KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal–assisted labeling

Keth-seq for transcriptome-wide RNA structure mapping

(2020) Xiaocheng Weng et al.   Nature Chemical Biology

ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis

(2020) Jacob Paiano et al.   Nature Communications

Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ

(2020) Tong Wu et al.   NATURE METHODS

The Configuration of RPA, RAD51, and DMC1 Binding in Meiosis Reveals the Nature of Critical Recombination Intermediates

(2020) Anjali Gupta Hinch et al.   MOLECULAR CELL

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

I-motif DNA structures are formed in the nuclei of human cells

(2018) Mahdi Zeraati et al.   Nature Chemistry

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The control of DNA repair by the cell cycle

(2017) Nicole Hustedt et al.   NATURE CELL BIOLOGY

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

(2017) Fedor Kouzine et al.   Cell Systems

The Landscape of Mouse Meiotic Double-Strand Break Formation, Processing, and Repair

(2016) Julian Lange et al.   CELL

Use of conditioned media is critical for studies of regulation in response to rapid heat shock

(2016) Dig B. Mahat et al.   CELL STRESS & CHAPERONES

Nascent Connections: R-Loops and Chromatin Patterning

(2016) Frédéric Chédin   TRENDS IN GENETICS

Sequence-Dependent Elasticity and Electrostatics of Single-Stranded DNA: Signatures of Base-Stacking

(2014) Dustin B. McIntosh et al.   BIOPHYSICAL JOURNAL

Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability

(2014) Julie Sollier et al.   MOLECULAR CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides

(2014) Roberto Laos et al.   Frontiers in Microbiology

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

(2014) Gilad Fuchs et al.   GENOME BIOLOGY

Global Regulation of Promoter Melting in Naive Lymphocytes

(2013) Fedor Kouzine et al.   CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response

(2013) M. T. Paulsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RPA Accumulation during Class Switch Recombination Represents 5′–3′ DNA-End Resection during the S–G2/M Phase of the Cell Cycle

(2013) Arito Yamane et al.   Cell Reports

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

(2012) E. E. Schadt et al.   GENOME RESEARCH

Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method

(2012) Z.-X. Zhou et al.   GENOME RESEARCH

Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA

(2012) P. P. Khil et al.   GENOME RESEARCH

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools

(2012) Regina Z. Cer et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Double-strand DNA breaks recruit the centromeric histone CENP-A

(2009) S. G. Zeitlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homologous recombination in DNA repair and DNA damage tolerance

(2008) Xuan Li et al.   CELL RESEARCH

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE