A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

(2015) Gireesh K. Bogu et al.   MOLECULAR AND CELLULAR BIOLOGY

Long noncoding RNA, CCDC26, controls myeloid leukemia cell growth through regulation of KIT expression

(2015) Tetsuo Hirano et al.   Molecular Cancer

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

(2015) Tanmoy Mondal et al.   Nature Communications

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application

(2015) Guoliang Li et al.   BMC GENOMICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

(2014) Thomas Trimarchi et al.   CELL

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Activation ofLTBP3Gene by a Long Noncoding RNA (lncRNA)MALAT1Transcript in Mesenchymal Stem Cells from Multiple Myeloma

(2014) Bingzong Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

LincRNAs MONC and MIR100HG act as oncogenes in acute megakaryoblastic leukemia

(2014) Stephan Emmrich et al.   Molecular Cancer

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

(2014) Wenxiu Ma et al.   NATURE METHODS

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

(2014) Tanvir Alam et al.   PLoS One

Long noncoding RNAs: an emerging link between gene regulation and nuclear organization

(2014) Sofia Quinodoz et al.   TRENDS IN CELL BIOLOGY

Transcriptional regulatory functions of nuclear long noncoding RNAs

(2014) Keith W. Vance et al.   TRENDS IN GENETICS

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dissecting the chromatin interactome of microRNA genes

(2013) D. Chen et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

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

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells

(2012) T. Gutschner et al.   CANCER RESEARCH

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Cis-acting noncoding RNAs: friends and foes

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

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Epstein-Barr Virus, Human Papillomavirus and Mouse Mammary Tumour Virus as Multiple Viruses in Breast Cancer

(2012) Wendy K. Glenn et al.   PLoS One

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

(2012) Kuljeet Singh Sandhu et al.   Cell Reports

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

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

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics

(2010) István A. Kovács et al.   PLoS One

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Germline Genetic Variation in an Organic Anion Transporter Polypeptide Associated With Methotrexate Pharmacokinetics and Clinical Effects

(2009) Lisa R. Treviño et al.   JOURNAL OF CLINICAL ONCOLOGY

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

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

(2009) Mitchell Guttman et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Genomic analysis reveals few genetic alterations in pediatric acute myeloid leukemia

(2009) I. Radtke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA