Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

SvABA: genome-wide detection of structural variants and indels by local assembly

(2018) Jeremiah A. Wala et al.   GENOME RESEARCH

Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics

(2018) Annie N. Cowell et al.   SCIENCE

Gene duplicates cause hybrid lethality between sympatric species of Mimulus

(2018) Matthew P. Zuellig et al.   PLoS Genetics

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

(2018) Andrés Mansisidor et al.   MOLECULAR CELL

Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity

(2017) Kristen M. Turner et al.   NATURE

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

Copy number variation and disease resistance in plants

(2017) Aria Dolatabadian et al.   THEORETICAL AND APPLIED GENETICS

Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage

(2017) Stefano A. Iantorno et al.   mBio

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Environmental change drives accelerated adaptation through stimulated copy number variation

(2017) Ryan M. Hull et al.   PLOS BIOLOGY

Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection

(2017) Magdalena Steinrueck et al.   eLife

Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

(2016) Edoardo M. Airoldi et al.   MOLECULAR BIOLOGY OF THE CELL

Mechanisms underlying structural variant formation in genomic disorders

(2016) Claudia M. B. Carvalho et al.   NATURE REVIEWS GENETICS

Genetic basis of priority effects: insights from nectar yeast

(2016) Manpreet K. Dhami et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Cost of Protein Production

(2016) Moshe Kafri et al.   Cell Reports

High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations

(2016) Celia Payen et al.   PLoS Genetics

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements

(2015) Cynthia J. Sakofsky et al.   MOLECULAR CELL

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

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

Extrachromosomal circular DNA is common in yeast

(2015) Henrik D. Møller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of Gene Duplication and Amplification

(2015) Andrew B. Reams et al.   Cold Spring Harbor Perspectives in Biology

Genome-wide construction of a series of designed segmental aneuploids in Saccharomyces cerevisiae

(2015) Waranya Natesuntorn et al.   Scientific Reports

Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification

(2015) Bonita J. Brewer et al.   PLoS Genetics

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

Large transcription units unify copy number variants and common fragile sites arising under replication stress

(2014) Thomas E. Wilson et al.   GENOME RESEARCH

The enduring utility of continuous culturing in experimental evolution

(2014) David Gresham et al.   GENOMICS

CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis

(2014) Lu Chen et al.   HUMAN MOLECULAR GENETICS

High Fitness Costs and Instability of Gene Duplications Reduce Rates of Evolution of New Genes by Duplication-Divergence Mechanisms

(2014) M. Adler et al.   MOLECULAR BIOLOGY AND EVOLUTION

The role of microhomology in genomic structural variation

(2014) Diego Ottaviani et al.   TRENDS IN GENETICS

Transcription and Recombination: When RNA Meets DNA

(2014) A. Aguilera et al.   Cold Spring Harbor Perspectives in Biology

Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

(2014) Jungeui Hong et al.   PLoS Genetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Copy number polymorphism in plant genomes

(2013) Agnieszka Żmieńko et al.   THEORETICAL AND APPLIED GENETICS

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

(2013) Celia Payen et al.   G3-Genes Genomes Genetics

The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress

(2013) Erika Shor et al.   PLoS Genetics

Copy number variation in the genomes of domestic animals

(2012) A. Clop et al.   ANIMAL GENETICS

Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses

(2012) Nels C. Elde et al.   CELL

The Regulation of Filamentous Growth in Yeast

(2012) Paul J. Cullen et al.   GENETICS

Regulatory element copy number differences shape primate expression profiles

(2012) R. C. Iskow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Role of Clonal Interference in the Evolutionary Dynamics of Plasmid-Host Adaptation

(2012) J. M. Hughes et al.   mBio

De Novo CNV Formation in Mouse Embryonic Stem Cells Occurs in the Absence of Xrcc4-Dependent Nonhomologous End Joining

(2012) Martin F. Arlt et al.   PLoS Genetics

Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects, and Dominance

(2012) Jonathan D. Gruber et al.   PLoS Genetics

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection

(2011) Yo Suzuki et al.   NATURE METHODS

Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape

(2011) Daniel J. Kvitek et al.   PLoS Genetics

Origin-Dependent Inverted-Repeat Amplification: A Replication-Based Model for Generating Palindromic Amplicons

(2011) Bonita J. Brewer et al.   PLoS Genetics

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

(2010) Heng Li et al.   BIOINFORMATICS

Identification of Aneuploidy-Tolerating Mutations

(2010) Eduardo M. Torres et al.   CELL

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

(2010) A. McKenna et al.   GENOME RESEARCH

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

(2010) D. Gresham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Extrachromosomal Circular DNA in Eukaryotes: Possible Involvement in the Plasticity of Tandem Repeats

(2009) S. Cohen et al.   CYTOGENETIC AND GENOME RESEARCH

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans

(2009) Feng Zhang et al.   NATURE GENETICS

Mechanisms of change in gene copy number

(2009) P. J. Hastings et al.   NATURE REVIEWS GENETICS

Copy number variations and cancer

(2009) Adam Shlien et al.   Genome Medicine

A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation

(2009) P. J. Hastings et al.   PLoS Genetics

Natural selection has driven population differentiation in modern humans

(2008) Luis B Barreiro et al.   NATURE GENETICS

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

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

Segmental Duplications Arise from Pol32-Dependent Repair of Broken Forks through Two Alternative Replication-Based Mechanisms

(2008) Celia Payen et al.   PLoS Genetics

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL