Calibration and analysis of genome-based models for microbial ecology

Transient dynamics of competitive exclusion in microbial communities

(2015) Stilianos Louca et al.   ENVIRONMENTAL MICROBIOLOGY

Gene-centric approach to integrating environmental genomics and biogeochemical models

(2014) Daniel C. Reed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli

(2014) J. Plucain et al.   SCIENCE

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

The Genotypic View of Social Interactions in Microbial Communities

(2013) Sara Mitri et al.   Annual Review of Genetics

Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis

(2013) Filip Husnik et al.   CELL

Dynamic metabolic flux analysis—tools for probing transient states of metabolic networks

(2013) Maciek R Antoniewicz   CURRENT OPINION IN BIOTECHNOLOGY

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

(2013) Matthew D. Herron et al.   PLOS BIOLOGY

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

(2013) William R. Harcombe et al.   PLoS Computational Biology

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

(2012) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

(2012) Sung Yoon et al.   GENOME BIOLOGY

Integration of expression data in genome-scale metabolic network reconstructions

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

Ecosystems biology of microbial metabolism

(2011) Niels Klitgord et al.   CURRENT OPINION IN BIOTECHNOLOGY

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Prospects for systems biology and modeling of the gut microbiome

(2011) Fredrik H. Karlsson et al.   TRENDS IN BIOTECHNOLOGY

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Aerobic growth at nanomolar oxygen concentrations

(2010) D. A. Stolper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation

(2009) Adam L. Meadows et al.   METABOLIC ENGINEERING

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

DEFINED ORDER OF EVOLUTIONARY ADAPTATIONS: EXPERIMENTAL EVIDENCE

(2008) Erez Oxman et al.   EVOLUTION

Metabolic Changes Associated With Adaptive Diversification in Escherichia coli

(2008) M. Le Gac et al.   GENETICS

Reconstruction of biochemical networks in microorganisms

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

Adaptation increases the likelihood of diversification in an experimental bacterial lineage

(2008) C. C. Spencer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY