The hemagglutinin of human influenza virus evolves rapidly to erode neutralizing antibody immunity. Twice per year, new vaccine strains are selected with the goal of providing maximum protection again...

Phylogenetic studies examining the origins, emergence, and spread of viruses have arguably been one of the most active and successful areas of evolutionary biology and form the bedrock of the flourishing field of genomic epidemiology. This, in part, reflects the ability of viruses, particularly those with RNA genomes, to evolve at rates much greater than their cellular counterparts (1). The rapid rate at which viruses evolve and accumulate mutations enables evolutionary signals to be identified through comparative genomics at short timescales relevant for outbreak investigation and response. The integration of phylogenetics and epidemiology, known as phylodynamics, has become a vital tool in response to numerous viral outbreaks, epidemics, and pandemics, including Ebola (2), Zika (3), and, more recently, COVID-19 (4) and mpox (5).

Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase...

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.