Yunjiang Qiu

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

The paper introduces BNBC, a normalization and batch correction method for Hi-C data, improving cross-sample comparisons and analyses.

The paper creates a deep population reference panel of tandem repeat variation using whole genome sequencing and develops a method to genotype over 1.7 million TR loci, identifying novel eQTL signals and a phased haplotype panel for imputation.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper identifies T1D risk genes and regulatory elements that influence beta cell survival under proinflammatory cytokine exposure using functional genomics and genetics.

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

The paper creates a chromatin accessibility atlas across 25 adult human tissues, identifying over 750,000 cis-regulatory elements and linking them to gene regulatory programs and disease-associated variants.

The paper identifies 491,818 candidate cis regulatory elements in adult mouse brain sub-types and links them to target genes and transcriptional regulators involved in various pathways.

The paper uses single-cell chromatin accessibility to identify cell type- and state-specific regulatory programs associated with type 2 diabetes risk.

The paper identifies T2D risk variants in pancreatic progenitor-specific enhancers and shows their role in regulating developmental genes involved in pancreas morphogenesis.

FIREcaller detects frequently interacting regions from Hi-C data and shows their association with gene regulation and GWAS variants in human tissues.

The paper shows FOXA pioneer factors prime some enhancers but require lineage-specific TFs to activate others, influencing endodermal organ fate decisions.

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

This study identifies DNA sequence variants that influence 3D chromatin conformation and links them to gene expression and disease risk.

The paper investigates chromatin architecture changes during human cardiomyocyte differentiation and identifies HERV-H retrotransposons as key regulators of TAD boundaries and gene regulation.

The paper identifies distal enhancer networks in pancreatic islets associated with type 2 diabetes risk by integrating chromatin accessibility, conformation, and genetic data.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

MAPS processes PLAC-seq and HiChIP data to identify long-range chromatin interactions by removing biases and analyzing contact frequencies.

This study shows that MLL3/4 proteins regulate chromatin interactions at enhancers by depositing H3K4me1, which recruits Cohesin to facilitate chromatin looping.