Eduardo Rocha

Eduardo Rocha is a Professor and Head of the Microbial Evolutionary Genomics laboratory at the Institut Pasteur, within the Department of Genomes and Genetics. His research integrates bioinformatics, molecular evolution, and genomics to understand bacterial genome organization and dynamics, particularly focusing on mobile genetic elements and their role in adaptation and antibiotic resistance.

His research interests include microbial evolutionary genomics, genome organization, horizontal gene transfer, mobile genetic elements (plasmids, phages, integrons), bacterial pathogen evolution, and computational biology. His work lies at the intersection of molecular evolution, population genetics, and molecular epidemiology, with strong translational implications for understanding antimicrobial resistance and infectious disease emergence.

The recent publications highlight a consistent focus on mobile genetic elements, genome plasticity, and bacterial adaptation. Key themes include the role of integrons and CRISPR-Cas systems in bacterial immunity, plasmid-mediated spread of antibiotic resistance, phage-plasmid interactions, and the development of bioinformatics tools for microbial genomics. These works frequently appear in high-impact journals such as Science, Nature Microbiology, and PLoS Biology, reflecting significant contributions to the field.

• Eduardo Rocha leads multiple funded research projects, including ERC-2011-StG EVOMOBILOME, ANR Magisbac, and ANR SHAPE.
• He has developed and maintains several widely used bioinformatics software tools: IntegronFinder, MacSyFinder, PanACoTA, SatelliteFinder, CapsuleFinder, TXSScan, and others.
• He mentors a large team of PhD students, postdoctoral researchers, and engineers, and has supervised numerous former students who now hold independent research positions worldwide.

Eduardo Rocha has received research funding from major agencies including the European Research Council (ERC) and the French National Research Agency (ANR). His work is central to the LabEx IBEID and the INCEPTION convergence program, where he serves on the steering committee, promoting interdisciplinary research in infectious disease emergence.

His laboratory, part of the Genomes and Genetics department, actively contributes to microbial evolutionary genomics through both methodological development and biological discovery. The team participates in networks such as Phages.fr, GDR BIM, and GDR AIEM, reinforcing its collaborative and integrative approach.