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 …

Metagenomic experiments expose the wide range of microscopic organisms in any
microbial environment through high-throughput DNA sequencing. The computational …

Deep-learning language models have shown promise in various biotechnological
applications, including protein design and engineering. Here we describe ProGen, a …

Proteins are key to all cellular processes and their structure is important in understanding
their function and evolution. Sequence-based predictions of protein structures have …

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions
and activities,. Exploration of this vast sequence space has been limited to a comparative …

Metagenomic binning is the step in building metagenome-assembled genomes (MAGs)
when sequences predicted to originate from the same genome are automatically grouped …

Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome
assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer) …

Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse
entities in the biosphere. There is accumulating evidence revealing their important roles in …

The decreasing cost of sequencing and concomitant augmentation of publicly available
genomes have created an acute need for automated software to assess genomic …

Background Long-read shotgun metagenomic sequencing is gaining in popularity and offers
many advantages over short-read sequencing. The higher information content in long reads …