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

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts

(2016) Margarida Gonçalves et al.   CURRENT BIOLOGY

Independent Origins of Yeast Associated with Coffee and Cacao Fermentation

(2016) Catherine L. Ludlow et al.   CURRENT BIOLOGY

Evidence of Natural Hybridization in Brazilian Wild Lineages ofSaccharomyces cerevisiae

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

Revealing a 5,000-y-old beer recipe in China

(2016) Jiajing Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Saccharomyces eubayanusandSaccharomyces arboricolareside in North Island native New Zealand forests

(2015) Velimir Gayevskiy et al.   ENVIRONMENTAL MICROBIOLOGY

Saccharomyces cerevisiae: a nomadic yeast with no niche?

(2015) Matthew R. Goddard et al.   FEMS YEAST RESEARCH

Genomic Insights into the Saccharomyces sensu stricto Complex

(2015) Anthony R. Borneman et al.   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

Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages

(2015) François Tapsoba et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

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

Genetic isolation between two recently diverged populations of a symbiotic fungus

(2015) Sara Branco et al.   MOLECULAR ECOLOGY

The fascinating and secret wild life of the budding yeast S. cerevisiae

(2015) Gianni Liti   eLife

Genomic Insights into the Saccharomyces sensu stricto Complex

(2015) Anthony R. Borneman et al.   GENETICS

Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

(2014) Sam Crauwels et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Chromosomal Rearrangements as a Major Mechanism in the Onset of Reproductive Isolation in Saccharomyces cerevisiae

(2014) Jing Hou et al.   CURRENT BIOLOGY

Evidence for a Far East Asian origin of lager beer yeast

(2014) Jian Bing et al.   CURRENT BIOLOGY

Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation

(2014) Sarah Knight et al.   ISME Journal

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

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

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Current perspectives and the future of domestication studies

(2014) G. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles

(2013) Heidi E.L. Lischer et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Heterosis Is Prevalent Among Domesticated but not Wild Strains of Saccharomyces cerevisiae

(2013) Marcin Plech et al.   G3-Genes Genomes Genetics

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

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

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Life History Shapes Trait Heredity by Accumulation of Loss-of-Function Alleles in Yeast

(2012) E. Zorgo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

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

(2011) H. Li   BIOINFORMATICS

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

(2011) Delphine Sicard et al.   COMPTES RENDUS BIOLOGIES

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

Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae

(2011) Anthony R. Borneman et al.   PLoS Genetics

Trait Variation in Yeast Is Defined by Population History

(2011) Jonas Warringer et al.   PLoS Genetics

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Flocculation in Saccharomyces cerevisiae: a review

(2010) E.V. Soares   JOURNAL OF APPLIED MICROBIOLOGY

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Evidence for widespread adaptive evolution of gene expression in budding yeast

(2010) H. B. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A distinct population ofSaccharomyces cerevisiaein New Zealand: evidence for local dispersal by insects and human-aided global dispersal in oak barrels

(2009) Matthew R. Goddard et al.   ENVIRONMENTAL MICROBIOLOGY

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

(2009) J. L. Argueso et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Evidence for autotetraploidy associated with reproductive isolation inSaccharomyces cerevisiae: towards a new domesticated species

(2009) W. ALBERTIN et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer et al.   NATURE

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

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

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

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

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH