A unique ecological niche fosters hybridization of oak-tree and vineyard isolates ofSaccharomyces cerevisiae

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

Ecological and Genetic Barriers Differentiate Natural Populations ofSaccharomyces cerevisiae

(2015) Katie J. Clowers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dosage compensation can buffer copy-number variation in wild yeast

(2015) James Hose et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Isolation by environment

(2014) Ian J. Wang et al.   MOLECULAR ECOLOGY

QTL Dissection of Lag Phase in Wine Fermentation Reveals a New Translocation Responsible for Saccharomyces cerevisiae Adaptation to Sulfite

(2014) Adrien Zimmer et al.   PLoS One

Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks

(2013) Christian Brion et al.   BMC GENOMICS

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

(2013) Jason P. Sexton et al.   EVOLUTION

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

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

Mixing of vineyard and oak-tree ecotypes ofSaccharomyces cerevisiaein North American vineyards

(2013) Katie E. Hyma et al.   MOLECULAR ECOLOGY

Hybridization may facilitate in situ survival of endemic species through periods of climate change

(2013) Matthias Becker et al.   Nature Climate Change

Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq

(2013) Gareth A. Cromie et al.   G3-Genes Genomes Genetics

Small- and Large-Effect Quantitative Trait Locus Interactions Underlie Variation in Yeast Sporulation Efficiency

(2012) K. Lorenz et al.   GENETICS

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Bread, beer and wine: Yeast domestication in the Saccharomyces sensu stricto complex

(2011) Delphine Sicard et al.   COMPTES RENDUS BIOLOGIES

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

(2011) D. Libkind et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution inSaccharomyces cerevisiae

(2011) Paul M. Magwene et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

(2011) Paul M. Magwene et al.   PLoS Computational Biology

Trait Variation in Yeast Is Defined by Population History

(2011) Jonas Warringer et al.   PLoS Genetics

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

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

A sulphite-inducible form of the sulphite efflux gene SSU1 in a Saccharomyces cerevisiae wine yeast

(2010) T. Nardi et al.   MICROBIOLOGY-SGM

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

(2010) Jessica L. Will et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Genetic analysis ofSaccharomyces cerevisiaestrains isolated from palm wine in eastern Nigeria. Comparison with other African strains

(2009) O.U. Ezeronye et al.   JOURNAL OF APPLIED MICROBIOLOGY

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

Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae

(2009) Sandra Merz et al.   GENOME BIOLOGY

Natural Populations of Saccharomyces kudriavzevii in Portugal Are Associated with Oak Bark and Are Sympatric with S. cerevisiae and S. paradoxus

(2008) J. P. Sampaio et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

ECOLOGICAL REPRODUCTIVE ISOLATION OF COAST AND INLAND RACES OFMIMULUS GUTTATUS

(2008) David B. Lowry et al.   EVOLUTION

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

(2008) Daniel J. Kvitek et al.   PLoS Genetics