Short open reading frames (sORFs) are a common feature of all genomes, but their coding
potential has mostly been disregarded, partly because of the difficulty in determining …

Pfam, available via servers in the UK (http://pfam. sanger. ac. uk/) and the USA (http://pfam.
janelia. org/), is a widely used database of protein families, containing 14 831 manually …

Language models have recently emerged as a powerful machine-learning approach for
distilling information from massive protein sequence databases. From readily available …

In the field of artificial intelligence, a combination of scale in data and model capacity
enabled by unsupervised learning has led to major advances in representation learning and …

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan,
gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community …

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions
since the dawn of agriculture. Their large genomes are characterized by a high content of …

Generative modeling for protein engineering is key to solving fundamental problems in
synthetic biology, medicine, and material science. We pose protein engineering as an …

Anaerobic oxidation of methane (AOM) is a major biological process that reduces global
methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate …

Phylogenetic tree confidence is often estimated from a multiple sequence alignment (MSA)
using the Felsenstein bootstrap heuristic. However, this does not account for systematic …

Background System-wide profiling of genes and proteins in mammalian cells produce lists of
differentially expressed genes/proteins that need to be further analyzed for their collective …