Stephen Hwang

Ok-k-mer selects optimal k-mer length ensembles to improve genomic distance estimation by maximizing correlation with phylogenetic branch distances.

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

The paper benchmarks ANI estimation algorithms using simulated and real datasets, showing that ANIb is most accurate but least efficient, while k-mer approaches are efficient and accurate, with some clades requiring multiple k-values.

The paper introduces MEMO, a pangenome indexing method that efficiently handles k-mer queries and conservation analysis across pangenomes.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.