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

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

(2013) Gianni Liti et al.   BMC GENOMICS

High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population

(2013) Francisco A. Cubillos et al.   GENETICS

Evolution and diversity of copy number variation in the great ape lineage

(2013) P. H. Sudmant et al.   GENOME RESEARCH

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

Inferring Genome-Wide Recombination Landscapes from Advanced Intercross Lines: Application to Yeast Crosses

(2013) Christopher J. R. Illingworth et al.   PLoS One

Saccharomyces diversity and evolution: a budding model genus

(2013) Chris Todd Hittinger   TRENDS IN GENETICS

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

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

Meiotic Recombination Initiation in and around Retrotransposable Elements in Saccharomyces cerevisiae

(2013) Mariko Sasaki et al.   PLoS Genetics

Duplication and Retention Biases of Essential and Non-Essential Genes Revealed by Systematic Knockdown Analyses

(2013) Shane Woods et al.   PLoS Genetics

A Loss-of-Function Mutation in the PAS Kinase Rim15p Is Related to Defective Quiescence Entry and High Fermentation Rates of Saccharomyces cerevisiae Sake Yeast Strains

(2012) Daisuke Watanabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329

(2012) Dao-Qiong Zheng et al.   BMC GENOMICS

Functional divergence of gene duplicates through ectopic recombination

(2012) Joaquin F Christiaens et al.   EMBO REPORTS

A complete sequence ofSaccharomyces paradoxusmitochondrial genome that restores the respiration inS. cerevisiae

(2012) Emanuel Procházka et al.   FEMS YEAST RESEARCH

On the Prospects of Whole-Genome Association Mapping in Saccharomyces cerevisiae

(2012) C. F. Connelly et al.   GENETICS

Nutritional Control of Growth and Development in Yeast

(2012) J. R. Broach   GENETICS

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

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

(2012) E. W. Loomis et al.   GENOME RESEARCH

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

(2012) Jurgen F Nijkamp et al.   Microbial Cell Factories

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

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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Systematic identification of gene annotation errors in the widely used yeast mutation collections

(2012) Taly Ben-Shitrit et al.   NATURE METHODS

The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae

(2012) Francisco Salinas et al.   PLoS One

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

At the cutting-edge of grape and wine biotechnology

(2012) Anthony R. Borneman et al.   TRENDS IN GENETICS

The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt

(2012) M. Ralser et al.   Open Biology

Genetic Architecture of Highly Complex Chemical Resistance Traits across Four Yeast Strains

(2012) Ian M. Ehrenreich et al.   PLoS Genetics

Advances in Quantitative Trait Analysis in Yeast

(2012) Gianni Liti et al.   PLoS Genetics

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

The rise of yeast population genomics

(2011) Gianni Liti et al.   COMPTES RENDUS BIOLOGIES

Whole-Genome Sequencing of Sake Yeast Saccharomyces cerevisiae Kyokai no. 7

(2011) T. Akao et al.   DNA RESEARCH

Divergence in wine characteristics produced by wild and domesticated strains of Saccharomyces cerevisiae

(2011) Katie E. Hyma et al.   FEMS YEAST RESEARCH

Revealing the genetic structure of a trait by sequencing a population under selection

(2011) L. Parts et al.   GENOME RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Assessing the complex architecture of polygenic traits in diverged yeast populations

(2011) FRANCISCO A. CUBILLOS et al.   MOLECULAR ECOLOGY

Predicting phenotypic variation in yeast from individual genome sequences

(2011) Rob Jelier et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Deciphering the Molecular Basis of Wine Yeast Fermentation Traits Using a Combined Genetic and Genomic Approach

(2011) Chloé Ambroset et al.   G3-Genes Genomes Genetics

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

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

Microindel detection in short-read sequence data

(2010) Peter Krawitz et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

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

Saccharomyces paradoxus and Saccharomyces cerevisiae reside on oak trees in New Zealand: evidence for migration from Europe and interspecies hybrids

(2010) Hanyao Zhang et al.   FEMS YEAST RESEARCH

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Yeast evolutionary genomics

(2010) Bernard Dujon   NATURE REVIEWS 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

Genotype to Phenotype: A Complex Problem

(2010) R. D. Dowell et al.   SCIENCE

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

(2010) Jared W. Wenger et al.   PLoS Genetics

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA

(2010) Nils Homer et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) J. L. Argueso et al.   GENOME 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

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer 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

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

Segregating YKU80 and TLC1 Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast

(2009) Gianni Liti et al.   PLoS Genetics

Comparative genome analysis of aSaccharomyces cerevisiaewine strain

(2008) Anthony R. Borneman et al.   FEMS YEAST RESEARCH

Sequential Elimination of Major-Effect Contributors Identifies Additional Quantitative Trait Loci Conditioning High-Temperature Growth in Yeast

(2008) Himanshu Sinha et al.   GENETICS

KnotInFrame: prediction of −1 ribosomal frameshift events

(2008) Corinna Theis et al.   NUCLEIC ACIDS RESEARCH

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

A Catalog of Neutral and Deleterious Polymorphism in Yeast

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