In situ CRISPR‐Cas9 base editing for the development of genetically engineered mouse models of breast cancer

Comparative oncogenomics identifies combinations of driver genes and drug targets in BRCA1-mutated breast cancer

(2019) Stefano Annunziato et al.   Nature Communications

Engineering of high-precision base editors for site-specific single nucleotide replacement

(2019) Junjie Tan et al.   Nature Communications

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

Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies

(2019) Yi-Zhou Jiang et al.   CANCER CELL

Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors

(2019) Tony P. Huang et al.   NATURE BIOTECHNOLOGY

Continuous evolution of base editors with expanded target compatibility and improved activity

(2019) Benjamin W. Thuronyi et al.   NATURE BIOTECHNOLOGY

BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity

(2018) Wen Jiang et al.   CELL RESEARCH

Optimized base editors enable efficient editing in cells, organoids and mice

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

Web-based design and analysis tools for CRISPR base editing

(2018) Gue-Ho Hwang et al.   BMC BIOINFORMATICS

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma

(2017) Sjors M Kas et al.   NATURE GENETICS

BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance

(2017) Alexandra A Duarte et al.   NATURE METHODS

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

(2017) Alexis C. Komor et al.   Science Advances

Modeling invasive lobular breast carcinoma by CRISPR/Cas9-mediated somatic genome editing of the mammary gland

(2016) Stefano Annunziato et al.   GENES & DEVELOPMENT

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

(2016) Alexis C. Komor et al.   NATURE

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

(2016) Bastiaan Evers et al.   NATURE BIOTECHNOLOGY

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma

(2016) Mirjam C. Boelens et al.   Cell Reports

Selective resistance to the PARP inhibitor olaparib in a mouse model for BRCA1-deficient metaplastic breast cancer

(2015) Linda Henneman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Rapid target gene validation in complex cancer mouse models using re-derived embryonic stem cells

(2014) Ivo J Huijbers et al.   EMBO Molecular Medicine

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Easy quantitative assessment of genome editing by sequence trace decomposition

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

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Preclinical Mouse Model of Invasive Lobular Breast Cancer Metastasis

(2012) C. W. Doornebal et al.   CANCER RESEARCH

A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes

(2012) Benjamin Haibe-Kains et al.   JNCI-Journal of the National Cancer Institute

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS