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Computing the shortest elementary flux modes in genome-scale metabolic networks
TLDR
We show that the full set of elementary flux modes in large-scale metabolic networks can be enumerated in increasing order of number of reactions via integer linear programming. Expand
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BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
TLDR
We combine spatial and temporal multi-scale modeling approaches such as BacArena to generate novel biological insights into Pseudomonas aeruginosa biofilm formation as well as a seven species model community of human gut. Expand
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Integrated network reconstruction, visualization and analysis using YANAsquare
TLDR
YANAsquare provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview, calculation of metabolic fluxes and testing the robustness of the network. Expand
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Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
TLDR
Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. Expand
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Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis
TLDR
We predicted a set of five novel TF - target gene interactions in E. coli. Expand
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Using chemical organization theory for model checking
TLDR
We introduce an algorithm that uncovers stoichiometric information that might be hidden in the kinetic laws of a reaction network. Expand
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Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach
TLDR
We show that in the case of low or moderate synthesis costs for the enzymes of the high-yield pathway, maximizing pathway flux is in line with maximizing molar yield while in the cases of high costs, it is not. Expand
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Computing chemical organizations in biological networks
TLDR
MOTIVATION Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. Expand
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Can sugars be produced from fatty acids? A test case for pathway analysis tools
TLDR
MOTIVATION In recent years, several methods have been proposed for determining metabolic pathways in an automated way based on network topology. Expand
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In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans
TLDR
The question whether fatty acids can be converted into glucose in humans has a long standing tradition in biochemistry, and the expected answer is “No”. Expand
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