 v1
Image document

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-04358357 v1

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-04357657 v1
Image document

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-04356218 v1

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-04286744 v1
Image document

Des génomes au métabolisme des microorganismes

David Vallenet
Bio-Informatique, Biologie Systémique [q-bio.QM]. Université d'Évry-Val-d'Essonne, 2020
HDR tel-04355465 v1