A steady-state model of microbial acclimation to substrate limitation

Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation

(2020) Hong Zeng et al.   Scientific Reports

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann et al.   Nature Communications

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

(2016) Dan Davidi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glucose Transport in Escherichia coli Mutant Strains with Defects in Sugar Transport Systems

(2012) S. Steinsiek et al.   JOURNAL OF BACTERIOLOGY

Trait-based models of nutrient uptake in microbes extend the Michaelis-Menten framework

(2012) Øyvind Fiksen et al.   LIMNOLOGY AND OCEANOGRAPHY

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

Optimality-based modeling of planktonic organisms

(2011) S. Lan Smith et al.   LIMNOLOGY AND OCEANOGRAPHY

Inherent and apparent traits in microbial nutrient uptake

(2011) DL Aksnes et al.   MARINE ECOLOGY PROGRESS SERIES

Dynamic model of flexible phytoplankton nutrient uptake

(2011) J. A. Bonachela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimal uptake kinetics: physiological acclimation explains the pattern of nitrate uptake by phytoplankton in the ocean

(2009) SL Smith et al.   MARINE ECOLOGY PROGRESS SERIES

Nutrient uptake rate as a function of cell size and surface transporter density: A Michaelis-like approximation to the model of Pasciak and Gavis

(2008) Robert A. Armstrong   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS