Genomic and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae

5-Hydroxymethylfurfural induces ADH7 and ARI1 expression in tolerant industrial Saccharomyces cerevisiae strain P6H9 during bioethanol production

(2013) Nicole Teixeira Sehnem et al.   BIORESOURCE TECHNOLOGY

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

(2013) Hamid Mirzaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved motifs in the Msn2-activating domain are important for Msn2-mediated yeast stress response

(2012) A. Sadeh et al.   JOURNAL OF CELL SCIENCE

Functional Survey for Heterologous Sugar Transport Proteins, Using Saccharomyces cerevisiae as a Host

(2011) Eric Young et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP

(2011) J. R. Grant et al.   BIOINFORMATICS

Engineered NADH-dependent GRE2 from Saccharomyces cerevisiae by directed enzyme evolution enhances HMF reduction using additional cofactor NADPH

(2011) Jaewoong Moon et al.   ENZYME AND MICROBIAL TECHNOLOGY

Characterization of CpSte11, a MAPKKK gene of Cryphonectria parasitica, and initial evidence of its involvement in the pheromone response pathway

(2011) JIN-AH PARK et al.   MOLECULAR PLANT PATHOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

FPG1, a gene involved in foam formation in Saccharomyces cerevisiae

(2011) Lucía Blasco et al.   YEAST

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

Stereochemistry of Furfural Reduction by a Saccharomyces cerevisiae Aldehyde Reductase That Contributes to In Situ Furfural Detoxification

(2010) M. J. Bowman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae

(2010) Dragana Stanley et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Comparison of heterologous xylose transporters in recombinant Saccharomyces cerevisiae

(2010) David Runquist et al.   Biotechnology for Biofuels

DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data

(2010) Stacy Duncan et al.   BMC BIOINFORMATICS

Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae

(2010) Menggen Ma et al.   BMC GENOMICS

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

(2010) J. A. Lewis et al.   GENETICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Comparative Proteomic Analysis of Tolerance and Adaptation of Ethanologenic Saccharomyces cerevisiae to Furfural, a Lignocellulosic Inhibitory Compound

(2009) F.-M. Lin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Stress-tolerance of baker's-yeast (Saccharomyces cerevisiae) cells: stress-protective molecules and genes involved in stress tolerance

(2009) Jun Shima et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast

(2009) Craig Lawless et al.   BMC GENOMICS

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

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

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

Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis

(2009) B. U. Stambuk et al.   GENOME RESEARCH

Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways

(2009) Z. Lewis Liu et al.   MOLECULAR GENETICS AND GENOMICS

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer et al.   NATURE

Temporal quantitative proteomics of Saccharomyces cerevisiae in response to a nonlethal concentration of furfural

(2009) Feng-Ming Lin et al.   PROTEOMICS

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

(2008) A. D. Johnson et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

iPath: interactive exploration of biochemical pathways and networks

(2008) Ivica Letunic et al.   TRENDS IN BIOCHEMICAL SCIENCES