Sebastian Duchene

Sebastian Duchene is a researcher at the Institut Pasteur in Paris, where he serves as Principal Investigator (PI) for the TraM project, which focuses on trait-driven molecular clocks to date the long-term evolution of re-emerging bacterial pathogens. His work integrates genomics, evolutionary biology, and phylodynamics to understand infectious disease dynamics.

• Institution: Institut Pasteur, Paris
• Research Focus: Molecular clocks, phylodynamics, genomic epidemiology, bacterial evolution

His research interests center on the evolutionary genomics of bacterial pathogens, with a focus on developing and applying computational methods for molecular dating, phylodynamic inference, and genomic surveillance. He investigates how pathogens such as Mycobacterium lepromatosis and Streptococcus pyogenes evolve over time and spread across populations.

The trends in his recent publications reveal a strong emphasis on methodological innovation in phylodynamics and molecular clock modeling, including tools like Clockor2 for root-to-tip regression and studies on temporal signal detection. His work bridges computational biology with public health applications, particularly in understanding antibiotic resistance and historical disease spread.

His scientific contributions have been published in top-tier journals including Science, Nature, PLoS Computational Biology, and Systematic Biology.

• Pre-European contact leprosy in the Americas and its current persistence. (Science, 2025)
• Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin. (Nature, 2024)
• Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression (Systematic Biology, 2024)
• How does date-rounding affect phylodynamic inference for public health? (PLoS Comput Biol, 2025)

Duchene leads a research team and collaborates with post-doctoral fellows, research engineers, and students. While specific grant details are not listed, his active publication record and PI status suggest ongoing funding for projects in evolutionary genomics and infectious disease modeling. He contributes to open science through publicly available tools like Clockor2.

He is part of the research team focused on the evolutionary dynamics of infectious diseases at the Institut Pasteur, working alongside experts in genomics, microbiology, and epidemiology to advance understanding of pathogen evolution and public health threats.