Eli Levy Karin

BFVD v3-UniProt-complete, improved viral protein structure predictions

5,776,417 ColabFold-AlphaFold2 structures cover 98.9% of viral UniProt 2025_03 sequences, 16.4-fold more than earlier versions, with 75.3% high-confidence and 72.6% of viral reference proteomes fully covered.

Metagenomic-scale analysis of the predicted protein structure universe

The paper combines AlphaFold and ESMfold predictions to create a large structural dataset, identifies novel protein folds and domain combinations, and highlights the value of metagenomic data for structural diversity.

Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer

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

BFVD - a large repository of predicted viral protein structures

BFVD provides a large repository of predicted viral protein structures, enhancing annotation of bacteriophage proteins compared to sequence-based methods.

Petascale Homology Search for Structure Prediction

The paper uses petabase-scale homology searches from SRA data to improve protein structure prediction accuracy using ColabFold, achieving better results than default methods.

Identification of selective sweeps in bacteria

The paper introduces SINCOPA, a phylogeny-based method for detecting locus-specific selective sweeps in bacterial strains, and applies it to over 500 microbial genomes to identify sweeps in genes related to biofilm formation and environmental adaptation.

SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts

SpacePHARER identifies phage-host relationships by matching CRISPR spacers to phage genomes in genomic or metagenomic data, improving sensitivity through protein-level comparisons and multiple match evidence.

Fast and sensitive taxonomic assignment to metagenomic contigs

MMseqs2 taxonomy assigns taxonomic labels to metagenomic contigs using fragment extraction and weighted voting, achieving 2-18x speed improvements over existing tools.

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

MetaEuk annotates protein-coding genes in eukaryotic metagenomic data with high sensitivity and speed, discovering many novel proteins from under-sampled eukaryotic groups.