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

Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks

(2018) Benedict Borer et al.   Nature Communications

Emergence of Escherichia coli critically buckled motile helices under stress

(2018) Trung V. Phan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

(2017) Oliver Hädicke et al.   Scientific Reports

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

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

(2017) Eugen Bauer et al.   PLoS Computational Biology

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model

(2016) Ali Ebrahimi et al.   GLOBAL CHANGE BIOLOGY

Bacterial flagellar motility on hydrated rough surfaces controlled by aqueous film thickness and connectedness

(2016) Robin Tecon et al.   Scientific Reports

Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

(2015) Parizad Babaei et al.   Molecular BioSystems

Microbial hotspots and hot moments in soil: Concept & review

(2015) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

(2015) Ali Ebrahimi et al.   WATER RESOURCES RESEARCH

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Spatial Ecology of Bacteria at the Microscale in Soil

(2014) Xavier Raynaud et al.   PLoS One

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

(2014) Ali N. Ebrahimi et al.   WATER RESOURCES RESEARCH

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

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

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

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

Hydration dynamics promote bacterial coexistence on rough surfaces

(2012) Gang Wang et al.   ISME Journal

iDynoMiCS: next-generation individual-based modelling of biofilms

(2011) Laurent A. Lardon et al.   ENVIRONMENTAL MICROBIOLOGY

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Aqueous films limit bacterial cell motility and colony expansion on partially saturated rough surfaces

(2010) Gang Wang et al.   ENVIRONMENTAL MICROBIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Hydration-controlled bacterial motility and dispersal on surfaces

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

Dynamics of Microbial Growth and Coexistence on Variably Saturated Rough Surfaces

(2009) Tao Long et al.   MICROBIAL ECOLOGY

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology