PhD Ecophysiologist & Data Scientist
Experiences
Researcher Bioinformatics & Data Science
- From Jan. 2019 to sept. 2023
- Company: LIRMM-UM-CNRS
- Location: Montpellier, France
I work on different subjects related to cancer research (specific gene impact, chemiotherapy), to fundamental research (mRNA modelisation), to plant adaptation mechanisms and to biodiversity.
I develop methods and design workflows for diverses NGS sequencing, realize statistical analysis and perform new visualisations.
I co-anime a formation for profesionals in data analysis and bioinformatics through the CNRS Formations (Bioinformatique pour le traitement de données de séquençage (NGS)).
Projects:
- GEM
- dipwmsearch
- FTO
- 5-FU
- translatome
- RESIST2OME (coming soon)
- TRANSLATOL (coming soon)
- MELANOMA (coming soon)
- Splicing (coming soon)
Languages: python, R, shell, java, yaml, html, css, pandas Workflow: snakemake, conda, docker
Post-doc Bioinformatics & Data Science
- From nov. 2018 to dec. 2018
- Company: Institut Agronomique néo-Calédonien
- Location: Noumea, New Caledonia
Data management and analyses for the CNRT BioIndic project.
- Languages: shell, R, python, yaml
- Workflow: snakemake, conda
Post-doc Bioinformatics & Data Science
- From august 2017 to oct. 2018
- Company: IRD
- Location: UMR 9220 Entropie, Noumea, New Caledonia
Bioinformatic analyses of metatranscriptomic data for the ANR CARIOCA.
- Languages: shell, R, perl, yaml, python
- Workflow: snakemake, conda
Post-doc Bioinformatic & Data Science
- From nov. 2016 to juin 2017
- Company: University of Avignon
- Location Avignon, France
Lactuca genome comparisons in different postharvest conditions for Bonduelle Lactuca.
- Software: IGV, KEGG pathway, Blastx, R / BioConductor
Post-doc Data analysis & Data Science
- From nov. 2015 to sept. 2016
- Company: University of Avignon
- Location Avignon, France
Projects:
Study of plant and fruit metabolisms responses to abiotic stress (water stress, elicitors, UV and light) and biotic stress (botrytis cinerea, phytophthora infestans).
- Experimentation: Hormonal dosage/ Chlorophyll a fluorescence / Phytopathologic test
- Plants: tomato, lactuca, grappes, pepper
- Software: FIJI (language: jython), R (multivariate analyses), PEA+
PhD student Ecophysiology & Data Science
- From oct. 2011 to apr. 2015
- Company: INRA UR1115 PSH & University of Avignon
- Location: Avignon, France
“Effects of water stress, only or in interaction with a pathogen, on plant functioning and fruit quality of Solanum lycopersicum L., depending on genetic variation” Thesis
- Projects: ADAPTOM, TOMSEC and ANR-08-STRA-14
- Funding: SFR Tersys
- Teaching in Licence (72h per year): vegetal physiology, climate change adaptation and laboratory methodology
- Students training (trainee from licence to master degree)
- Software: R, PEA+, Shimadzu, ImageJ
Internship engineer
- From feb. 2010 to sept. 2010
- Company: USDA-ARS European Biological Control Laboratory
- Location: Montpellier, France
“Contribution of genetic and life history traits to the invasive power of Sylverleaf nightshade as part of a biological control program” Solanum elaeagnifolium
Internship engineer
- From feb. 2009 to july 2009
- Company: CIRAD
- Location: Montpellier, France & Kribi, Cameroon
“Interactions between the inflorescences of the oil palm Elaeis guineensis J. and their pollinators of the genus Elaeidobius spp. F. (Coleoptera: Curculionidae) in Central Africa” Elaeidobius
Expertise details
Biostatistics
- correlation networks
- parametric & non-parametric analyses
- multivariate analysis
- time-series analysis
- statistical & machine learnings
- deep learning
Bioinformatics
- computational sciences
- workflows
- integration
- tool knowledges
- multi-omics
Biology
- abiotic and biotic stresses
- photosynthesis
- plant development / fruit quality / plant defense
- co-evolution with micro-organisms
- senescence / oncology
Laboratory
- extraction and dosage
- volatil organic compounds
- microscopy
- chemistry: GC-MS, LC-MS, HPLC
- molecular biology
Qualifications
Recent qualifications
Teaching in University:
- Qualifications CNU (2022): sections 64 (bioinformatics), and 68 (organisms biology)
- Qualifications CNU (2017): sections 66 (physiology), 67 (ecology) and 68 (organisms biology)
Other:
- Training CNRS (2022): FIDLE deep learning
- Training CINES (2019): Atos Quantum Learning Machine
- MOOC INRIA (2015): 41001S02 'Python' (validated 100%)
Thesis in Agronomic Sciences
- University of Avignon
- Validated with mention TH (2015)
- Keywords: Physiology, Fruit quality, Water deficit, B. cinerea, OJIP model, Genetic variability
Master Bio-engineering
- University of Montpellier
- Validated with mention B (2010)
- Keywords: Biodetection kit, DNA chips, RFID, Project managing, ISO 9001 and 14001, HACCP, Sequencing, Bioinformatics
Bachelor degrees Biology-Ecology
- University of Perpignan
- Validated with mention P (2008)
- Keywords: Cellular and bacterial cultures, API gallery, Antibiogram, SIG, Fire risk training, Ecology, Parasitology
Monitoring / Teaching
- Trainee frames (BTS to PhD student)
- Supervision of engineers
- Teaching at University (Classes: Vegetal physiology, Initiation to laboratory working, Introduction to R, Climate Change adaptation)
- Professional formations for researchers & companies (in data analysis) on Bioinformatics for NGS with CNRS Formation
Professional associations
- Member of French Society of Bioinformatics (SFBI) since 2018
- Member of French Society of Statistics in 2016, 2017
- Member of the GSO, GDR Ecostat, GDR BIM, COST Translacore, MBI network and RNA Club