Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier

JACKS: joint analysis of CRISPR/Cas9 knockout screens

(2019) Felicity Allen et al.   GENOME RESEARCH

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials

(2019) Ann Lin et al.   Science Translational Medicine

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

(2019) Joshua M. Dempster et al.   Nature Communications

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

(2018) Francesco Iorio et al.   BMC GENOMICS

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

(2018) James M. McFarland et al.   Nature Communications

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

(2018) Kendall R. Sanson et al.   Nature Communications

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

(2017) Robin M Meyers et al.   NATURE GENETICS

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

(2017) Shashikant Pujar et al.   NUCLEIC ACIDS RESEARCH

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

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

The KEAP1–NRF2 System in Cancer

(2017) Keiko Taguchi et al.   Frontiers in Oncology

BAGEL: a computational framework for identifying essential genes from pooled library screens

(2016) Traver Hart et al.   BMC BIOINFORMATICS

CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

(2016) Bastiaan Evers et al.   NATURE BIOTECHNOLOGY

Genome-wide CRISPR screens reveal a Wnt–FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors

(2016) Zachary Steinhart et al.   NATURE 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

The impact of amplification on differential expression analyses by RNA-seq

(2016) Swati Parekh et al.   Scientific Reports

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

(2015) Traver Hart et al.   CELL

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

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

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

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

(2014) Yuexin Zhou et al.   NATURE

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Protein Interaction Network of the Mammalian Hippo Pathway Reveals Mechanisms of Kinase-Phosphatase Interactions

(2013) A. L. Couzens et al.   Science Signaling

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Loss of Keap1 Function Activates Nrf2 and Provides Advantages for Lung Cancer Cell Growth

(2008) T. Ohta et al.   CANCER RESEARCH