Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome

On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

(2020) Alexandra N. Khristich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Distinct DNA repair pathways cause genomic instability at alternative DNA structures

(2020) Jennifer A. McKinney et al.   Nature Communications

Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations

(2020) David S. M. Lee 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

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

(2019) Kathleen T. Xie et al.   SCIENCE

Functional data analysis for computational biology

(2019) Marzia A Cremona et al.   BIOINFORMATICS

DNA G‐quadruplex stability, position and chromatin accessibility are associated with CpG island methylation

(2019) Manuel Jara‐Espejo et al.   FEBS Journal

Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes

(2019) Ipsita Agarwal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters

(2019) Aaron M. Fleming et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

IWTomics: testing high-resolution sequence-based ‘Omics’ data at multiple locations and scales

(2018) Marzia A Cremona et al.   BIOINFORMATICS

Role of specialized DNA polymerases in the limitation of replicative stress and DNA damage transmission

(2018) Elodie Bournique et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing

(2018) Robert Hänsel-Hertsch et al.   Nature Protocols

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes

(2018) Niek van Wietmarschen et al.   Nature Communications

Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes

(2018) Junhua Zhao et al.   Cell Reports

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

(2018) Ilias Georgakopoulos-Soares et al.   GENOME RESEARCH

DNA G-quadruplex structures mold the DNA methylome

(2018) Shi-Qing Mao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

(2018) Wilfried M. Guiblet et al.   GENOME RESEARCH

Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress

(2018) Wei-Chung Tsao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition

(2018) Nishita Shastri et al.   MOLECULAR CELL

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition

(2017) Aleksandr B Sahakyan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition

(2017) Aleksandr B Sahakyan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2017) Fedor Kouzine et al.   Cell Systems

Machine learning model for sequence-driven DNA G-quadruplex formation

(2017) Aleksandr B. Sahakyan et al.   Scientific Reports

G4-Interacting DNA Helicases and Polymerases: Potential Therapeutic Targets

(2017) Katrina N. Estep et al.   CURRENT MEDICINAL CHEMISTRY

Evidence of selection for an accessible nucleosomal array in human

(2016) Guénola Drillon et al.   BMC GENOMICS

Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands

(2016) Pey Jiun Lai et al.   GENES TO CELLS

PrimPol Is Required for Replicative Tolerance of G Quadruplexes in Vertebrate Cells

(2016) Davide Schiavone et al.   MOLECULAR CELL

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

G-quadruplex structures mark human regulatory chromatin

(2016) Robert Hänsel-Hertsch et al.   NATURE GENETICS

Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences

(2016) Albino Bacolla et al.   NUCLEIC ACIDS RESEARCH

G-Quadruplexes in DNA Replication: A Problem or a Necessity?

(2016) Anne-Laure Valton et al.   TRENDS IN GENETICS

The hidden side of unstable DNA repeats: Mutagenesis at a distance

(2015) Kartik A. Shah et al.   DNA REPAIR

Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites

(2015) A. Piazza et al.   EMBO JOURNAL

G4-associated human diseases

(2015) N. Maizels   EMBO REPORTS

Error-Prone Repair of DNA Double-Strand Breaks

(2015) Kasey Rodgers et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Vicki S Chambers et al.   NATURE BIOTECHNOLOGY

The effects of chromatin organization on variation in mutation rates in the genome

(2015) Kateryna D. Makova et al.   NATURE REVIEWS GENETICS

Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes

(2015) Albino Bacolla et al.   NUCLEIC ACIDS RESEARCH

Fate of a mutation in a fluctuating environment

(2015) Ivana Cvijović et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutagenic consequences of a single G-quadruplex demonstrate mitotic inheritance of DNA replication fork barriers

(2015) Bennie Lemmens et al.   Nature Communications

Telomeric G-quadruplexes are a substrate and site of localization for human telomerase

(2015) Aaron L. Moye et al.   Nature Communications

A Role for the Fifth G-Track in G-Quadruplex Forming Oncogene Promoter Sequences during Oxidative Stress: Do These “Spare Tires” Have an Evolved Function?

