Algebra, Geometry and Topology of ERK Kinetics.

Lewis Marsh, Emilie Dufresne, Helen M Byrne, Heather A Harrington

Open access · hybridAbstract read

In one paragraph

Article in Bulletin of mathematical biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

0.9field-weighted citation impact, top 24% of its field

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

1 citing paper in PubMed, 6 citations in OpenAlex.

Simulating BRAFV600E-MEK-ERK signalling dynamics in response to vertical inhibition treatment strategies.NPJ systems biology and applications · 2024
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

4 authors at 2 institutions in 2 countries.

Lewis MarshMathematical Institute, University of Oxford, Oxford, UK. lewis.marsh@maths.ox.ac.uk.ORCID http://orcid.org/0000-0002-6740-8436

Emilie DufresneDepartment of Mathematics, The University of York, York, UK.

Helen M ByrneMathematical Institute, University of Oxford, Oxford, UK.

Heather A HarringtonMathematical Institute, University of Oxford, Oxford, UK.

University of Oxford · GBUniversity of York · GB

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The MEK/ERK signalling pathway is involved in cell division, cell specialisation, survival and cell death (Shaul and Seger in Biochim Biophys Acta (BBA)-Mol Cell Res 1773(8):1213-1226, 2007). Here we study a polynomial dynamical system describing the dynamics of MEK/ERK proposed by Yeung et al. (Curr Biol 2019, https://doi.org/10.1016/j.cub.2019.12.052 ) with their experimental setup, data and known biological information. The experimental dataset is a time-course of ERK measurements in different phosphorylation states following activation of either wild-type MEK or MEK mutations associated with cancer or developmental defects. We demonstrate how methods from computational algebraic geometry, differential algebra, Bayesian statistics and computational algebraic topology can inform the model reduction, identification and parameter inference of MEK variants, respectively. Throughout, we show how this algebraic viewpoint offers a rigorous and systematic analysis of such models.

Indexed as

Mathematical ConceptsModels, BiologicalBayes TheoremKineticsMAP Kinase Signaling SystemMitogen-Activated Protein Kinase KinasesPhosphorylationMitogen-Activated Protein Kinase KinasesAlgebraic model reduction and identificationSystems biologyTopological data analysis

Identifiers

PMID36273372

DOI10.1007/s11538-022-01088-2

PMCPMC9588486

OpenAlexW3216549283

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

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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.