Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition

Mutational landscape of yeast mutator strains

(2014) Alexandre Serero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

(2014) Stacia R. Engel et al.   G3-Genes Genomes Genetics

DNA polymerase ɛ and δ exonuclease domain mutations in endometrial cancer

(2013) David N. Church et al.   HUMAN MOLECULAR GENETICS

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

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

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

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

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Mutation Rates, Spectra, and Genome-Wide Distribution of Spontaneous Mutations in Mismatch Repair Deficient Yeast

(2013) Gregory I. Lang et al.   G3-Genes Genomes Genetics

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences

(2013) Ephraim Kenigsberg et al.   PLoS Genetics

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

(2012) Amnon Koren et al.   AMERICAN JOURNAL OF HUMAN GENETICS

NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model

(2012) A. Polishko et al.   BIOINFORMATICS

Exonuclease 1 preferentially repairs mismatches generated by DNA polymerase α

(2012) Sascha E. Liberti et al.   DNA REPAIR

Conservation of replication timing reveals global and local regulation of replication origin activity

(2012) C. A. Muller et al.   GENOME RESEARCH

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes

(2012) Yong H Woo et al.   Nature Communications

Mutation Hot Spots in Yeast Caused by Long-Range Clustering of Homopolymeric Sequences

(2012) Xin Ma et al.   Cell Reports

Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity

(2012) Scott A. Lujan et al.   PLoS Genetics

Visualization of Eukaryotic DNA Mismatch Repair Reveals Distinct Recognition and Repair Intermediates

(2011) Hans Hombauer et al.   CELL

Balancing eukaryotic replication asymmetry with replication fidelity

(2011) Thomas A Kunkel   CURRENT OPINION IN CHEMICAL BIOLOGY

Mutation Rates across Budding Yeast Chromosome VI Are Correlated with Replication Timing

(2011) Gregory I. Lang et al.   Genome Biology and Evolution

Widespread signatures of recent selection linked to nucleosome positioning in the human lineage

(2011) J. G. D. Prendergast et al.   GENOME RESEARCH

The large-scale distribution of somatic mutations in cancer genomes

(2011) Alan Hodgkinson et al.   HUMAN MUTATION

Replication-Associated Mutational Asymmetry in the Human Genome

(2011) Chun-Long Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Mutational Profile of the Yeast Genome Is Shaped by Replication

(2011) N. Agier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Late-Replicating Domains Have Higher Divergence and Diversity in Drosophila melanogaster

(2011) Claudia C. Weber et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of chromatin structure on sequence variability in the human genome

(2011) Michael Y Tolstorukov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

OriDB, the DNA replication origin database updated and extended

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

A genome-wide view of mutation rate co-variation using multivariate analyses

(2011) Guruprasad Ananda et al.   GENOME BIOLOGY

Detection of Heterozygous Mutations in the Genome of Mismatch Repair Defective Diploid Yeast Using a Bayesian Approach

(2010) S. Zanders et al.   GENETICS

Functional Conservation of Nucleosome Formation Selectively Biases Presumably Neutral Molecular Variation in Yeast Genomes

(2010) Gregory A. Babbitt et al.   Genome Biology and Evolution

Evolutionary Rates and Gene Dispensability Associate with Replication Timing in the Archaeon Sulfolobus islandicus

(2010) Kenneth M. Flynn et al.   Genome Biology and Evolution

Differential correction of lagging-strand replication errors made by DNA polymerases   and  

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

Genome-wide model for the normal eukaryotic DNA replication fork

(2010) Andres A. Larrea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast

(2010) Ephraim Kenigsberg et al.   PLoS Computational Biology

Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase

(2010) Amnon Koren et al.   PLoS Genetics

Mutational Heterogeneity in Human Cancers: Origin and Consequences

(2009) Jesse J. Salk et al.   Annual Review of Pathology-Mechanisms of Disease

Genomic mutation rates: what high-throughput methods can tell us

(2009) Koodali T. Nishant et al.   BIOESSAYS

Nucleosome positioning: How is it established, and why does it matter?

(2009) Marta Radman-Livaja et al.   DEVELOPMENTAL BIOLOGY

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

Evidence that Localized Variation in Primate Sequence Divergence Arises from an Influence of Nucleosome Placement on DNA Repair

(2009) H. Ying et al.   MOLECULAR BIOLOGY AND EVOLUTION

Timing of Replication Is a Determinant of Neutral Substitution Rates but Does Not Explain Slow Y Chromosome Evolution in Rodents

(2009) C. J. Pink et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

(2009) D. R. Denver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA polymerase   and   proofreading suppress discrete mutator and cancer phenotypes in mice

(2009) T. M. Albertson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Transcription induces strand-specific mutations at the 5' end of human genes

(2008) P. Polak et al.   GENOME RESEARCH

Transcription-Induced Mutational Strand Bias and Its Effect on Substitution Rates in Human Genes

(2008) C. F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Division of Labor at the Eukaryotic Replication Fork

(2008) Stephanie A. Nick McElhinny et al.   MOLECULAR CELL

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites

(2008) S. Sasaki et al.   SCIENCE

Dividing the workload at a eukaryotic replication fork

(2008) Thomas A. Kunkel et al.   TRENDS IN CELL BIOLOGY

Evolutionary footprints of nucleosome positions in yeast

(2008) Stefan Washietl et al.   TRENDS IN GENETICS

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology

Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection

(2008) Steffen Schmidt et al.   PLoS Genetics