Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

A new artificial intelligence model, DeepSeek-R1, is introduced, demonstrating that the reasoning abilities of large language models can be incentivized through pure reinforcement learning, removing the need for human-annotated demonstrations.

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).

Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i

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 flourish...

Artificial intelligence is opening new perspectives in virus research, providing advanced tools to analyze viral evolution and to understand protein structure and dynamics on a large scale. To explore...

Abstract. Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the

Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...