Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

The long noncoding RNA THRIL regulates TNF  expression through its interaction with hnRNPL

(2013) Z. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

(2013) T. Shay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Long Noncoding RNA Mediates Both Activation and Repression of Immune Response Genes

(2013) S. Carpenter et al.   SCIENCE

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

(2013) Nicole A Rapicavoli et al.   eLife

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Treating inflammation by blocking interleukin-1 in a broad spectrum of diseases

(2012) Charles A. Dinarello et al.   NATURE REVIEWS DRUG DISCOVERY

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

The Emerging Role of Interleukin-1β in Autoinflammatory Diseases

(2011) Thirusha Lane et al.   CURRENT ALLERGY AND ASTHMA REPORTS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

A Global Clustering Algorithm to Identify Long Intergenic Non-Coding RNA - with Applications in Mouse Macrophages

(2011) Lana X. Garmire et al.   PLoS One

Discovery of active enhancers through bidirectional expression of short transcripts

(2011) Michael F Melgar et al.   GENOME BIOLOGY

Identification of LPS-inducible genes downregulated by ubiquinone in human THP-1 monocytes

(2010) Constance Schmelzer et al.   BIOFACTORS

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

Enhancers make non-coding RNA

(2010) Bing Ren   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Effects of formoterol and salmeterol on cytokine release from monocyte-derived macrophages

(2009) L. E. Donnelly et al.   EUROPEAN RESPIRATORY JOURNAL

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

(2008) A. G. Robertson et al.   GENOME RESEARCH

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

microRNAs and the immune response

(2008) Mark A. Lindsay   TRENDS IN IMMUNOLOGY