Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

Transparency in metabolic network reconstruction enables scalable biological discovery

(2015) Benjamin D Heavner et al.   CURRENT OPINION IN BIOTECHNOLOGY

Understanding carbon catabolite repression in Escherichia coli using quantitative models

(2015) A. Kremling et al.   TRENDS IN MICROBIOLOGY

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

(2014) Matthew N. Benedict et al.   PLoS Computational Biology

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

(2014) Esa Pitkänen et al.   PLoS Computational Biology

Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

(2014) Benjamin VanderSluis et al.   GENOME BIOLOGY

Assimilating genome-scale metabolic reconstructions with modelBorgifier

(2013) John T. Sauls et al.   BIOINFORMATICS

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

(2013) Tobias Österlund et al.   BMC Systems Biology

Dead End Metabolites - Defining the Known Unknowns of the E. coli Metabolic Network

(2013) Amanda Mackie et al.   PLoS One

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

(2013) Benjamin D. Heavner et al.   Database-The Journal of Biological Databases and Curation

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

(2012) Benjamin D Heavner et al.   BMC Systems Biology

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

(2012) Jeffrey D Orth et al.   BMC Systems Biology

Nutritional requirements of the BY series ofSaccharomyces cerevisiaestrains for optimum growth

(2012) Michael Hanscho et al.   FEMS YEAST RESEARCH

A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae

(2012) Magalie Celton et al.   METABOLIC ENGINEERING

YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

(2012) Rama Balakrishnan et al.   Database-The Journal of Biological Databases and Curation

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

(2011) Ali R Zomorrodi et al.   BMC Systems Biology

Engineering strategy of yeast metabolism for higher alcohol production

(2011) Fumio Matsuda et al.   Microbial Cell Factories

An integrated approach to characterize genetic interaction networks in yeast metabolism

(2011) Balázs Szappanos et al.   NATURE GENETICS

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Why does yeast ferment? A flux balance analysis study

(2010) Evangelos Simeonidis et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Further developments towards a genome-scale metabolic model of yeast

(2010) Paul D Dobson et al.   BMC Systems Biology

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

BioMet Toolbox: genome-wide analysis of metabolism

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

Reconstruction and Validation of RefRec: A Global Model for the Yeast Molecular Interaction Network

(2010) Tommi Aho et al.   PLoS One

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

(2009) Caroline B. Milne et al.   Biotechnology Journal

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

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

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

(2008) Intawat Nookaew et al.   BMC Systems Biology

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

(2008) Evan S Snitkin et al.   GENOME BIOLOGY