U2020.4 equations in PDF Version 1
PDF of U2020.4 equations
SEEK ID: https://fairdomhub.org/documents/4174?version=1
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U2020.4.pdf
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Created: 9th Apr 2023 at 06:36
Last updated: 19th Dec 2024 at 11:29
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Version 1 (earliest) Created 9th Apr 2023 at 06:36 by Uriel Urquiza-Garcia
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Projects: Millar group, PlaSMo model repository, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, Light and plant development, Light control of leaf development, Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
Institutions: University of Edinburgh, Heinrich Heine University of Düsseldorf
https://orcid.org/0000-0002-7975-5013
Group Leader in Plant Synthetic Genomics at Heinrich Heine University Düsseldorf and the Cluster of Excellence on Plant Sciences (CEPLAS). My research develops the genetic and cellular methods required for synthetic plant chromosomes to function in living cells — including telomere seeding, neocentromere activation, and heritable gene expression — using Physcomitrium patens as a programmable plant chassis. I use the circadian clock as a quantitative test system to test whether complex gene ...
The Centre for Engineering Biology is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2023 as the successor to SynthSys, itself founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE). CSBE was newly founded in 2007. The Centre for Engineering Biology is a hub organisation that links across multiple, major funding awards, including an Engineering Biology Mission Hub, and EPSRC C-loop.
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository, BioDare1
Web page: https://biology.ed.ac.uk/centre-engineering-biology
Andrew Millar's research group, University of Edinburgh
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: http://www.amillar.org
The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025 doi 10.1038/s44320-025-00086-5.
Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted ...
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Studies: Construction of NanoLUC-tagged plants, Estimating DNA-binding affinities for Arabidopsis proteins, Measuring absolute levels of clock proteins with calibrated NanoLUC assays, Predicting absolute levels of clock proteins with a simple model, Recalibrating the clock models for absolute protein levels, to create mo..., Reproducibility documentation
Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, Gatway maps of genomic regions of clock genes, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi..., Jupyter notebook Predicting Protein Numbers, Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Protein level time series, Python packages, Reproducibility tool set, Selection of complemented transgenic lines, TiMet RNA timeseries data, promoter binding affinity calculations on the genome based on PBMs and E...
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Investigation: Absolute units for proteins in Arabidopsis cloc...
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Jupyter lab notebook that contains the models and data that for predicting protein levels based on mRNA data from TiMet projecto
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Biological problem addressed: Model Analysis Type
Investigation: Absolute units for proteins in Arabidopsis cloc...
