A systems-level approach for metabolic engineering of yeast cell factories

Enzymatic glutathione production using metabolically engineered Saccharomyces cerevisiae as a whole-cell biocatalyst

(2011) Hideyo Yoshida et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Improving ethanol fermentation performance of Saccharomyces cerevisiae in very high-gravity fermentation through chemical mutagenesis and meiotic recombination

(2011) Jing-Jing Liu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Use of chemometrics in the selection of a Saccharomyces cerevisiae expression system for recombinant cyprosin B production

(2011) P. N. Sampaio et al.   BIOTECHNOLOGY LETTERS

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

(2011) José Otero et al.   BMC GENOMICS

Codon usage variability determines the correlation between proteome and transcriptome fold changes

(2011) Roberto Olivares-Hernández et al.   BMC Systems Biology

Statistical Inference Methods for Sparse Biological Time Series Data

(2011) Juliet Ndukum et al.   BMC Systems Biology

Expanding a dynamic flux balance model of yeast fermentation to genome-scale

(2011) Felipe A Vargas et al.   BMC Systems Biology

Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins

(2011) Jeffery G Saven   CURRENT OPINION IN CHEMICAL BIOLOGY

Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae

(2011) Jeremiah Wright et al.   FEMS YEAST RESEARCH

Oral treatment with Saccharomyces cerevisiae strain UFMG 905 modulates immune responses and interferes with signal pathways involved in the activation of inflammation in a murine model of typhoid fever

(2011) Flaviano S. Martins et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Metabolomics, Pathway Regulation, and Pathway Discovery

(2011) Guo-Fang Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bridging the Gap between Fluxomics and Industrial Biotechnology

(2011) Xueyang Feng et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Metabolic and bioprocess engineering for production of selenized yeast with increased content of seleno-methylselenocysteine

(2011) Valeria Mapelli et al.   METABOLIC ENGINEERING

An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data

(2011) André B. Canelas et al.   METABOLIC ENGINEERING

Targeted proteomics for metabolic pathway optimization: Application to terpene production

(2011) Alyssa M. Redding-Johanson et al.   METABOLIC ENGINEERING

Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae

(2011) Tomohisa Hasunuma et al.   Microbial Cell Factories

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

(2011) J. Zhang et al.   Molecular Systems Biology

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules

(2011) Andrew H. Babiskin et al.   NUCLEIC ACIDS RESEARCH

Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity

(2011) Andrew H. Babiskin et al.   NUCLEIC ACIDS RESEARCH

Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers

(2011) Karina M. Madsen et al.   PLoS One

The Stress Response Factors Yap6, Cin5, Phd1, and Skn7 Direct Targeting of the Conserved Co-Repressor Tup1-Ssn6 in S. cerevisiae

(2011) Sean E. Hanlon et al.   PLoS One

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

Engineered riboswitches: Overview, problems and trends

(2011) Beatrix Suess et al.   RNA Biology

Synthetic Biology Moving into the Clinic

(2011) W. C. Ruder et al.   SCIENCE

Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant

(2011) Sarah B. Smith et al.   YEAST

Metabolomics: a second-generation platform for crop and food analysis

(2011) Louise VT Shepherd et al.   Bioanalysis

Beyond the Transcripts: What Controls Protein Variation?

(2011) Laura Straub   PLOS BIOLOGY

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

(2011) Eric J. Foss et al.   PLOS BIOLOGY

Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape

(2011) Daniel J. Kvitek et al.   PLoS Genetics

Sensitive and Convenient Yeast Reporter Assay for High-Throughput Analysis by Using a Secretory Luciferase fromCypridina noctiluca

(2010) Yuki Tochigi et al.   ANALYTICAL CHEMISTRY

Metabolic Engineering ofSaccharomyces cerevisiaefor Production of Eicosapentaenoic Acid, Using a Novel Δ5-Desaturase fromParamecium tetraurelia

(2010) Sabina Tavares et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversion of Flux toward Sesquiterpene Production inSaccharomyces cerevisiaeby Fusion of Host and Heterologous Enzymes

(2010) Line Albertsen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced Production of a Plant Monoterpene by Overexpression of the 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase Catalytic Domain in Saccharomyces cerevisiae

