Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

Ribonucleotides in DNA: Origins, repair and consequences

(2014) Jessica S. Williams et al.   DNA REPAIR

RNA intrusions change DNA elastic properties and structure

(2014) Hsiang-Chih Chiu et al.   Nanoscale

Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms

(2014) Catherine J. Potenski et al.   NATURE

Ribonuclease L and metal-ion–independent endoribonuclease cleavage sites in host and viral RNAs

(2014) Daphne A. Cooper et al.   NUCLEIC ACIDS RESEARCH

How the misincorporation of ribonucleotides into genomic DNA can be both harmful and helpful to cells

(2014) Catherine J. Potenski et al.   NUCLEIC ACIDS RESEARCH

Distinctive kinetics and substrate specificities of plant and fungal tRNA ligases

(2014) B. S. Remus et al.   RNA

Ribose--An Internal Threat to DNA

(2014) K. W. Caldecott   SCIENCE

Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

(2014) Aziz El Hage et al.   PLoS Genetics

Two distinct mechanisms of Topoisomerase 1-dependent mutagenesis in yeast

(2013) Jang-Eun Cho et al.   DNA REPAIR

Topoisomerase 1-Mediated Removal of Ribonucleotides from Nascent Leading-Strand DNA

(2013) Jessica S. Williams et al.   MOLECULAR CELL

Ribonucleotides Are Signals for Mismatch Repair of Leading-Strand Replication Errors

(2013) Scott A. Lujan et al.   MOLECULAR CELL

Cost of rNTP/dNTP pool imbalance at the replication fork

(2013) N. Y. Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development

(2012) Martin A.M. Reijns et al.   CELL

Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ɛ

(2012) Jessica S. Williams et al.   DNA REPAIR

Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ

(2012) Anders R. Clausen et al.   DNA REPAIR

RNase H2-Initiated Ribonucleotide Excision Repair

(2012) Justin L. Sparks et al.   MOLECULAR CELL

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Mechanisms Employed by Escherichia coli to Prevent Ribonucleotide Incorporation into Genomic DNA by Pol V

(2012) John P. McDonald et al.   PLoS Genetics

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Ribonucleotide Discrimination and Reverse Transcription by the Human Mitochondrial DNA Polymerase

(2011) Rajesh Kasiviswanathan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

OriDB, the DNA replication origin database updated and extended

(2011) C. C. Siow et al.   NUCLEIC ACIDS RESEARCH

Mutagenic Processing of Ribonucleotides in DNA by Yeast Topoisomerase I

(2011) N. Kim et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Strand Invasion Structures in the Inverted Repeat of Candida albicans Mitochondrial DNA Reveal a Role for Homologous Recombination in Replication

(2010) Joachim M. Gerhold et al.   MOLECULAR CELL

Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases

(2010) S. A. Nick McElhinny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates

(2010) K. Schutz et al.   RNA

Mechanism and evolution of DNA primases

(2009) Robert D. Kuchta et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Ribonuclease H: the enzymes in eukaryotes

(2009) Susana M. Cerritelli et al.   FEBS Journal

Elevated dNTP levels suppress hyper-recombination in Saccharomyces cerevisiae S-phase checkpoint mutants

(2009) Michael Fasullo et al.   NUCLEIC ACIDS RESEARCH

Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH Monoribonucleotide

(2008) Hui Zhu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY