The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology.

Fiona Achcar; Abeer Fadda; Jurgen R. Haanstra; Eduard J. Kerkhoven; Dong Hyun Kim; Alejandro E. Leroux; Theodore Papamarkou; Federico Rojas; Barbara M. Bakker; Michael P. Barrett; Christine Clayton; Mark Girolami; R. Luise Krauth-Siegel; Keith R. Matthews; Rainer Breitling

doi:10.1016/B978-0-12-800143-1.00003-8

The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology.

Fiona Achcar, Abeer Fadda, Jurgen R. Haanstra, Eduard J. Kerkhoven, Dong Hyun Kim, Alejandro E. Leroux, Theodore Papamarkou, Federico Rojas, Barbara M. Bakker, Michael P. Barrett, Christine Clayton, Mark Girolami, R. Luise Krauth-Siegel, Keith R. Matthews, Rainer Breitling

Research output: Chapter in Book/Conference proceeding › Chapter

Abstract

The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology. © 2014 Elsevier Ltd.

Original language	English
Title of host publication	Advances in Microbial Physiology\|Adv. Microb. Physiol.
Publisher	Academic Press, Ltd
Pages	115-143
Number of pages	28
Volume	64
DOIs	https://doi.org/10.1016/B978-0-12-800143-1.00003-8
Publication status	Published - 2014

Keywords

Differential equations
Dynamic modelling
Metabolomics
Systems biology
Transcriptomics
Trypanosoma brucei
Uncertainty

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10.1016/B978-0-12-800143-1.00003-8

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Achcar, F., Fadda, A., Haanstra, J. R., Kerkhoven, E. J., Kim, D. H., Leroux, A. E., Papamarkou, T., Rojas, F., Bakker, B. M., Barrett, M. P., Clayton, C., Girolami, M., Krauth-Siegel, R. L., Matthews, K. R., & Breitling, R. (2014). The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology. In Advances in Microbial Physiology|Adv. Microb. Physiol. (Vol. 64, pp. 115-143). Academic Press, Ltd. https://doi.org/10.1016/B978-0-12-800143-1.00003-8

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title = "The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology.",

abstract = "The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology. {\textcopyright} 2014 Elsevier Ltd.",

keywords = "Differential equations, Dynamic modelling, Metabolomics, Systems biology, Transcriptomics, Trypanosoma brucei, Uncertainty",

author = "Fiona Achcar and Abeer Fadda and Haanstra, {Jurgen R.} and Kerkhoven, {Eduard J.} and Kim, {Dong Hyun} and Leroux, {Alejandro E.} and Theodore Papamarkou and Federico Rojas and Bakker, {Barbara M.} and Barrett, {Michael P.} and Christine Clayton and Mark Girolami and Krauth-Siegel, {R. Luise} and Matthews, {Keith R.} and Rainer Breitling",

year = "2014",

doi = "10.1016/B978-0-12-800143-1.00003-8",

language = "English",

volume = "64",

pages = "115--143",

booktitle = "Advances in Microbial Physiology|Adv. Microb. Physiol.",

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Achcar, F, Fadda, A, Haanstra, JR, Kerkhoven, EJ, Kim, DH, Leroux, AE, Papamarkou, T, Rojas, F, Bakker, BM, Barrett, MP, Clayton, C, Girolami, M, Krauth-Siegel, RL, Matthews, KR & Breitling, R 2014, The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology. in Advances in Microbial Physiology|Adv. Microb. Physiol.. vol. 64, Academic Press, Ltd, pp. 115-143. https://doi.org/10.1016/B978-0-12-800143-1.00003-8

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T1 - The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology.

AU - Achcar, Fiona

AU - Fadda, Abeer

AU - Haanstra, Jurgen R.

AU - Kerkhoven, Eduard J.

AU - Kim, Dong Hyun

AU - Leroux, Alejandro E.

AU - Papamarkou, Theodore

AU - Rojas, Federico

AU - Bakker, Barbara M.

AU - Barrett, Michael P.

AU - Clayton, Christine

AU - Girolami, Mark

AU - Krauth-Siegel, R. Luise

AU - Matthews, Keith R.

AU - Breitling, Rainer

PY - 2014

Y1 - 2014

N2 - The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology. © 2014 Elsevier Ltd.

AB - The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology. © 2014 Elsevier Ltd.

KW - Differential equations

KW - Dynamic modelling

KW - Metabolomics

KW - Systems biology

KW - Transcriptomics

KW - Trypanosoma brucei

KW - Uncertainty

U2 - 10.1016/B978-0-12-800143-1.00003-8

DO - 10.1016/B978-0-12-800143-1.00003-8

M3 - Chapter

VL - 64

SP - 115

EP - 143

BT - Advances in Microbial Physiology|Adv. Microb. Physiol.

PB - Academic Press, Ltd

ER -

The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology.

Abstract

Keywords

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