Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation

(2013) Tyson A Clark et al.   BMC BIOLOGY

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

(2013) Osman Doluca et al.   CHEMICAL REVIEWS

Quantitative visualization of DNA G-quadruplex structures in human cells

(2013) Giulia Biffi et al.   Nature Chemistry

Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements

(2013) Sterling Sawaya et al.   PLoS One

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

(2013) Zhixing Feng et al.   PLoS Computational Biology

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution

(2013) Maria Lluch-Senar et al.   PLoS Genetics

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

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

(2012) E. W. Loomis et al.   GENOME RESEARCH

Single-molecule investigation of G-quadruplex using a nanopore sensor

(2012) Jiwook Shim et al.   METHODS

Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals

(2012) Aradhita Baral et al.   NUCLEIC ACIDS RESEARCH

The methylomes of six bacteria

(2012) Iain A. Murray et al.   NUCLEIC ACIDS RESEARCH

QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences

(2012) Camille Menendez et al.   NUCLEIC ACIDS RESEARCH

The Role of Methylation in the Intrinsic Dynamics of B- and Z-DNA

(2012) Nuri A. Temiz et al.   PLoS One

FMR1 CGG repeat lengths mediate different regulation of reporter gene expression in comparative transient and locus specific integration assays

(2011) Christina Sølvsten et al.   GENE

Non-B DNA-forming Sequences and WRN Deficiency Independently Increase the Frequency of Base Substitution in Human Cells

(2011) Albino Bacolla et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

(2011) Chun-Xiao Song et al.   NATURE METHODS

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes

(2011) J. Eddy et al.   NUCLEIC ACIDS RESEARCH

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

(2011) Tyson A. Clark et al.   NUCLEIC ACIDS RESEARCH

Mapping the sequences of potential guanine quadruplex motifs

(2011) Alan K. Todd et al.   NUCLEIC ACIDS RESEARCH

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

5'-UTR G-quadruplex structures acting as translational repressors

(2010) J.-D. Beaudoin et al.   NUCLEIC ACIDS RESEARCH

Z-DNA-forming silencer in the first exon regulates human ADAM-12 gene expression

(2010) B. K. Ray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension

(2010) M. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of G-quadruplex/i-motif secondary structures as cis-acting regulatory elements

(2010) Samantha Kendrick et al.   PURE AND APPLIED CHEMISTRY

Predicting and understanding the stability of G-quadruplexes

(2009) Oliver Stegle et al.   BIOINFORMATICS

Identification and Prevention of Genotyping Errors Caused by G-Quadruplex- and i-Motif-Like Sequences

(2009) J. J. Wenzel et al.   CLINICAL CHEMISTRY

The Importance of Negative Superhelicity in Inducing the Formation of G-Quadruplex and i-Motif Structures in the c-Myc Promoter: Implications for Drug Targeting and Control of Gene Expression

(2009) Daekyu Sun et al.   JOURNAL OF MEDICINAL CHEMISTRY

Non-B DNA conformations as determinants of mutagenesis and human disease

(2009) Albino Bacolla et al.   MOLECULAR CARCINOGENESIS

Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility

(2009) Irina Voineagu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human genomic Z-DNA segments probed by the Zα domain of ADAR1

(2009) Heng Li et al.   NUCLEIC ACIDS RESEARCH

Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells

(2009) Anjali Verma et al.   NUCLEIC ACIDS RESEARCH

Single molecule measurement of the "speed limit" of DNA polymerase

(2009) J. J. Schwartz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE