Genomic signatures of adaptation to wine biological ageing conditions in biofilm-forming flor yeasts

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae

(2016) Anthony R. Borneman et al.   G3-Genes Genomes Genetics

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi

(2015) Jeanne Ropars et al.   CURRENT BIOLOGY

The genomics of microbial domestication in the fermented food environment

(2015) John G Gibbons et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Role of Phosphatidylinositol Phosphate Signaling in the Regulation of the Filamentous-Growth Mitogen-Activated Protein Kinase Pathway

(2015) Hema Adhikari et al.   EUKARYOTIC CELL

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

Detection of selective sweeps in structured populations: a comparison of recent methods

(2015) Alexandra I. Vatsiou et al.   MOLECULAR ECOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

The Genotype–Phenotype Map of Yeast Complex Traits: Basic Parameters and the Role of Natural Selection

(2014) Wei-Chin Ho et al.   MOLECULAR BIOLOGY AND EVOLUTION

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Population Structure and Comparative Genome Hybridization of European Flor Yeast Reveal a Unique Group of Saccharomyces cerevisiae Strains with Few Gene Duplications in Their Genome

(2014) Jean-Luc Legras et al.   PLoS One

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

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

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

(2013) Stacia R. Engel et al.   Database-The Journal of Biological Databases and Curation

ZRT1 Harbors an Excess of Nonsynonymous Polymorphism and Shows Evidence of Balancing Selection in Saccharomyces cerevisiae

(2013) Elizabeth K. Engle 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

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

(2013) Daniel J. Kvitek et al.   PLoS Genetics

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition

(2012) Mohammad Hossein Moradi et al.   BMC GENETICS

Response to Hyperosmotic Stress

(2012) H. Saito et al.   GENETICS

The Regulation of Filamentous Growth in Yeast

(2012) Paul J. Cullen et al.   GENETICS

Regulation of Mat Responses by a Differentiation MAPK Pathway in Saccharomyces cerevisiae

(2012) Sheelarani Karunanithi et al.   PLoS One

Global Gene Deletion Analysis Exploring Yeast Filamentous Growth

(2012) O. Ryan et al.   SCIENCE

Candida albicans Scavenges Host Zinc via Pra1 during Endothelial Invasion

(2012) Francesco Citiulo et al.   PLoS Pathogens

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

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

(2011) T. Akao et al.   DNA 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

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

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Population differentiation as a test for selective sweeps

(2010) H. Chen 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

FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter

(2010) V. Galeote et al.   MICROBIOLOGY-SGM

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tracking footprints of artificial selection in the dog genome

(2010) J. M. Akey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

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

Expression of the yeast aquaporin Aqy2 affects cell surface properties under the control of osmoregulatory and morphogenic signalling pathways

(2009) Kentaro Furukawa et al.   MOLECULAR MICROBIOLOGY

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

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-Wide Scan for Signatures of Human Population Differentiation and Their Relationship with Natural Selection, Functional Pathways and Diseases

(2009) Roberto Amato et al.   PLoS One

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

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

(2009) S. L. Bumgarner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biofilm Matrix Regulation by Candida albicans Zap1

(2009) Clarissa J. Nobile et al.   PLOS BIOLOGY

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

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

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

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics