Laboratory evolution of new lactate transporter genes in a jen1Δ mutant of Saccharomyces cerevisiae and their identification as ADY2 alleles by whole-genome resequencing and transcriptome analysis

Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution

(2011) R. DHAR et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Engineering topology and kinetics of sucrose metabolism in Saccharomyces cerevisiae for improved ethanol yield

(2011) Thiago O. Basso et al.   METABOLIC ENGINEERING

Increasing free-energy (ATP) conservation in maltose-grown Saccharomyces cerevisiae by expression of a heterologous maltose phosphorylase

(2011) Stefan de Kok et al.   METABOLIC ENGINEERING

Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis

(2011) K.-K. Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

(2010) D.-H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks

(2010) Stefan J. Jol et al.   BIOPHYSICAL JOURNAL

A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution

(2010) Pier-Luc Tremblay et al.   ENVIRONMENTAL MICROBIOLOGY

Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems

(2010) Minou Nowrousian   EUKARYOTIC CELL

Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae

(2010) H. Wouter Wisselink et al.   METABOLIC ENGINEERING

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli

(2010) Shota Atsumi et al.   Molecular Systems Biology

Quantitative Physiology of Saccharomyces cerevisiae at Near-Zero Specific Growth Rates

(2009) L. G. M. Boender et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Catalase Overexpression Reduces Lactic Acid-Induced Oxidative Stress in Saccharomyces cerevisiae

(2009) D. A. Abbott et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol

(2009) Hongbo Hu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Saltational evolution: hopeful monsters are here to stay

(2009) Günter Theißen   THEORY IN BIOSCIENCES

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

(2009) Tom M Conrad et al.   GENOME BIOLOGY

Comparing whole genomes using DNA microarrays

(2008) David Gresham et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics

Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling

(2008) Chandran Vijayendran et al.   GENOME BIOLOGY