A nucleotide-level pangenome simulator. Contribute to samhorsfield96/PansimNuc development by creating an account on GitHub.

A dataset of diverse bacterial genomes across habitats. Includes deduplicated genomes, proteins and intergenic sequences.

Quantifying short-term evolutionary rates of microbial genomes is essential for understanding the processes that shape within-host evolution and for establishing thresholds needed to track transmissio...

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

Browser-based prophage prediction using PhiSpy, Pyodide, and WebAssembly

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A cluster of meningitis cases is currently dominating the UK news. At least five of the cases have been confirmed as serotype B (menB), from what I can tell the others have not yet been analysed. My P...

Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the e…

Staphylococcus aureus lineages vary widely in the frequency of gene exchange and the diversity of genome content. Gorzynski and Harling-Lee et al. show that both host ecology and the horizontal acquis...

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Silva et al. perform a global analysis of over 11,000 gut microbiomes and reveal that uncultured bacteria are key markers of gut health. The uncultured genus CAG-170 is strongly linked to low gut dysb...

We’re on a journey to advance and democratize artificial intelligence through open source and open science.

Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...

Surface layers (S-layers) are ubiquitous protein assemblies that coat prokaryotic cells, with their functional roles increasingly coming into focus. In this Review, Isbilir and colleagues discuss rece...

Pangenome graphs as a new paradigm in comparative genomics -

Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

Hackathon held in Hinxton 2026

Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.

Background Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, a...

Mathematical modelling for biologists - Modelling concepts in biological research

Nature Genetics - A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for...

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 evolu...

As well as undergoing mutational selection, bacterial genomes are shaped by a complex evolutionary interplay among diverse accessory genome elements (AGEs). In this study we define AGEs as encompassin...

Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but...

AI has the potential to transform health and medicine. It won't be straightforward, but if we get it right, the benefits could be enormous. Andres Floto, Mihaela van der Schaar and Eoin McKinney expla...