Contact
Email: anne-laure.abraham@inrae.fr Adress: INRAE - MaIAGE Unit Domaine de Vilvert - Bat 233 78352 JOUY-EN-JOSAS CEDEX Phone: +33 1 34 65 22 36 |
Research interest
I am interested in the development of new methods to study microbial ecosystem with metagenomic sequencing.
On-going projects
- Holovini (2023-2026)
- TANDEM (2021-2023)
- Metachick-2 (2021-2022)
Publications
All my publications and communications are available on HAL INRAE and google schoolar
Bioinformatics working groups
- 2013-now Co-organiser of metagenomics working group of PEPI IBIS
- 2019-now In charge of the Workpackage ANNOT of the CATI BOOM
- 2015-2021 Board member of PEPI IBIS
Supervising and co-supervising
- 2023 - Mia Legras M2 internship - Master of Bioinformatics - University Paris City (6 months)
Identification of strain fluxes in a dairy food chain - 2021-2023 - Solène Pety M2 apprenticeship - Master of Bioinformatics - Rouen University (17 months)
Development of methods for strain and genes fluxes from metagenomic datasets along an food production chain - 2019-2022 - Benoit Goutorbe Ph. D student - Paris Saclay University
Developement & implementation of a precise method for human microbiota study with a clinical application - 2021 - Nathan Godart L3 internship, Poitiers University (3 months)
Test of Antobiotic Resistance Gene haplotype reconstructions methods in metagenomic datasets 2020-2021 - Anne-Carmen Sanchez M2 internship - Paris 6 University - Fixed-term contract engineer (11 months)
Analysis of microbial diversity in metagenomic datasets - Analysis of genes and strains fluxes in chicken metagenomes2019 - Yassin El Djoudi L3 internship, Poitiers University (3 months)
Intraspecific polymorphism study on gut microbiota prevalent species from sequenced genomes.2018 - Daniel de Murat M1 internship - Master of Bioinformatics, Paris 7 University (4 months)
Comparative analysis of metagenomic analysis tools.2017-2019 - Quentin Cavaillé Fixed-term contract engineer (18 months).
Development of a tool for cheese ecosystem analysis with metagenomic datasets.2015-2017 - Thibaut Guirimand Fixed-term contract engineer (23 months).
Development of a tool for cheese ecosystem analysis with metagenomic datasets.2014-2016 - Charlie Pauvert M1 internship and M2 apprenticeship (2 years) - Master of Bioinformatics - Rouen University.
Cheese ecosystems metagenomics - Explorations & improvements around a bioinformatics tool- 2012 - Amira Hamdi M2 internship - Master of Bioinformatics - Evry Universty Cheese ecosystem analyses
Teaching
- 2013-2019: Introduction to metagenomic 16S analysis - 4 days - Migale plateform training
- 2017 & 2019: Analysis of shotgun metagenomic data with FoodMicrobiomeTransfert tool - 2 days
- 2018: Metabarcoding - 5 days - Roscoff Abyms plateform
Background
Since 2017 : Research engineer in bioinformatics in MaIAGE Unit, team StatInfOmics
2011- 2016 : Research engineer in bioinformatics in Micalis, teams FME, Fine, IFE
2010 - 2011 : Post-Doc at IBENS (12 months) - Supervisor: Lionel Navarro
2009 - 2010 : Post Doc at ENS-Lyon (18 months) - Supervisor: Gaël Yvert
2005 - 2009 : Ph. D in bioinformatics in Atelier de Bioinformatique de Paris 6 - Supervisors: Eduardo Rocha and Joël Pothier