Zhi-Luo Deng

Metax improves cross-domain taxonomic profiling by using coverage-informed probabilistic modeling, showing accuracy across bacteria, archaea, eukaryotes, and viruses in diverse samples.

CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest by analyzing lineage frequency dynamics and antigenic changes from GISAID data.

This study uses long-read metagenomics to detect Paracoccus yeei in SBP patients, revealing its pathogenicity and antimicrobial resistance profile.

This study benchmarks ML and rule-based methods for predicting antimicrobial resistance from microbial genomes, finding significant variation in performance across species and antibiotics.

The paper presents a multi-omics analysis of Prorocentrum cordatum under heat stress, revealing RNA editing and exon usage regulation of biomolecules.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Haploflow assembles viral strain genomes from mixed samples, outperforming existing assemblers in speed and accuracy on benchmark datasets.

This study benchmarks assemblers and variant callers for strain-resolved analysis of large DNA viruses, identifying best practices and challenges in handling low-divergent viral populations.