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

Fiona Achcar, Abeer A. 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: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)115-143
Number of pages29
JournalAdvances in Microbial Physiology
Volume64
DOIs
Publication statusPublished - 2014
Externally publishedYes

Fingerprint

African Trypanosomiasis
Systems Biology
Trypanosomiasis
Silicon
Parasites
Trypanosoma brucei brucei
Glycolysis
Uncertainty

Keywords

  • Differential equations
  • Dynamic modelling
  • Metabolomics
  • Systems biology
  • Transcriptomics
  • Trypanosoma brucei
  • Uncertainty

ASJC Scopus subject areas

  • Microbiology
  • Physiology

Cite this

The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology. / Achcar, Fiona; Fadda, Abeer A.; Haanstra, Jurgen R.; Kerkhoven, Eduard J.; Kim, Dong Hyun; Leroux, Alejandro E.; Papamarkou, Theodore; Rojas, Federico; Bakker, Barbara M.; Barrett, Michael P.; Clayton, Christine; Girolami, Mark; Krauth-Siegel, R. Luise; Matthews, Keith R.; Breitling, Rainer.

In: Advances in Microbial Physiology, Vol. 64, 2014, p. 115-143.

Research output: Contribution to journalArticle

Achcar, F, Fadda, AA, 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
Achcar, Fiona ; Fadda, Abeer A. ; Haanstra, Jurgen R. ; Kerkhoven, Eduard J. ; Kim, Dong Hyun ; Leroux, Alejandro E. ; Papamarkou, Theodore ; Rojas, Federico ; Bakker, Barbara M. ; Barrett, Michael P. ; Clayton, Christine ; Girolami, Mark ; Krauth-Siegel, R. Luise ; Matthews, Keith R. ; Breitling, Rainer. / The Silicon Trypanosome. A Test Case of Iterative Model Extension in Systems Biology. In: Advances in Microbial Physiology. 2014 ; Vol. 64. pp. 115-143.
@article{bf1163cfaa784727953f869c47675f1b,
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 = "Differential equations, Dynamic modelling, Metabolomics, Systems biology, Transcriptomics, Trypanosoma brucei, Uncertainty",
author = "Fiona Achcar and Fadda, {Abeer A.} 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",
journal = "Advances in Microbial Physiology",
issn = "0065-2911",
publisher = "Academic Press Inc.",

}

TY - JOUR

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

AU - Achcar, Fiona

AU - Fadda, Abeer A.

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.

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 - Differential equations

KW - Dynamic modelling

KW - Metabolomics

KW - Systems biology

KW - Transcriptomics

KW - Trypanosoma brucei

KW - Uncertainty

UR - http://www.scopus.com/inward/record.url?scp=84899678173&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84899678173&partnerID=8YFLogxK

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

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

M3 - Article

C2 - 24797926

AN - SCOPUS:84899678173

VL - 64

SP - 115

EP - 143

JO - Advances in Microbial Physiology

JF - Advances in Microbial Physiology

SN - 0065-2911

ER -