Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance

Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance

(2016) Maria Sardi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae

(2016) Yingying Chen et al.   Biotechnology for Biofuels

Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae

(2016) Jean-Paul Meijnen et al.   Biotechnology for Biofuels

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

The Power of Natural Variation for Model Organism Biology

(2016) Audrey P. Gasch et al.   TRENDS IN GENETICS

Genetic dissection of acetic acid tolerance in Saccharomyces cerevisiae

(2016) Peng Geng et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction

(2016) You Tang et al.   Plant Genome

Phenolic Amides Are Potent Inhibitors ofDe NovoNucleotide Biosynthesis

(2015) Tippapha Pisithkul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance

(2015) Tim Snoek et al.   Biotechnology for Biofuels

Natural Variation in Gene Expression Modulates the Severity of Mutant Phenotypes

(2015) Victoria Vu et al.   CELL

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

Ecological and Genetic Barriers Differentiate Natural Populations ofSaccharomyces cerevisiae

(2015) Katie J. Clowers et al.   MOLECULAR BIOLOGY AND EVOLUTION

The laboratory domestication of Caenorhabditis elegans

(2015) Mark G. Sterken et al.   TRENDS IN GENETICS

Dosage compensation can buffer copy-number variation in wild yeast

(2015) James Hose et al.   eLife

Changes in the Sterol Composition of the Plasma Membrane Affect Membrane Potential, Salt Tolerance and the Activity of Multidrug Resistance Pumps in Saccharomyces cerevisiae

(2015) Marie Kodedová et al.   PLoS One

Stress Tolerance Variations in Saccharomyces cerevisiae Strains from Diverse Ecological Sources and Geographical Locations

(2015) Yan-Lin Zheng et al.   PLoS One

Flocculation Causes Inhibitor Tolerance in Saccharomyces cerevisiae for Second-Generation Bioethanol Production

(2014) Johan O. Westman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Physiological response ofSaccharomyces cerevisiaeto weak acids present in lignocellulosic hydrolysate

(2014) Zhongpeng Guo et al.   FEMS YEAST RESEARCH

High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces

(2014) W. G. Alexander et al.   GENETICS

Causes and Consequences of Genetic Background Effects Illuminated by Integrative Genomic Analysis

(2014) Christopher H. Chandler et al.   GENETICS

Heritability and genetic basis of protein level variation in an outbred population

(2014) Leopold Parts et al.   GENOME RESEARCH

Preservation of genetic and regulatory robustness in ancient gene duplicates ofSaccharomyces cerevisiae

(2014) Orla M. Keane et al.   GENOME RESEARCH

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

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

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

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

Genetic Basis of Metabolome Variation in Yeast

(2014) Jeffrey S. Breunig et al.   PLoS Genetics

Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors

(2014) Jeff S. Piotrowski et al.   Frontiers in Microbiology

Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation

(2013) Georg Hubmann et al.   Biotechnology for Biofuels

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

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

Vanillin causes the activation of Yap1 and mitochondrial fragmentation in Saccharomyces cerevisiae

(2013) Trinh Thi My Nguyen et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Vanillin Inhibits Translation and Induces Messenger Ribonucleoprotein (mRNP) Granule Formation in Saccharomyces cerevisiae: Application and Validation of High-Content, Image-Based Profiling

(2013) Aya Iwaki et al.   PLoS One

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

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

A strain of Saccharomyces cerevisiae evolved for fermentation of lignocellulosic biomass displays improved growth and fermentative ability in high solids concentrations and in the presence of inhibitory compounds

(2012) Gary M Hawkins et al.   Biotechnology for Biofuels

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

(2012) Pablo Cingolani et al.   FLY

Local Ancestry Corrects for Population Structure in Saccharomyces cerevisiae Genome-Wide Association Studies

(2012) Liyang Diao et al.   GENETICS

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

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

Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis

(2012) S. Swinnen et al.   GENOME RESEARCH

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

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

Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

(2012) Jun Zhu et al.   PLOS BIOLOGY

Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster

(2012) Ulrike Ober et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

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

(2011) L. Parts et al.   GENOME RESEARCH

Mne1 Is a Novel Component of the Mitochondrial Splicing Apparatus Responsible for Processing of aCOX1Group I Intron in Yeast

(2011) Talina Watts et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparative metabolic profiling of parental and inhibitors-tolerant yeasts during lignocellulosic ethanol fermentation

(2011) Ming-Zhu Ding et al.   Metabolomics

Assessing the complex architecture of polygenic traits in diverged yeast populations

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

Introduction: Next generation biofuels

(2011) Peter Fairley   NATURE

Highly efficient bioethanol production by a Saccharomyces cerevisiae strain with multiple stress tolerance to high temperature, acid and ethanol

(2011) Suthee Benjaphokee et al.   New Biotechnology

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals

(2011) Shishir P.S. Chundawat et al.   Annual Review of Chemical and Biomolecular Engineering

Trait Variation in Yeast Is Defined by Population History

(2011) Jonas Warringer et al.   PLoS Genetics

Bioinformatics challenges for genome-wide association studies

(2010) J. H. Moore et al.   BIOINFORMATICS

Multifaceted characterization of cell wall decomposition products formed during ammonia fiber expansion (AFEX) and dilute acid based pretreatments

(2010) Shishir P.S. Chundawat et al.   BIORESOURCE TECHNOLOGY

Furfural induces reactive oxygen species accumulation and cellular damage in Saccharomyces cerevisiae

(2010) Sandra A Allen et al.   Biotechnology for Biofuels

Genome shuffling to improve fermentation properties of top-fermenting yeast by the improvement of stress tolerance

(2010) Haiyong Wang et al.   FOOD SCIENCE AND BIOTECHNOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid

(2010) Nuno P Mira et al.   Microbial Cell Factories

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

(2010) Ian M. Ehrenreich et al.   NATURE

Genotype to Phenotype: A Complex Problem

(2010) R. D. Dowell 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

Genome-Wide Identification of Saccharomyces cerevisiae Genes Required for Maximal Tolerance to Ethanol

(2009) M. C. Teixeira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Novel methods of genome shuffling in Saccharomyces cerevisiae

(2009) Lihua Hou   BIOTECHNOLOGY LETTERS

Involvement of ergosterol in tolerance to vanillin, a potential inhibitor of bioethanol fermentation, inSaccharomyces cerevisiae

(2009) Ayako Endo et al.   FEMS MICROBIOLOGY LETTERS

Genetic improvement  of  thermo-tolerance in wineSaccharomyces cerevisiae  strains by a backcross approach

(2009) Philippe Marullo et al.   FEMS YEAST RESEARCH

A novel NADPH-dependent aldehyde reductase gene from Saccharomyces cerevisiae NRRL Y-12632 involved in the detoxification of aldehyde inhibitors derived from lignocellulosic biomass conversion

(2009) Z. Lewis Liu et al.   GENE

Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability of Saccharomyces cerevisiae S288C Strains

(2009) L. N. Dimitrov et al.   GENETICS

QTL mapping of sake brewing characteristics of yeast

(2009) Taku Katou et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

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

Effects of the S288c genetic background and common auxotrophic markers on mitochondrial DNA function inSaccharomyces cerevisiae

(2009) M. J. Young et al.   YEAST

Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae

(2008) Z. Lewis Liu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

NADH- vs NADPH-coupled reduction of 5-hydroxymethyl furfural (HMF) and its implications on product distribution in Saccharomyces cerevisiae

(2008) João R. M. Almeida et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Pretreatments to enhance the digestibility of lignocellulosic biomass

(2008) A.T.W.M. Hendriks et al.   BIORESOURCE TECHNOLOGY

A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms

(2008) Xiaoyi Gao et al.   GENETIC EPIDEMIOLOGY

The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes

(2008) M. E. Hillenmeyer et al.   SCIENCE

Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain

(2008) Dominik Heer et al.   Microbial Biotechnology

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

(2008) Daniel J. Kvitek et al.   PLoS Genetics