Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

Augmenting zero-shot mutant prediction by retrieval-based logits fusion.

A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes

RNAlien - unsupervised RNA family model construction

Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.

Algebraic topology based header only library to extract insight of complex high dimensional data.

Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.

A kmer-based homology searching tool

Using structure information only for protein homology detection (IEEE BIBM 2024).

Searching proteins against a database of embeddings

A simple pipeline to create and search HMM models against reference protein databases.

A snakemake workflow for iterative sequence profile searching using jackhmmer from the HMMer3 package.