We are interested in themes including the genetics of behavior, the interplay between social evolution and genome evolution, and the molecular mechanisms responsible for differences between castes.

For example we:

• reviewed the most up-to-date research on ant omics (Current Opinion in Insect Science 2018).
• characterized the genomic features of the variants of the social chromosome, showing high genetic diversity between them (Molecular Ecology 2017 and Evolution Letters 2017).
• discovered that the number of queens accepted in a fire ant colony is determined by variants of a social chromosome (Nature 2013).
• sequenced and analyzed the genome of the invasive red fire ant Solenopsis invicta (PNAS 2011).
• described the gene expression changes that occur in a virgin queen when she is given the opportunity of replacing her mother (Molecular Ecology 2010).
• examined selective regime (positive vs. neutral selection) and fate of duplicated genes (conserved vs. subfunctionalized vs. neofunctionalization) for gene families including sex-determination loci (tranfsormer/feminiser), clock genes, chemosensory proteins (CSPs), olfactory binding proteins (OBPs), olfactory receptors and vitellogenin genes.

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• BLAST is the most commonly used bioinformatics tool. But setting it up for private data and using it is counter-intuitive. Furthermore the standard graphical user interfaces for BLAST are clunky. We developed SequenceServer to overcome these hurdles.
• Sequencing genomes has become straightforward. But correctly identifying genes in a genome sequence remains challenging. This is a huge problem for multi-species multi-gene analyses on emerging model organisms (trash in trash out).
  • We developed GeneValidator for automated identification and visualization of problems with gene predictions.
  • Many gene predictions need to be inspected and manually fixed before performing analyses. We are developing infrastructure to crowd-source gene curation to students as part of improved learning experience.
• Because genomics data types and analysis algorithms remain young, many analyses require jumping back and forth between multiple tools. The tools themselves are young, can be challenging to install and can require frequent updates. But for reproducibility a given project may want to stick to specific versions of specific tools. Based on the docker container architecture, oSwitch enables lightweight switching from one virtual operating system to another. It is a powerful tool for pipelines and for hacking.
• We are also developping BioNode, an Open Source community to build highly reusable tools and code for bioinformatics by leveraging the Node.JS ecosystem. We want to process big genomic data using Node.JS Streams. We welcome all kinds of contributions at all levels of experience.

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• We are quantifying the effects of pesticide exposure on gene expression in various bee species. (Trends in Ecology & Evolution 2020).
• We are characterising the selection pressures affecting wild bees using population genomics approaches.
• We have contributed to several experiments examining the impact of pesticides on field colonies.

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