Since September 2023, I am leading the Environmental Bioinformatics Group at the SIB Swiss Institute of Bioinformatics. Our activities and research aim to build capacities in coordinating biodata resources and developing data science tools and services that contribute to planetary preservation and restoration by addressing the global crisis and delivering direct benefits for society, with a focus on genomics data as part of developing the broader biodiversity knowledge graph to connect and integrate diverse data types for enhanced understanding and monitoring of the health of species and ecosystems.
Previously at the University of Lausanne's Department of Ecology and Evolution, my Group's research focus has been on elucidating interactions between gene evolution and gene function through developing computational approaches to interrogate evolutionary and functional genomics data, with a biological focus on insects and other arthropods as their countless adaptations mean that they are ideal for investigating how conservation or divergence of functional genomic elements give rise to the splendour of animal biology.
Arthropod Evolutionary-Functional Genomics
Functional constraints on insect immune system components govern their evolutionary trajectories. Our results identified three main axes of evolutionary trajectories and suggest that where and how genes participate in immune responses limit the range of possible evolutionary scenarios they exhibit.
Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet, immunity and detoxification.
Gene content evolution in the arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations.
Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles. We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders.
Exploring new genomic territories with emerging model insects. New genome resources are expanding possibilities for developing insect model systems. Technological advances are supporting new models by delivering high-quality data. Emerging model systems advance understanding of insect biology and evolution.
Anopheles mosquitoes reveal new principles of 3D genome organization in insects. We profile genome organisations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other, revealing conservation of chromatin architecture for tens of millions of years.
Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles. Using genomic and transcriptomic data from 38 species of ladybird beetles, we identified a set of acquired bacterial cell wall hydrolase genes with putative roles in immunity linked to a successful species radiation.
Of genes and genomes: mosquito evolution and diversity. Evolutionary genomics analyses have unveiled dynamic patterns of gene and genome evolution likely linked to mosquito adaptability, and enhance the interpretation of results from multispecies studies with an evolutionary perspective.