Daniel Thedie

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About Daniel Thedie:

Research Software Engineer in the Biological Research Data Management team (BioRDM) at the University of Edinburgh.

SEEK ID: https://fairdomhub.org/people/2847

Location: United Kingdom

ORCID: https://orcid.org/0000-0002-1352-7245

Joined: 19th May 2026

Expertise: Data Management, Python, R, Programming, microscopy, fluorescence protein fusions, Software Engineering

Tools: Data Management, Python, R, Fluorescence and confocal microscopy, Time-lapse fluorescence microscopy Flow cytometry, Fluorecence based reporter gene analyses/single cell analyses

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Centre for Engineering Biology (prev. SynthSys)

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

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BioDare1

Experiment data previously hosted on the original version of BioDare (biodare.ed.ac.uk).

Programme: Centre for Engineering Biology (prev. SynthSys)

Public web page: Not specified

Organisms: Not specified

Millar group

Andrew Millar's research group, University of Edinburgh

Programme: Centre for Engineering Biology (prev. SynthSys)

Public web page: http://www.amillar.org

Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri

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University of Edinburgh

ROR ID: Not specified

Department: Not specified

Country: United Kingdom

City: Edinburgh

Web page: http://www.ed.ac.uk/

School of Biological Sciences, University of Edinburgh

ROR ID: https://ror.org/https://ror.org/01nrxwf90

Department: School of Biological Sciences

Country: United Kingdom

City: Edinburgh

Web page: https://www.ed.ac.uk

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Flis, Anna

BioDare1

Collection of experiments created by Flis, Anna on the original BioDare and automatically transferred to FAIRDOM Hub.

Submitter: Daniel Thedie

Studies: Flis et al. (2025)

Assays: TiMet WP1.1 qRT-PCR LD to LL and LD

Snapshots: No snapshots

Created: 5th Jun 2026 at 16:17

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Flis et al. (2025)

BioDare1

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

Flis et al. (2025)

DOI: 10.1098/rsob.150042

Submitter: Daniel Thedie

Investigation: Flis, Anna

Assays: TiMet WP1.1 qRT-PCR LD to LL and LD

Snapshots: No snapshots

Created: 5th Jun 2026 at 16:18

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TiMet WP1.1 qRT-PCR LD to LL and LD

BioDare1

TiMet WP1.1 qRT-PCR LD to LL and LD

Property	Value
BioDare ID	2841
Author	Anna Flis
Institution	MPI of Molecular Plant Physiology, Golm, Germany
License	CC_BY

Description

2 WT (Col, Ws) and 5 clock mutants, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvest every 2 hours. Numbers are in transcript copy per cell, obtained ...

Submitter: Daniel Thedie

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Flis, Anna

Study: Flis et al. (2025)

Organisms: No organisms

SOPs: No SOPs

Data files: Metadata, Primers_TiMet_AnnaFlis2013, RNA LD to Both LL and DD, Readme, Sample_list

Snapshots: No snapshots

Created: 5th Jun 2026 at 16:18, Last updated: 5th Jun 2026 at 16:19

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Primers_TiMet_AnnaFlis2013

BioDare1

Primers_TiMet_AnnaFlis2013 (from BioDare)

Creator: Anna Flis

Submitter: Daniel Thedie

Investigations: Flis, Anna

Studies: Flis et al. (2025)

Assays: TiMet WP1.1 qRT-PCR LD to LL and LD

Download

Created: 5th Jun 2026 at 16:19, Last updated: 5th Jun 2026 at 16:20

RNA LD to Both LL and DD

BioDare1

RNA LD to Both LL and DD (from BioDare)

Creator: Anna Flis

Submitter: Daniel Thedie

Investigations: Flis, Anna

Studies: Flis et al. (2025)

Assays: TiMet WP1.1 qRT-PCR LD to LL and LD

Download

Created: 5th Jun 2026 at 16:19, Last updated: 5th Jun 2026 at 16:19

Sample_list

BioDare1

List of samples used in the assay (extracted from original BioDare metadata and converted to csv)

Creator: Anna Flis

Submitter: Daniel Thedie

Investigations: Flis, Anna

Studies: Flis et al. (2025)

Assays: TiMet WP1.1 qRT-PCR LD to LL and LD

Download

Created: 5th Jun 2026 at 16:19, Last updated: 5th Jun 2026 at 16:19

Metadata

BioDare1

Original BioDare metadata, converted to json format

Creator: Anna Flis

Submitter: Daniel Thedie

Investigations: Flis, Anna

Studies: Flis et al. (2025)

Assays: TiMet WP1.1 qRT-PCR LD to LL and LD

Download

Created: 5th Jun 2026 at 16:18, Last updated: 5th Jun 2026 at 16:19

Readme

BioDare1

Readme file

Creator: Anna Flis

Submitter: Daniel Thedie

Investigations: Flis, Anna

Studies: Flis et al. (2025)

Assays: TiMet WP1.1 qRT-PCR LD to LL and LD

Download

Created: 5th Jun 2026 at 16:18, Last updated: 5th Jun 2026 at 16:18

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The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

BioDare1

(Show All)

Abstract (Expand)

Abstract Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators …

Authors: Yin Hoon Chew, Daniel D Seaton, Virginie Mengin, Anna Flis, Sam T Mugford, Gavin M George, Michael Moulin, Alastair Hume, Samuel C Zeeman, Teresa B Fitzpatrick, Alison M Smith, Mark Stitt, Andrew J Millar

Date Published: 30th May 2022

Publication Type: Journal Article

DOI: 10.1093/insilicoplants/diac010

Citation: in silico Plants 4(2):diac010.

Created: 8th Jun 2026 at 14:32, Last updated: 8th Jun 2026 at 14:35

Photoperiod‐dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis

BioDare1

Abstract (Expand)

AbstractPlants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light‐sensitive clock output coincides with light …

Authors: Anna Flis, Ronan Sulpice, Daniel D. Seaton, Alexander A. Ivakov, Magda Liput, Christin Abel, Andrew J. Millar, Mark Stitt

Date Published: 15th Jul 2016

Publication Type: Journal Article

DOI: 10.1111/pce.12754

Citation: Plant Cell & Environment 39(9):1955-1981.

Created: 8th Jun 2026 at 14:29

Changing planetary rotation rescues the biological clock mutant lhy cca1 of Arabidopsis thaliana

BioDare1

Abstract (Expand)

Background: Pervasive, 24-hour rhythms from the biological clock affect diverse biological processes in metabolism and behaviour, including the human cell division cycle and sleep-wake cycle, nightly … transpiration and energy balance in plants, and seasonal breeding in both plants and animals. The clock mechanism in the laboratory model plant species Arabidopsis thaliana is complex, in part due to the multiple interlocking, negative feedback loops that link the clock genes. Clock gene mutants are powerful tools to manipulate and understand the clock mechanism and its effects on physiology. The LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK ASSOCIATED 1 genes encode dawn-expressed, Myb-related repressor proteins that delay the expression of other clock genes until late in the day. Double mutant plants (lhy cca1) have low-amplitude, short-period rhythms that have been used in multiple studies of the plant circadian clock. Results: We used in vivo imaging of several luciferase (LUC) reporter genes to test how the rhythmic gene expression of wild-type and lhy cca1 mutant plants responded to light:dark cycles. Red, blue and red+blue light were similarly able to entrain these gene expression rhythms. The timing of expression rhythms in double mutant plants showed little or no response to the duration of light under 24h light:dark cycles (dusk sensitivity), in contrast to the wild type. As the period of the mutant clock is about 18h, we tested light:dark cycles of different duration (T cycles), simulating altered rotation of planet Earth. lhy cca1 double mutants regained as much dusk sensitivity in 20h T cycles as the wild type in 24h cycles, though the phase of the rhythm in the mutants was much earlier than wild type. The severe, triple lhy cca1 gi mutants also regained dusk sensitivity in 20h cycles. The double mutant showed some dusk sensitivity under 28h cycles. lhy cca1 double mutants under 28h cycles with short photoperiods, however, had the same apparent phase as wild-type plants. Conclusion: Simulating altered planetary rotation with light:dark cycles can reveal normal circadian performance in clock mutants that have been described as arrhythmic under standard conditions. The features rescued here comprise a dynamic behaviour (apparent phase under 28h cycles) and a dynamic property (dusk sensitivity under 20h cycles). These conditional clock phenotypes indicate that parts of the clock mechanism continue to function independently of LHY and CCA1, despite the major role of these genes in wild-type plants under standard conditions. Accessibility: Most results here will be published only in this format, citable by the DOI. Data and analysis are publicly accessible on the BioDare resource (www.biodare.ed.ac.uk), as detailed in the links below. Transgenic lines are linked to Stock Centre IDs below (Table 7).

Authors: Andrew J. Millar, Jamie T. Carrington, Wei Ven Tee, Sarah K. Hodge

Date Published: 17th Dec 2015

Publication Type: Preprint

DOI: 10.1101/034629

Citation: Preprint. https://doi.org/10.1101/034629

Created: 8th Jun 2026 at 14:37

Light and circadian regulation of clock components aids flexible responses to environmental signals

BioDare1

Abstract (Expand)

Summary The circadian clock measures time across a 24 h period, increasing fitness by phasing biological processes to the most appropriate time of day. The interlocking feedback loop mechanism of the …

Authors: Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar

Date Published: 20th May 2014

Publication Type: Journal Article

DOI: 10.1111/nph.12853

Citation: New Phytologist 203(2):568-577.

Created: 8th Jun 2026 at 14:35, Last updated: 8th Jun 2026 at 14:36

Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf

BioDare1

Abstract (Expand)

The circadian clocks that drive daily rhythms in animals are tightly coupled among the cells of some tissues. The coupling profoundly affects cellular rhythmicity and is central to contemporary …

Authors: Bénédicte Wenden, David L. K. Toner, Sarah K. Hodge, Ramon Grima, Andrew J. Millar

Date Published: 10th Apr 2012

Publication Type: Journal Article

DOI: 10.1073/pnas.1118814109

Citation: Proc. Natl. Acad. Sci. U.S.A. 109(17):6757-6762.

Created: 8th Jun 2026 at 14:36, Last updated: 8th Jun 2026 at 14:36

Quantitative analysis of regulatory flexibility under changing environmental conditions

BioDare1

Abstract

Not specified

Authors: Kieron D Edwards, Ozgur E Akman, Kirsten Knox, Peter J Lumsden, Adrian W Thomson, Paul E Brown, Alexandra Pokhilko, Laszlo Kozma‐Bognar, Ferenc Nagy, David A Rand, Andrew J Millar

Date Published: 2nd Nov 2010

Publication Type: Journal Article

DOI: 10.1038/msb.2010.81

Citation: Mol Syst Biol 6(1):MSB201081.

Created: 8th Jun 2026 at 14:33