Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

Advancing metabolic models with kinetic information

(2014) Hannes Link et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook

(2014) Christopher P Long et al.   CURRENT OPINION IN BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803

(2014) T. R. Maarleveld et al.   PLANT PHYSIOLOGY

The environmental controls that govern the end product of bacterial nitrate respiration

(2014) B. Kraft et al.   SCIENCE

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

(2014) J. H. van Heerden et al.   SCIENCE

Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example

(2014) Wilfred F. M. Röling et al.   Frontiers in Microbiology

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms

(2013) Yoshihiro Toya et al.   BIOTECHNOLOGY ADVANCES

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

(2013) David D. Myrold et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing

(2012) Ruo He et al.   ENVIRONMENTAL MICROBIOLOGY

Piecewise affine approximations of fluxes and enzyme kinetics fromin vivo13C labeling experiments

(2012) Alessandro Abate et al.   INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL

A road map for the development of community systems (CoSy) biology

(2012) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

Carbon availability triggers fungal nitrogen uptake and transport in arbuscular mycorrhizal symbiosis

(2012) C. R. Fellbaum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

(2012) Steven M. Kelk et al.   Scientific Reports

Shrinking the Metabolic Solution Space Using Experimental Datasets

(2012) Jennifer L. Reed   PLoS Computational Biology

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Subpopulation-Specific Metabolic Pathway Usage in Mixed Cultures as Revealed by Reporter Protein-Based13C Analysis

(2011) Martin Rühl et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterizing microbial communities through space and time

(2011) Antonio Gonzalez et al.   CURRENT OPINION IN BIOTECHNOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures

(2010) Timothy J. Hanly et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing

(2010) Fahimeh Salimi et al.   Biotechnology Journal

Systems approaches to microbial communities and their functioning

(2010) Wilfred FM Röling et al.   CURRENT OPINION IN BIOTECHNOLOGY

13C metabolic flux analysis in complex systems

(2010) Nicola Zamboni   CURRENT OPINION IN BIOTECHNOLOGY

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

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

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

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Genome-scale constraint-based modeling of Geobacter metallireducens

(2009) Jun Sun et al.   BMC Systems Biology

Flux balance analysis of biological systems: applications and challenges

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

The application of flux balance analysis in systems biology

(2009) Erwin P. Gianchandani et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation

(2009) Bas Teusink et al.   PLoS Computational Biology

Isotopomer Distributions in Amino Acids from a Highly Expressed Protein as a Proxy for Those from Total Protein

(2008) Afshan S. Shaikh et al.   ANALYTICAL CHEMISTRY

13C labeling experiments at metabolic nonstationary conditions: An exploratory study

(2008) Sebastian Wahl et al.   BMC BIOINFORMATICS

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

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

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Simultaneous analysis of microbial identity and function using NanoSIMS

(2007) Tianlun Li et al.   ENVIRONMENTAL MICROBIOLOGY