Barrier Trees for Metabolic Adjustment Landscapes

Christoph Flamm, Chris Hemmingsen, Daniel Merkle

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

We construct and analyze a discrete fitness landscape called metabolic adjustment landscape, from sub-networks covered by different productive flux distributions of a metabolic network. The topological structure of this landscape, i.e., the local minima and saddle points, can be compactly represented as a hierarchical structure called barrier tree. The switching from one local optimal flux pattern to another one is accompanied by adjustment costs, since genes have to be turned on or off. This phenomenon gives raise to saddle points in the
metabolic adjustment landscape. Our approach allows calculating the minimal cost pathway that connects any two local minima in the landscape. Furthermore, our method yields a detailed ordering which reactions have to be (de-)activated to switch from one flux distribution to another one with minimal adjustment costs. Such a mechanistic hypothesis can guide experimental verification. We apply our approaches to a network describing the central carbon metabolism of E. coli.
Original languageEnglish
Title of host publicationProceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems : Advances in Artificial Life
Publication date2013
Pages1151-1158
DOIs
Publication statusPublished - 2013

Fingerprint

cost
fitness
metabolism
gene
carbon
distribution
method

Cite this

Flamm, C., Hemmingsen, C., & Merkle, D. (2013). Barrier Trees for Metabolic Adjustment Landscapes. In Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life (pp. 1151-1158) https://doi.org/10.7551/978-0-262-31709-2-ch175
Flamm, Christoph ; Hemmingsen, Chris ; Merkle, Daniel. / Barrier Trees for Metabolic Adjustment Landscapes. Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life. 2013. pp. 1151-1158
@inproceedings{8e65d69315cf4b05b8da305e01dab0a5,
title = "Barrier Trees for Metabolic Adjustment Landscapes",
abstract = "We construct and analyze a discrete fitness landscape called metabolic adjustment landscape, from sub-networks covered by different productive flux distributions of a metabolic network. The topological structure of this landscape, i.e., the local minima and saddle points, can be compactly represented as a hierarchical structure called barrier tree. The switching from one local optimal flux pattern to another one is accompanied by adjustment costs, since genes have to be turned on or off. This phenomenon gives raise to saddle points in themetabolic adjustment landscape. Our approach allows calculating the minimal cost pathway that connects any two local minima in the landscape. Furthermore, our method yields a detailed ordering which reactions have to be (de-)activated to switch from one flux distribution to another one with minimal adjustment costs. Such a mechanistic hypothesis can guide experimental verification. We apply our approaches to a network describing the central carbon metabolism of E. coli.",
author = "Christoph Flamm and Chris Hemmingsen and Daniel Merkle",
year = "2013",
doi = "10.7551/978-0-262-31709-2-ch175",
language = "English",
pages = "1151--1158",
booktitle = "Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems",

}

Flamm, C, Hemmingsen, C & Merkle, D 2013, Barrier Trees for Metabolic Adjustment Landscapes. in Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life. pp. 1151-1158. https://doi.org/10.7551/978-0-262-31709-2-ch175

Barrier Trees for Metabolic Adjustment Landscapes. / Flamm, Christoph; Hemmingsen, Chris; Merkle, Daniel.

Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life. 2013. p. 1151-1158.

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

TY - GEN

T1 - Barrier Trees for Metabolic Adjustment Landscapes

AU - Flamm, Christoph

AU - Hemmingsen, Chris

AU - Merkle, Daniel

PY - 2013

Y1 - 2013

N2 - We construct and analyze a discrete fitness landscape called metabolic adjustment landscape, from sub-networks covered by different productive flux distributions of a metabolic network. The topological structure of this landscape, i.e., the local minima and saddle points, can be compactly represented as a hierarchical structure called barrier tree. The switching from one local optimal flux pattern to another one is accompanied by adjustment costs, since genes have to be turned on or off. This phenomenon gives raise to saddle points in themetabolic adjustment landscape. Our approach allows calculating the minimal cost pathway that connects any two local minima in the landscape. Furthermore, our method yields a detailed ordering which reactions have to be (de-)activated to switch from one flux distribution to another one with minimal adjustment costs. Such a mechanistic hypothesis can guide experimental verification. We apply our approaches to a network describing the central carbon metabolism of E. coli.

AB - We construct and analyze a discrete fitness landscape called metabolic adjustment landscape, from sub-networks covered by different productive flux distributions of a metabolic network. The topological structure of this landscape, i.e., the local minima and saddle points, can be compactly represented as a hierarchical structure called barrier tree. The switching from one local optimal flux pattern to another one is accompanied by adjustment costs, since genes have to be turned on or off. This phenomenon gives raise to saddle points in themetabolic adjustment landscape. Our approach allows calculating the minimal cost pathway that connects any two local minima in the landscape. Furthermore, our method yields a detailed ordering which reactions have to be (de-)activated to switch from one flux distribution to another one with minimal adjustment costs. Such a mechanistic hypothesis can guide experimental verification. We apply our approaches to a network describing the central carbon metabolism of E. coli.

U2 - 10.7551/978-0-262-31709-2-ch175

DO - 10.7551/978-0-262-31709-2-ch175

M3 - Article in proceedings

SP - 1151

EP - 1158

BT - Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems

ER -

Flamm C, Hemmingsen C, Merkle D. Barrier Trees for Metabolic Adjustment Landscapes. In Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life. 2013. p. 1151-1158 https://doi.org/10.7551/978-0-262-31709-2-ch175