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

Family-Wide Comparative Analysis of Cytidine and Methylcytidine Deamination by Eleven Human APOBEC Proteins

(2017) Fumiaki Ito et al.   JOURNAL OF MOLECULAR BIOLOGY

Active DNA demethylation by DNA repair: Facts and uncertainties

(2016) David Schuermann et al.   DNA REPAIR

Enigmatic 5-hydroxymethyluracil: Oxidatively modified base, epigenetic mark or both?

(2016) Ryszard Olinski et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

5-Hydroxymethylcytosine Marks Sites of DNA Damage and Promotes Genome Stability

(2016) Georgia Rose Kafer et al.   Cell Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships

(2015) Daniel Gackowski et al.   PLoS One

Uracil excision by endogenous SMUG1 glycosylase promotes efficient Ig class switching and impacts on A:T substitutions during somatic mutation

(2014) Felix A. Dingler et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA

(2014) Toni Pfaffeneder et al.   Nature Chemical Biology

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

A robust, sensitive assay for genomic uracil determination by LC/MS/MS reveals lower levels than previously reported

(2013) Anastasia Galashevskaya et al.   DNA REPAIR

Deamination, Oxidation, and C–C Bond Cleavage Reactivity of 5-Hydroxymethylcytosine, 5-Formylcytosine, and 5-Carboxycytosine

(2013) Stefan Schiesser et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Genomic HyperBrowser: an analysis web server for genome-scale data

(2013) Geir K. Sandve et al.   NUCLEIC ACIDS RESEARCH

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

(2013) Benjamin JM Taylor et al.   eLife

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Strikingly different properties of uracil-DNA glycosylases UNG2 and SMUG1 may explain divergent roles in processing of genomic uracil

(2012) Berit Doseth et al.   DNA REPAIR

The Human Base Excision Repair Enzyme SMUG1 Directly Interacts with DKC1 and Contributes to RNA Quality Control

(2012) Laure Jobert et al.   MOLECULAR CELL

Germline ablation of SMUG1 DNA glycosylase causes loss of 5-hydroxymethyluracil- and UNG-backup uracil-excision activities and increases cancer predisposition of Ung−/−Msh2−/− mice

(2012) Kristin Kemmerich et al.   NUCLEIC ACIDS RESEARCH

Uracil-DNA Glycosylase in Base Excision Repair and Adaptive Immunity

(2011) Berit Doseth et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

(2009) Agus Darwanto et al.   ANALYTICAL BIOCHEMISTRY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Extracts of proliferating and non-proliferating human cells display different base excision pathways and repair fidelity

(2009) Mansour Akbari et al.   DNA REPAIR

Base Excision by Thymine DNA Glycosylase Mediates DNA-Directed Cytotoxicity of 5-Fluorouracil

(2009) Christophe Kunz et al.   PLOS BIOLOGY