Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency

Targeting bivalency de-represses Indian Hedgehog and inhibits self-renewal of colorectal cancer-initiating cells

(2019) Evelyne Lima-Fernandes et al.   Nature Communications

Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas

(2019) Brian Krug et al.   CANCER CELL

Clonally Expanded T Cells Reveal Immunogenicity of Rhabdoid Tumors

(2019) Amaury Leruste et al.   CANCER CELL

Tools and best practices for retrotransposon analysis using high-throughput sequencing data

(2019) Aurélie Teissandier et al.   Mobile DNA

OUP accepted manuscript

(2018)   BIOINFORMATICS

Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown

(2018) Hachung Chung et al.   CELL

Breaching Self-Tolerance to Alu Duplex RNA Underlies MDA5-Mediated Inflammation

(2018) Sadeem Ahmad et al.   CELL

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade

(2018) Wanqiang Sheng et al.   CELL

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

(2018) Peter J Skene et al.   Nature Protocols

The Cancer Epigenome: Exploiting Its Vulnerabilities for Immunotherapy

(2018) Helen Loo Yau et al.   TRENDS IN CELL BIOLOGY

Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade

(2018) Jeffrey J. Ishizuka et al.   NATURE

Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells

(2018) Hugh S. Gannon et al.   Nature Communications

­­­Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia­­

(2017) Trinna L. Cuellar et al.   JOURNAL OF CELL BIOLOGY

CDK4/6 inhibition triggers anti-tumour immunity

(2017) Shom Goel et al.   NATURE

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

(2016) Vagheesh Narasimhan et al.   BIOINFORMATICS

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

(2016) Andreas J. Gruber et al.   GENOME RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Inhibition of DNA Methylation Suppresses Intestinal Tumor Organoids by Inducing an Anti-Viral Response

(2016) Yoshimasa Saito et al.   Scientific Reports

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

(2015) Katherine B. Chiappinelli et al.   CELL

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data

(2015) Goo Jun et al.   GENOME RESEARCH

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself

(2015) B. J. Liddicoat et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Self-renewal as a therapeutic target in human colorectal cancer

(2013) Antonija Kreso et al.   NATURE MEDICINE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

MAVS Forms Functional Prion-like Aggregates to Activate and Propagate Antiviral Innate Immune Response

(2011) Fajian Hou et al.   CELL

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral

(2011) Charles E. Samuel   VIROLOGY

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Targeting DNA Methylation

(2009) J.-P. J. Issa et al.   CLINICAL CANCER RESEARCH

ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays

(2009) Yifang Hu et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY