Daofeng Li

This study develops pangenome-based frameworks to analyze DNA methylome variation across diverse human genomes, identifying genetic factors influencing methylation patterns and their associations with complex traits.

The paper analyzes polymorphic transposable elements in human pangenomes to reveal regulatory evolution mechanisms before fixation.

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 presents a human panepigenome map of DNA methylation, revealing epigenomic diversity across populations and highlighting the role of genetic variation in CpG presence and absence.

Pansoma improves somatic variant calling using pangenome graphs, enhancing accuracy by avoiding reference bias and preserving graph-specific variant representations.

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

This paper creates a multimodal single-cell atlas of the human basal ganglia, revealing epigenomic and 3D genome features across cell types and linking them to disease-associated genetic risk.

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 integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

This paper creates a high-resolution spatial transcriptomic atlas of the human basal ganglia, identifying 60 cell types and their spatial organization across multiple nuclei.

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 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 uses single-cell multi-omics to identify cell type-specific regulatory networks and novel therapeutic targets in MASLD.

The paper integrates single-cell multi-omics and 3D genome data from human hearts to identify gene regulatory changes and causal genetic contributors in heart failure.

The paper introduces BAllC, a binary format for single-cell DNA methylation data, and BAllCools, a toolkit to improve storage and operational efficiency.

The paper introduces a comparative epigenome browser that enables visualization and comparison of genomic and epigenomic data across species and genome assemblies.

The paper analyzes gene regulatory programs in the neocortex of rodents and primates using single-cell multiomics, finding rapid evolution of cell type-specific gene expression and TE-driven cCREs.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper introduces a 3D visualization module to the WashU Epigenome Browser, enabling integration of 1D and 2D genomic data with 3D chromatin structures for better interpretation of genomic information.

The paper introduces a genome browser track for visualizing dynamic DNA sequence features at single nucleotide resolution using machine learning-derived scores.

The paper introduces the qBED format and track for visualizing calling card data and other genomic datasets in the WashU Epigenome Browser.

The paper introduces the WashU Virus Genome Browser, a web-based tool for viewing and comparing viral genomic data, including 16 complete 2019-nCoV sequences and related viruses.

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

The paper introduces a web-based browser for visualizing 3D genome organization and chromatin interactions, enabling integration with other omics data to study gene regulation.