Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9–Cas12a platform

Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing

(2019) Benjamin P. Kleinstiver et al.   NATURE BIOTECHNOLOGY

Global Genetic Networks and the Genotype-to-Phenotype Relationship

(2019) Michael Costanzo et al.   CELL

In vivo profiling of metastatic double knockouts through CRISPR–Cpf1 screens

(2019) Ryan D. Chow et al.   NATURE METHODS

Essential Gene Profiles for Human Pluripotent Stem Cells Identify Uncharacterized Genes and Substrate Dependencies

(2019) Barbara Mair et al.   Cell Reports

Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts

(2019) Carlo C. Campa et al.   NATURE METHODS

Mapping the Genetic Landscape of Human Cells

(2018) Max A. Horlbeck et al.   CELL

The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression

(2018) Cindy Meyer et al.   MOLECULAR CELL

Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis

(2018) Dongxin Zhao et al.   MOLECULAR CELL

Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity

(2018) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Dual gene activation and knockout screen reveals directional dependencies in genetic networks

(2018) Michael Boettcher et al.   NATURE BIOTECHNOLOGY

Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer

(2018) Srinivas R. Viswanathan et al.   NATURE GENETICS

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs

(2018) Jennifer Listgarten et al.   Nature Biomedical Engineering

A case of mistaken identity

(2018) Ruth E Hanna et al.   NATURE BIOTECHNOLOGY

Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function

(2018) Eric Shifrut et al.   CELL

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

(2018) Thomas Gonatopoulos-Pournatzis et al.   MOLECULAR CELL

Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens

(2018) Michael S. Haney et al.   NATURE GENETICS

Autism spectrum disorder: insights into convergent mechanisms from transcriptomics

(2018) Mathieu Quesnel-Vallières et al.   NATURE REVIEWS GENETICS

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

Identification of essential genes for cancer immunotherapy

(2017) Shashank J. Patel et al.   NATURE

Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens

(2017) Fadi J Najm et al.   NATURE BIOTECHNOLOGY

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

(2017) Kyuho Han et al.   NATURE BIOTECHNOLOGY

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions

(2017) John Paul Shen et al.   NATURE METHODS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

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

(2017) John G. Doench   NATURE REVIEWS GENETICS

Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia

(2017) Martin Moder et al.   Nature Communications

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

(2017) David W. Morgens et al.   Nature Communications

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

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

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

(2016) Britt Adamson et al.   CELL

Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering

(2016) Addison V. Wright et al.   CELL

Data Independent Acquisition analysis in ProHits 4.0

(2016) Guomin Liu et al.   Journal of Proteomics

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

(2016) Ines Fonfara 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

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

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array

(2016) Bernd Zetsche et al.   NATURE BIOTECHNOLOGY

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

(2016) Ryan J Park et al.   NATURE GENETICS

In vivo high-throughput profiling of CRISPR–Cpf1 activity

(2016) Hui K Kim et al.   NATURE METHODS

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

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

(2016) M. Costanzo et al.   SCIENCE

Sources of Error in Mammalian Genetic Screens

(2016) Laura Magill Sack et al.   G3-Genes Genomes Genetics

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

(2015) Traver Hart et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

Sequence determinants of improved CRISPR sgRNA design

(2015) Han Xu et al.   GENOME RESEARCH

mTOR Complex 2 Stabilizes Mcl-1 Protein by Suppressing Its Glycogen Synthase Kinase 3-Dependent and SCF-FBXW7-Mediated Degradation

(2015) Junghui Koo et al.   MOLECULAR AND CELLULAR BIOLOGY

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries

(2015) Joana A. Vidigal et al.   Nature Communications

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

(2015) Param Priya Singh et al.   PLoS Computational Biology

Maintaining Glycogen Synthase Kinase-3 Activity Is Critical for mTOR Kinase Inhibitors to Inhibit Cancer Cell Growth

(2014) J. Koo et al.   CANCER RESEARCH

A Global Regulatory Mechanism for Activating an Exon Network Required for Neurogenesis

(2014) Bushra Raj et al.   MOLECULAR CELL

Ral and Rheb GTPase Activating Proteins Integrate mTOR and GTPase Signaling in Aging, Autophagy, and Tumor Cell Invasion

(2014) Timothy D. Martin et al.   MOLECULAR CELL

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Genetic Interactions in Cancer Progression and Treatment

(2011) Alan Ashworth et al.   CELL

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

An ATP-competitive Mammalian Target of Rapamycin Inhibitor Reveals Rapamycin-resistant Functions of mTORC1

(2009) Carson C. Thoreen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The mTORC2 Complex Regulates Terminal Differentiation of C2C12 Myoblasts

(2009) L. Shu et al.   MOLECULAR AND CELLULAR BIOLOGY

Lentiviral Vector Design for Multiple shRNA Expression and Durable HIV-1 Inhibition

(2008) Olivier ter Brake et al.   MOLECULAR THERAPY