Research engineer



David Goudenège is in charge of bioinformatics related to different omics data (metagenomics, metaviromics) used to highlight the complex eco-evolutionary dynamics of environmental pathogens and to explore disease emergence and virulence mechanisms. Having acquired substantial background and experience in comparative genomic, phylogenomic and NGS data analysis, his work consists in using and/or developing in silico tools and pipelines.



2021              Bioinformatic research engineer, IFREMER, Marine station of Sorbonne University,Roscoff (France).

2014-2021   Bioinformatician in clinical and research genetics at Angers University Hospital Centre (France).

2011-2014   Postdoctoral research fellow with Dr Frédérique Le Roux,  Marine station of Sorbonne University,
                        Roscoff (France). ResearchProject: "Bioinformatic to study the emergence of marine invertebrate
                        pathogens in Vibrio  populations". 

2007-2011   Ph.D. degree (Bioinformatic) with Dr Frédérique Barloy-Hubler, Rennes 1 University (France).
                        Title: Subcellular protein localization in silico prediction in prokaryotes.

2005-2007   Master 2 degree (Bioinformatic), Nantes University (France)

1999-2004   Master 1 degree (Population and Ecosytem Biology), La Réunion University (France)



2016 to 2021- Bioinformatic, DUT 2, IUT Angers





1- Charif M, Bris C, Goudenège D, Desquiret-Dumas V, Colin E, Ziegler A, Procaccio V, Reynier P, Bonneau D, Lenaers G, Amati-Bonneau P.

 Use of Next-Generation Sequencing for the Molecular Diagnosis of 1,102 Patients With a Autosomal Optic Neuropathy. Front Neurol. 2021 Mar 25;12:602979.

2- Aurrière J, Goudenège D, Baris OR, Boguenet M, May-Panloup P, Lenaers G, Khiati S. Cancer/Testis Antigens into mitochondria: a hub between spermatogenesis, tumorigenesis and mitochondrial physiology adaptation. Mitochondrion. 2021 Jan;56:73-81.

3- Ziegler A, Colin E, Goudenège D, Bonneau D. A snapshot of some pLI score pitfalls. Hum Mutat. 2019 Jul;40(7):839-841.

4- Bris C, Goudenege D, Desquiret-Dumas V, Charif M, Colin E, Bonneau D, Amati-Bonneau P, Lenaers G, Reynier P, Procaccio V. Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing. Front Genet. 2018 Dec 11;9:632.

5- Goudenège D, Bris C, Hoffmann V, Desquiret-Dumas V, Jardel C, Rucheton B, Bannwarth S, Paquis-Flucklinger V, Lebre AS, Colin E, Amati-Bonneau P, Bonneau D, Reynier P, Lenaers G, Procaccio V. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med. 2019 Jun;21(6):1407-1416.

6- Wakim J, Goudenege D, Perrot R, Gueguen N, Desquiret-Dumas V, Chao de la Barca JM, Dalla Rosa I, Manero F, Le Mao M, Chupin S, Chevrollier A, Procaccio V, Bonneau D, Logan DC, Reynier P, Lenaers G, Khiati S. CLUH couples mitochondrial distribution to the energetic and metabolic status. J Cell Sci. 2017 Jun 1;130(11):1940-1951.

7- Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F. Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. ISME J. 2015 Jul;9(7):1523-31.

8- Goudenège D, Travers MA, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A, Le roux F. A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters. Environ Microbiol. 2015 Nov;17(11):4189-99.

9- Goudenège D, Boursicot V, Versigny T, Bonnetot S, Ratiskol J, Sinquin C, LaPointe G, Le Rous F, Delbarre-Ladrat C. Genome sequence of Vibrio diabolicus and identification of the exopolysaccharide HE800 biosynthesis locus. Appl Microbiol Biotechnol. 2014 Dec;98(24):10165-76.

10- Vanhove AS, Duperthuy M, Charrière GM, Le Roux F, Goudenège D, Gourbal B, Kieffer-Jaquinod S, Couté Y, Wai SN, Destoumieux-Garzón D. Outer membrane vesicles are vehicles for the delivery of Vibrio tasmaniensis virulence factors to oyster immune cells. Environ Microbiol. 2015 Apr;17(4):1152-65.

11- Goudenège D, Labreuche Y, Krin E, Ansquer D, Mangenot S, Calteau A, Médigue C, Mazel D, Polz MF, Le Roux F. Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits. ISME J. 2013 Oct;7(10):1985-96.

12- Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F. CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC Microbiol. 2010 Mar 23;10:88.