Xiaoting Chen

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

This study provides a reference genome and transcriptome atlas of the Rocky Mountain wood tick, identifying genes involved in blood feeding and developmental-stage-specific gene expression.

This study systematically investigates EBV transcriptional regulators' interactions with the human genome, identifying extensive gene expression alterations and chromatin changes.

This study shows that EBNA2 activity is increased in MS patients, altering gene expression and chromatin accessibility in EBV-transformed B cells.

The paper identifies memory-specific AP-1 recruitment in T cells, driven by epigenetic changes and co-factor interactions, and links it to disease risk variants.

This study evaluates over 3,000 congenital heart disease-risk variants using SNP Bind-n-Seq and MPRA to identify variants with allelic TF binding and regulatory activity.

The paper identifies a splicing mechanism in AML independent of mutations, showing it drives poor prognosis and can be targeted with PRMT5 inhibition.

The paper identifies functional regulatory SNPs in SLE risk loci by testing their impact on transcription factor binding and gene expression.

The paper links IBD polygenic risk to TNFi response using multiome-seq and genetic data from pediatric IBD patients.

The paper presents a chromosome-level genome assembly and manual annotation of Diaphorina citri, along with transcriptome and endosymbiont genomes, providing genomic resources for pest control research.

The paper identifies a regulatory pathway involving rs7034653, FRA2, and TRAF1 that explains how a non-coding variant increases risk of inflammatory arthritis.

maxATAC provides deep learning models for predicting transcription factor binding sites from ATAC-seq data, improving prediction in primary and single-cell contexts.

The paper identifies a non-coding variant that increases ICOS expression, leading to more T peripheral helper cells and contributing to autoimmune diseases.

The paper maps promoter interactions in human ILC3s using PCHi-C and links GWAS risk variants to target genes, identifying new autoimmune disease risk genes.

NOMe-HiC jointly profiles genetic variants, DNA methylation, chromatin accessibility, and 3D genome structure from the same DNA molecule, showing high concordance with mono-omic assays and revealing coordinated chromatin accessibility in spatially proximal regions.

This study identifies epigenetic and transcriptional dysregulation in CD4+ T cells of atopic dermatitis patients, linking genetic risk variants to altered chromatin accessibility and NFKB1 binding.

The paper identifies 482 SLE risk variants with enhancer activity and characterizes allelic regulatory mechanisms at 27 risk loci using MPRA.

The paper identifies alternative splicing programs in three germ layers and shows Quaking's role in cardiac mesoderm specification through splicing regulation.

This study shows Gli3 and Hand2 work together to control gene expression in craniofacial development without relying on a graded Hh signal.

The paper identifies Sox17 and β-catenin interactions at enhancers that regulate endoderm gene expression and repression of mesectoderm fates during Xenopus gastrulation.

The paper shows that super-enhancer switching drives bursts in germline gene expression during the mitosis-to-meiosis transition in testis.

This study provides insights into the biology of the stable fly by combining genome sequencing, microbiome analysis, and RNA-seq to identify genes related to reproduction, host interactions, and pest control.

This study identifies a fetal genome-wide association signal near pro-inflammatory cytokine genes on 2q13 linked to gestational duration and preterm/postterm birth.