Chao Jiang

MetaNet is an R package for scalable multi-omics network analysis, offering faster computation and better memory efficiency than existing tools, with applications in microbial and exposome-transcriptome studies.

The paper presents a longitudinal transcriptomic atlas of maternal peripheral blood during healthy pregnancy, identifying 720 pregnancy-specific genes and nine transcriptional modules associated with immune and metabolic changes.

This study identifies microhomology-mediated tandem duplication (MTD) as a universal mechanism for tandem repeat formation across all domains of life, including human pathogenic mutations.

TidyMass2 improves untargeted metabolomics by inferring metabolite origins and analyzing functional modules, increasing biologically interpretable features from 5.8% to 58.8% in pregnancy urine data.

MAPA uses large language models to reduce redundancy in pathway analysis and improve biological interpretation of multi-omics data.

Kun-peng is a metagenomic classifier that outperforms existing tools in speed, memory efficiency, and accuracy for large-scale pan-domain classification.

The paper introduces the iPhylo suite, an interactive platform for building and annotating biological and chemical taxonomic trees, with web and command-line modules for analysis and visualization.

This study analyzes longitudinal vaginal microbiome data from diverse ethnic groups, revealing ethnic signatures in microbial diversity, community states, and evolutionary dynamics, with Lactobacillus adhesins showing positive selection.

This study shows bacterial ExoIII can cleave single-stranded DNA (ssDNA) via exonuclease and endonuclease activities, revealing new enzymatic functions and implications for biosensor design.

This study tracks microbiome changes across four body sites in 86 participants over six years, revealing site-specific stability, individualized dynamics, and altered patterns in insulin-resistant individuals.

The paper introduces GRSA, a generalized reporter score-based method for multi-group and longitudinal omics data, showing increased sensitivity and applied it to microbiome, transcriptome, and metabolome data.

This study shows that microplastics from disposable paper cups accumulate in mouse placenta and fetus, causing metabolic and reproductive toxicity at exposure levels considered safe.

This study uses high-throughput evolution to explore antibiotic resistance landscapes in E. coli exposed to low-level antibiotics, identifying key mutations and developing predictive models.

This study examines the long-term microbial changes in desert soil during ecological restoration, finding shifts in community structure, functional diversity, and biogeochemical cycles over 17 years.

This study integrates longitudinal personal exposome and multi-omics data to show dynamic interactions between environmental exposures and internal biomolecules, highlighting key agrochemicals and fungi.

The paper maps the host protein interactome of SARS-CoV-2 non-coding regions in human cell lines, revealing core and cell-type-specific interactions and their functional roles.

This study shows that tyrosine kinase inhibitors cause mitochondrial dysfunction in cardiomyocytes by altering GATA4-mediated networks, and GATA4 overexpression can rescue these effects.