Maxime Borry, PhD.
Bioinformatics scientist

Developing Bioinformatics statistical tools and workflows for scalable and reproducible, and actionable results.

Maxime Borry, PhD.

Max Planck Institute for Evolutionary Anthropology

Hey there,

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.

Interests

Bioinformatics
Metagenomics
Machine Learning

Education

PhD candidate in Bioinformatics, 2018-2023
Friedrich-Schiller-Universität Jena 🇩🇪
M.Sc. in Bioinformatics, 2016-2018
Université Paris Diderot 🇫🇷
M.Sc. in Ecology and Environmental sciences, 2014-2015
Université Joseph Fourier, Grenoble 🇫🇷
Exchange Semester, 2013
University of Nordland 🇳🇴
B.Sc. in Life Sciences, 2011-2014
Université Paris Descartes 🇫🇷

Recent Publications

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James A. Fellows Yates, Christina Warinner, Aida Andrades Valtueña, Maxime Borry, Meriam Guellil, Alexander Herbig, Alina Hiß, Alexander Hübner, Arthur Kocher, Thiseas C. Lamnidis, Megan E. Michel, Kevin Nota, Nikolay Oskolkov, Aleksandra Laura Pach, Vilma Pérez, Clemens Schmid, Irina M. Velsko, Robin Warner, Giulia Zampirolo, Teresa Zeibig. Introduction to Ancient Metagenomics Textbook. Zenodo, 2024.

Maxime Borry et al. Facilitating Accessible, Rapid, and Appropriate Processing of Ancient Metagenomic Data with AMDirT. F1000Research, 2024.

Moritz E. Beber, Maxime Borry, Sofia Stamouli, James A. Fellows Yates. TAXPASTA: TAXonomic Profile Aggregation and STAndardisation. Journal of Open Source Software, 2023.

Martin Klapper, Alexander Hübner, Anan Ibrahim, Ina Wasmuth, Maxime Borry, Veit G. Haensch, Shuaibing Zhang, Walid K. Al-Jammal, Harikumar Suma, James A. Fellows Yates, Jasmin Frangenberg, Irina M. Velsko, Somak Chowdhury, Rosa Herbst, Evgeni V. Bratovanov, Hans-Martin Dahse, Therese Horch, Christian Hertweck, Manuel Ramon González Morales, Lawrence Guy Straus, Ivan Vilotijevic, Christina Warinner, Pierre Stallforth. Natural Products from Reconstructed Bacterial Genomes of the Middle and Upper Paleolithic. Science, 2023.

Sofia Stamouli, Moritz E. Beber, Tanja Normark, Thomas A. Christensen, Lili Andersson-Li, Maxime Borry, Mahwash Jamy, nf-core community, James A. Fellows Yates. nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. bioRxiv, 2023.

Maxime Borry, Alexander Hübner, Christina Warinner. sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files. Journal of Open Source Software, 2022.

Maxime Borry, Alexander Hübner, Adam B. Rohrlach, Christina Warinner. PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ, 2021.

Marsha C. Wibowo, Zhen Yang, Maxime Borry, Alexander Hübner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto García-Ortiz, Angélica Martínez-Hernández, Jacob M. Luber, Philipp Kirstahler, Tre Blohm, Francis E. Smiley, Richard Arnold, Sonia A. Ballal, Sünje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc, Aleksandar D. Kostic. Reconstruction of ancient microbial genomes from the human gut. Nature, 2021.

James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ, 2021.

James A. Fellows Yates, Aida Andrades Valtueña, Åshild J. Vågene, Becky Cribdon, Irina M. Velsko, Maxime Borry, Miriam J. Bravo-Lopez, Antonio Fernandez-Guerra, Eleanor J. Green, Shreya L. Ramachandran, Peter D. Heintzman, Maria A. Spyrou, Alexander Hübner, Abigail S. Gancz, Jessica Hider, Aurora F. Allshouse, Valentina Zaro, Christina Warinner. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 2021.

Maxime Borry et al. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ, 2020.

Maxime Borry. Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification. Journal of Open Source Software, 2019.

Experience

Bioinformatics Scientist

TRON - Translational Oncology Mainz

Jun 2024 – Nov 2025 Mainz, Germany

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

Apr 2023 – Mar 2025 Leipzig, Germany

Bioinformatic metagenomic analysis of ancient fermentation microbiomes.

Doctoral Researcher in Bioinformatics

Max Planck Institute for Evolutionary Anthropology

Sep 2021 – Mar 2023 Leipzig, Germany

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

Sep 2018 – Present Jena, Germany

Development of tools and pipelines for the analysis of ancient DNA metagenomics data.

Bioinformatics Research intern

Natural History Museum - CNRS

Jan 2018 – Jul 2018 Paris, France

Development of tools and pipelines for the analysis of ancient DNA metagenomics data.

Bioinformatics Research intern

Institut Pasteur

Mar 2017 – May 2017 Paris, France

Development of a tool in R and Shiny for comparison of expression level in multi-omics data.

Bioinformatics Research assistant

CRG

Jun 2016 – Aug 2016 Barcelona, Spain

Exploration of the human oral mycobiome.

Research intern

MPI-EVA

Dec 2015 – Feb 2016 Leipzig, Germany

Detection of gene duplications between Neanderthal and Mordern Humans.

Guest researcher

University of Oslo

Jun 2015 – Oct 2015 Oslo, Norway

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.