Epigenomic landscape study reveals molecular subtypes and EBV-associated regulatory epigenome reprogramming in nasopharyngeal carcinoma

Comprehensive single-cell sequencing reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of nasopharyngeal carcinoma

(2021) Lanqi Gong et al.   Nature Communications

Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution

(2021) Yang Liu et al.   Nature Communications

The Impact of Epstein-Barr Virus Infection on Epigenetic Regulation of Host Cell Gene Expression in Epithelial and Lymphocytic Malignancies

(2021) Merrin Man Long Leong et al.   Frontiers in Oncology

IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility

(2021) Ran Song et al.   Cell Reports

Phase separation of Epstein-Barr virus EBNA2 protein reorganizes chromatin topology for epigenetic regulation

(2021) Yiting Yang et al.   Communications Biology

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

(2020) Yu-Pei Chen et al.   CELL RESEARCH

CTCF loss mediates unique DNA hypermethylation landscapes in human cancers

(2020) Nathan A. Damaschke et al.   Clinical Epigenetics

Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma

(2020) Shanzhao Jin et al.   CELL RESEARCH

Clinical Outcome-Related Mutational Signatures Identified by Integrative Genomic Analysis in Nasopharyngeal Carcinoma

(2020) Wei Dai et al.   CLINICAL CANCER RESEARCH

TET repression and increased DNMT activity synergistically induce aberrant DNA methylation

(2020) Hideyuki Takeshima et al.   JOURNAL OF CLINICAL INVESTIGATION

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci

(2020) Lvwen Ning et al.   Communications Biology

Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

(2019) Lindsay F. Rizzardi et al.   NATURE NEUROSCIENCE

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

MIF family proteins in genitourinary cancer: tumorigenic roles and therapeutic potential

(2019) Justin C. Penticuff et al.   Nature Reviews Urology

Macrophage migration inhibitory factor‐ CD 74 interaction regulates the expression of programmed cell death ligand 1 in melanoma cells

(2019) Masako Imaoka et al.   CANCER SCIENCE

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Nasopharyngeal carcinoma

(2019) Yu-Pei Chen et al.   LANCET

Genome sequencing analysis identifies Epstein–Barr virus subtypes associated with high risk of nasopharyngeal carcinoma

(2019) Miao Xu et al.   NATURE GENETICS

EBV infection is associated with histone bivalent switch modifications in squamous epithelial cells

(2019) Merrin Man Long Leong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IRF1 Inhibits Antitumor Immunity through the Upregulation of PD-L1 in the Tumor Cell

(2019) Lulu Shao et al.   Cancer Immunology Research

L1EM: a tool for accurate locus specific LINE-1 RNA quantification

(2019) Wilson McKerrow et al.   BIOINFORMATICS

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Mutant cellular AP-1 proteins promote expression of a subset of Epstein-Barr virus late genes in the absence of lytic viral DNA replication

(2018) Danielle E. Lyons et al.   JOURNAL OF VIROLOGY

Establishment of a nasopharyngeal carcinoma cell line capable of undergoing lytic Epstein–Barr virus reactivation

(2018) Yim Ling Yip et al.   LABORATORY INVESTIGATION

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML

(2018) Mathijs A. Sanders et al.   BLOOD

High risk Epstein‐Barr virus variants characterized by distinct polymorphisms in the EBER locus are strongly associated with nasopharyngeal carcinoma

(2018) Kwai Fung Hui et al.   INTERNATIONAL JOURNAL OF CANCER

Establishment and characterization of new tumor xenografts and cancer cell lines from EBV-positive nasopharyngeal carcinoma

(2018) Weitao Lin et al.   Nature Communications

CTCFdeletion syndrome: clinical features and epigenetic delineation

(2017) Ikumi Hori et al.   JOURNAL OF MEDICAL GENETICS

Epstein-Barr virus infection induces genome-wide de novo DNA methylation in non-neoplastic gastric epithelial cells

(2017) Keisuke Matsusaka et al.   JOURNAL OF PATHOLOGY

Whole-exome sequencing reveals critical genes underlying metastasis in oesophageal squamous cell carcinoma

(2017) Wei Dai et al.   JOURNAL OF PATHOLOGY

Differentiation-Dependent LMP1 Expression Is Required for Efficient Lytic Epstein-Barr Virus Reactivation in Epithelial Cells

(2017) Dhananjay M. Nawandar et al.   JOURNAL OF VIROLOGY

Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-Based Subtypes

(2017) Li Zhang et al.   MOLECULAR CANCER RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA

(2017) Emily K. Schutsky et al.   NUCLEIC ACIDS RESEARCH

Epstein–Barr virus-associated lymphomas

(2017) Claire Shannon-Lowe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epstein–Barr virus infection and nasopharyngeal carcinoma

(2017) Sai Wah Tsao et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The multifaceted roles of the invariant chain CD74 — More than just a chaperone

(2016) Bernd Schröder   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Epstein-Barr virus lytic reactivation regulation and its pathogenic role in carcinogenesis

(2016) Hongde Li et al.   International Journal of Biological Sciences

Tumour hypoxia causes DNA hypermethylation by reducing TET activity

(2016) Bernard Thienpont et al.   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Whole-exome sequencing identifies multiple loss-of-function mutations of NF-κB pathway regulators in nasopharyngeal carcinoma

(2016) Hong Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites

(2015) Alfonso Bellacosa et al.   DNA REPAIR

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

(2015) Frank Jühling et al.   GENOME RESEARCH

Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma

(2015) W. Jiang et al.   MOLECULAR CANCER THERAPEUTICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Upregulated long non-coding RNA AFAP1-AS1 expression is associated with progression and poor prognosis of nasopharyngeal carcinoma

(2015) Hao Bo et al.   Oncotarget

Differentiation-Dependent KLF4 Expression Promotes Lytic Epstein-Barr Virus Infection in Epithelial Cells

(2015) Dhananjay M. Nawandar et al.   PLoS Pathogens

Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma

(2015) Wei Dai et al.   Cancer Medicine

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Regulation of Epstein-Barr virus reactivation from latency

(2014) Takayuki Murata   MICROBIOLOGY AND IMMUNOLOGY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

(2014) Christopher J. Kemp et al.   Cell Reports

Constitutive activation of distinct NF-κB signals in EBV-associated nasopharyngeal carcinoma

(2013) Grace Tin-Yun Chung et al.   JOURNAL OF PATHOLOGY

Identification of active regulatory regions from DNA methylation data

(2013) Lukas Burger et al.   NUCLEIC ACIDS RESEARCH

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma: An Integrated Analysis at the Genetic and Expression Levels

(2012) Chunfang Hu et al.   PLoS One

Cyclin D1 overexpression supports stable EBV infection in nasopharyngeal epithelial cells

(2012) C. M. Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD74 and macrophage migration inhibitory factor as therapeutic targets in gastric cancer

(2012) Ying-Xia Zheng   WORLD JOURNAL OF GASTROENTEROLOGY

Classification of Epstein-Barr Virus-Positive Gastric Cancers by Definition of DNA Methylation Epigenotypes

(2011) K. Matsusaka et al.   CANCER RESEARCH

Leukemic IDH1 and IDH2 Mutations Result in a Hypermethylation Phenotype, Disrupt TET2 Function, and Impair Hematopoietic Differentiation

(2010) Maria E. Figueroa et al.   CANCER CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY