Wang Lab Research

Click the links below to learn more about the research that takes place at Wang Lab

Research

Cis-regulatory evolution of the recently expanded Ly49 gene family

Abstract: Comparative genomics has revealed the rapid expansion of multiple gene families involved in…

Learn More (Link to external site)

Towards targeting transposable elements for cancer therapy

Abstract: Transposable elements (TEs) represent almost half of the human genome. Historically deemed ‘junk…

Learn More (Link to external site)

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

Abstract: Recent studies have shown that the noncoding genome can produce unannotated proteins as antigens…

Learn More (Link to external site)

Modbed track: Visualization of modified bases in single-molecule sequencing

Abstract: Recent advances in long-read sequencing technologies have not only dramatically increased…

Learn More (Link to external site)

Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers

Abstract: Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence…

Learn More (Link to external site)

Transposable elements in mammalian chromatin organization

Abstract: Transposable elements (TEs) are mobile DNA elements that comprise almost 50% of mammalian genomic…

Learn More (Link to external site)

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

Abstract: Genome browsers have become an intuitive and critical tool to visualize and analyze genomic…

Learn More (Link to external site)

Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements

Abstract: Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in tumors…

Learn More (Link to external site)

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

Abstract: Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These…

Learn More (Link to external site)

Functional characterization of enhancer activity during a long terminal repeat's evolution

Abstract: Many transposable elements (TEs) contain transcription factor binding sites and are implicated as…

Learn More (Link to external site)

Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser

Three-dimensional (3D) genomic structures are vital for gene regulation and cell function1. High-throughput…

Learn More (Link to external site)

Epigenomic landscape of zebrafish TEs

Abstract: Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple…

Learn More (Link to external site)

Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression

Abstract: Allele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed…

Learn More (Link to external site)

The Human Pangenome Project: a global resource to map genomic diversity

Abstract: The human reference genome is the most widely used resource in human genetics and is due for a…

Learn More (Link to external site)

WashU Epigenome Browser update 2022

Abstract: WashU Epigenome Browser (https://epigenomegateway.wustl.edu/browser/) is a web-based genomic data…

Learn More (Link to external site)

A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

Summary: Retrotransposons mediate gene regulation in important developmental and pathological processes.…

Learn More (Link to external site)

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

Abstract: Background: Zebrafish pigment cell differentiation provides an attractive model for studying cell…

Learn More (Link to external site)

Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis

Abstract: Trends in altered DNA methylation have been defined across human cancers, revealing global loss of…

Learn More (Link to external site)

Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease

Summary: The human placenta and its specialized cytotrophoblasts rapidly develop, have a compressed lifespan,…

Learn More (Link to external site)

Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data

Abstract: Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding…

Learn More (Link to external site)

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation

Abstract: Structural variation (SV), including insertions and deletions (indels), is a primary mechanism of…

Learn More (Link to external site)

Tissue-specific usage of transposable element-derived promoters in mouse development

Background: Transposable elements (TEs) are a significant component of eukaryotic genomes and play essential…

Learn More (Link to external site)

Exploring the coronavirus pandemic with the WashU Virus Genome Browser

The WashU Virus Genome Browser is a web-based portal for efficient visualization of viral ‘omics’ data in the…

Learn More (Link to external site)

Cellular diversity of the regenerating caudal fin

Abstract: Zebrafish faithfully regenerate their caudal fin after amputation. During this process, both…

Learn More (Link to external site)

DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods

Abstract: Increased appreciation of 5-hydroxymethylcytosine (5hmC) as a stable epigenetic mark, which defines…

Learn More (Link to external site)

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility

Abstract: Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a…

Learn More (Link to external site)

Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Abstract: Background: Transposable elements (TEs) make up half of mammalian genomes and shape genome…

Learn More (Link to external site)

The epigenomic landscape of transposable elements across normal human development and anatomy

Abstract: Transposable elements (TEs) have deposited functional regulatory elements throughout the human…

Learn More (Link to external site)

WashU Epigenome Browser update 2019

Abstract: The WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) provides visualization,…

Learn More (Link to external site)

Transposable elements drive widespread expression of oncogenes in human cancers

Abstract: Transposable elements (TEs) are an abundant and rich genetic resource of regulatory sequences1,2,3.…

Learn More (Link to external site)

Epigenomic landscape of nicotinic receptor genes

Abstract: Background: Nicotinic acetylcholine receptors (nAChRs) play an important role in cellular…

Learn More (Link to external site)

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

Abstract: Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate the…

Learn More (Link to external site)

Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer

Abstract: Evidence that noncoding mutation can result in cancer driver events is mounting. However, it is…

Learn More (Link to external site)

Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma

Abstract: Uterine carcinosarcoma (UCS) is a form of endometrial cancer simultaneously exhibiting…

Learn More (Link to external site)

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

Abstract: DNA methylation undergoes dynamic changes during development and cell differentiation. Recent…

Learn More (Link to external site)

Integrative analysis of 111 reference human epigenomes

Abstract: The reference human genome sequence set the stage for studies of genetic variation and its…

Learn More (Link to external site)

Intermediate DNA methylation is a conserved signature of genome regulation Learn More

Abstract: The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify…

Learn More (Link to external site)

Evolution of Epigenetic Regulation in Vertebrate Genomes

Empirical models of sequence evolution have spurred progress in the field of evolutionary genetics for…

Learn More (Link to external site)

DNA Methylation Signatures of Embryonic Surface Ectoderm and Human Skin Cells

Companion website for the vertebrate surface ectoderm and human skin project.

Learn More (Link to external site)

Widespread contribution of transposable elements to the innovation of gene regulatory networks

Abstract: Transposable elements (TEs) have been shown to contain functional binding sites for certain…

Learn More (Link to external site)

Mapping of Variable DNA Methylation Across Multiple Cell Types

Abstract: DNA methylation is an important epigenetic modification involved in many biological processes and…

Learn More (Link to external site)

Combining MeDIP-seq and MRE-seq to estimate single CpG methylation genome wide

Overview: No current assay of DNA methylation provides single-CpG resolution, comprehensive genome-wide…

Learn More (Link to external site)

Jointly analyzing MeDIP-seq and MRE-seq data

Introduction: methyMnM was developed for jointly analyzing MeDIP-seq and MRE-seq data, which were derived…

Learn More (Link to external site)