(2010) J. Rico et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Production of tranilast [N-(3′,4′-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae

(2010) Aymerick Eudes et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Engineering of glycerol utilization pathway for ethanol production by Saccharomyces cerevisiae

(2010) Kyung Ok Yu et al.   BIORESOURCE TECHNOLOGY

Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level

(2010) Roberto Olivares-Hernández et al.   BIOTECHNOLOGY AND BIOENGINEERING

Improved galactose fermentation of Saccharomyces cerevisiae through inverse metabolic engineering

(2010) Ki-Sung Lee et al.   BIOTECHNOLOGY AND BIOENGINEERING

Implementation of communication-mediating domains for non-ribosomal peptide production in Saccharomyces cerevisiae

(2010) Verena Siewers et al.   BIOTECHNOLOGY AND BIOENGINEERING

Optimizing pentose utilization in yeast: the need for novel tools and approaches

(2010) Eric Young et al.   Biotechnology for Biofuels

Fast sampling for quantitative microbial metabolomics

(2010) Walter M van Gulik   CURRENT OPINION IN BIOTECHNOLOGY

Metabolomics in systems microbiology

(2010) Marshall Louis Reaves et al.   CURRENT OPINION IN BIOTECHNOLOGY

Random Mutagenesis Methods for In Vitro Directed Enzyme Evolution

(2010) Nikolaos Labrou   CURRENT PROTEIN & PEPTIDE SCIENCE

CE-MS for metabolomics: Developments and applications in the period 2008-2010

(2010) Rawi Ramautar et al.   ELECTROPHORESIS

Use of genome-scale metabolic models for understanding microbial physiology

(2010) Liming Liu et al.   FEBS LETTERS

Differential glucose repression in common yeast strains in response to HXK2 deletion

(2010) Anne Kümmel et al.   FEMS YEAST RESEARCH

Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics

(2010) Stefan Christen et al.   FEMS YEAST RESEARCH

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

(2010) J. A. Lewis et al.   GENETICS

Feed-Forward Regulation of a Cell Fate Determinant by an RNA-Binding Protein Generates Asymmetry in Yeast

(2010) J. J. Wolf et al.   GENETICS

Optimizing the secondary structure of human papillomavirus type 16 L1 mRNA enhances L1 protein expression in Saccharomyces cerevisiae

(2010) Hyoung Jin Kim et al.   JOURNAL OF BIOTECHNOLOGY

RAPYD — Rapid Annotation Platform for Yeast Data

(2010) Jessica Schneider et al.   JOURNAL OF BIOTECHNOLOGY

Metabolic engineering of Saccharomyces cerevisiae for the biotechnological production of succinic acid

(2010) Andreas M. Raab et al.   METABOLIC ENGINEERING

Improved vanillin production in baker's yeast through in silico design

(2010) Ana Brochado et al.   Microbial Cell Factories

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

BioMet Toolbox: genome-wide analysis of metabolism

(2010) M. Cvijovic et al.   NUCLEIC ACIDS RESEARCH

Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae

(2010) James Kirby et al.   PHYTOCHEMISTRY

Manufacturing Molecules Through Metabolic Engineering

(2010) J. D. Keasling   SCIENCE

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae

(2010) Siavash Partow et al.   YEAST

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

(2010) André B. Canelas et al.   Nature Communications

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

How to make a minimal genome for synthetic minimal cell

(2010) Liu-yan Zhang et al.   Protein & Cell

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

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

Elimination of Glycerol Production in Anaerobic Cultures of a Saccharomyces cerevisiae Strain Engineered To Use Acetic Acid as an Electron Acceptor

(2009) V. G. Medina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhancing the flux of D-glucose to the pentose phosphate pathway in Saccharomyces cerevisiae for the production of D-ribose and ribitol

(2009) Mervi H. Toivari et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Construction of a xylose-fermenting Saccharomyces cerevisiae strain by combined approaches of genetic engineering, chemical mutagenesis and evolutionary adaptation

(2009) Enkai Liu et al.   BIOCHEMICAL ENGINEERING JOURNAL

Constraints-based genome-scale metabolic simulation for systems metabolic engineering

