G-quadruplex structures mark human regulatory chromatin

G4-associated human diseases

(2015) N. Maizels   EMBO REPORTS

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

(2015) Michael S. Foulk et al.   GENOME RESEARCH

High-throughput sequencing of DNA G-quadruplex structures in the human genome

(2015) Vicki S Chambers et al.   NATURE BIOTECHNOLOGY

Guanine quadruplex structures localize to heterochromatin

(2015) Roland F. Hoffmann et al.   NUCLEIC ACIDS RESEARCH

Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

(2015) Eleni M. Tomazou et al.   Cell Reports

The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage

(2014) Nasim Sabouri et al.   BMC BIOLOGY

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

(2014) Andrew L. Wolfe et al.   NATURE

C9orf72 nucleotide repeat structures initiate molecular cascades of disease

(2014) Aaron R. Haeusler et al.   NATURE

Regulation of RNA polymerase II activation by histone acetylation in single living cells

(2014) Timothy J. Stasevich et al.   NATURE

G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD

(2014) Lucas T Gray et al.   Nature Chemical Biology

Unravelling the genomic targets of small molecules using high-throughput sequencing

(2014) Raphaël Rodriguez et al.   NATURE REVIEWS GENETICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Elevated Levels of G-Quadruplex Formation in Human Stomach and Liver Cancer Tissues

(2014) Giulia Biffi et al.   PLoS One

PAVIS: a tool for Peak Annotation and Visualization

(2013) Weichun Huang et al.   BIOINFORMATICS

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Statistical tests for measures of colocalization in biological microscopy

(2013) JOHN H. MCDONALD et al.   JOURNAL OF MICROSCOPY

Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences

(2013) Vineeth Thachappilly Mukundan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells

(2013) Giulia Biffi et al.   Nature Chemistry

Quantitative visualization of DNA G-quadruplex structures in human cells

(2013) Giulia Biffi et al.   Nature Chemistry

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

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

Detection of G-quadruplex DNA in mammalian cells

(2013) A. Henderson et al.   NUCLEIC ACIDS RESEARCH

G-quadruplex structures are stable and detectable in human genomic DNA

(2013) Enid Yi Ni Lam et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Small-molecule–induced DNA damage identifies alternative DNA structures in human genes

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

DNA secondary structures: stability and function of G-quadruplex structures

(2012) Matthew L. Bochman et al.   NATURE REVIEWS GENETICS

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

(2012) Emilie Besnard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop

(2012) P. H. Wanrooij et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation

(2012) Simon S. McDade et al.   NUCLEIC ACIDS RESEARCH

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

DNA Replication through G-Quadruplex Motifs Is Promoted by the Saccharomyces cerevisiae Pif1 DNA Helicase

(2011) Katrin Paeschke et al.   CELL

Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?

(2011) Shankar Balasubramanian et al.   NATURE REVIEWS DRUG DISCOVERY

Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling

(2011) Yoko Hayashi-Takanaka et al.   NUCLEIC ACIDS RESEARCH

A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro

(2011) Eun-Ang Raiber et al.   NUCLEIC ACIDS RESEARCH

ATR-X Syndrome Protein Targets Tandem Repeats and Influences Allele-Specific Expression in a Size-Dependent Manner

(2010) Martin J. Law et al.   CELL

How long is too long? Effects of loop size on G-quadruplex stability

(2010) Aurore Guédin et al.   NUCLEIC ACIDS RESEARCH

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

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

Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential

(2009) Jay E. Johnson et al.   NUCLEIC ACIDS RESEARCH

Fast interscale wavelet denoising of Poisson-corrupted images

(2009) Florian Luisier et al.   SIGNAL PROCESSING

The Yeast Pif1 Helicase Prevents Genomic Instability Caused by G-Quadruplex-Forming CEB1 Sequences In Vivo

(2009) Cyril Ribeyre et al.   PLoS Genetics

The Organization of Histone H3 Modifications as Revealed by a Panel of Specific Monoclonal Antibodies

(2008) Hiroshi Kimura et al.   CELL STRUCTURE AND FUNCTION

A Novel Small Molecule That Alters Shelterin Integrity and Triggers a DNA-Damage Response at Telomeres

(2008) Raphaël Rodriguez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY