Jianshu Zhao

TurboANI is a fast, homology-aware ANI estimator with up to ~40,000x speedup over alignment-based methods and better accuracy than FastANI and skani.

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

DartUniFrac is a fast, scalable algorithm for microbiome analysis that matches the statistical performance of exact UniFrac methods.

The paper introduces GraphEmbed, a scalable network embedding tool that efficiently handles large biological datasets with speed and accuracy improvements over existing methods.

The paper defines rare biosphere and generalists using metagenomic and macroecological metrics, showing their roles in microbial resilience to disturbances like tropical cyclones and warming.

The paper shows SAR11 bacteria use promiscuous recombination to form sequence-discrete species with lower ANI thresholds than other microbes.

GSearch efficiently searches and classifies microbial or viral genomes using k-mer hashing and HNSW graphs, achieving high speed and accuracy with low memory usage.

BinDash 2.0 improves genome comparison speed using new MinHash algorithms and SIMD optimizations, achieving faster and accurate large-scale genomic distance estimation.

This paper introduces an improved non-linear dimension reduction algorithm using HNSW for nearest neighbor search and applies it to visualize large-scale biological data with competitive accuracy.