(2009) Jong Myoung Park et al.   BIOTECHNOLOGY ADVANCES

Directed evolution of a secretory leader for the improved expression of heterologous proteins and full-length antibodies inSaccharomyces cerevisiae

(2009) J. Andy Rakestraw et al.   BIOTECHNOLOGY AND BIOENGINEERING

Industrial biotechnology: Tools and applications

(2009) Weng Lin Tang et al.   Biotechnology Journal

Direct spectroscopic (FTIR) detection of intraspecific binary contaminations in yeast cultures

(2009) Paolo Rellini et al.   FEMS YEAST RESEARCH

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

(2009) C. J. Kennedy et al.   GENETICS

Expression of hepatitis B surface antigen S domain in recombinant Saccharomyces cerevisiae using GAL1 promoter

(2009) Eun-Jeong Kim et al.   JOURNAL OF BIOTECHNOLOGY

A comprehensive method for the quantification of the non-oxidative pentose phosphate pathway intermediates in Saccharomyces cerevisiae by GC–IDMS

(2009) Chiara Cipollina et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Heterologous production of non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae

(2009) Verena Siewers et al.   METABOLIC ENGINEERING

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering

(2009) Mohammad A. Asadollahi et al.   METABOLIC ENGINEERING

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

(2009) Lake-Ee Quek et al.   Microbial Cell Factories

Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

(2009) Renata Usaite et al.   Molecular Systems Biology

Synthetic protein scaffolds provide modular control over metabolic flux

(2009) John E Dueber et al.   NATURE BIOTECHNOLOGY

A fast and efficient translational control system for conditional expression of yeast genes

(2009) Peter Kötter et al.   NUCLEIC ACIDS RESEARCH

Strong Eukaryotic IRESs Have Weak Secondary Structure

(2009) Xuhua Xia et al.   PLoS One

Isotope dilution quantification of ultratrace gamma-glutamyl-Se-methylselenocysteine species using HPLC with enhanced ICP–MS detection by ultrasonic nebulisation or carbon-loaded plasma

(2008) Heidi Goenaga Infante et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Engineered enzymes for chemical production

(2008) Stephan Luetz et al.   BIOTECHNOLOGY AND BIOENGINEERING

Determination of the cytosolic free NAD/NADH ratio inSaccharomyces cerevisiaeunder steady-state and highly dynamic conditions

(2008) André B. Canelas et al.   BIOTECHNOLOGY AND BIOENGINEERING

Appropriate sampling for intracellular amino acid analysis in five phylogenetically different yeasts

(2008) Christoph J. Bolten et al.   BIOTECHNOLOGY LETTERS

De novo biosynthetic pathways: rational design of microbial chemical factories

(2008) Kristala L Jones Prather et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineering of a mammalian O-glycosylation pathway in the yeast Saccharomyces cerevisiae: production of O-fucosylated epidermal growth factor domains

(2008) Y. Chigira et al.   GLYCOBIOLOGY

Synthetic biology with RNA motifs

(2008) Hirohide Saito et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose RepressionSaccharomyces cerevisiaeStrains: The Comparison of Two Quantitative Methods

(2008) Renata Usaite et al.   JOURNAL OF PROTEOME RESEARCH

Leakage-free rapid quenching technique for yeast metabolomics

(2008) André B. Canelas et al.   Metabolomics

Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol

(2008) Eric J Steen et al.   Microbial Cell Factories

Progress in Metabolic Engineering of Saccharomyces cerevisiae

(2008) E. Nevoigt   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

(2008) Zengyi Shao et al.   NUCLEIC ACIDS RESEARCH

Promoter library designed for fine-tuned gene expression in Pichia pastoris

(2008) Franz S. Hartner et al.   NUCLEIC ACIDS RESEARCH

Application of systems biology for bioprocess development

(2008) Jin Hwan Park et al.   TRENDS IN BIOTECHNOLOGY

Impact of systems biology on metabolic engineering ofSaccharomyces cerevisiae

(2007) Jens Nielsen et al.   FEMS YEAST RESEARCH