Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast

Global genomic instability caused by reduced expression of DNA polymerase ε in yeast

(2022) Ke Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

rDNA array length is a major determinant of replicative lifespan in budding yeast

(2022) Manuel Hotz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Under the magnifying glass: The ups and downs of rDNA copy number

(2022) Selina M. Kindelay et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations

(2022) Diksha Sharma et al.   GENOMICS

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

(2021) David Sehnal et al.   NUCLEIC ACIDS RESEARCH

The rate and molecular spectrum of mutation are selectively maintained in yeast

(2021) Haoxuan Liu et al.   Nature Communications

Concerted evolution of ribosomal DNA: Somatic peace amid germinal strife

(2021) David Haig   BIOESSAYS

Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

(2020) Ajith V. Pankajam et al.   G3-Genes Genomes Genetics

Metal exposure causes rDNA copy number to fluctuate in mutation accumulation lines of Daphnia pulex

(2020) Eleanor F. Harvey et al.   AQUATIC TOXICOLOGY

The cruciform DNA‐binding protein Crp1 stimulates the endonuclease activity of Mus81–Mms4 in Saccharomyces cerevisiae

(2020) Huong Thi Thu Phung et al.   FEBS LETTERS

Ribosomal DNA instability and genome adaptability

(2019) Devika Salim et al.   CHROMOSOME RESEARCH

RNA Polymerase I Activators Count and Adjust Ribosomal RNA Gene Copy Number

(2019) Tetsushi Iida et al.   MOLECULAR CELL

Depletion of Limiting rDNA Structural Complexes Triggers Chromosomal Instability and Replicative Aging of Saccharomyces cerevisiae

(2019) Ryan D. Fine et al.   GENETICS

How do cells count multi-copy genes?: “Musical Chair” model for preserving the number of rDNA copies

(2019) Tetsushi Iida et al.   CURRENT GENETICS

Yeast Spontaneous Mutation Rate and Spectrum Vary with Environment

(2019) Haoxuan Liu et al.   CURRENT BIOLOGY

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

(2019) Symonová   Genes

Adaptation by Loss of Heterozygosity in Saccharomyces cerevisiae Clones Under Divergent Selection

(2019) Timothy Y. James et al.   GENETICS

Mechanisms of rDNA Copy Number Maintenance

(2019) Jonathan O. Nelson et al.   TRENDS IN GENETICS

Challenges and Approaches to Genotyping Repetitive DNA

(2019) Elizabeth A. Morton et al.   G3-Genes Genomes Genetics

Primer3_masker: integrating masking of template sequence with primer design software

(2018) Triinu Kõressaar et al.   BIOINFORMATICS

Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii

(2018) Jullien M Flynn et al.   Genome Biology and Evolution

Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis

(2018) Mikael S. Lindström et al.   ONCOGENE

The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast

(2018) Nathaniel P. Sharp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive genome duplication affects patterns of molecular evolution in Saccharomyces cerevisiae

(2018) Kaitlin J. Fisher et al.   PLoS Genetics

Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks

(2018) Shin‐ichiro Hiraga et al.   EMBO REPORTS

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Genomic Copy-Number Loss Is Rescued by Self-Limiting Production of DNA Circles

(2018) Andrés Mansisidor et al.   MOLECULAR CELL

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

(2018) Lotus A. Lofgren et al.   MOLECULAR ECOLOGY

Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex

(2017) Jullien M. Flynn et al.   GENETICS

Loss of Heterozygosity Drives Adaptation in Hybrid Yeast

(2017) Caiti S. Smukowski Heil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends

(2017) Stefano Mattarocci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends

(2017) Stefano Mattarocci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR

(2017) Jennifer Lu et al.   Scientific Reports

DNA replication stress restricts ribosomal DNA copy number

(2017) Devika Salim et al.   PLoS Genetics

Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation

(2017) Meng Wang et al.   PLoS Genetics

Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex

(2017) Jullien M. Flynn et al.   GENETICS

Mutation Is a Sufficient and Robust Predictor of Genetic Variation for Mitotic Spindle Traits in Caenorhabditis elegans

(2016) Reza Farhadifar et al.   GENETICS

More than 10% of yeast genes are related to genome stability and influence cellular senescence via rDNA maintenance

(2016) Kimiko Saka et al.   NUCLEIC ACIDS RESEARCH

rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants

(2016) Elizabeth X. Kwan et al.   G3-Genes Genomes Genetics

Budding Yeast Rif1 Controls Genome Integrity by Inhibiting rDNA Replication

(2016) Maksym Shyian et al.   PLoS Genetics

Spontaneous mutations and the origin and maintenance of quantitative genetic variation

(2016) Wen Huang et al.   eLife

Mutation Is a Sufficient and Robust Predictor of Genetic Variation for Mitotic Spindle Traits in Caenorhabditis elegans

(2016) Reza Farhadifar et al.   GENETICS

A physiological significance of the functional interaction between Mus81 and Rad27 in homologous recombination repair

(2015) Huong Phung Thi Thu et al.   NUCLEIC ACIDS RESEARCH

Regulation of ribosomal DNA amplification by the TOR pathway

(2015) Carmen V. Jack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Causes of natural variation in fitness: Evidence from studies ofDrosophilapopulations

(2015) Brian Charlesworth   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes

(2015) John G. Gibbons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of copy number variants in whole-genome data using Reference Coverage Profiles

(2015) Gustavo Glusman et al.   Frontiers in Genetics

Ribosomal RNA gene repeats, their stability and cellular senescence

(2014) Takehiko KOBAYASHI   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Yeast mutation accumulation experiment supports elevated mutation rates at highly transcribed sites

(2014) Xiaoshu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans

(2014) John G. Gibbons et al.   Nature Communications

RIF1 Is Essential for 53BP1-Dependent Nonhomologous End Joining and Suppression of DNA Double-Strand Break Resection

(2013) J. Ross Chapman et al.   MOLECULAR CELL

A Natural Polymorphism in rDNA Replication Origins Links Origin Activation with Calorie Restriction and Lifespan

(2013) Elizabeth X. Kwan et al.   PLoS Genetics

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Transcription as a source of genome instability

(2012) Nayun Kim et al.   NATURE REVIEWS GENETICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

(2011) Benjamin J. Hindson et al.   ANALYTICAL CHEMISTRY

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

(2011) H. Li   BIOINFORMATICS

Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast

(2011) Takehiko Kobayashi   CELLULAR AND MOLECULAR LIFE SCIENCES

GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes

(2011) Juan S. Escobar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Monitoring the Rate and Dynamics of Concerted Evolution in the Ribosomal DNA Repeats of Saccharomyces cerevisiae Using Experimental Evolution

(2011) Austen R.D. Ganley et al.   MOLECULAR BIOLOGY AND EVOLUTION

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Replicative Age Induces Mitotic Recombination in the Ribosomal RNA Gene Cluster of Saccharomyces cerevisiae

(2011) Derek L. Lindstrom et al.   PLoS Genetics

Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: “rDNA–Sensitive” Genes and Natural Variation

(2011) Silvana Paredes et al.   PLoS Genetics

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

(2010) Daniel Wegmann et al.   BMC BIOINFORMATICS

Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity

(2010) S. Ide et al.   SCIENCE

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Spontaneous Mutation Accumulation Studies in Evolutionary Genetics

(2009) Daniel L. Halligan et al.   Annual Review of Ecology Evolution and Systematics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

(2009) S. A. James et al.   GENOME RESEARCH

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

ESTIMATING NONLINEAR SELECTION GRADIENTS USING QUADRATIC REGRESSION COEFFICIENTS: DOUBLE OR NOTHING?

(2008) John R. Stinchcombe et al.   EVOLUTION

Spontaneous mutations in diploid Saccharomyces cerevisiae: another thousand cell generations

(2008) DAVID W. HALL et al.   Genetics Research

Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle

(2008) I. J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA