Wang Lab Research

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Research

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…

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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…

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Epigenomic landscape of zebrafish TEs

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

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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…

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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…

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WashU Epigenome Browser update 2022

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

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

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

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Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

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

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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…

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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,…

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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…

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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…

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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…

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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…

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Cellular diversity of the regenerating caudal fin

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

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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…

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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…

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

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

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

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

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WashU Epigenome Browser update 2019

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

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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.…

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Epigenomic landscape of nicotinic receptor genes

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

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

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

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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…

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

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

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

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

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Integrative analysis of 111 reference human epigenomes

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

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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…

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Evolution of Epigenetic Regulation in Vertebrate Genomes

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

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DNA Methylation Signatures of Embryonic Surface Ectoderm and Human Skin Cells

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

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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…

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Mapping of Variable DNA Methylation Across Multiple Cell Types

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

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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…

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Jointly analyzing MeDIP-seq and MRE-seq data

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

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