Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

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

Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding

(2017) Shinsuke Ohnuki et al.   G3-Genes Genomes Genetics

Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts

(2017) Christian Brion et al.   PLoS Genetics

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

(2017) Benjamin Istace et al.   GigaScience

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

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

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale

(2016) Jackson Peter et al.   YEAST

The Hidden Complexity of Mendelian Traits across Natural Yeast Populations

(2016) Jing Hou et al.   Cell Reports

Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

(2016) Yuan O. Zhu et al.   G3-Genes Genomes Genetics

Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion

(2016) Raphaëlle Laureau et al.   PLoS Genetics

Genomics and the making of yeast biodiversity

(2015) Chris Todd Hittinger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

(2015) Anna B. Sunshine et al.   PLOS BIOLOGY

Dosage compensation can buffer copy-number variation in wild yeast

(2015) James Hose et al.   eLife

Genomic Insights into the Saccharomyces sensu stricto Complex

(2015) Anthony R. Borneman et al.   GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Population Genomics Reveals Chromosome-Scale Heterogeneous Evolution in a Protoploid Yeast

(2014) Anne Friedrich et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images

(2014) Omar Wagih et al.   G3-Genes Genomes Genetics

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

(2013) Gianni Liti et al.   BMC GENOMICS

The molecular basis of phenotypic variation in yeast

(2013) Justin C Fay   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Aneuploidy underlies a multicellular phenotypic switch

(2013) Z. Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient Evolutionary Trade-Offs between Yeast Ploidy States

(2013) Enikö Zörgö et al.   PLoS Genetics

A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach

(2012) Estelle Proux-Wéra et al.   BMC BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments

(2012) B. Dunn et al.   GENOME RESEARCH

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

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

The mystery of missing heritability: Genetic interactions create phantom heritability

(2012) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosomal duplication is a transient evolutionary solution to stress

(2012) A. H. Yona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Yeast: An Experimental Organism for 21st Century Biology

(2011) David Botstein et al.   GENETICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

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 Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

(2011) Devin R. Scannell et al.   G3-Genes Genomes Genetics

Break-induced replication: What is it and what is it for?

(2010) Bertrand Llorente et al.   CELL CYCLE

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

(2010) Chris A. Brown et al.   CURRENT BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Remarkably ancient balanced polymorphisms in a multi-locus gene network

(2010) Chris Todd Hittinger et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer et al.   NATURE

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

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