Functional interrogation of DNA damage response variants with base editing screens

In vivo base editing rescues Hutchinson–Gilford progeria syndrome in mice

(2021) Luke W. Koblan et al.   NATURE

Massively parallel assessment of human variants with base editor screens

(2021) Ruth E. Hanna et al.   CELL

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Perturbing proteomes at single residue resolution using base editing

(2020) Philippe C. Després et al.   Nature Communications

Functional analysis of BARD1 missense variants in homology-directed repair and damage sensitivity

(2019) Aleksandra I. Adamovich et al.   PLoS Genetics

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

(2019) Junjie Tan et al.   Nature Communications

TRAIP is a master regulator of DNA interstrand crosslink repair

(2019) R. Alex Wu et al.   NATURE

Shieldin – the protector of DNA ends

(2019) Dheva Setiaputra et al.   EMBO REPORTS

Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?

(2019) Sirawit Ittisoponpisan et al.   JOURNAL OF MOLECULAR BIOLOGY

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants

(2019) Jiyeon Kweon et al.   ONCOGENE

Identifying chemogenetic interactions from CRISPR screens with drugZ

(2019) Medina Colic et al.   Genome Medicine

A consensus set of genetic vulnerabilities to ATR inhibition

(2019) Nicole Hustedt et al.   Open Biology

TRAIP drives replisome disassembly and mitotic DNA repair synthesis at sites of incomplete DNA replication

(2019) Remi Sonneville et al.   eLife

Functional characterization of 84 PALB2 variants of uncertain significance

(2019) Timothy Wiltshire et al.   GENETICS IN MEDICINE

Functional analysis of genetic variants in the high-risk breast cancer susceptibility gene PALB2

(2019) Rick A. C. M. Boonen et al.   Nature Communications

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

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

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells

(2018) Robert J. Ihry et al.   NATURE MEDICINE

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

(2018) Emma Haapaniemi et al.   NATURE MEDICINE

In vivo base editing of post-mitotic sensory cells

(2018) Wei-Hsi Yeh et al.   Nature Communications

The BRCT Domains of the BRCA1 and BARD1 Tumor Suppressors Differentially Regulate Homology-Directed Repair and Stalled Fork Protection

(2018) David Billing et al.   MOLECULAR CELL

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

53BP1 cooperation with the REV7–shieldin complex underpins DNA structure-specific NHEJ

(2018) Hind Ghezraoui et al.   NATURE

The shieldin complex mediates 53BP1-dependent DNA repair

(2018) Sylvie M. Noordermeer et al.   NATURE

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

ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response

(2017) Andrew N. Blackford et al.   MOLECULAR CELL

CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons

(2017) Pierre Billon et al.   MOLECULAR CELL

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

CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations

(2017) Cem Kuscu et al.   NATURE METHODS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

BRCA2 suppresses replication stress-induced mitotic and G1 abnormalities through homologous recombination

(2017) Weiran Feng et al.   Nature Communications

Aurora kinase B dependent phosphorylation of 53BP1 is required for resolving merotelic kinetochore-microtubule attachment errors during mitosis

(2017) Haibo Wang et al.   Oncotarget

Structures of closed and open conformations of dimeric human ATM

(2017) Domagoj Baretić et al.   Science Advances

53BP1 Integrates DNA Repair and p53-Dependent Cell Fate Decisions via Distinct Mechanisms

(2016) Raquel Cuella-Martin et al.   MOLECULAR CELL

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

(2016) Alexis C. Komor et al.   NATURE

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

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

TRAIP/RNF206 is required for recruitment of RAP80 to sites of DNA damage

(2016) Nam Soo Lee et al.   Nature Communications

TRAIP regulates replication fork recovery and progression via PCNA

(2016) Wanjuan Feng et al.   Cell Discovery

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

(2015) Traver Hart et al.   CELL

Functional Analysis of BARD1 Missense Variants in Homology-Directed Repair of DNA Double Strand Breaks

(2015) Cindy Lee et al.   HUMAN MUTATION

TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress

(2015) Saskia Hoffmann et al.   JOURNAL OF CELL BIOLOGY

TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism

(2015) Margaret E Harley et al.   NATURE GENETICS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

A novel recurrent CHEK2 Y390C mutation identified in high-risk Chinese breast cancer patients impairs its activity and is associated with increased breast cancer risk

(2015) N Wang et al.   ONCOGENE

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

USP28 Is Recruited to Sites of DNA Damage by the Tandem BRCT Domains of 53BP1 but Plays a Minor Role in Double-Strand Break Metabolism

(2014) P. A. Knobel et al.   MOLECULAR AND CELLULAR BIOLOGY

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Deciphering key features in protein structures with the new ENDscript server

(2014) Xavier Robert et al.   NUCLEIC ACIDS RESEARCH

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Functional Assays for Analysis of Variants of Uncertain Significance inBRCA2

(2013) Lucia Guidugli et al.   HUMAN MUTATION

Double-strand break repair: 53BP1 comes into focus

(2013) Stephanie Panier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A High-Throughput Functional Complementation Assay for Classification of BRCA1 Missense Variants

(2013) P. Bouwman et al.   Cancer Discovery

Double-Strand Break Repair-Independent Role for BRCA2 in Blocking Stalled Replication Fork Degradation by MRE11

(2011) Katharina Schlacher et al.   CELL

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

(2011) D. Blazek et al.   GENES & DEVELOPMENT

53BP1 Inhibits Homologous Recombination in Brca1-Deficient Cells by Blocking Resection of DNA Breaks

(2010) Samuel F. Bunting et al.   CELL

The DNA Damage Response: Making It Safe to Play with Knives

(2010) Alberto Ciccia et al.   MOLECULAR CELL

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase

(2009) Zhenjian Cai et al.   MOLECULAR CELL

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

DNA repair deficiency and neurological disease

(2009) Peter J. McKinnon   NATURE REVIEWS NEUROSCIENCE

Functional Assays for Classification of BRCA2 Variants of Uncertain Significance

(2008) D. J. Farrugia et al.   CANCER RESEARCH