Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth

Review and perspective on mathematical modeling of microbial ecosystems

(2018) Antonella Succurro et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia

(2017) Antonella Succurro et al.   JOURNAL OF BACTERIOLOGY

Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments

(2017) Coco van Boxtel et al.   Journal of the Royal Society Interface

Limited by sensing - A minimal stochastic model of the lag-phase during diauxic growth

(2017) Dominique Chu   JOURNAL OF THEORETICAL BIOLOGY

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Synthetic Ecology of Microbes: Mathematical Models and Applications

(2016) Ali R. Zomorrodi et al.   JOURNAL OF MOLECULAR BIOLOGY

Identifying Metabolic Subpopulations from Population Level Mass Spectrometry

(2016) Christine M. DeGennaro et al.   PLoS One

Acetate Exposure Determines the Diauxic Behavior of Escherichia coli during the Glucose-Acetate Transition

(2015) Brice Enjalbert et al.   JOURNAL OF BACTERIOLOGY

Shifting Sugars and Shifting Paradigms

(2015) Mark L. Siegal   PLOS BIOLOGY

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

(2015) Zachary A. King et al.   PLoS Computational Biology

DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

(2014) Jose A Gomez et al.   BMC BIOINFORMATICS

Phenotypic bistability in Escherichia coli's central carbon metabolism

(2014) O. Kotte et al.   Molecular Systems Biology

Bet-hedging during bacterial diauxic shift

(2014) A. Solopova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

(2014) Ali R. Zomorrodi et al.   ACS Synthetic Biology

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

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

Memory and Fitness Optimization of Bacteria under Fluctuating Environments

(2014) Guillaume Lambert et al.   PLoS Genetics

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

(2014) Hyun-Seob Song et al.   Processes

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Single-Cell Dynamics Reveals Sustained Growth during Diauxic Shifts

(2013) Sarah Boulineau et al.   PLoS One

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

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology