Evidence map›Paper›PMID 25161236›Full record

ArticleBioinformatics (Oxford, England)2014

Effects of small particle numbers on long-term behaviour in discrete biochemical systems.

Peter Kreyssig, Christian Wozar, Stephan Peter, Tomás Veloz, Bashar Ibrahim, Peter Dittrich

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Goals as Emergent Autopoietic Processes.Frontiers in bioengineering and biotechnology · 2021
    Article
  6. Article
  7. Trends in mathematical modeling of host-pathogen interactions.Cellular and molecular life sciences : CMLS · 2020
    Review
  8. Article
  9. Article
  10. Article
  11. Article
  12. Active transport can greatly enhance Cdc20:Mad2 formation.International journal of molecular sciences · 2014
    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

6 authors.

Peter KreyssigBio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia.
Christian WozarBio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia.
Stephan PeterBio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia.
Tomás VelozBio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia Bio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia Bio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia.
Bashar IbrahimBio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia Bio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia Bio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia.
Peter DittrichBio Systems Analysis Group, Department of Mathematics and Computer Science and Jena Centre for Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany, Mathematics Department, University of British Columbia, Kelowna, BC V1V 1V7, Canada, Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Los Alerces 3024 Ñuñoa, Santiago, Chile, Center Leo Apostel, Vrije Universiteit Brussel, B-1160 Brussels, Belgium, Umm Al-Qura University, 1109 Makkah Al-Mukarramah and Al-Qunfudah Center for Scientific Research (QCSR), 21912 Al-Qunfudah, Kingdom of Saudi Arabia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

motivationThe functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state.

resultsWe provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism. AVAILABILITY AND IMPLEMENTATION: http://www.biosys.uni-jena.de/Services.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Models, BiologicalDatabases, FactualSpindle ApparatusSystems Biology

Identifiers

PMID25161236
PMCPMC4147906

What OpenQuestion holds

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LicenceCC BY-NC
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.