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

APOBEC3B is an enzymatic source of mutation in breast cancer

(2013) Michael B. Burns et al.   NATURE

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

Oxidatively induced DNA damage: Mechanisms, repair and disease

(2012) Miral Dizdaroglu   CANCER LETTERS

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

Disease gene identification strategies for exome sequencing

(2012) Christian Gilissen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Melanoma Genetics: Recent Findings Take Us Beyond Well-Traveled Pathways

(2012) Matthew H. Law et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Lifetimes and Reaction Pathways of Guanine Radical Cations and Neutral Guanine Radicals in an Oligonucleotide in Aqueous Solutions

(2012) Yekaterina Rokhlenko et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Oxidative genome damage and its repair: Implications in aging and neurodegenerative diseases

(2012) Muralidhar L. Hegde et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions

(2012) Steven A. Roberts et al.   MOLECULAR CELL

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

(2012) Michael Krauthammer et al.   NATURE GENETICS

Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

(2012) Natalie B. Muren et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Dependence of DNA–Protein Cross-Linking via Guanine Oxidation upon Local DNA Sequence As Studied by Restriction Endonuclease Inhibition

(2011) Amanda L. Madison et al.   BIOCHEMISTRY

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Whole genome sequencing of matched primary and metastatic acral melanomas

(2011) S. Turajlic et al.   GENOME RESEARCH

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

Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes

(2011) Dobril Ivanov 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

Increased complexity of gene structure and base composition in vertebrates

(2011) Ying Wu et al.   Journal of Genetics and Genomics

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

(2011) Zheng Yang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Electron Donor–Acceptor Interactions with Flanking Purines Influence the Efficiency of Thymine Photodimerization

(2011) Zhengzheng Pan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Base Pairing Enhances Fluorescence and Favors Cyclobutane Dimer Formation Induced upon Absorption of UVA Radiation by DNA

(2011) Akos Banyasz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman et al.   NATURE

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing

(2011) Mitchell S Stark et al.   NATURE GENETICS

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma

(2011) Sergey I Nikolaev et al.   NATURE GENETICS

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

High-resolution characterization of a hepatocellular carcinoma genome

(2011) Yasushi Totoki et al.   NATURE GENETICS

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer

(2011) Kai Wang et al.   NATURE GENETICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin cancer

(2011) Gerd P. Pfeifer et al.   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

(2011) N. Agrawal et al.   SCIENCE

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

(2011) N. Stransky et al.   SCIENCE

Pause locally, splice globally

(2011) Fernando Carrillo Oesterreich et al.   TRENDS IN CELL BIOLOGY

Base Excision Repair and Lesion-Dependent Subpathways for Repair of Oxidative DNA Damage

(2010) David Svilar et al.   ANTIOXIDANTS & REDOX SIGNALING

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

(2010) Ksenia B. Bravaya et al.   JOURNAL OF PHYSICAL CHEMISTRY A

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

Diverse somatic mutation patterns and pathway alterations in human cancers

(2010) Zhengyan Kan et al.   NATURE

Structure-Dependent DNA Damage and Repair in a Trinucleotide Repeat Sequence

(2009) Daniel A. Jarem et al.   BIOCHEMISTRY

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis

(2009) Ming Yi et al.   BMC BIOINFORMATICS

Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences

(2009) Guy Baele et al.   BMC EVOLUTIONARY BIOLOGY

Large-scale inference of the point mutational spectrum in human segmental duplications

(2009) Sigve Nakken et al.   BMC GENOMICS

The Role of One-Electron Reduction of Lipid Hydroperoxides in Causing DNA Damage

(2009) Conor Crean et al.   CHEMISTRY-A EUROPEAN JOURNAL

SNP-based prediction of the human germ cell methylation landscape

(2009) Hehuang Xie et al.   GENOMICS

Mutational spectra of human cancer

(2009) Gerd P. Pfeifer et al.   HUMAN GENETICS

Acceleration of 5-Methylcytosine Deamination in Cyclobutane Dimers by G and Its Implications for UV-Induced C-to-T Mutation Hotspots

(2009) Vincent J. Cannistraro et al.   JOURNAL OF MOLECULAR BIOLOGY

Excited State, Charge Transfer, and Spin Dynamics in DNA Hairpin Conjugates with Perylenediimide Hairpin Linkers†

(2009) Raanan Carmieli et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Theoretical and Experimental Study of Valence-Shell Ionization Spectra of Guanine†

(2009) Irina L. Zaytseva et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent

(2009) Satoshi Yokojima et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures

(2009) G. Zheng et al.   NUCLEIC ACIDS RESEARCH

Mutation patterns in cancer genomes

(2009) A. F. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Density Functionals with Broad Applicability in Chemistry

(2008) Yan Zhao et al.   ACCOUNTS OF CHEMICAL RESEARCH

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

(2008) A. Bacolla et al.   GENOME RESEARCH

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Solving Non-Uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms

(2008) Alberto Fernández et al.   JOURNAL OF CLASSIFICATION

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Transcription-coupled DNA repair: two decades of progress and surprises

(2008) Philip C. Hanawalt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE

A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences

(2008) Guy Baele et al.   SYSTEMATIC BIOLOGY

Mutagenic potential of DNA–peptide crosslinks mediated by acrolein-derived DNA adducts

(2007) Irina G. Minko et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS