Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China

Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae

(2021) Da-Yong Han et al.   Frontiers in Microbiology

Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature

(2021) Liang Song et al.   GENOME RESEARCH

Defining and Disrupting Species Boundaries in Saccharomyces

(2020) Jasmine Ono et al.   Annual Review of Microbiology

Population size, sex, and purifying selection: comparative genomics of two sister taxa of the wild yeast Saccharomyces paradoxus

(2020) Vassiliki Koufopanou et al.   Genome Biology and Evolution

Hybridization is a recurrent evolutionary stimulus in wild yeast speciation

(2019) Chris Eberlein et al.   Nature Communications

Origins, evolution, domestication and diversity of Saccharomyces beer yeasts

(2018) Brigida Gallone et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

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

Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts

(2018) David J. Krause et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur

(2017) Samina Naseeb et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Heterosis in hybrids within and between yeast species

(2017) J. P. Bernardes et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeastSaccharomyces paradoxusin a natural woodland

(2017) Wenjing Xia et al.   MOLECULAR ECOLOGY

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

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

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

Summer temperature can predict the distribution of wild yeast populations

(2016) Heather A. Robinson et al.   Ecology and Evolution

Speciation driven by hybridization and chromosomal plasticity in a wild yeast

(2016) Jean-Baptiste Leducq et al.   Nature Microbiology

The Genome Sequence ofSaccharomyces eubayanusand the Domestication of Lager-Brewing Yeasts

(2015) EmilyClare Baker 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

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

Evidence for a Far East Asian origin of lager beer yeast

(2014) Jian Bing et al.   CURRENT BIOLOGY

Chromosomal variation segregates within incipient species and correlates with reproductive isolation

(2014) Guillaume Charron et al.   MOLECULAR ECOLOGY

Local climatic adaptation in a widespread microorganism

(2014) J.-B. Leducq et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

(2014) Stacia R. Engel et al.   G3-Genes Genomes Genetics

RACER: Rapid and accurate correction of errors in reads

(2013) Lucian Ilie et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

(2013) Gianni Liti et al.   BMC GENOMICS

Exploring the northern limit of the distribution ofSaccharomyces cerevisiaeandSaccharomyces paradoxusin North America

(2013) Guillaume Charron et al.   FEMS YEAST RESEARCH

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

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

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

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

Saccharomyces diversity and evolution: a budding model genus

(2013) Chris Todd Hittinger   TRENDS IN GENETICS

Molecular genetic diversity of the Saccharomyces yeasts in Taiwan: Saccharomyces arboricola, Saccharomyces cerevisiae and Saccharomyces kudriavzevii

(2012) Gennadi I. Naumov et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) Stéphane De Mita et al.   BMC GENETICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

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

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Evidence for Divergent Evolution of Growth Temperature Preference in Sympatric Saccharomyces Species

(2011) Paula Gonçalves et al.   PLoS One

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

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

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

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

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Rapid Differentiation of Phenotypically Similar Yeast Species by Single-Strand Conformation Polymorphism Analysis of Ribosomal DNA

(2008) Q.-M. Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

Saccharomyces sensu stricto as a model system for evolution and ecology

(2008) T REPLANSKY et al.   TRENDS IN ECOLOGY & EVOLUTION