CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs

(2016) Mohammad A. Mandegar et al.   Cell Stem Cell

Unlinking an lncRNA from Its Associated cis Element

(2016) Vikram R. Paralkar et al.   MOLECULAR CELL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

(2016) Shiyou Zhu et al.   NATURE BIOTECHNOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation

(2016) Christian J. Braun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

In Vivo Characterization of Linc-p21 Reveals Functional cis -Regulatory DNA Elements

(2016) Abigail F. Groff et al.   Cell Reports

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

(2016) Nathan Salomonis et al.   Stem Cell Reports

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs

(2015) Estel Aparicio-Prat et al.   BMC GENOMICS

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

(2015) Xiaohui Yan et al.   CANCER CELL

Crystal Structure of Staphylococcus aureus Cas9

(2015) Hiroshi Nishimasu et al.   CELL

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

The Long Noncoding RNA Pnky Regulates Neuronal Differentiation of Embryonic and Postnatal Neural Stem Cells

(2015) Alexander D. Ramos et al.   Cell Stem Cell

Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

(2015) Yafei Yin et al.   Cell Stem Cell

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

(2015) Junwei Shi et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

(2015) James A. Briggs et al.   NEURON

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

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

(2014) Nianwei Lin et al.   MOLECULAR CELL

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

PVT1 dependence in cancer with MYC copy-number increase

(2014) Yuen-Yi Tseng et al.   NATURE

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

(2014) Wenxiu Ma et al.   NATURE METHODS

Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines

(2014) Tsui-Ting Ho et al.   NUCLEIC ACIDS RESEARCH

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Gene regulation by the act of long non-coding RNA transcription

(2013) Aleksandra E Kornienko et al.   BMC BIOLOGY

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells

(2013) M. Kampmann 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

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

Genome Regulation by Long Noncoding RNAs

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

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

(2012) T. Gutschner et al.   CANCER RESEARCH

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response

(2012) Britt Adamson et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom 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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

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

(2009) Ben Langmead et al.   GENOME BIOLOGY