ArticleNature communications2020
Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Single-cell analysis and control of microbial systems using optogenetics.Current opinion in microbiology · 2026Review
- Exploring the computing power of microbes that shapes the environment.Current opinion in microbiology · 2026Review
- Closed-loop optogenetic control of cell biology enables outcome-driven microscopy.Nature communications · 2025Article
- Review
- Protein design accelerates the development and application of optogenetic tools.Computational and structural biotechnology journal · 2025Review
- Image-guided optogenetic spatiotemporal tissue patterning using μPatternScope.Nature communications · 2024Article
- AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis.PLoS computational biology · 2024Article
- Deep model predictive control of gene expression in thousands of single cells.Nature communications · 2024Article
- Quantitative insights in tissue growth and morphogenesis with optogenetics.Physical biology · 2023Review
- Mechanochemical feedback loops in contact-dependent fate patterning.Current opinion in systems biology · 2023Review
- An optogenetic toolkit for light-inducible antibiotic resistance.Nature communications · 2023Article
- The space between us: Modeling spatial heterogeneity in synthetic microbial consortia dynamics.Biophysical reports · 2022Article
- A synthetic synthesis to explore animal evolution and development.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- CyberSco.Py an open-source software for event-based, conditional microscopy.Scientific reports · 2022Article
- Advances and challenges in programming pattern formation using living cells.Current opinion in chemical biology · 2022Review
- Synthetic Morphogenesis: introducing IEEE journal readers to programming living mammalian cells to make structures.Proceedings of the IEEE. Institute of Electrical and Electronics Engineers · 2022Article
- Enabling reactive microscopy with MicroMator.Nature communications · 2022Article
- Platforms for Optogenetic Stimulation and Feedback Control.Frontiers in bioengineering and biotechnology · 2022Review
- A light tunable differentiation system for the creation and control of consortia in yeast.Nature communications · 2021Article
- Cells and computers, better together.Nature reviews. Microbiology · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Designing and implementing synthetic biological pattern formation remains challenging due to underlying theoretical complexity as well as the difficulty of engineering multicellular networks biochemically. Here, we introduce a cell-in-the-loop approach where living cells interact through in silico signaling, establishing a new testbed to interrogate theoretical principles when internal cell dynamics are incorporated rather than modeled. We present an easy-to-use theoretical test to predict the emergence of contrasting patterns in gene expression among laterally inhibiting cells. Guided by the theory, we experimentally demonstrate spontaneous checkerboard patterning in an optogenetic setup, where cell-to-cell signaling is emulated with light inputs calculated in silico from real-time gene expression measurements. The scheme successfully produces spontaneous, persistent checkerboard patterns for systems of sixteen patches, in quantitative agreement with theoretical predictions. Our research highlights how tools from dynamical systems theory may inform our understanding of patterning, and illustrates the potential of cell-in-the-loop for engineering synthetic multicellular systems.
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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.