ArticleSTAR protocols2021
Building predictive signaling models by perturbing yeast cells with time-varying stimulations resulting in distinct signaling responses.
Article in STAR protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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.
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.
Who cites it
7 citing papers in PubMed.
- DANSE: a pipeline for dynamic modelling of time-series multi-omics data.BMC bioinformatics · 2025Article
- TrueSpot: a robust automated tool for quantifying signal puncta in fluorescent imaging.Genome biology · 2025Article
- Measuring Regulatory Network Inheritance in Dividing Yeast Cells Using Ordinary Differential Equations.bioRxiv : the preprint server for biology · 2025Article
- TrueSpot: A robust automated tool for quantifying signal puncta in fluorescent imaging.bioRxiv : the preprint server for biology · 2025Article
- Article
- Phenotypic consequences of logarithmic signaling in MAPK stress response.bioRxiv : the preprint server for biology · 2023Article
- Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments.Frontiers in cell and developmental biology · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
This protocol provides a step-by-step approach to perturb single cells with time-varying stimulation profiles, collect distinct signaling responses, and use these to infer a system of ordinary differential equations to capture and predict dynamics of protein-protein regulation in signal transduction pathways. The models are validated by predicting the signaling activation upon new cell stimulation conditions. In comparison to using standard step-like stimulations, application of diverse time-varying cell stimulations results in better inference of model parameters and substantially improves model predictions. For complete details on the use and results of this protocol, please refer to Jashnsaz et al. (2020).
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Registered trials
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.