Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Mutation signatures specific to DNA alkylating agents in yeast and cancers

(2020) Natalie Saini et al.   NUCLEIC ACIDS RESEARCH

The emerging role of RNA modifications in the regulation of mRNA stability

(2020) Sung Ho Boo et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2

(2020) Salvatore Di Giorgio et al.   Science Advances

Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots

(2020) Pégah Jalili et al.   Nature Communications

Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

(2020) Roman Matyášek et al.   Genes

Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

(2020) P. Simmonds   mSphere

Adenosine deaminase acting on RNA (ADAR1), a suppressor of double-stranded RNA–triggered innate immune responses

(2019) Charles E. Samuel   JOURNAL OF BIOLOGICAL CHEMISTRY

Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature

(2019) Natalya P. Degtyareva et al.   PLOS BIOLOGY

Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features

(2019) Rémi Buisson et al.   SCIENCE

Viral quasispecies

(2019) Esteban Domingo et al.   PLoS Genetics

Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies

(2019) Ludmila Perelygina et al.   PLoS Pathogens

Biogenesis and functions of aminocarboxypropyluridine in tRNA

(2019) Mayuko Takakura et al.   Nature Communications

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes

(2017) Clara C. Posthuma et al.   VIRUS RESEARCH

Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1

(2017) Lene Alsøe et al.   Scientific Reports

Identification of the long, edited dsRNAome of LPS-stimulated immune cells

(2016) Matthew G. Blango et al.   GENOME RESEARCH

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts

(2016) Natalie Saini et al.   PLoS Genetics

Clusters of Multiple Mutations: Incidence and Molecular Mechanisms

(2015) Kin Chan et al.   Annual Review of Genetics

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

(2015) Kin Chan et al.   NATURE GENETICS

APOBECs and virus restriction

(2015) Reuben S. Harris et al.   VIROLOGY

APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages

(2015) Shraddha Sharma et al.   Nature Communications

Genome-Wide Estimates of Mutation Rates and Spectrum in Schizosaccharomyces pombe Indicate CpG Sites are Highly Mutagenic Despite the Absence of DNA Methylation

(2015) Megan G. Behringer et al.   G3-Genes Genomes Genetics

APOBEC3A Is Implicated in a Novel Class of G-to-A mRNA Editing in WT1 Transcripts

(2015) Ahmadreza Niavarani et al.   PLoS One

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

(2014) Fiona Tulloch et al.   eLife

Oxidative stress-induced mutagenesis in single-strand DNA occurs primarily at cytosines and is DNA polymerase zeta-dependent only for adenines and guanines

(2013) N. P. Degtyareva et al.   NUCLEIC ACIDS RESEARCH

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

Creative deaminases, self-inflicted damage, and genome evolution

(2012) Silvestro G. Conticello   Annals of the New York Academy of Sciences

Base Damage within Single-Strand DNA Underlies In Vivo Hypermutability Induced by a Ubiquitous Environmental Agent

(2012) Kin Chan et al.   PLoS Genetics

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Coronaviruses

(2011) Mark R. Denison et al.   RNA Biology

Functions and regulation of the APOBEC family of proteins

(2011) Harold C. Smith et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Predicting sites of ADAR editing in double-stranded RNA

(2011) Julie M. Eggington et al.   Nature Communications

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH