Deep model predictive control of gene expression in thousands of single cells
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-024-46361-1
Download full text from publisher
References listed on IDEAS
- Sant Kumar & Marc Rullan & Mustafa Khammash, 2021. "Rapid prototyping and design of cybergenetic single-cell controllers," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
- Sydney M. Shaffer & Margaret C. Dunagin & Stefan R. Torborg & Eduardo A. Torre & Benjamin Emert & Clemens Krepler & Marilda Beqiri & Katrin Sproesser & Patricia A. Brafford & Min Xiao & Elliott Eggan , 2017. "Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance," Nature, Nature, vol. 546(7658), pages 431-435, June.
- Melinda Liu Perkins & Dirk Benzinger & Murat Arcak & Mustafa Khammash, 2020. "Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
- Remy Chait & Jakob Ruess & Tobias Bergmiller & Gašper Tkačik & Călin C. Guet, 2017. "Shaping bacterial population behavior through computer-interfaced control of individual cells," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
- Andreas Milias-Argeitis & Marc Rullan & Stephanie K. Aoki & Peter Buchmann & Mustafa Khammash, 2016. "Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
- Om Patange & Christian Schwall & Matt Jones & Casandra Villava & Douglas A. Griffith & Andrew Phillips & James C. W. Locke, 2018. "Escherichia coli can survive stress by noisy growth modulation," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
- Zachary R. Fox & Steven Fletcher & Achille Fraisse & Chetan Aditya & Sebastián Sosa-Carrillo & Julienne Petit & Sébastien Gilles & François Bertaux & Jakob Ruess & Gregory Batt, 2022. "Enabling reactive microscopy with MicroMator," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Michael B. Sheets & Nathan Tague & Mary J. Dunlop, 2023. "An optogenetic toolkit for light-inducible antibiotic resistance," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Lucas Henrion & Juan Andres Martinez & Vincent Vandenbroucke & Mathéo Delvenne & Samuel Telek & Andrew Zicler & Alexander Grünberger & Frank Delvigne, 2023. "Fitness cost associated with cell phenotypic switching drives population diversification dynamics and controllability," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Joaquín Gutiérrez Mena & Sant Kumar & Mustafa Khammash, 2022. "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Maurice Filo & Sant Kumar & Mustafa Khammash, 2022. "A hierarchy of biomolecular proportional-integral-derivative feedback controllers for robust perfect adaptation and dynamic performance," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- François Bertaux & Sebastián Sosa-Carrillo & Viktoriia Gross & Achille Fraisse & Chetan Aditya & Mariela Furstenheim & Gregory Batt, 2022. "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Sebastián Sosa-Carrillo & Henri Galez & Sara Napolitano & François Bertaux & Gregory Batt, 2023. "Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Zachary R. Fox & Steven Fletcher & Achille Fraisse & Chetan Aditya & Sebastián Sosa-Carrillo & Julienne Petit & Sébastien Gilles & François Bertaux & Jakob Ruess & Gregory Batt, 2022. "Enabling reactive microscopy with MicroMator," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
- Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Jun Dai & Shuyu Zheng & Matías M. Falco & Jie Bao & Johanna Eriksson & Sanna Pikkusaari & Sofia Forstén & Jing Jiang & Wenyu Wang & Luping Gao & Fernando Perez-Villatoro & Olli Dufva & Khalid Saeed & , 2024. "Tracing back primed resistance in cancer via sister cells," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Franziska Haderk & Yu-Ting Chou & Lauren Cech & Celia Fernández-Méndez & Johnny Yu & Victor Olivas & Ismail M. Meraz & Dora Barbosa Rabago & D. Lucas Kerr & Carlos Gomez & David V. Allegakoen & Juan G, 2024. "Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Singh, Abhyudai & Vahdat, Zahra & Xu, Zikai, 2019. "Time-triggered stochastic hybrid systems with two timer-dependent resets," OSF Preprints u8fzg, Center for Open Science.
- Xue Zhang & Shishir M. Pant & Cecily C. Ritch & Hsin-Yao Tang & Hongguang Shao & Harsh Dweep & Yao-Yu Gong & Rebekah Brooks & Patricia Brafford & Adam J. Wolpaw & Yool Lee & Ashani Weeraratna & Amita , 2024. "Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Heike Chauvistré & Batool Shannan & Sheena M. Daignault-Mill & Robert J. Ju & Daniel Picard & Stefanie Egetemaier & Renáta Váraljai & Christine S. Gibhardt & Antonio Sechi & Farnusch Kaschani & Oliver, 2022. "Persister state-directed transitioning and vulnerability in melanoma," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Jonathan Liu & Donald Hansen & Elizabeth Eck & Yang Joon Kim & Meghan Turner & Simon Alamos & Hernan Garcia, 2021. "Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage," PLOS Computational Biology, Public Library of Science, vol. 17(5), pages 1-26, May.
- Jaishree Tripathi & Lei Zhu & Sourav Nayak & Michal Stoklasa & Zbynek Bozdech, 2022. "Stochastic expression of invasion genes in Plasmodium falciparum schizonts," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Caitlin E. Mills & Kartik Subramanian & Marc Hafner & Mario Niepel & Luca Gerosa & Mirra Chung & Chiara Victor & Benjamin Gaudio & Clarence Yapp & Ajit J. Nirmal & Nicholas Clark & Peter K. Sorger, 2022. "Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Zhou Fang & Ankit Gupta & Sant Kumar & Mustafa Khammash, 2024. "Advanced methods for gene network identification and noise decomposition from single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Xinrui Zhou & Wan Yi Seow & Norbert Ha & Teh How Cheng & Lingfan Jiang & Jeeranan Boonruangkan & Jolene Jie Lin Goh & Shyam Prabhakar & Nigel Chou & Kok Hao Chen, 2024. "Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- G. Gambardella & G. Viscido & B. Tumaini & A. Isacchi & R. Bosotti & D. di Bernardo, 2022. "A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Anđela Davidović & Remy Chait & Gregory Batt & Jakob Ruess, 2022. "Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level," PLOS Computational Biology, Public Library of Science, vol. 18(3), pages 1-22, March.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46361-1. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.