Associate professor at Université Paris Cité.

A taste for challenges at the interfaces (both human and scientific) and teamwork. Strong interest in computational problem solving in biology. High scientific appeal for data management and analysis of biological data.

Research activities

Since 2024

My research is conducted at the Laboratory of Theoretical Biochemistry (Institut de Biologie Physico-Chimique). I study the sharing and reuse of data produced during molecular dynamics simulations. I also analyze this data using systemic approaches.

Related publication:

• MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations (2023)

2017-2023

I am working with the Mitochondria, Metals and Oxidative Stress research group and the Proteomics & mass spectrometry facility, at Institut Jacques Monod.

In tight collaboration with wet-lab biologists, I develop new methods to analyse mass spectrometry data.

Related publications:

• Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy (2021),
• AutoClassWrapper: a Python wrapper for AutoClass C classification (2019),
• Pixel: a content management platform for quantitative omics data (2019).

2014-2016

Visiting scientist at the Fondation Congolaise pour la Recherche Médicale (FCRM).

I am studying high-burden deseases like HIV (especially prevention of mother-to-child transmission), tuberculosis (improvement of clinical diagnosis) and malaria.

One of my projects concerns the development of digital solutions to fight malaria. By digital solutions I mean web or mobile applications to improve the diagnosis of malaria or the prevention and knowledge of this disease. To achieve this goal, I am working with Fongwama, the Congolese Plateforme for open-source development, created by Fondation ECAir and Skepsos.

Related publications:

• HIV-1 Genetic Diversity in the Republic of Congo: Seventeen Years in Review (2015),
• Diagnosis of smear-negative pulmonary tuberculosis based on clinical signs in the Republic of Congo (2015),
• Factors influencing acceptability of voluntary HIV testing among pregnant women in Gamboma, Republic of Congo (2015),
• Prevention of Mother-to-Child HIV Transmission (PMTCT) in the Republic of Congo: Challenges to Implementation (2015).

2007 - 2012

Research work performed in the DSIMB bioinformatics group of the lab “Protéines de La Membrane Erythrocytaire et Homologues Non-Erythroides” (Inserm UMR-S 665 and University Paris Diderot – Paris 7), hosted at the INTS.
topics: macromolecular assemblies, structural bioinformatics
collaborators: D. Flatters (now at MTi), JC. Gelly (DSIMB), C. Etchebest (DSIMB), A. de Brevern (DSIMB), V. Jallu (Laboratoire d’Immunologie Plaquettaire, INTS), C. Prévost (Laboratoire de Biochimie Théorique, IBPC, CNRS).

Related publications:

• Protein flexibility in the light of structural alphabets (2015),
• An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA (2015),
• Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants (2014),
• Cis–trans isomerization of omega dihedrals in proteins (2013),
• The αIIb p.Leu841Met (Cab3a+) Polymorphism Results in a New Human Platelet Alloantigen Involved in Neonatal Alloimmune Thrombocytopenia (2013),
• Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIbβ3 Integrin (2012),
• Ten Simple Rules for Getting Help from Online Scientific Communities (2011),
• Detection and Architecture of Small Heat Shock Protein Monomers (2010).

2006 - 2007

Post-doc at Laboratoire de Biochimie Théorique , UPR 9080 CNRS, Paris, France.
topics : flexible protein/DNA docking, coarse grain DNA model development, C++/Python library (PTools)
collaborators : A. Saladin and C. Prévost

Publications:

• Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments (2010).
• PTools: an opensource molecular docking library (2009),
• Insights on protein-DNA recognition by coarse grain modelling (2008),

2003 - 2006

PhD student at Laboratoire de spectrométie ionique et moléculaire (Lasim) , UMR 5579, CNRS and Université Lyon 1, France.
topics : statistical approach of the structure and dynamics of isolated proteines
supervisor: P. Dugourd, head of the "Electric dipole, biomolecules and clusters" group.
abstract : this work is a theoretical study of the thermodynamical properties of polypeptides in the gas phase. We aim to a better understanding of the fundamental mechanisms involved in protein folding. A statistical approach based on Monte Carlo algorithms applied in generalized ensembles, such as Replica Exchange Method or Wang-Landau method, has been used to sample the rugged energy landscape of these molecules. The peptides were composed of 2 to 20 amino acids and have been modelized by the Amber 96 forcefield. Simulations have been realized in strong relation with experimental progress of the group. We thus tried to understand the influence of the secondary structure on photofragmentation mechanism, the role of entropy in the stabilisation of beta sheets and the effect of intense and static electric field on peptide conformation.
Download my PhD thesis locally [PDF, 4.9 Mb, French] or on the CNRS TEL multidisciplinary thesis server.

Publications:

• Transitions between secondary structures in isolated polyalanines (2009),
• Competition between secondary structures in gas phase polyalanines (2007),
• Performances of Wang-Landau algorithms for continuous systems (2006),
• Comparison of the fragmentation pattern induced by collisions, laser excitation and electron capture. Influence of the initial excitation (2006),
• Monte Carlo simulations of flexible molecules in a static electric field: electric dipole and conformation (2005),

Older & shorter

March - September 2003

Biomolecular Sciences department, UMIST, Manchester, UK
topics: automatic extraction of the toxic properties of compounds from the biomedical literature
supervisor: B. J. Stapley
abstract: Automatic information extraction from free-text documents encompasse a set of techniques and tools already well known, but its application to biology is relatively new. Thus, this project aims to predict and/or extract toxicological properties of some compounds using information extraction and retrieval techniques. Nowadays, toxicological data are issued from in vitro and in vivo tests that are expensive and time-consuming for the pharmaceutical industry. As a consequence, and given the large body of information latent in bibliographic databases, the prediction of toxic information on possible therapeutic compounds becomes particularly important.

July - August 2001

Laboratoire d'ImmunoGénétique Moléculaire (LIGM) , Montpellier, France.
topics: 3D visualization tools for IMGT structural data
supervisors: M. Ruiz and M.-P. Lefranc
abstract: IMGT, the international ImMunoGeneTics database is an integrated database, specializing in immunoglobulins (Ig), T-cells receptors (TcR) and major histocompatibily complex (MHC) molecules of all species that was created in 1989 by Marie-Paule Lefranc (Montpellier II Unversity, CNRS, Montpellier, France) We aim to implement PERL scripts in order to compare 3D structures of proteins picked up in the IMGT database (use of STAMP).

Teaching activities

High involvement in pedagogy:

• Certificate in pedagogy in 2019 (Certifiens).
• Awards in digital educational innovations: EdTech 2018 for the Plasma project, IN2018 (live coding), Idex2020 (flipped classroom).

2007 - to present
Université de Paris.
Python programming, unix, proteomics, open science, bioinformatics project management (data, source code...).
Creation of two professionnal trainings in bioinformatics and omics data analysis.

2003 - 2006
Multidisciplanary engineering university Institut National des Sciences Appliquées de Lyon (INSA Lyon)
First year chemistry workshops (total of 288 hours, 255 students).

22 - 27/05/2005
Summer school "Modelisation, dynamique et thermodynamique des agrégats et molécules complexes"
Modelisation workshop: simulated annealing and parallel tempering simulations of a dipeptide.

Collective duty

Member of the steering committee of :

• the integrative platform for omics projects at Université de Paris (iPOP-UP)
• the bioinformatics and biostatistics platform of Epigenetics and Cell Fate lab
• IT departement of Institut Jacques Monod

Head of the IT service of the Life Sciences Department

Academic training

2003 - 2006
PhD in Physics, Lasim, Université Lyon 1, France

2002 - 2003
MSc in Cheminformatics, UMIST, Manchester, U.K.

2000 - 2003
"Diplôme d'Ingénieur Chimiste" at the Ecole Nationale Supérieure de Chimie de Montpellier (the National Graduate School of Chemistry, Montpellier)

1997 - 2000
Classes Préparatoires aux Grandes Ecoles, preparatory classes leading to French institutes. Lycée Henri Bergson, Angers, France.

1997
Baccalauréat in Sciences, i.e. High School diploma
Lycée David d'Angers, France.

Languages

• French: native fluency
• English: good level in spoken and written English
• Munukutuba: elementary proficiency

Computers skills

• operating systems [administration]: GNU/Linux (Ubuntu, Debian)
• office software: Microsoft Office and OpenOffice.org
• programming: Python, Bash
• data analysis and visualisation with Python: Pandas, Matplotlib, Plotly
• text formating: LaTeX, HTML, Markdown

Professional address

Institut Jacques Monod (IJM)
Building Buffon
15 rue Hélène Brion
75015 Paris France

My office is on the third floor, room 390B. Here are directions for visitors to find the IJM.