Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

(2020) Pierre Salvy et al.   Nature Communications

Predictive biology: modelling, understanding and harnessing microbial complexity

(2020) Allison J. Lopatkin et al.   NATURE REVIEWS MICROBIOLOGY

Slower growth of Escherichia coli leads to longer survival in carbon starvation due to a decrease in the maintenance rate

(2020) Elena Biselli et al.   Molecular Systems Biology

Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments

(2020) Elena Perrin et al.   Nature Communications

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

(2019) Laurence Yang et al.   BMC Systems Biology

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

(2019) Antonella Succurro et al.   mSystems

Growth strategy of microbes on mixed carbon sources

(2019) Xin Wang et al.   Nature Communications

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

(2018) Colton J. Lloyd et al.   PLoS Computational Biology

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

(2017) Meric Ataman et al.   PLoS Computational Biology

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

(2017) Meric Ataman et al.   PLoS Computational Biology

solveME: fast and reliable solution of nonlinear ME models

(2016) Laurence Yang et al.   BMC BIOINFORMATICS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

(2015) Noushin Hadadi et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2015) Brice Enjalbert et al.   JOURNAL OF BACTERIOLOGY

Understanding carbon catabolite repression in Escherichia coli using quantitative models

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

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

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

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

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

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY