ArticleACS synthetic biology2020
FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data.
Article in ACS synthetic biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers, 1 of them a synthesis that pooled 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.
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
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers.PLoS computational biology · 2022Pooled it
- Making GFP count: a validated framework for absolute protein quantification in precision fermentation.Applied microbiology and biotechnology · 2026Article
- Characterization of Synthetic Gene Circuits with Absolute Quantification in Continuous Culture.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Construction of aACS omega · 2025Article
- Bacterial microcompartment utilization in the human commensalJournal of bacteriology · 2024Article
- A bacteriocin expression platform for targeting pathogenic bacterial species.Nature communications · 2024Article
- Emergent digital bio-computation through spatial diffusion and engineered bacteria.Nature communications · 2024Article
- Data hazards in synthetic biology.Synthetic biology (Oxford, England) · 2024Review
- Parsley: a web app for parsing data from plate readers.Bioinformatics (Oxford, England) · 2023Article
- Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence.Molecular & cellular proteomics : MCP · 2023Article
- PLATERO: A calibration protocol for plate reader green fluorescence measurements.Frontiers in bioengineering and biotechnology · 2023Article
- Advancing reproducibility can ease the 'hard truths' of synthetic biology.Synthetic biology (Oxford, England) · 2023Review
- Absolute protein quantification using fluorescence measurements with FPCountR.Nature communications · 2022Article
- Toehold switch based biosensors for sensing the highly trafficked rosewoodSynthetic and systems biotechnology · 2022Article
- Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system.Biotechnology and bioengineering · 2021Article
- Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes.Trends in biotechnology · 2021Review
- Single strain control of microbial consortia.Nature communications · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
The measurement of gene expression using fluorescence markers has been a cornerstone of synthetic biology for the past two decades. However, the use of arbitrary units has limited the usefulness of these data for many quantitative purposes. Calibration of fluorescence measurements from flow cytometry and plate reader spectrophotometry has been implemented previously, but the tools are disjointed. Here we pull together, and in some cases improve, extant methods into a single software tool, written as a package in the R statistical framework. The workflow is validated using
Indexed as
Identifiers
What OpenQuestion holds
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.