Cameron L. M. Gilchrist

Foldseek-Interface clusters protein interaction interfaces from PDB data, revealing 77,167 interface clusters and novel interface types.

FoldMason uses Foldseek's 3Di+AA alphabet for progressive multiple structure alignment, beating structure aligners' LDDT on AlphaFold DB clusters at near sequence-aligner speed, scaling to 100,000 structures.

This study identifies ancient immune convergence between prokaryotes and primates through SAMD9/9L proteins and reveals recent adaptations in bonobos and chimps enhancing HIV resistance.

The paper introduces Metabuli App, a desktop tool for metagenomic taxonomic profiling, offering user-friendly interfaces and local execution without requiring command-line skills or high-performance computing.

The paper presents an nf-core framework for comparing multiple sequence aligners, aiming to streamline deployment and evaluation of MSA tools in HPC environments.

Foldseek-Multimer rapidly aligns protein complexes by clustering superposition vectors, outperforming the gold standard in speed while maintaining alignment quality.

A Foldseek-based linear-time structural clustering groups 52 million AlphaFold DB representatives into 2.27 million non-singleton clusters; 31% lack known structural or domain annotation.

Foldseek's 3Di tertiary-interaction alphabet enables structure search four to five orders of magnitude faster than Dali and TM-align at 86% and 88% of their respective sensitivities.

CAGECAT enables rapid homology searches and visualization of gene clusters across genomes, aiding in the discovery of novel metabolites through comparative analysis.

The paper introduces a database of universal fungal core genes and an automated pipeline for phylogenetic analysis of fungi, providing curated genes and tools for genome-wide studies.

clinker aligns translated genes from GenBank gene clusters, orders clusters by homology-plus-synteny similarity, and renders interactive, editable comparison figures via the D3-based clustermap.js library.

cblaster identifies and visualizes homologous gene clusters across local and remote databases, enhancing comparative genomics analysis.

A dLbCas12a-VPR CRISPR activation system works in Aspergillus nidulans, boosting microperfuranone output from the native micA gene and revealing dehydromicroperfuranone as the mic cluster product.