A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

Genomes are an integral component of the biological information about an organism; thus,
the more complete the genome, the more informative it is. Historically, bacterial and …

Proteins are essential to life, and understanding their structure can facilitate a mechanistic
understanding of their function. Through an enormous experimental effort 1, 2, 3, 4, the …

The Pfam database is a widely used resource for classifying protein sequences into families
and domains. Since Pfam was last described in this journal, over 350 new families have …

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …

The genome sequences of many species of the human gut microbiome remain unknown,
largely owing to challenges in cultivating microorganisms under laboratory conditions. Here …

Metagenomic datasets contain billions of protein sequences that could greatly enhance
large-scale functional annotation and structure prediction. Utilizing this enormous resource …

Cell-surface receptors play pivotal roles in many biological processes, including immunity,
development, and reproduction, across diverse organisms. How cell-surface receptors …

Abstract Large-scale Protein Language Models (PLMs) have improved performance in
protein prediction tasks, ranging from 3D structure prediction to various function predictions …

The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health
and disease states. Here, we sequence the genomes of 41 fungal isolates representative of …