Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination

Linking genetic, metabolic and phenotypic diversity among S. cerevisiae strains using multi-omics associations

(2019) Kang Kang et al.   GigaScience

A polyploid admixed origin of beer yeasts derived from European and Asian wine populations

(2019) Justin C. Fay et al.   PLOS BIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Multiple rounds of artificial selection promote microbe secondary domestication – the case of cachaça yeasts

(2018) Raquel Barbosa et al.   Genome Biology and Evolution

The origin and adaptive evolution of domesticated populations of yeast from Far East Asia

(2018) Shou-Fu Duan et al.   Nature Communications

Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus

(2018) Casey M. Bergman   Mobile DNA

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut

(2018) Matteo Ramazzotti et al.   ENVIRONMENTAL MICROBIOLOGY

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites

(2017) Pedro Almeida et al.   MOLECULAR ECOLOGY

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii

(2017) Indu Khatri et al.   Scientific Reports

How retrotransposons shape genome regulation

(2016) Paolo Mita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Evidence of Natural Hybridization in Brazilian Wild Lineages ofSaccharomyces cerevisiae

(2016) Raquel Barbosa et al.   Genome Biology and Evolution

Ty1 Integrase Interacts with RNA Polymerase III-specific Subcomplexes to Promote Insertion of Ty1 Elements Upstream of Polymerase (Pol) III-transcribed Genes

(2016) Stephanie Cheung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

A self-encoded capsid derivative restricts Ty1 retrotransposition in Saccharomyces

(2015) David J. Garfinkel et al.   CURRENT GENETICS

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

Atrans-Dominant Form of Gag Restricts Ty1 Retrotransposition and Mediates Copy Number Control

(2015) Agniva Saha et al.   JOURNAL OF VIROLOGY

Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts

(2015) Souhir Marsit et al.   MOLECULAR BIOLOGY AND EVOLUTION

A population genomics insight into the Mediterranean origins of wine yeast domestication

(2015) Pedro Almeida et al.   MOLECULAR ECOLOGY

Ty1 retrovirus-like element Gag contains overlapping restriction factor and nucleic acid chaperone functions

(2015) Yuri Nishida et al.   NUCLEIC ACIDS RESEARCH

An RNA polymerase III subunit determines sites of retrotransposon integration

(2015) A. Bridier-Nahmias et al.   SCIENCE

The Ty1 Retrotransposon Restriction Factor p22 Targets Gag

(2015) Jessica M. Tucker et al.   PLoS Genetics

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae

(2015) Giltae Song et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

(2014) Anders Bergström et al.   MOLECULAR BIOLOGY AND EVOLUTION

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Mobilomics in Saccharomyces cerevisiae strains

(2013) Giulia Menconi et al.   BMC BIOINFORMATICS

Genome-wide analysis of intraspecific transposon diversity in yeast

(2013) Claudine Bleykasten-Grosshans et al.   BMC GENOMICS

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome

(2013) Gianni Liti et al.   BMC GENOMICS

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

(2013) D. A. Skelly et al.   GENOME RESEARCH

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

(2012) Qi-Ming Wang et al.   MOLECULAR ECOLOGY

Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding

(2012) SAMUEL D. J. BROWN et al.   Molecular Ecology Resources

Evolutionary Genomics of Transposable Elements in Saccharomyces cerevisiae

(2012) Martin Carr et al.   PLoS One

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Generation of a large set of genetically tractable haploid and diploidSaccharomyces strains

(2009) Francisco A. Cubillos et al.   FEMS YEAST RESEARCH

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Saccharomyces cerevisiae: Population Divergence and Resistance to Oxidative Stress in Clinical, Domesticated and Wild Isolates

(2009) Stephanie Diezmann et al.   PLoS One

Posttranslational interference of Ty1 retrotransposition by antisense RNAs

(2009) E. Matsuda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAi in Budding Yeast

(2009) I. A. Drinnenberg et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

A Catalog of Neutral and Deleterious Polymorphism in Yeast

(2008) Scott W. Doniger et al.   PLoS Genetics