Abstract. Amino acid-based phylogenetics usually relies on first clustering and aligning orthologous proteins. This approach is powerful but computationall

CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...

This year I went on two puffin watching experiences, and it is about time I reflect on this with a listicle / ranking. All on islands with decreasing populations of people and increasing populations o...

Agentic coding models such as codex and claude code are really useful for software engineering tasks. We sadly (and unsurprisingly) seem to be exiting the era of highly subsidised costs to get us hook...

The decision for the one-off vaccine programme follows the unprecedented outbreak in Kent this year.

Bacteria have evolved a vast diversity of functions and behaviours which are currently incompletely understood and poorly predicted from DNA sequence alone. To understand the syntax of bacterial evolution and discover genome-to-phenotype relationships, we curated over 1.3 million genomes spanning bacterial phylogenetic space, representing each as an ordered sequence of proteins which collectively were used to train a transformer-based, contextualised protein language model, Bacformer . By pretraining the model to learn genome-wide evolutionary patterns, Bacformer captures the compositional and positional relationships of proteins and can accurately: predict protein-protein interactions, operon structure (which we validated experimentally), and protein function; infer phenotypic traits and identify likely causal genes; and design template synthethic genomes with desired properties. Thus, Bacformer represents a new foundation model for bacterial genomics that provide biological insights and a framework for prediction, inference, and generative tasks. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 226602/Z/22/Z LifeArc, IH001 Ineos (United Kingdom), Oxbridge AMR Doctoral training programme NIHR Cambridge Biomedical Research Centre Cambridge Centre for AI in Medicine (CCAIM) doctoral training programme Swiss National Science Foundation, TMSGI2_226252/1, IC00I0_23192 Peter und Traudl Engelhorn Foundation Engineering and Physical Sciences Research Council, EP/T022159/1 Science and Technology Facilities Council, DiRAC

This is a brief update to the previous menB analysis we’d posted here. UKHSA have released a technical briefing and further data which includes four further isolates from the outbreak, and a high qual...

A snakelike pipeline combining ggCaller and Panaroo. - samhorsfield96/ggCallaroo

Working with us

We’ve done a quick analysis on the meningitis outbreak genome to try and answer whether there is anything obviously genetically unusual about the publicly available outbreak strain. We aimed for three...