A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …
biology tool for modeling cellular physiology and growth. Extensions of this approach are …
Convex optimization for trajectory generation: A tutorial on generating dynamically feasible trajectories reliably and efficiently
Reliable and efficient trajectory generation methods are a fundamental need for
autonomous dynamical systems. The goal of this article is to provide a comprehensive …
autonomous dynamical systems. The goal of this article is to provide a comprehensive …
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis
Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex
manner, the full potential of which has yet to be established for any individual bacterial …
manner, the full potential of which has yet to be established for any individual bacterial …
Convex optimization for trajectory generation
Reliable and efficient trajectory generation methods are a fundamental need for
autonomous dynamical systems of tomorrow. The goal of this article is to provide a …
autonomous dynamical systems of tomorrow. The goal of this article is to provide a …
Bacillus subtilis: from soil bacterium to super-secreting cell factory
JM van Dijl, M Hecker - Microbial cell factories, 2013 - Springer
The biotechnology industry has become a key element in modern societies. Within this
industry, the production of recombinant enzymes and biopharmaceutical proteins is of major …
industry, the production of recombinant enzymes and biopharmaceutical proteins is of major …
Automatic construction of metabolic models with enzyme constraints
PS Bekiaris, S Klamt - BMC bioinformatics, 2020 - Springer
Background In order to improve the accuracy of constraint-based metabolic models, several
approaches have been developed which intend to integrate additional biological …
approaches have been developed which intend to integrate additional biological …
Quantitative prediction of genome-wide resource allocation in bacteria
A Goelzer, J Muntel, V Chubukov, M Jules, E Prestel… - Metabolic …, 2015 - Elsevier
Predicting resource allocation between cell processes is the primary step towards decoding
the evolutionary constraints governing bacterial growth under various conditions …
the evolutionary constraints governing bacterial growth under various conditions …
Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters
R Adadi, B Volkmer, R Milo… - PLoS computational …, 2012 - journals.plos.org
Identifying the factors that determine microbial growth rate under various environmental and
genetic conditions is a major challenge of systems biology. While current genome-scale …
genetic conditions is a major challenge of systems biology. While current genome-scale …
Constrained allocation flux balance analysis
New experimental results on bacterial growth inspire a novel top-down approach to study
cell metabolism, combining mass balance and proteomic constraints to extend and …
cell metabolism, combining mass balance and proteomic constraints to extend and …
Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth
AM Reimers, H Knoop, A Bockmayr… - Proceedings of the …, 2017 - National Acad Sciences
Cyanobacteria are an integral part of Earth's biogeochemical cycles and a promising
resource for the synthesis of renewable bioproducts from atmospheric CO2. Growth and …
resource for the synthesis of renewable bioproducts from atmospheric CO2. Growth and …