Evidence map›Paper›PMID 24797926›Full record

ReviewAdvances in microbial physiology2014

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 and 5 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Advances in microbial physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. An adaptableMolecular omics · 2024
    Article
  2. Article
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Fiona AchcarInstitute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
Abeer FaddaZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany.
Jurgen R HaanstraDepartment of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands.
Eduard J KerkhovenWellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
Dong-Hyun KimWellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
Alejandro E LerouxBiochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany.
Theodore PapamarkouThe Department of Statistical Science and The Centre for Computational Statistics and Machine Learning University College London, London, United Kingdom.
Federico RojasCentre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.
Barbara M BakkerDepartment of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Michael P BarrettWellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
Christine ClaytonZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany.
Mark GirolamiThe Department of Statistical Science and The Centre for Computational Statistics and Machine Learning University College London, London, United Kingdom.
R Luise Krauth-SiegelBiochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany.
Keith R MatthewsCentre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.
Rainer BreitlingManchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom. Electronic address: rainer.breitling@manchester.ac.uk.

Funding

Biotechnology and Biological Sciences Research Council BB/I004599/1Biotechnology and Biological Sciences Research Council BB/I004602/1Wellcome Trust 104111
6 · The paper itself

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.

Indexed as

Systems BiologyAnimalsGlycolysisHumansProtozoan ProteinsTrypanosoma brucei bruceiTrypanosomiasis, AfricanProtozoan ProteinsDifferential equationsDynamic modellingMetabolomicsSystems biologyTranscriptomicsTrypanosoma bruceiUncertainty

Identifiers

PMID24797926
PMCPMC4773886

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.