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

Biomedical and Life Sciences

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The silicon trypanosome: a test case of iterative model extension in systems biology. / Achcar, F; Fadda, A; Haanstra, JR et al.
In: Advances in Microbial Physiology, Vol. 64, 31.05.2014, p. 115-143.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Harvard

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.', Advances in Microbial Physiology, vol. 64, pp. 115-143. https://doi.org/10.1016/B978-0-12-800143-1.00003-8

APA

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, 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, 115-143. https://doi.org/10.1016/B978-0-12-800143-1.00003-8

Vancouver

Achcar F, Fadda A, Haanstra JR, Kerkhoven EJ, Kim DH, Leroux AE et al. The silicon trypanosome: a test case of iterative model extension in systems biology. Advances in Microbial Physiology. 2014 May 31;64:115-143. doi: 10.1016/B978-0-12-800143-1.00003-8

Author

Achcar, F ; Fadda, A ; Haanstra, JR et al. / The silicon trypanosome: a test case of iterative model extension in systems biology. In: Advances in Microbial Physiology. 2014 ; Vol. 64. pp. 115-143.

Bibtex

@article{b640922c0df94cfebf88f28aa88eb99f,

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

author = "F Achcar and A Fadda and JR Haanstra and EJ Kerkhoven and DH Kim and AE Leroux and T Papamarkou and F Rojas and BM Bakker and MP Barrett and C Clayton and M Girolami and R.L. Krauth-Siegel and Matthews, {Keith R.} and R Breitling",

year = "2014",

month = may,

day = "31",

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

language = "English",

volume = "64",

pages = "115--143",

journal = "Advances in Microbial Physiology",

issn = "0065-2911",

publisher = "Academic Press Inc.",

}

RIS

TY - JOUR

T1 - The silicon trypanosome: a test case of iterative model extension in systems biology.

AU - Achcar, F

AU - Fadda, A

AU - Haanstra, JR

AU - Kerkhoven, EJ

AU - Kim, DH

AU - Leroux, AE

AU - Papamarkou, T

AU - Rojas, F

AU - Bakker, BM

AU - Barrett, MP

AU - Clayton, C

AU - Girolami, M

AU - Krauth-Siegel, R.L.

AU - Matthews, Keith R.

AU - Breitling, R

PY - 2014/5/31

Y1 - 2014/5/31

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 - Dynamic modelling

KW - Uncertainty

KW - Metabolomics

KW - Transcriptomics

KW - Trypanosoma brucei

KW - Systems biology

KW - Differential equations

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

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

M3 - Journal article

C2 - 24797926

VL - 64

SP - 115

EP - 143

JO - Advances in Microbial Physiology

JF - Advances in Microbial Physiology

SN - 0065-2911

ER -

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