Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

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

(2020) Pierre Salvy et al.   Nature Communications

Short-range interactions govern the dynamics and functions of microbial communities

(2020) Alma Dal Co et al.   Nature Ecology & Evolution

Acetate metabolism and the inhibition of bacterial growth by acetate

(2019) Stéphane Pinhal et al.   JOURNAL OF BACTERIOLOGY

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

(2019) Benedict Borer et al.   PLoS Computational Biology

Energy metabolism controls phenotypes by protein efficiency and allocation

(2019) Yu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single microcolony diffusion analysis in Pseudomonas aeruginosa biofilms

(2019) Jagadish Sankaran et al.   npj Biofilms and Microbiomes

Metabolic heterogeneity in clonal microbial populations

(2018) Vakil Takhaveev et al.   CURRENT OPINION IN MICROBIOLOGY

Extracellular-matrix-mediated osmotic pressure drives Vibrio cholerae biofilm expansion and cheater exclusion

(2017) Jing Yan et al.   Nature Communications

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

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

Biofilms: an emergent form of bacterial life

(2016) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

Spatial structure, cooperation and competition in biofilms

(2016) Carey D. Nadell et al.   NATURE REVIEWS MICROBIOLOGY

Fast and accurate determination of 3D temperature distribution using fraction-step semi-implicit method

(2016) Wei Cen et al.   AIP Advances

The Influence of Crowding Conditions on the Thermodynamic Feasibility of Metabolic Pathways

(2015) Liliana Angeles-Martinez et al.   BIOPHYSICAL JOURNAL

A Lattice-Boltzmann scheme for the simulation of diffusion in intracellular crowded systems

(2015) Liliana Angeles-Martinez et al.   BMC BIOINFORMATICS

Spatially-resolved metabolic cooperativity within dense bacterial colonies

(2015) John A Cole et al.   BMC Systems Biology

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

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

Metabolic costs of amino acid and protein production inEscherichia coli

(2013) Christoph Kaleta et al.   Biotechnology Journal

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

(2013) Matthew B. Biggs et al.   PLoS One

Spatial self-organization favors heterotypic cooperation over cheating

(2013) Babak Momeni et al.   eLife

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

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

New insights into diffusion in 3D crowded media by Monte Carlo simulations: effect of size, mobility and spatial distribution of obstacles

(2011) Eudald Vilaseca et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Social evolution in multispecies biofilms

(2011) S. Mitri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying Diffusion in a Biofilm ofStreptococcus mutans

(2010) Zeshi Zhang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Diffusion of Macromolecules in Model Oral Biofilms

(2009) S. Takenaka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

(2009) Anu Raghunathan et al.   BMC Systems Biology

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY