DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats

Combining Epigenetic and Immunotherapy to Combat Cancer

(2016) Katherine B. Chiappinelli et al.   CANCER RESEARCH

5-Azacytidine and DLI can induce long-term remissions in AML patients relapsed after allograft

(2015) J Steinmann et al.   BONE MARROW TRANSPLANTATION

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

Comprehensive identification of genes driven by ERV9-LTRs reveals TNFRSF10B as a re-activatable mediator of testicular cancer cell death

(2015) U Beyer et al.   CELL DEATH AND DIFFERENTIATION

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

(2015) Kosuke Hashimoto et al.   GENOME RESEARCH

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

(2015) Thomas Wiesner et al.   NATURE

Epigenetic silencing of TH1-type chemokines shapes tumour immunity and immunotherapy

(2015) Dongjun Peng et al.   NATURE

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR

(2015) Miguel Vizoso et al.   NATURE MEDICINE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes

(2015) Min Zhao et al.   NUCLEIC ACIDS RESEARCH

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

(2015) Scott Sherrill-Mix et al.   Retrovirology

Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions

(2015) Martin Sokol et al.   Retrovirology

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers

(2015) Huili Li et al.   Oncotarget

5-azacytidine inhibits nonsense-mediated decay in a MYC-dependent fashion

(2014) M. Bhuvanagiri et al.   EMBO Molecular Medicine

Vascular histone deacetylation by pharmacological HDAC inhibition

(2014) Haloom Rafehi et al.   GENOME RESEARCH

At the tipping point for epigenetic therapies in cancer

(2014) Peter A. Jones   JOURNAL OF CLINICAL INVESTIGATION

New and emerging HDAC inhibitors for cancer treatment

(2014) Alison C. West et al.   JOURNAL OF CLINICAL INVESTIGATION

Clinical development of demethylating agents in hematology

(2014) Shyamala C. Navada et al.   JOURNAL OF CLINICAL INVESTIGATION

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma

(2014) F. E. Lock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eradication of metastatic mouse cancers resistant to immune checkpoint blockade by suppression of myeloid-derived cells

(2014) K. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

(2014) Sebastiaan van Heesch et al.   GENOME BIOLOGY

Genomic impact of transient low-dose decitabine treatment on primary AML cells

(2013) J. M. Klco et al.   BLOOD

Azacitidine and donor lymphocyte infusions as first salvage therapy for relapse of AML or MDS after allogeneic stem cell transplantation

(2013) T Schroeder et al.   LEUKEMIA

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex

(2013) John R Prensner et al.   NATURE GENETICS

Tagmentation-based whole-genome bisulfite sequencing

(2013) Qi Wang et al.   Nature Protocols

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Association of Endogenous Retroviruses and Long Terminal Repeats with Human Disorders

(2013) Iyoko Katoh et al.   Frontiers in Oncology

HDAC inhibitor-based therapies: Can we interpret the code?

(2012) Maria New et al.   Molecular Oncology

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Quantitative analyses of DAPK1 methylation in AML and MDS

(2011) Rainer Claus et al.   INTERNATIONAL JOURNAL OF CANCER

Systematic Clustering of Transcription Start Site Landscapes

(2011) Xiaobei Zhao et al.   PLoS One

Combination Epigenetic Therapy Has Efficacy in Patients with Refractory Advanced Non-Small Cell Lung Cancer

(2011) R. A. Juergens et al.   Cancer Discovery

The DNA demethylating agent 5-aza-2′-deoxycytidine induces expression of NY-ESO-1 and other cancer/testis antigens in myeloid leukemia cells

(2010) Maika Almstedt et al.   LEUKEMIA RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Long-range function of an intergenic retrotransposon

(2010) W. Pi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

(2009) Carla J. Cohen et al.   GENE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

(2009) Giorgio Grillo et al.   NUCLEIC ACIDS RESEARCH

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Enhancement of Antigen Processing and Presentation Promotes Immune Recognition of Tumors

(2008) A. F. Setiadi et al.   CANCER RESEARCH

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

(2008) L. G. Almeida et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY