Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

Harnessing Genetic Diversity in Saccharomyces cerevisiae for Fermentation of Xylose in Hydrolysates of Alkaline Hydrogen Peroxide-Pretreated Biomass

(2013) Trey K. Sato et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phenotypic selection of a wild Saccharomyces cerevisiae strain for simultaneous saccharification and co-fermentation of AFEX™ pretreated corn stover

(2013) Mingjie Jin et al.   Biotechnology for Biofuels

Adaptively evolved yeast mutants on galactose show trade-offs in carbon utilization on glucose

(2013) Kuk-Ki Hong et al.   METABOLIC ENGINEERING

Adaptive laboratory evolution – principles and applications for biotechnology

(2013) Martin Dragosits et al.   Microbial Cell Factories

Coevolution Trumps Pleiotropy: Carbon Assimilation Traits Are Independent of Metabolic Network Structure in Budding Yeast

(2013) Dana A. Opulente et al.   PLoS One

Genetic Basis of Variations in Nitrogen Source Utilization in Four Wine Commercial Yeast Strains

(2013) Alicia Gutiérrez et al.   PLoS One

Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes

(2013) P. A. Gibney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae

(2012) Andrea Hodgins-Davis et al.   Genome Biology and Evolution

Surprisingly diverged populations ofSaccharomyces cerevisiaein natural environments remote from human activity

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

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1

(2012) Farbod Babrzadeh et al.   MOLECULAR GENETICS AND GENOMICS

Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor

(2012) Jeffrey A. Lewis et al.   G3-Genes Genomes Genetics

Advances in Quantitative Trait Analysis in Yeast

(2012) Gianni Liti et al.   PLoS Genetics

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

(2011) T. Akao et al.   DNA RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Saccharomyces Genome Database: the genomics resource of budding yeast

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

Amplification of a Zygosaccharomyces bailii DNA Segment in Wine Yeast Genomes by Extrachromosomal Circular DNA Formation

(2011) Virginie Galeote et al.   PLoS One

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

A Tradeoff Drives the Evolution of Reduced Metal Resistance in Natural Populations of Yeast

(2011) Shang-Lin Chang et al.   PLoS 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

Enhancement of the Initial Rate of Ethanol Fermentation Due to Dysfunction of Yeast Stress Response Components Msn2p and/or Msn4p

(2010) Daisuke Watanabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

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

Exploiting Natural Variation in Saccharomyces cerevisiae to Identify Genes for Increased Ethanol Resistance

(2010) J. A. Lewis et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

(2010) Hani Goodarzi et al.   Molecular Systems Biology

Remarkably ancient balanced polymorphisms in a multi-locus gene network

(2010) Chris Todd Hittinger et al.   NATURE

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays

(2010) Y. S. Dufour et al.   NUCLEIC ACIDS RESEARCH

Polygenic and directional regulatory evolution across pathways in Saccharomyces

(2010) J. H. Bullard 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

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

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

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

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

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass: a comparative evaluation between ammonia fiber expansion and dilute acid pretreatment

(2009) Ming W Lau et al.   Biotechnology for Biofuels

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

(2009) J. L. Argueso et al.   GENOME RESEARCH

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

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

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

Comparative genome analysis of aSaccharomyces cerevisiaewine strain

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

Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress inSaccharomyces cerevisiae

(2008) Katsunori Yoshikawa et al.   FEMS YEAST RESEARCH

Stress-activated Genomic Expression Changes Serve a Preparative Role for Impending Stress in Yeast

(2008) David B. Berry et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

A Catalog of Neutral and Deleterious Polymorphism in Yeast

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

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics