Loss-of-function genetic tools for animal models: cross-species and cross-platform differences

Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish

(2016) Isabel Brocal et al.   BMC GENOMICS

Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes

(2016) Alexa Burger et al.   DEVELOPMENT

Regulated protein depletion by the auxin-inducible degradation system inDrosophila melanogaster

(2016) Martina Trost et al.   FLY

The application of somatic CRISPR-Cas9 to conditional genome editing inCaenorhabditis elegans

(2016) Wei Li et al.   GENESIS

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9

(2016) Dominik Paquet 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

Organoids as an in vitro model of human development and disease

(2016) Aliya Fatehullah et al.   NATURE CELL BIOLOGY

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

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

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

Comparison of Cas9 activators in multiple species

(2016) Alejandro Chavez et al.   NATURE METHODS

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

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

DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data

(2016) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

Effective knockdown ofDrosophilalong non-coding RNAs by CRISPR interference

(2016) Sanjay Ghosh et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta 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

Reverse Genetics in Zebrafish: Mutants, Morphants, and Moving Forward

(2016) Nathan D. Lawson   TRENDS IN CELL BIOLOGY

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

Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors

(2016) Toyoaki Natsume et al.   Cell Reports

A genome-wide resource for the analysis of protein localisation in Drosophila

(2016) Mihail Sarov et al.   eLife

Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis

(2015) Luyuan Pan et al.   BMC GENOMICS

Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer

(2015) Lukas E. Dow et al.   CELL

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

(2015) Sidi Chen et al.   CELL

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

(2015) Oren Parnas et al.   CELL

Regulation of transcriptionally active genes via the catalytically inactive Cas9 in C. elegans and D. rerio

(2015) Lijiang Long et al.   CELL RESEARCH

A photosensitive degron enables acute light-induced protein degradation in the nervous system

(2015) Anke Hermann et al.   CURRENT BIOLOGY

Anillin Regulates Neuronal Migration and Neurite Growth by Linking RhoG to the Actin Cytoskeleton

(2015) Dong Tian et al.   CURRENT BIOLOGY

The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans

(2015) L. Zhang et al.   DEVELOPMENT

Making Sense of Anti-Sense Data

(2015) Didier Y.R. Stainier et al.   DEVELOPMENTAL CELL

Morpholinos: Antisense and Sensibility

(2015) Martin Blum et al.   DEVELOPMENTAL CELL

A CRISPR/Cas9 Vector System for Tissue-Specific Gene Disruption in Zebrafish

(2015) Julien Ablain et al.   DEVELOPMENTAL CELL

Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish

(2015) Fatma O. Kok et al.   DEVELOPMENTAL CELL

Potential pitfalls of CRISPR/Cas9-mediated genome editing

(2015) Rongxue Peng et al.   FEBS Journal

Genetic screens and functional genomics using CRISPR/Cas9 technology

(2015) Ella Hartenian et al.   FEBS Journal

A Transparent Window into Biology: A Primer on Caenorhabditis elegans

(2015) Ann K. Corsi et al.   GENETICS

In VivoTranscriptional Activation Using CRISPR/Cas9 inDrosophila

(2015) Shuailiang Lin et al.   GENETICS

High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR-Cas9 Ribonucleoprotein Complexes

(2015) A. Paix et al.   GENETICS

Enabling functional genomics with genome engineering

(2015) Isaac B. Hilton et al.   GENOME RESEARCH

Somatic CRISPR–Cas9-induced mutations reveal roles of embryonically essential dynein chains inCaenorhabditis eleganscilia

(2015) Wenjing Li et al.   JOURNAL OF CELL BIOLOGY

Big Data in Caenorhabditis elegans: quo vadis?

(2015) Harald Hutter et al.   MOLECULAR BIOLOGY OF THE CELL

Global genetic analysis in mice unveils central role for cilia in congenital heart disease

(2015) You Li et al.   NATURE

Genetic compensation induced by deleterious mutations but not gene knockdowns

(2015) Andrea Rossi et al.   NATURE

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

(2015) Silvana Konermann et al.   NATURE

Inducible in vivo genome editing with CRISPR-Cas9

(2015) Lukas E Dow 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

The promise and peril of chemical probes

(2015) Cheryl H Arrowsmith et al.   Nature Chemical Biology

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

(2015) Nicola A Kearns et al.   NATURE METHODS

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez 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

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

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

Auxin binding protein 1 (ABP1) is not required for either auxin signaling orArabidopsisdevelopment

(2015) Yangbin Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi

(2015) Benjamin E. Housden et al.   Science Signaling

Quantifying on- and off-target genome editing

(2015) Ayal Hendel et al.   TRENDS IN BIOTECHNOLOGY

RIPK1 and RIPK3: critical regulators of inflammation and cell death

(2015) Kim Newton   TRENDS IN CELL BIOLOGY

Optogenetic mutagenesis in Caenorhabditis elegans

(2015) Kentaro Noma et al.   Nature Communications

Recombinase-based conditional and reversible gene regulation via XTR alleles

(2015) Camila Robles-Oteiza et al.   Nature Communications

Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins

(2015) Yeong Ju Shin et al.   Scientific Reports

Probing Yeast Polarity with Acute, Reversible, Optogenetic Inhibition of Protein Function

(2015) Anna Payne-Tobin Jost et al.   ACS Synthetic Biology

A Multifunctional Mutagenesis System for Analysis of Gene Function in Zebrafish

(2015) H. N. B. Quach et al.   G3-Genes Genomes Genetics

A Transparent Window into Biology: A Primer on Caenorhabditis elegans

(2015) Ann K. Corsi et al.   GENETICS

In VivoTranscriptional Activation Using CRISPR/Cas9 inDrosophila

(2015) Shuailiang Lin et al.   GENETICS

Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi

(2015) Benjamin E. Housden et al.   Science Signaling

klf2ash317 Mutant Zebrafish Do Not Recapitulate Morpholino-Induced Vascular and Haematopoietic Phenotypes

(2015) Peter Novodvorsky et al.   PLoS One

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

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

(2014) Luke A. Gilbert et al.   CELL

Chemical Biology Strategies for Posttranslational Control of Protein Function

(2014) Rishi Rakhit et al.   CHEMISTRY & BIOLOGY

Repurposing an endogenous degradation system for rapid and targeted depletion of C. elegans proteins

(2014) S. T. Armenti et al.   DEVELOPMENT

Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library

(2014) N. Lowe et al.   DEVELOPMENT

Out with the old, in with the new: reassessing morpholino knockdowns in light of genome editing technology

(2014) S. Schulte-Merker et al.   DEVELOPMENT

High-Resolution Temporal Analysis Reveals a Functional Timeline for the Molecular Regulation of Cytokinesis

(2014) Tim Davies et al.   DEVELOPMENTAL CELL

Conditional Knockouts Generated by Engineered CRISPR-Cas9 Endonuclease Reveal the Roles of Coronin in C. elegans Neural Development

(2014) Zhongfu Shen et al.   DEVELOPMENTAL CELL

Resources for Functional Genomics Studies in Drosophila melanogaster

(2014) Stephanie E. Mohr et al.   GENETICS

Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans

(2014) Alexandre Paix et al.   GENETICS

Efficient Marker-Free Recovery of Custom Genetic Modifications with CRISPR/Cas9 in Caenorhabditis elegans

(2014) J. A. Arribere et al.   GENETICS

Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

(2014) Patrick Essletzbichler et al.   GENOME RESEARCH

Chemical mutagens, transposons, and transgenes to interrogate gene function in Drosophila melanogaster

(2014) Koen J.T. Venken et al.   METHODS

RNAi screening in Drosophila cells and in vivo

(2014) Stephanie E. Mohr   METHODS

RNAi screening comes of age: improved techniques and complementary approaches

(2014) Stephanie E. Mohr et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Serine-Threonine Protein Kinase PAK4 Is Dispensable in Zebrafish: Identification of a Morpholino-Generated Pseudophenotype

(2014) Sheran H. W. Law et al.   PLoS One

CRISPR/Cas9 Mediates Efficient Conditional Mutagenesis in Drosophila

(2014) Zhaoyu Xue et al.   G3-Genes Genomes Genetics

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

(2013) Vincent C. Auyeung et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos

(2013) Nannan Chang et al.   CELL RESEARCH

A combinatorial regulatory signature controls terminal differentiation of the dopaminergic nervous system in C. elegans

(2013) M. Doitsidou et al.   GENES & DEVELOPMENT

Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease

(2013) Scott J. Gratz et al.   GENETICS

A large-scale zebrafish gene knockout resource for the genome-wide study of gene function

(2013) G. K. Varshney et al.   GENOME RESEARCH

The million mutation project: A new approach to genetics in Caenorhabditis elegans

(2013) O. Thompson et al.   GENOME RESEARCH

Genome-wide Consequences of Deleting Any Single Gene

(2013) Xinchen Teng et al.   MOLECULAR CELL

A systematic genome-wide analysis of zebrafish protein-coding gene function

(2013) Ross N. W. Kettleborough et al.   NATURE

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

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

Stable RNA interference rules for silencing

(2013) Christof Fellmann et al.   NATURE CELL BIOLOGY

Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination

(2013) Daniel J Dickinson et al.   NATURE METHODS

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

A reversible gene trap collection empowers haploid genetics in human cells

(2013) Tilmann Bürckstümmer et al.   NATURE METHODS

Heritable genome editing in C. elegans via a CRISPR-Cas9 system

(2013) Ari E Friedland et al.   NATURE METHODS

Treatment of HCV Infection by Targeting MicroRNA

(2013) Harry L.A. Janssen et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses

(2013) R. A. Neumuller et al.   Science Signaling

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

PAPTi: A Peptide Aptamer Interference Toolkit for Perturbation of Protein-Protein Interaction Networks

(2013) Johannes T. -H. Yeh et al.   Scientific Reports

An Optimized microRNA Backbone for Effective Single-Copy RNAi

(2013) Christof Fellmann et al.   Cell Reports

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases

(2013) Shimin Lim et al.   GENOME BIOLOGY

Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9

(2013) A. R. Bassett et al.   Biology Open

The Loop Position of shRNAs and Pre-miRNAs Is Critical for the Accuracy of Dicer Processing In Vivo

(2012) Shuo Gu et al.   CELL

Generation of Genetically Modified Mice by Oocyte Injection of Androgenetic Haploid Embryonic Stem Cells

(2012) Hui Yang et al.   CELL

Essential metabolic, anti-inflammatory, and anti-tumorigenic functions of miR-122 in liver

(2012) Shu-hao Hsu et al.   JOURNAL OF CLINICAL INVESTIGATION

MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis

(2012) Wei-Chih Tsai et al.   JOURNAL OF CLINICAL INVESTIGATION

A Genome-Wide Collection of Mos1 Transposon Insertion Mutants for the C. elegans Research Community

(2012) Elodie Vallin et al.   PLoS One

Knockout of the prion protein (PrP)-like Sprn gene does not produce embryonic lethality in combination with PrPC-deficiency

(2012) N. Daude et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells

(2012) A. J. Holland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-Scale Screening for Targeted Knockouts in the Caenorhabditis elegans Genome

(2012)   G3-Genes Genomes Genetics

The use of RNAi technologies for gene knockdown in zebrafish

(2011) A. Kelly et al.   Briefings in Functional Genomics

A Rapid and Scalable System for Studying Gene Function in Mice Using Conditional RNA Interference

(2011) Prem K. Premsrirut et al.   CELL

A versatile gene trap to visualize and interrogate the function of the vertebrate proteome

(2011) L. A. Trinh et al.   GENES & DEVELOPMENT

Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay

(2011) Christof Fellmann et al.   MOLECULAR CELL

Derivation of haploid embryonic stem cells from mouse embryos

(2011) Martin Leeb et al.   NATURE

Small-molecule displacement of a cryptic degron causes conditional protein degradation

(2011) Kimberly M Bonger et al.   Nature Chemical Biology

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

(2011) Thomas Horn et al.   NATURE METHODS

Quantification of PtdInsP3 molecular species in cells and tissues by mass spectrometry

(2011) Jonathan Clark et al.   NATURE METHODS

MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes

(2011) Koen J T Venken et al.   NATURE METHODS

Fluorescent fusion protein knockout mediated by anti-GFP nanobody

(2011) Emmanuel Caussinus et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Survey of New Temperature-Sensitive, Embryonic-Lethal Mutations in C. elegans: 24 Alleles of Thirteen Genes

(2011) Sean M. O'Rourke et al.   PLoS One

Reversible suppression of an essential gene in adult mice using transgenic RNA interference

(2011) K. McJunkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells

(2011) Richard Marcotte et al.   Cancer Discovery

Synthetic lethality: General principles, utility and detection using genetic screens in human cells

(2010) Sebastian M.B. Nijman   FEBS LETTERS

Analysis of Multiple Ethyl Methanesulfonate-Mutagenized Caenorhabditis elegans Strains by Whole-Genome Sequencing

(2010) S. Sarin et al.   GENETICS

Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi

(2010) Johannes Zuber et al.   NATURE BIOTECHNOLOGY

Autonomous role of medullary thymic epithelial cells in central CD4+ T cell tolerance

(2010) Maria Hinterberger et al.   NATURE IMMUNOLOGY

In vivo RNAi: Today and Tomorrow

(2010) N. Perrimon et al.   Cold Spring Harbor Perspectives in Biology

Targeted chromosomal deletions in human cells using zinc finger nucleases

(2009) H. J. Lee et al.   GENOME RESEARCH

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Haploid Genetic Screens in Human Cells Identify Host Factors Used by Pathogens

(2009) J. E. Carette et al.   SCIENCE

Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: Implications for the therapeutic development of RNAi

(2008) J. L. McBride et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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