Small proteins (exact definitions vary, but < 100 amino acids is a common threshold) have generally been ignored as standard bioinformatics approaches fail when applied to these short sequences. Nonetheless, it has also become clear that small proteins are abundant across all domains of life.
As an initial project in this domain, we have focused on antimicrobial peptides (AMPs) and developed macrel, a tool to mine them from genomes and metagenomes. We are currently building up a catalog of AMPs in the global microbiome and analysing how this mechanism is used to shape microbial communities.
Antimicrobial resistance (AMR), whereby bacteria become resistant to antibiotics, is a major global public health problem. Our research interests are centered around antimicrobial resistome – bacterial genes encoding antibiotic resistance found just about everywhere, from the deep ocean to healthy human gut, and important for both environmental and clinical settings. We are a part of the international EMBARK project, which analyses AMR at a global scale.
We are interested in looking at different habitats and comparing their microbial ecology.
What are the common features of different microbiota (for example, the gut of different mammals)? Are strains biome-specific?
We are interested both in developing new algorithms with applications to large-scale metagenomics and in exploring tools that enable reproducible science.
In particular, we are interested in the potential of designing domain specific languages to concisely specify data handling pipelines in a way that is (1) intuitive, (2) enables defensive programming, (3) computational efficient, (4) extensible.
We want to push the boundaries on bioimage informatics. This can mean work on larger datasets or build detailed models from images or link images and metagenomics or something else you can think of.
We are interested in working with clinical groups on issues of relevance to human health or with groups with access to environmental samples.
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