AbstractMotivation. The Encyclopedia of Domains (TED) provides domain annotations for proteins in the AlphaFold Protein Structure Database (AFDB) using a c

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...

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 ...

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

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

Kinetoplastids are a group of parasites that cause severe diseases in the poorest regions of the world. Despite the increasing amount of genomic information available on these parasites, predicting th...

The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...

DNA sequencing of the yerba mate (Ilex paraguariensis) genome reveals convergent genomic changes, biochemical pathways, mutations, and substrate-binding orientations responsible for caffeine biosynthe...

Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...