Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Mongersen, an Oral SMAD7 Antisense Oligonucleotide, and Crohn’s Disease

(2015) Giovanni Monteleone et al.   NEW ENGLAND JOURNAL OF MEDICINE

Man's best friend: what can pet dogs teach us about non-Hodgkin's lymphoma?

(2014) Kristy L. Richards et al.   IMMUNOLOGICAL REVIEWS

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Long Non-Coding RNA PCAT-1 Promotes Prostate Cancer Cell Proliferation through cMyc

(2014) John R. Prensner et al.   NEOPLASIA

EZH2 Is Required for Germinal Center Formation and Somatic EZH2 Mutations Promote Lymphoid Transformation

(2013) Wendy Béguelin et al.   CANCER CELL

Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

(2013) Bjoern Chapuy et al.   CANCER CELL

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris

(2013) Marie Mooney et al.   PLoS One

Noncoding RNA and Polycomb recruitment

(2013) N. Brockdorff   RNA

A Hybrid Mechanism of Action for BCL6 in B Cells Defined by Formation of Functionally Distinct Complexes at Enhancers and Promoters

(2013) Katerina Hatzi et al.   Cell Reports

STAT3 Targets Suggest Mechanisms of Aggressive Tumorigenesis in Diffuse Large B-Cell Lymphoma

(2013) Jennifer Hardee et al.   G3-Genes Genomes Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Non-coding RNAs and EZH2 interactions in cancer: Long and short tales from the transcriptome

(2012) Leonidas Benetatos et al.   INTERNATIONAL JOURNAL OF CANCER

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Intronic RNAs mediate EZH2 regulation of epigenetic targets

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis

(2010) I. Velichutina et al.   BLOOD

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

(2010) Ryan D Morin et al.   NATURE GENETICS

Oncogenic Activation of NF- B

(2010) L. M. Staudt   Cold Spring Harbor Perspectives in Biology

Using Alu Elements as Polyadenylation Sites: A Case of Retroposon Exaptation

(2008) C. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stromal Gene Signatures in Large-B-Cell Lymphomas

(2008) G. Lenz et al.   NEW ENGLAND JOURNAL OF MEDICINE