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Genetics

D-Index
50
Citations
14778
World Ranking
3903
National Ranking
204

Overview

David Vallenet is affiliated with the University of Paris-Saclay in France. Their research focusses primarily on the field of Biochemistry, Genetics and Molecular Biology, with a strong emphasis on Molecular Biology. Other subfields include Genetics, Ecology, Materials Chemistry, and Plant Science.

The main topics of their academic work cover a range of areas within molecular and microbial biology such as:

  • Genomics and Phylogenetic Studies
  • Bioinformatics and Genomic Networks
  • RNA and protein synthesis mechanisms
  • Bacterial Genetics and Biotechnology
  • Machine Learning in Bioinformatics
  • Microbial Metabolic Engineering and Bioproduction
  • Microbial Community Ecology and Physiology

Recent publications by David Vallenet illustrate their involvement in bioinformatics and microbial genomics. Notable works include:

  • PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph, 2020, PLoS Computational Biology
  • A roadmap for the functional annotation of protein families: a community perspective, 2022, Database
  • panRGP: a pangenome-based method to predict genomic islands and explore their diversity, 2020, Bioinformatics
  • A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century, 2023, Microbial Biotechnology
  • From Strain Characterization to Field Authorization: Highlights on Bacillus velezensis Strain B25 Beneficial Properties for Plants and Its Activities on Phytopathogenic Fungi, 2021, Microorganisms

David Vallenet frequently publishes in several scientific venues, including:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Microbiology Resource Announcements
  • PLoS Computational Biology
  • Bioinformatics
  • Nature Communications

Their collaborative work involves regular co-authorship with several researchers, most frequently with Alexandra Calteau, Adelme Bazin, Claudine Médigue, Eddy Elisée, and Guillaume Gautreau.

Best Publications

  • Deciphering the evolution and metabolism of an anammox bacterium from a community genome

    Marc Strous;Eric Pelletier;Sophie Mangenot;Thomas Rattei

  • Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

    Marie Touchon;Marie Touchon;Claire Hoede;Olivier Tenaillon;Valérie Barbe

  • Comparative Genomics of Multidrug Resistance in Acinetobacter baumannii

    Pierre-Edouard Fournier;David Vallenet;Valérie Barbe;Stéphane Audic

  • Legumes Symbioses: Absence of Nod Genes in Photosynthetic Bradyrhizobia

    Eric Giraud;Lionel Moulin;David Vallenet;Valérie Barbe

  • Genome sequences of Escherichia coli B strains REL606 and BL21(DE3).

    Haeyoung Jeong;Valérie Barbe;Choong Hoon Lee;Choong Hoon Lee;David Vallenet

  • 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

  • Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125

    Claudine Médigue;Evelyne Krin;Géraldine Pascal;Valérie Barbe

  • MaGe: a microbial genome annotation system supported by synteny results

    David Vallenet;Laurent Labarre;Zoé Rouy;Valérie Barbe

  • Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

    Valérie Barbe;David Vallenet;Nuria Fonknechten;Annett Kreimeyer

  • 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

  • MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

    David Vallenet;Eugeni Belda;Alexandra Calteau;Stéphane Cruveiller

  • Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

    David Vallenet;Patrice Nordmann;Valérie Barbe;Laurent Poirel

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

    Véronique de Berardinis;David Vallenet;Vanina Castelli;Marielle Besnard

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

    Eugeni Belda;Eugeni Belda;Ruben G. A. van Heck;Maria Jose Lopez-Sanchez;Stephane Cruveiller

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

    Nicolas Vodovar;David Vallenet;Stéphane Cruveiller;Zoé Rouy

  • MicroScope: a platform for microbial genome annotation and comparative genomics

    David Vallenet;Stefan Engelen;Damien Mornico;Stéphane Cruveiller

  • 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

  • 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

  • A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

    Daniel Muller;Claudine Médigue;Sandrine Koechler;Valérie Barbe

  • MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

    David Vallenet;Alexandra Calteau;Stéphane Cruveiller;Mathieu Gachet

Frequent Co-Authors

Claudine Médigue
Claudine Médigue University of Paris-Saclay
Jean Weissenbach
Jean Weissenbach Centre national de la recherche scientifique, CNRS
Valérie Barbe
Valérie Barbe Centre national de la recherche scientifique, CNRS
Antoine Danchin
Antoine Danchin Institut Cochin
Philippe Normand
Philippe Normand Claude Bernard University Lyon 1
David Pignol
David Pignol Aix-Marseille University
Erick Denamur
Erick Denamur Université Paris Cité
Eduardo P. C. Rocha
Eduardo P. C. Rocha Institut Pasteur
Gurvan Michel
Gurvan Michel Université Paris Cité
Arnaud Couloux
Arnaud Couloux French Alternative Energies and Atomic Energy Commission (CEA)

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