Yufen Huang

SILO improves detection of disease susceptible variants in short IBD segments, outperforming existing models in simulated and real data.

Pangaea improves metagenome assembly using short-reads with barcodes, achieving better contig continuity and more complete genomes than existing assemblers.

The paper assesses how genome topology and viral selection affect biological interpretation in the human gut virome, highlighting the need for standardized reporting of circular-to-linear genome ratios and dereplication thresholds.

LRTK is a platform-agnostic toolkit for linked-read analysis of human genomes and metagenomes, offering simulation, alignment, variant calling, and taxonomic classification.

Deepurify uses a multi-modal deep language model with contrastive learning to improve MAG decontamination by leveraging genomic sequences and taxonomic lineages.