(2015) Aaron M. Fleming et al.   ACS Central Science

Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability

(2014) Guliang Wang et al.   DNA REPAIR

Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations

(2014) Rebeca Campos-Sánchez et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation

(2014) Xiangjun Du et al.   NUCLEIC ACIDS RESEARCH

A Polymerase Theta-dependent repair pathway suppresses extensive genomic instability at endogenous G4 DNA sites

(2014) Wouter Koole et al.   Nature Communications

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Segmenting the human genome based on states of neutral genetic divergence

(2013) Prabhani Kuruppumullage Don et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy

(2013) Libo Yuan et al.   Scientific Reports

Fragile DNA Motifs Trigger Mutagenesis at Distant Chromosomal Loci in Saccharomyces cerevisiae

(2013) Natalie Saini et al.   PLoS Genetics

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

(2013) Albino Bacolla et al.   PLoS Genetics

The G4 Genome

(2013) Nancy Maizels et al.   PLoS Genetics

c-Myc and Cancer Metabolism

(2012) D. M. Miller et al.   CLINICAL CANCER RESEARCH

A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

(2012) Arkarachai Fungtammasan et al.   GENOME RESEARCH

The yin and yang of repair mechanisms in DNA structure-induced genetic instability

(2012) Karen M. Vasquez et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

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

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

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

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

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

(2012) Aradhita Baral et al.   NUCLEIC ACIDS RESEARCH

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

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Cruciform structures are a common DNA feature important for regulating biological processes

(2011) Václav Brázda et al.   BMC MOLECULAR BIOLOGY

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

(2011) Katrin Paeschke et al.   CELL

On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease

(2011) David N. Cooper et al.   HUMAN MUTATION

The large-scale distribution of somatic mutations in cancer genomes

(2011) Alan Hodgkinson et al.   HUMAN MUTATION

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

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

DNA secondary structures and epigenetic determinants of cancer genome evolution

(2011) Subhajyoti De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Beyond translesion synthesis: polymerase κ fidelity as a potential determinant of microsatellite stability

(2011) Suzanne E. Hile et al.   NUCLEIC ACIDS RESEARCH

A genome-wide view of mutation rate co-variation using multivariate analyses

(2011) Guruprasad Ananda et al.   GENOME BIOLOGY

Guanine quadruplex DNA structure restricts methylation of CpG dinucleotides genome-wide

(2010) Rashi Halder et al.   Molecular BioSystems

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes

(2010) R. Z. Cer et al.   NUCLEIC ACIDS RESEARCH

Mechanisms and implications of transcription blockage by guanine-rich DNA sequences

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

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae

(2010) John A. Capra et al.   PLoS Computational Biology

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Non-B DNA structure-induced genetic instability and evolution

(2009) Junhua Zhao et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Involvement of Nucleotide Excision and Mismatch Repair Mechanisms in Double Strand Break Repair

(2009) Ye Zhang et al.   CURRENT GENOMICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Gene conversion causing human inherited disease: Evidence for involvement of non-B-DNA-forming sequences and recombination-promoting motifs in DNA breakage and repair

(2009) Nadia Chuzhanova et al.   HUMAN MUTATION

Evidence that Localized Variation in Primate Sequence Divergence Arises from an Influence of Nucleosome Placement on DNA Repair

(2009) H. Ying et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts

(2009) S. Nakken et al.   NUCLEIC ACIDS RESEARCH

Dramatic effect of single-base mutation on the conformational dynamics of human telomeric G-quadruplex

(2009) Ja Yil Lee et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analyses of Recombination Prone Regions Predict Role of DNA Structural Motif in Recombination

(2009) Prithvi Mani et al.   PLoS One

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins

(2008) I. Voineagu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics

Human-macaque comparisons illuminate variation in neutral substitution rates

(2008) Svitlana Tyekucheva et al.   GENOME BIOLOGY

Discovery of alternative DNA structures: a heroic decade (1979-1989)

(2007) Sergei et al.   Frontiers in Bioscience-Landmark