Development of a versatile high-throughput mutagenesis assay with multiplexed short-read NGS using DNA-barcoded supF shuttle vector library amplified in E. coli

Single-cell profiling of tumour evolution in multiple myeloma — opportunities for precision medicine

(2022) Ankit K. Dutta et al.   Nature Reviews Clinical Oncology

Paradoxical role of the major DNA repair protein, OGG1, in action-at-a-distance mutation induction by 8-oxo-7,8-dihydroguanine

(2022) Tetsuya Suzuki et al.   DNA REPAIR

Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination

(2022) Riccardo Pecori et al.   NATURE REVIEWS GENETICS

Human activation-induced deaminase lacks strong replicative strand bias or preference for cytosines in hairpin loops

(2022) Ramin Sakhtemani et al.   NUCLEIC ACIDS RESEARCH

A novel role of DNA polymerase λ in translesion synthesis in conjunction with DNA polymerase ζ

(2021) Jung-Hoon Yoon et al.   Life Science Alliance

Daughter-strand gaps in DNA replication – substrates of lesion processing and initiators of distress signalling

(2021) Ronald P. Wong et al.   DNA REPAIR

Implications of inhibition of Rev1 interaction with Y family DNA polymerases for cisplatin chemotherapy

(2021) Jung-Hoon Yoon et al.   GENES & DEVELOPMENT

Single-cell measurement of higher-order 3D genome organization with scSPRITE

(2021) Mary V. Arrastia et al.   NATURE BIOTECHNOLOGY

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

(2021) Jonathan Foox et al.   NATURE BIOTECHNOLOGY

The promise of toxicogenomics for genetic toxicology: past, present and future

(2020) Rhiannon David   MUTAGENESIS

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Error-Prone Replication through UV Lesions by DNA Polymerase θ Protects against Skin Cancers

(2019) Jung-Hoon Yoon et al.   CELL

An Error-Prone Polymerase in the Fight against Cancer

(2019) Yathish Jagadheesh Achar et al.   CELL

In vitro mammalian cell mutation assays based on transgenic reporters: A report of the International Workshop on Genotoxicity Testing (IWGT)

(2019) Paul A. White et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light

(2019) Markus Lindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Reduction of Werner Syndrome Protein Enhances G:C → A:T Transition byO6-Methylguanine in Human Cells

(2018) Tetsuya Suzuki et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods

(2018) Daniel B. Sloan et al.   TRENDS IN BIOTECHNOLOGY

Biochemical Basis of APOBEC3 Deoxycytidine Deaminase Activity on Diverse DNA Substrates

(2018) Madison B. Adolph et al.   ACS Infectious Diseases

Next-Generation Sequencing Technologies

(2018) W. Richard McCombie et al.   Cold Spring Harbor Perspectives in Medicine

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

DNA sequencing at 40: past, present and future

(2017) Jay Shendure et al.   NATURE

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair

(2016) Nicholas J. Haradhvala et al.   CELL

APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication

(2016) Vladimir B. Seplyarskiy et al.   GENOME RESEARCH

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing

(2016) Justin Jee et al.   NATURE

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

(2016) Peng Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis

(2016) Kaile Wang et al.   Scientific Reports

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing

(2014) Sunyoung Kwon et al.   BMC BIOINFORMATICS

Having a direct look: Analysis of DNA damage and repair mechanisms by next generation sequencing

(2014) Bettina Meier et al.   EXPERIMENTAL CELL RESEARCH

The genetic landscape of high-risk neuroblastoma

(2013) Trevor J Pugh et al.   NATURE GENETICS

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

PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data

(2013) Johanna Brodin et al.   PLoS One

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Biochemical Analysis of Hypermutation by the Deoxycytidine Deaminase APOBEC3A

(2012) Robin P. Love et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

En bloc transfer of polyubiquitin chains to PCNA in vitro is mediated by two different human E2–E3 pairs

(2012) Yuji Masuda et al.   NUCLEIC ACIDS RESEARCH

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The Mechanisms of UV Mutagenesis

(2011) Hironobu IKEHATA et al.   JOURNAL OF RADIATION RESEARCH

SHPRH and HLTF Act in a Damage-Specific Manner to Coordinate Different Forms of Postreplication Repair and Prevent Mutagenesis

(2011) Jia-Ren Lin et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS