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

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

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.

Original language	English
Pages (from-to)	115-43
Number of pages	29
Journal	Advances in microbial physiology
Volume	64
DOIs	https://doi.org/10.1016/B978-0-12-800143-1.00003-8
Publication status	Published - 4 May 2014

Keywords / Materials (for Non-textual outputs)

animals
glycolysis
humans
protozoan proteins
systems Biology
trypanosoma brucei brucei
trypanosomiasis
African

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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. Advances in microbial physiology, 64, 115-43. 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.",

keywords = "animals, glycolysis, humans, protozoan proteins, systems Biology, trypanosoma brucei brucei, trypanosomiasis, African",

author = "Fiona Achcar and Abeer Fadda and Haanstra, {Jurgen R} and Kerkhoven, {Eduard J} and Dong-Hyun Kim 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",

month = may,

day = "4",

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

language = "English",

volume = "64",

pages = "115--43",

journal = "Advances in microbial physiology",

issn = "0065-2911",

publisher = "Academic Press",

}

Achcar, F, Fadda, A, Haanstra, JR, Kerkhoven, EJ, Kim, D-H, 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', Advances in microbial physiology, vol. 64, pp. 115-43. https://doi.org/10.1016/B978-0-12-800143-1.00003-8

TY - JOUR

T1 - The silicon trypanosome

T2 - 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 - 2014/5/4

Y1 - 2014/5/4

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.

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.

KW - animals

KW - glycolysis

KW - humans

KW - protozoan proteins

KW - systems Biology

KW - trypanosoma brucei brucei

KW - trypanosomiasis

KW - African

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

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

M3 - Article

C2 - 24797926

SN - 0065-2911

VL - 64

SP - 115

EP - 143

JO - Advances in microbial physiology

JF - Advances in microbial physiology

ER -

The silicon trypanosome: A test case of iterative model extension in systems biology

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Keywords / Materials (for Non-textual outputs)

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