coGSEA
comparative Analysis of Gene Set Enrichment analysis. R and transcriptomics. Also available as a Shiny GUI.
Professional Summary
I am Maxime, a Bioinformatics scientist specializing in the development of statistical tools and workflows for the analysis of omics data. I have extensive experience working with prokaryotic, eukaryotic, and human systems, and I excel at transforming complex biological datasets into scientific results through rigorous approaches and scalable bioinformatics solutions.
After an undergraduate degree in biology, I initially pursued studies in population and environmental sciences. After realizing I wanted to focus more on statistics and data analysis, I returned to complete an M.Sc. in Bioinformatics.
I completed my PhD in the Microbiome Sciences research group at the MPI-EVA, studying ancient DNA metagenomics, and continued this work as a postdoctoral researcher at the Leibniz-HKI with a focus on fermentation microbiomes. Recently, I transitioned to computational oncology and cancer research, focusing on personalized cancer vaccine development and the analysis of cancer genomics datasets.
Education
PhD candidate in Bioinformatics
Friedrich-Schiller-Universität Jena 🇩🇪
M.Sc. in Bioinformatics
Université Paris Diderot 🇫🇷
M.Sc. in Ecology and Environmental sciences
Université Joseph Fourier, Grenoble 🇫🇷
Exchange Semester
University of Nordland 🇳🇴
B.Sc. in Life Sciences
Université Paris Descartes 🇫🇷
Interests
Bioinformatics
Metagenomics
Machine Learning
Experience
Bioinformatics Scientist
TRON - Translational Oncology Mainz
Development of workflows and analysis of oncogenetics sequencing data for personalized cancer vaccine research.
Postdoctoral Researcher in Bioinformatics
Leibniz Institut for Natural Product Research and Infection Biology Hans Knöll Institute
Bioinformatic metagenomic analysis of ancient fermentation microbiomes.
Doctoral Researcher in Bioinformatics
Max Planck Institute for Evolutionary Anthropology
Development of tools and pipelines for the analysis of ancient DNA metagenomics data.
Bioinformatics Doctoral Researcher
Max Planck Institute for the Science of Human History
Development of tools and pipelines for the analysis of ancient DNA metagenomics data.
Bioinformatics Research intern
Natural History Museum - CNRS
Development of tools and pipelines for the analysis of ancient DNA metagenomics data.
Bioinformatics Research intern
Institut Pasteur
Development of a tool in R and Shiny for comparison of expression level in multi-omics data.
Bioinformatics Research assistant
CRG
Exploration of the human oral mycobiome.
Research intern
MPI-EVA
Detection of gene duplications between Neanderthal and Mordern Humans.
Guest researcher
University of Oslo
Development of new markers and metagenomics softwares for plant identification. De novo and mapping assembly of Illumina data, phylogeny of the Anacyclus genus, and metabarcoding visualization software development.
Education
PhD candidate in Bioinformatics
Friedrich-Schiller-Universität Jena 🇩🇪
2018-2023
M.Sc. in Bioinformatics
Université Paris Diderot 🇫🇷
2016-2018
M.Sc. in Ecology and Environmental sciences
Université Joseph Fourier, Grenoble 🇫🇷
2014-2015
Exchange Semester
University of Nordland 🇳🇴
2013
B.Sc. in Life Sciences
Université Paris Descartes 🇫🇷
2011-2014
Publications
(2026).
nf-core/coproID v2.0: An improved pipeline for the identification of (palaeo)faecal depositors.
Journal of Open Source Software.
(2024).
Introduction to Ancient Metagenomics Textbook.
Zenodo.
(2024).
Facilitating Accessible, Rapid, and Appropriate Processing of Ancient Metagenomic Data with AMDirT.
F1000Research.
(2023).
TAXPASTA: TAXonomic Profile Aggregation and STAndardisation.
Journal of Open Source Software.
(2023).
Natural Products from Reconstructed Bacterial Genomes of the Middle and Upper Paleolithic.
Science.
(2023).
nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling.
bioRxiv.
(2022).
sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files.
Journal of Open Source Software.
(2021).
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly.
PeerJ.
(2021).
Reconstruction of ancient microbial genomes from the human gut.
Nature.
(2021).
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.
PeerJ.
(2021).
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.
Scientific Data.
(2020).
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content.
PeerJ.
(2019).
Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification.
Journal of Open Source Software.
Projects
Dixit Diderot
Recreate the writing of Philosopher Denis Diderot using Markov Chains.
Phylogeny of the Anacyclus genus
Phylogeny of this Moroccan medicinal plant Anacyclus genus using the internal transcribed spacer marker.
Recent Posts
Using Python to solve the Monty Hall problem
What is the best strategy to win a 🚗 ? Keeping the original choice, or changing of door ?
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2 min read
A new E-score for KrakenUniq
How to distinguish between true and false positive assignations with KrakenUniq
noSQL: when it's too big for a dictionary
Recently, I’ve been working on a project where I need to store a key-value pairs for very large files. In Python, the first idea would be to use a dictionary. However, I had more …
Making Interactive maps in Python using GeoJSON and GitHub
Recently, I’ve been involved with the AncientMetagenomeDir project. Briefly, with this collaborative community effort, we aimed to regroup in one single repository, all the …
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2 min read