A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

(2017) Winston X. Yan et al.   Nature Communications

DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs

(2017) Francesca Rossiello et al.   Nature Communications

Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53

(2017) Ishwarya Venkata Narayanan et al.   Scientific Reports

DNA Breaks and End Resection Measured Genome-wide by End Sequencing

(2016) Andres Canela et al.   MOLECULAR CELL

DSBCapture: in situ capture and sequencing of DNA breaks

(2016) Stefanie V Lensing et al.   NATURE METHODS

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability

(2015) Jeongkyu Kim et al.   NUCLEIC ACIDS RESEARCH

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

Non-redundant Functions of ATM and DNA-PKcs in Response to DNA Double-Strand Breaks

(2015) Pierre Caron et al.   Cell Reports

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Quantifying DNA double-strand breaks induced by site-specific endonucleases in living cells by ligation-mediated purification

(2014) Catherine Chailleux et al.   Nature Protocols

Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks

(2014) François Aymard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation

(2014) S. Rashi-Elkeles et al.   Science Signaling

A Macrohistone Variant Links Dynamic Chromatin Compaction to BRCA1-Dependent Genome Maintenance

(2014) Simran Khurana et al.   Cell Reports

Preferential localization of γH2AX foci in euchromatin of retina rod cells after DNA damage induction

(2013) Laura Lafon-Hughes et al.   CHROMOSOME RESEARCH

Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA

(2013) Michelle T. Paulsen et al.   METHODS

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

Quantitation of DNA double-strand break resection intermediates in human cells

(2013) Yi Zhou et al.   NUCLEIC ACIDS RESEARCH

A direct role for small non-coding RNAs in DNA damage response

(2013) Fabrizio d’Adda di Fagagna   TRENDS IN CELL BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Role for Small RNAs in DNA Double-Strand Break Repair

(2012) Wei Wei et al.   CELL

Site-specific DICER and DROSHA RNA products control the DNA-damage response

(2012) Sofia Francia et al.   NATURE

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks

(2012) Tibor Pankotai et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ATM-Dependent Chromatin Changes Silence Transcription In cis to DNA Double-Strand Breaks

(2010) Niraj M. Shanbhag et al.   CELL

High-resolution profiling of γH2AX around DNA double strand breaks in the mammalian genome

(2010) Jason S Iacovoni et al.   EMBO JOURNAL

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Cellular senescence: hot or what?

(2009) Gerard I Evan et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcriptional control of human p53-regulated genes

(2008) Todd Riley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY