Wei Shen

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

LexicMap efficiently aligns sequences against millions of prokaryotic genomes, achieving comparable accuracy to existing tools with faster speed and lower memory use.

Designing efficient randstrobes for sequence similarity analyses

This paper introduces new randstrobe construction methods, identifies biases in previous approaches, and improves accuracy in short-read mapping.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

KMCP improves metagenomic profiling accuracy for prokaryotic and viral populations using k-mer-based methods with reduced false positives.

TaxonKit: a cross-platform and efficient NCBI taxonomy toolkit

TaxonKit is a dependency-free, cross-platform command-line toolkit written in Go for fast manipulation of National Center for Biotechnology Information (NCBI) taxonomy data without building a local database.

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.