Zhenmiao Zhang

This study evaluates long single-end barcoded reads for structural variant detection, showing improved accuracy with longer read lengths compared to short-read and pangenome-based methods.

CompleteBin improves short contig binning in complex microbial communities, recovering more complete genomes and novel genes, with applications in environmental metagenomics.

This study compares gut microbiome differences between Han Chinese and non-Chinese populations, identifying population-specific genome clusters and SNPs linked to functional traits.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

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.

This paper benchmarks 15 de novo metagenome assembly tools on 32 datasets from various sequencing technologies, finding that long-read assemblers produce the highest contig continuity but miss some MAGs, while hybrid assemblers offer a balance of continuity and MAG completeness.

METAMVGL improves metagenomic contig binning by integrating assembly and paired-end graphs to enhance accuracy for short contigs and correct binning errors.