Use of genome-scale metabolic models for understanding microbial physiology

A global map of gene function

(2010) Allison Doerr   NATURE METHODS

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

(2010) Ines Thiele et al.   Nature Protocols

Optimal In Silico Target Gene Deletion through Nonlinear Programming for Genetic Engineering

(2010) Chung-Chien Hong et al.   PLoS One

Toward systematic metabolic engineering based on the analysis of metabolic regulation by the integration of different levels of information

(2009) Kazuyuki Shimizu   BIOCHEMICAL ENGINEERING JOURNAL

KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways

(2009) Irena Spasić et al.   BIOINFORMATICS

Genetic modification of flux for flux prediction of mutants

(2009) Quanyu Zhao et al.   BIOINFORMATICS

Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli

(2009) R.M.T. Fleming et al.   BIOPHYSICAL CHEMISTRY

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

(2009) Jong Myoung Park et al.   BIOTECHNOLOGY ADVANCES

Industrial systems biology

(2009) José Manuel Otero et al.   BIOTECHNOLOGY AND BIOENGINEERING

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Fungal adaptation to the host environment

(2009) Bernhard Hube   CURRENT OPINION IN MICROBIOLOGY

Roles of NAD / NADH and NADP+ / NADPH in Cell Death

(2009) Weiliang Xia et al.   CURRENT PHARMACEUTICAL DESIGN

Transcriptional regulation of nonfermentable carbon utilization in budding yeast

(2009) Bernard Turcotte et al.   FEMS YEAST RESEARCH

Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug Targets

(2009) D.-S. Lee et al.   JOURNAL OF BACTERIOLOGY

Multiple redundant stress resistance mechanisms are induced in Salmonella enterica serovar Typhimurium in response to alteration of the intracellular environment via TLR4 signalling

(2009) J. A. Wright et al.   MICROBIOLOGY-SGM

Prediction of conditional gene essentiality through graph theoretical analysis of genome-wide functional linkages

(2009) P. Manimaran et al.   Molecular BioSystems

A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acid metabolism

(2009) Idit Diamant et al.   Molecular BioSystems

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism

(2009) Kenji Nakahigashi et al.   Molecular Systems Biology

PPI Finder: A Mining Tool for Human Protein-Protein Interactions

(2009) Min He et al.   PLoS One

Natural computation meta-heuristics for the in silico optimization of microbial strains

(2008) Miguel Rocha et al.   BMC BIOINFORMATICS

Exploiting the pathway structure of metabolism to reveal high-order epistasis

(2008) Marcin Imielinski et al.   BMC Systems Biology

Metabolic engineering for advanced biofuels production from Escherichia coli

(2008) Shota Atsumi et al.   CURRENT OPINION IN BIOTECHNOLOGY

Towards systems metabolic engineering of microorganisms for amino acid production

(2008) Jin Hwan Park et al.   CURRENT OPINION IN BIOTECHNOLOGY

Cofactor biosynthesis—still yielding fascinating new biological chemistry

(2008) Tadhg P Begley et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Systematic genome-wide scanning for genes involved in ATP generation in Escherichia coli

(2008) Kiyotaka Y. Hara et al.   METABOLIC ENGINEERING

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

(2008) R. Zhang et al.   NUCLEIC ACIDS RESEARCH

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

(2008) A. Chang et al.   NUCLEIC ACIDS RESEARCH

Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network Distance

(2008) Richard A. Notebaart et al.   PLoS Computational Biology

NADP Regulates the Yeast GAL Induction System

(2008) P. R. Kumar et al.   SCIENCE