Benpeng Miao

The paper investigates sex-specific molecular responses to early-life toxicant exposures in mice across multiple life stages using transcriptomic and epigenomic data.

The paper uses fully phased telomere-to-telomere assemblies and long-read epigenomes to study centromere genetic and epigenetic dynamics across inheritance and cell-fate transitions, finding positional stability of CDRs and dynamic epigenetic changes.

The paper presents an integrated single-cell and epigenomic resource for exploring basal ganglia datasets across species, enabling multi-omics and comparative analysis.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

The paper introduces a data repository containing epigenomic data from mice exposed to various environmental toxicants, enabling research on disease susceptibility.

The paper characterizes persistent epigenomic and transcriptomic changes in mice exposed to environmental toxicants across life stages, revealing widespread gene expression and chromatin alterations.

ToxiTaRGET provides a multi-omics resource of molecular responses to toxicants in mice, enabling researchers to explore transcriptomic and epigenomic changes across tissues and life stages.

This study examines how early-life exposure to environmental toxicants alters TE chromatin accessibility and expression in mouse liver, revealing exposure-specific and sex-dependent effects.

The paper analyzes TE-derived transcripts in 17,329 human transcriptomes across 47 adult tissues, revealing their broad expression, sex-specific regulation, and contribution to protein diversity and metabolic functions.

This study examines transcriptomic and epigenetic changes in four rat brain regions after a METH overdose, revealing region-specific responses and conserved regulatory elements linked to neurological functions.

This study performs genome assembly and transcriptome analysis of Microtus fortis to understand its resistance to Schistosoma japonicum infection, revealing differences in immune response timing and effectiveness compared to mice.

The paper introduces AIAP, an ATAC-seq analysis package that improves quality control and analysis, showing increased sensitivity in peak calling and differential analysis.