Epstein-Barr virus inactivates the transcriptome and disrupts the chromatin architecture of its host cell in the first phase of lytic reactivation

MYC Controls the Epstein-Barr Virus Lytic Switch

(2020) Rui Guo et al.   MOLECULAR CELL

An epigenetic journey: Epstein-Barr virus transcribes chromatinized and subsequently unchromatinized templates during its lytic cycle

(2019) Adityarup Chakravorty et al.   JOURNAL OF VIROLOGY

First Days in the Life of Naive Human B Lymphocytes Infected with Epstein-Barr Virus

(2019) Dagmar Pich et al.   mBio

Four-dimensional analyses show that replication compartments are clonal factories in which Epstein–Barr viral DNA amplification is coordinated

(2019) Thejaswi Nagaraju et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Superheat: An R Package for Creating Beautiful and Extendable Heatmaps for Visualizing Complex Data

(2018) Rebecca L. Barter et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data

(2018) Quan H Nguyen et al.   GigaScience

Stochastic switching in biology: from genotype to phenotype

(2017) Paul C Bressloff   Journal of Physics A-Mathematical and Theoretical

Seneca Valley Virus Suppresses Host Type I Interferon Production by Targeting Adaptor Proteins MAVS, TRIF, and TANK for Cleavage

(2017) Suhong Qian et al.   JOURNAL OF VIROLOGY

MicroRNAs of Epstein-Barr Virus Control Innate and Adaptive Antiviral Immunity

(2017) Manuel Albanese et al.   JOURNAL OF VIROLOGY

AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos

(2016) Johannes Stegmaier et al.   DEVELOPMENTAL CELL

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

K1 and K15 of Kaposi's Sarcoma-Associated Herpesvirus Are Partial Functional Homologues of Latent Membrane Protein 2A of Epstein-Barr Virus

(2015) Lisa Steinbrück et al.   JOURNAL OF VIROLOGY

Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth

(2015) Francesca Zanconato et al.   NATURE CELL BIOLOGY

Epstein–Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression

(2015) Sharada Ramasubramanyan et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Remodeling nuclear architecture allows efficient transport of herpesvirus capsids by diffusion

(2015) Jens B. Bosse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Damage Signaling Is Induced in the Absence of Epstein—Barr Virus (EBV) Lytic DNA Replication and in Response to Expression of ZEBRA

(2015) Ruth Wang'ondu et al.   PLoS One

Epstein-Barr virus BALF3 mediates genomic instability and progressive malignancy in nasopharyngeal carcinoma

(2015) Shih-Hsin Chiu et al.   Oncotarget

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

(2014) S. Anders et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Epstein-Barr Virus BALF3 Has Nuclease Activity and Mediates Mature Virion Production during the Lytic Cycle

(2014) S.-H. Chiu et al.   JOURNAL OF VIROLOGY

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Nuclear Translocation and Regulation of Intranuclear Distribution of Cytoplasmic Poly(A)-Binding Protein Are Distinct Processes Mediated by Two Epstein Barr Virus Proteins

(2014) Richard Park et al.   PLoS One

Regulation of the latent-lytic switch in Epstein–Barr virus

(2014) Shannon C. Kenney et al.   SEMINARS IN CANCER BIOLOGY

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

Epstein-Barr Viral Productive Amplification Reprograms Nuclear Architecture, DNA Replication, and Histone Deposition

(2013) Ya-Fang Chiu et al.   Cell Host & Microbe

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA sequence motifs

(2013) M. Gustems et al.   NUCLEIC ACIDS RESEARCH

Replication of Epstein-Barr Viral DNA

(2013) W. Hammerschmidt et al.   Cold Spring Harbor Perspectives in Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The "Bridge" in the Epstein-Barr Virus Alkaline Exonuclease Protein BGLF5 Contributes to Shutoff Activity during Productive Infection

(2012) D. Horst et al.   JOURNAL OF VIROLOGY

Suppression of the antiviral response by an influenza histone mimic

(2012) Ivan Marazzi et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

RNAs in Epstein-Barr virions control early steps of infection

(2012) S. Jochum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host restriction factors in retroviral infection: promises in virus-host interaction

(2012) Yong-Hui Zheng et al.   Retrovirology

BZLF1 Governs CpG-Methylated Chromatin of Epstein-Barr Virus Reversing Epigenetic Repression

(2012) Anne Woellmer et al.   PLoS Pathogens

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Human B cells on their route to latent infection – Early but transient expression of lytic genes of Epstein-Barr virus

(2011) Markus Kalla et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

The Lytic Phase of Epstein-Barr Virus Requires a Viral Genome with 5-Methylcytosine Residues in CpG Sites

(2011) M. Kalla et al.   JOURNAL OF VIROLOGY

Epigenetic Control of Viral Life-Cycle by a DNA-Methylation Dependent Transcription Factor

(2011) Kirsty Flower et al.   PLoS One

Epstein-Barr Virus Evades CD4+ T Cell Responses in Lytic Cycle through BZLF1-mediated Downregulation of CD74 and the Cooperation of vBcl-2

(2011) Jianmin Zuo et al.   PLoS Pathogens

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Epstein-Barr Virus BZLF1 Protein Inhibits Tumor Necrosis Factor Receptor 1 Expression through Effects on Cellular C/EBP Proteins

(2010) J. A. Bristol et al.   JOURNAL OF VIROLOGY

Nuclear Import of Cytoplasmic Poly(A) Binding Protein Restricts Gene Expression via Hyperadenylation and Nuclear Retention of mRNA

(2010) G. R. Kumar et al.   MOLECULAR AND CELLULAR BIOLOGY

CpG-Methylation Regulates a Class of Epstein-Barr Virus Promoters

(2010) Martin Bergbauer et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

EBV Zta protein induces the expression of interleukin-13, promoting the proliferation of EBV-infected B cells and lymphoblastoid cell lines

(2009) S.-C. Tsai et al.   BLOOD

The Epstein-Barr virus lytic cycle activator Zta interacts with methylated ZRE in the promoter of host target gene egr1

(2009) J. Heather et al.   JOURNAL OF GENERAL VIROLOGY

A Bridge Crosses the Active-Site Canyon of the Epstein–Barr Virus Nuclease with DNase and RNase Activities

(2009) Marlyse Buisson et al.   JOURNAL OF MOLECULAR BIOLOGY

Epstein–Barr Virus DNase (BGLF5) induces genomic instability in human epithelial cells

(2009) Chung-Chun Wu et al.   NUCLEIC ACIDS RESEARCH

AP-1 homolog BZLF1 of Epstein-Barr virus has two essential functions dependent on the epigenetic state of the viral genome

(2009) M. Kalla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methylation-Dependent Binding of the Epstein-Barr Virus BZLF1 Protein to Viral Promoters

(2009) Sarah J. Dickerson et al.   PLoS Pathogens

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Epstein-Barr Virus Lytic Transactivator Zta Enhances Chemotactic Activity through Induction of Interleukin-8 in Nasopharyngeal Carcinoma Cells

(2008) M. Hsu et al.   JOURNAL OF VIROLOGY

Long-Range Enhancer Associated with Chromatin Looping Allows AP-1 Regulation of the Peptidylarginine Deiminase 3 Gene in Differentiated Keratinocyte

(2008) Stéphane Chavanas et al.   PLoS One

Mutations of amino acids in the DNA-recognition domain of Epstein–Barr virus ZEBRA protein alter its sub-nuclear localization and affect formation of replication compartments

(2008) Richard Park et al.   VIROLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY