Am I ready for CRISPR? A user's guide to genetic screens

Applications of CRISPR genome editing technology in drug target identification and validation

(2017) Quinn Lu et al.   Expert Opinion on Drug Discovery

Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling

(2017) Markus Brockmann et al.   NATURE

In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target

(2017) Robert T. Manguso et al.   NATURE

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions

(2017) Kyuho Han et al.   NATURE BIOTECHNOLOGY

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci

(2017) Matthew C Canver et al.   NATURE GENETICS

Atomic segregation: Activity at the surface

(2017) Simon P. Ringer   NATURE MATERIALS

GUIDES: sgRNA design for loss-of-function screens

(2017) Joshua A Meier et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Flexible CRISPR library construction using parallel oligonucleotide retrieval

(2017) Abigail Read et al.   NUCLEIC ACIDS RESEARCH

Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis

(2017) Jonathan J. Ipsaro et al.   PLoS One

Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression

(2017) Joseph Rosenbluh et al.   Nature Communications

Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

(2017) Deborah Y. Kwon et al.   Nature Communications

ATXN1L, CIC, and ETS Transcription Factors Modulate Sensitivity to MAPK Pathway Inhibition

(2017) Belinda Wang et al.   Cell Reports

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

(2017) Traver Hart et al.   G3-Genes Genomes Genetics

KEAP1 loss modulates sensitivity to kinase targeted therapy in lung cancer

(2017) Elsa B Krall et al.   eLife

Synergistic interactions with PI3K inhibition that induce apoptosis

(2017) Yaara Zwang et al.   eLife

Creation of Novel Protein Variants with CRISPR/Cas9-Mediated Mutagenesis: Turning a Screening By-Product into a Discovery Tool

(2017) Katherine F. Donovan et al.   PLoS One

High-throughput Phenotyping of Lung Cancer Somatic Mutations

(2016) Alice H. Berger et al.   CANCER CELL

A Vulnerability of a Subset of Colon Cancers with Potential Clinical Utility

(2016) Loredana Vecchione et al.   CELL

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

CRISPR/Cas9 Screens Reveal Requirements for Host Cell Sulfation and Fucosylation in Bacterial Type III Secretion System-Mediated Cytotoxicity

(2016) Carlos J. Blondel et al.   Cell Host & Microbe

A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation

(2016) Jason D. Arroyo et al.   Cell Metabolism

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

Derivation and differentiation of haploid human embryonic stem cells

(2016) Ido Sagi et al.   NATURE

A CRISPR screen defines a signal peptide processing pathway required by flaviviruses

(2016) Rong Zhang et al.   NATURE

Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens

(2016) Caleb D. Marceau et al.   NATURE

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

(2016) Bastiaan Evers et al.   NATURE BIOTECHNOLOGY

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

(2016) David W Morgens et al.   NATURE BIOTECHNOLOGY

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification

(2016) Richard M Deans et al.   Nature Chemical Biology

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors

(2016) Ryan J Park et al.   NATURE GENETICS

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

(2016) Yunqing Ma et al.   NATURE METHODS

Comparison of Cas9 activators in multiple species

(2016) Alejandro Chavez et al.   NATURE METHODS

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases

(2016) Shengdar Q. Tsai et al.   NATURE REVIEWS GENETICS

GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens

(2016) Benedikt Rauscher et al.   NUCLEIC ACIDS RESEARCH

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression

(2016) Aliaksandra Radzisheuskaya et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Validation of Synthetic CRISPR Reagents as a Tool for Arrayed Functional Genomic Screening

(2016) Jenille Tan et al.   PLoS One

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

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM

(2016) Alan S. L. Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a proteinaceous cellular receptor for a norovirus

(2016) R. C. Orchard et al.   SCIENCE

Exploring genetic suppression interactions on a global scale

(2016) J. van Leeuwen et al.   SCIENCE

MTAPdeletion confers enhanced dependency on the PRMT5 arginine methyltransferase in cancer cells

(2016) Gregory V. Kryukov et al.   SCIENCE

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

(2016) S. John Liu et al.   SCIENCE

Hypoxia as a therapy for mitochondrial disease

(2016) I. H. Jain et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

(2016) Prarthana Mohanraju et al.   SCIENCE

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Disciplined approach to drug discovery and early development

(2016) Robert M. Plenge   Science Translational Medicine

CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions

(2016) D. M. Munoz et al.   Cancer Discovery

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter

(2016) Samrat Roy Choudhury et al.   Oncotarget

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia

(2016) Konstantinos Tzelepis et al.   Cell Reports

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens

(2015) Jan Winter et al.   BIOINFORMATICS

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

(2015) Traver Hart et al.   CELL

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

(2015) Oren Parnas et al.   CELL

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Genetic screens and functional genomics using CRISPR/Cas9 technology

(2015) Ella Hartenian et al.   FEBS Journal

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

(2015) Lauren R. Polstein et al.   GENOME RESEARCH

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

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

(2015) Junwei Shi et al.   NATURE BIOTECHNOLOGY

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns 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

Alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation

(2015) Asaf Rotem et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-generation libraries for robust RNA interference-based genome-wide screens

(2015) Martin Kampmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Strategies for precision modulation of gene expression by epigenome editing: an overview

(2015) Benjamin I. Laufer et al.   Epigenetics & Chromatin

A CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death

(2015) Hongming Ma et al.   Cell Reports

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects

(2015) Shantanu Singh et al.   PLoS One

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

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

(2014) Luke A. Gilbert et al.   CELL

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

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

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing

(2014) Dirk Heckl et al.   NATURE BIOTECHNOLOGY

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Microhomology-based choice of Cas9 nuclease target sites

(2014) Sangsu Bae et al.   NATURE METHODS

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Inducible RNAi in vivo reveals that the transcription factor BATF is required to initiate but not maintain CD8+T-cell effector differentiation

(2014) Jernej Godec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of Squamous Cell Carcinomas

(2014) D. Schramek et al.   SCIENCE

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

(2013) Lei S. Qi et al.   CELL

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

A melanocyte lineage program confers resistance to MAP kinase pathway inhibition

(2013) Cory M. Johannessen et al.   NATURE

RNAi screens in mice identify physiological regulators of oncogenic growth

(2013) Slobodan Beronja et al.   NATURE

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

(2013) Hiroko Koike-Yusa et al.   NATURE BIOTECHNOLOGY

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis

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

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali 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

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

(2011) H. W. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient tumour formation by single human melanoma cells

(2008) Elsa Quintana et al.   NATURE

Highly parallel identification of essential genes in cancer cells

(2008) B. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental validation of the importance of seed complement frequency to siRNA specificity

(2008) E. M. Anderson et al.   RNA