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

MIG: Multi-Image Genome viewer

(2013) S. J. McGowan et al.   BIOINFORMATICS

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

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

(2013) F. Schlesinger et al.   GENOME RESEARCH

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

(2013) F. S. J. de Souza et al.   MOLECULAR BIOLOGY AND EVOLUTION

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Claudia Kutter et al.   PLoS Genetics

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

(2012) David Kelley et al.   GENOME BIOLOGY

Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes

(2011) P. Wong et al.   BLOOD

From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications

(2011) S. M. Hattangadi et al.   BLOOD

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(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

Chromosome looping at the human  -globin locus is mediated via the major upstream regulatory element (HS -40)

(2009) D. Vernimmen et al.   BLOOD

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

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

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Resolving the distinct stages in erythroid differentiation based on dynamic changes in membrane protein expression during erythropoiesis

(2009) K. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH