Expression and functions of long noncoding RNAs during human T helper cell differentiation

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

(2014) V. R. Paralkar et al.   BLOOD

Multi-perspective quality control of Illumina exome sequencing data using QC3

(2014) Yan Guo et al.   GENOMICS

Methotrexate induces production of IL-1 and IL-6 in the monocytic cell line U937

(2014) Nancy J Olsen et al.   ARTHRITIS RESEARCH & THERAPY

Methotrexate Inhibits NF-κB Activity Via Long Intergenic (Noncoding) RNA-p21 Induction

(2014) Charles F. Spurlock et al.   Arthritis & Rheumatology

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

(2013) J. R. Alvarez-Dominguez et al.   BLOOD

Three-stage quality control strategies for DNA re-sequencing data

(2013) Y. Guo et al.   BRIEFINGS IN BIOINFORMATICS

The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-γ Locus

(2013) J. Antonio Gomez et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

Profiling of human CD4+ T-cell subsets identifies the TH2-specific noncoding RNA GATA3-AS1

(2013) Huan Zhang et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Reciprocal Regulation of HIF-1α and LincRNA-p21 Modulates the Warburg Effect

(2013) Fan Yang et al.   MOLECULAR CELL

Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation

(2013) Gangqing Hu et al.   NATURE IMMUNOLOGY

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

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

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

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

(2013) S. Carpenter et al.   SCIENCE

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

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Genome Regulation by Long Noncoding RNAs

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

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

Cutting Edge: Influence of Tmevpg1, a Long Intergenic Noncoding RNA, on the Expression of Ifng by Th1 Cells

(2012) S. P. Collier et al.   JOURNAL OF IMMUNOLOGY

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon et al.   MOLECULAR CELL

Chromatin loop formation in the β-globin locus and its role in globin gene transcription

(2012) AeRi Kim et al.   MOLECULES AND CELLS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

More than insulator: multiple roles of CTCF at the H19-Igf2 imprinted domain

(2012) Purnima Singh et al.   Frontiers in Genetics

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

No-Nonsense Functions for Long Noncoding RNAs

(2011) Takashi Nagano et al.   CELL

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

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

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

(2011) Ci Chu et al.   MOLECULAR CELL

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex

(2011) S. Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiation of Effector CD4 T Cell Populations

(2010) Jinfang Zhu et al.   Annual Review of Immunology

The Long Noncoding RNA, Jpx, Is a Molecular Switch for X Chromosome Inactivation

(2010) Di Tian et al.   CELL

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

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

(2010) Maite Huarte et al.   CELL

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

(2010) Rajnish A. Gupta 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

Th2 LCR is essential for regulation of Th2 cytokine genes and for pathogenesis of allergic asthma

(2010) B. H. Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Identification of Long Noncoding RNAs in CD8+ T Cells

(2009) K. C. Pang et al.   JOURNAL OF IMMUNOLOGY

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

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE