General

Benisch, Moritz, Stephanie K Aoki, and Mustafa Khammash. “Unlocking the Potential of Optogenetics in Microbial Applications.” Current Opinion in Microbiology 77 (2024): 102404. https://doi.org/10.1016/j.mib.2023.102404. Download

Holland, Ian, Wenmiao Shu, and Jamie A Davies. “Stratified Tissue Biofabrication by Rotational Internal Flow Layer Engineering.” Biofabrication 15, no. 4 (October 1, 2023): 045003. https://doi.org/10.1088/1758-5090/ace2ed. Download

Davies, Jamie, and Michael Levin. “Synthetic Morphology with Agential Materials.” Nature Reviews Bioengineering 1, no. 1 (January 19, 2023): 46–59. https://doi.org/10.1038/s44222-022-00001-9. Download

Pietsch, Jessica, Anna Deneer, Christian Fleck, and Martin Hülskamp. “Comparative Expression Analysis in Three Brassicaceae Species Revealed Compensatory Changes of the Underlying Gene Regulatory Network.” Frontiers in Plant Science 13 (January 4, 2023): 1086004. https://doi.org/10.3389/fpls.2022.1086004. Download

Pleyer, Jonas, and Christian Fleck. “Agent-Based Models in Cellular Systems.” Frontiers in Physics 10 (January 4, 2023): 968409. https://doi.org/10.3389/fphy.2022.968409. Download

Kumar, Sant, Stanislav Anastassov, Stephanie K. Aoki, Johannes Falkenstein, Ching-Hsiang Chang, Timothy Frei, Peter Buchmann, Paul Argast, and Mustafa Khammash. “Diya – A Universal Light Illumination Platform for Multiwell Plate Cultures.” IScience 26, no. 10 (2023): 107862. https://doi.org/10.1016/j.isci.2023.107862. Download

Jang, Jaewan, Kun Tang, Jeffrey Youn, Sherin McDonald, Hannes M. Beyer, Matias D. Zurbriggen, Maruti Uppalapati, and G. Andrew Woolley. “Engineering of Bidirectional, Cyanobacteriochrome-Based Light-Inducible Dimers (BICYCL)s.” Nature Methods 20, no. 3 (2023): 432–41. https://doi.org/10.1038/s41592-023-01764-8. Download

Kumar, Sant, and Mustafa Khammash. “Platforms for Optogenetic Stimulation and Feedback Control.” Frontiers in Bioengineering and Biotechnology 10 (June 8, 2022): 918917. https://doi.org/10.3389/fbioe.2022.918917. Download

Jamie A. Davies. “Synthetic Morphogenesis: Introducing IEEE Journal Readers to Programming Living Mammalian Cells to Make Structures.” Proceedings of the IEEE 110, no. 5 (May 2022): 688–707. https://doi.org/10.1109/JPROC.2021.3137077. Download

McKenzie, Rebecca E, Emma M Keizer, Jochem N A Vink, Jasper van Lopik, Ferhat Büke, Vera Kalkman, Christian Fleck, Sander J Tans, and Stan J J Brouns. “Single Cell Variability of CRISPR‐Cas Interference and Adaptation.” Molecular Systems Biology 18, no. 4 (April 1, 2022). https://doi.org/10.15252/msb.202110680. Download

Kun Tang, Hannes M. Beyer, Matias D. Zurbriggen, and Wolfgang Gärtner. “The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters.” Chemical Reviews 121, no. 24 (December 22, 2021): 14906–56. https://doi.org/10.1021/acs.chemrev.1c00194. Download

Kumar, Sant, Marc Rullan, and Mustafa Khammash. “Rapid Prototyping and Design of Cybergenetic Single-Cell Controllers.” Nature Communications 12, no. 1 (September 24, 2021): 5651. https://doi.org/10.1038/s41467-021-25754-6. Download

Jamie A. Davies, Mona Elhendawi, Anwar A. Palakkan, and May Sallam. “Renal Engineering: Strategies to Address the Problem of the Ureter.” Current Opinion in Biomedical Engineering 20 (2021): 100334. https://doi.org/10.1016/j.cobme.2021.100334. Download

Romano, Edoardo, Armin Baumschlager, Emir Bora Akmeriç, Navaneethan Palanisamy, Moustafa Houmani, Gregor Schmidt, Mehmet Ali Öztürk, Leonard Ernst, Mustafa Khammash, and Barbara Di Ventura. “Engineering AraC to Make It Responsive to Light Instead of Arabinose.” Nature Chemical Biology 17, no. 7 (2021): 817–27. https://doi.org/10.1038/s41589-021-00787-6. Download

Blomeier, Tim, Patrick Fischbach, Leonie‐Alexa Koch, Jennifer Andres, Miguel Miñambres, Hannes Michael Beyer, and Matias Daniel Zurbriggen. “Blue Light‐Operated CRISPR/Cas13b‐Mediated MRNA Knockdown (Lockdown).” Advanced Biology 5, no. 5 (2021): 2000307. https://doi.org/10.1002/adbi.202000307. Download

Baumschlager, Armin, and Mustafa Khammash. “Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light‐Control in Bacteria.” Advanced Biology 5, no. 5 (2021): 2000256. https://doi.org/10.1002/adbi.202000256. Download

Rosmalen, R.P. van, R.W. Smith, V.A.P. Martins dos Santos, C. Fleck, and M. Suarez-Diez. “Model Reduction of Genome-Scale Metabolic Models as a Basis for Targeted Kinetic Models.” Metabolic Engineering 64 (2021): 74–84. https://doi.org/10.1016/j.ymben.2021.01.008. Download

Christie, John M., and Matias D. Zurbriggen. “Optogenetics in Plants.” New Phytologist 229, no. 6 (2021): 3108–15. https://doi.org/10.1111/nph.17008. Download

Frei, Timothy, Federica Cella, Fabiana Tedeschi, Joaquín Gutiérrez, Guy-Bart Stan, Mustafa Khammash, and Velia Siciliano. “Characterization and Mitigation of Gene Expression Burden in Mammalian Cells.” Nature Communications 11 (September 15, 2020): 4641. https://doi.org/10.1038/s41467-020-18392-x. Download

Baumschlager, Armin, Marc Rullan, and Mustafa Khammash. “Exploiting Natural Chemical Photosensitivity of Anhydrotetracycline and Tetracycline for Dynamic and Setpoint Chemo-Optogenetic Control.” Nature Communications 11, no. 1 (July 31, 2020): 3834. https://doi.org/10.1038/s41467-020-17677-5. Download

Ochoa-Fernandez, Rocio, Nikolaj B. Abel, Franz-Georg Wieland, Jenia Schlegel, Leonie-Alexa Koch, J. Benjamin Miller, Raphael Engesser, et al. “Optogenetic Control of Gene Expression in Plants in the Presence of Ambient White Light.” Nature Methods 17, no. 7 (July 2020): 717–25. https://doi.org/10.1038/s41592-020-0868-y. Download

Davies, Jamie A., and Fokion Glykofrydis. “Engineering Pattern Formation and Morphogenesis.” Biochemical Society Transactions 48, no. 3 (June 30, 2020): 1177–85. https://doi.org/10.1042/BST20200013. Download

Perkins, Melinda Liu, Dirk Benzinger, Murat Arcak, and Mustafa Khammash. “Cell-in-the-Loop Pattern Formation with Optogenetically Emulated Cell-to-Cell Signaling.” Nature Communications 11, no. 1 (March 13, 2020): 1355. https://doi.org/10.1038/s41467-020-15166-3. Download

Kahle, Nikolai, David J. Sheerin, Patrick Fischbach, Leonie‐Alexa Koch, Philipp Schwenk, Dorothee Lambert, Ryan Rodriguez, et al. “COLD REGULATED 27 and 28 Are Targets of CONSTITUTIVELY PHOTOMORPHOGENIC 1 and Negatively Affect Phytochrome B Signalling.” The Plant Journal 104, no. 4 (2020): 1038–53. https://doi.org/10.1111/tpj.14979. Download

Davies, Jamie A, Patricia Murray, and Bettina Wilm. “Regenerative Medicine Therapies: Lessons from the Kidney.” Current Opinion in Physiology 14 (2020): 41–47. https://doi.org/10.1016/j.cophys.2019.12.008. Download

Fischbach, Patrick, Patrick Gonschorek, Julia Baaske, Jamie A. Davies, Wilfried Weber, and Matias D. Zurbriggen. “Optogenetic Downregulation of Protein Levels to Control Programmed Cell Death in Mammalian Cells with a Dual Blue-Light Switch.” In Photoswitching Proteins, edited by Dominik Niopek, 2173:159–70. New York, NY: Springer US, 2020. https://doi.org/10.1007/978-1-0716-0755-8_11. Download

Davies, Jamie A., and Paul S. Freemont, eds. Mammalian Synthetic Biology. Oxford Biology Primers. Oxford, United Kingdom ; New York, NY: Oxford University Press, 2020.

Golonka, David, Patrick Fischbach, Siddhartha G. Jena, Julius R. W. Kleeberg, Lars-Oliver Essen, Jared E. Toettcher, Matias D. Zurbriggen, and Andreas Möglich. “Deconstructing and Repurposing the Light-Regulated Interplay between Arabidopsis Phytochromes and Interacting Factors.” Communications Biology 2, no. 1 (December 2, 2019): 448. https://doi.org/10.1038/s42003-019-0687-9. Download

Khammash, M., M. Di Bernardo, and D. Di Bernardo. “Cybergenetics: Theory and Methods for Genetic Control System.” In 2019 IEEE 58th Conference on Decision and Control (CDC), 916–26, 2019. https://doi.org/10.1109/CDC40024.2019.9030209. Download

Aoki, Stephanie K., Gabriele Lillacci, Ankit Gupta, Armin Baumschlager, David Schweingruber, and Mustafa Khammash. “A Universal Biomolecular Integral Feedback Controller for Robust Perfect Adaptation.” Nature 570, no. 7762 (June 2019): 533–37. https://doi.org/10.1038/s41586-019-1321-1. Download

Yousefi, O Sascha, Matthias Günther, Maximilian Hörner, Julia Chalupsky, Maximilian Wess, Simon M Brandl, Robert W Smith, et al. “Optogenetic Control Shows That Kinetic Proofreading Regulates the Activity of the T Cell Receptor.” Edited by Arup K Chakraborty. ELife 8 (April 5, 2019): e42475. https://doi.org/10.7554/eLife.42475. Download

Andres, Jennifer, Tim Blomeier, and Matias D. Zurbriggen. “Synthetic Switches and Regulatory Circuits in Plants.” Plant Physiology 179, no. 3 (March 1, 2019): 862–84. https://doi.org/10.1104/pp.18.01362. Download

Davies, Jamie A. “Real-World Synthetic Biology: Is It Founded on an Engineering Approach, and Should It Be?” Life 9, no. 1 (January 7, 2019): 6. https://doi.org/10.3390/life9010006. Download

Waites, William, and Jamie A. Davies. “Emergence of Structure in Mouse Embryos: Structural Entropy Morphometry Applied to Digital Models of Embryonic Anatomy.” Journal of Anatomy 235, no. 4 (2019): 706–15. https://doi.org/10.1111/joa.13031. Download

Smith, Robert W., and Christian Fleck. “Basic Phytochrome B Calculations.” In Phytochromes, edited by Andreas Hiltbrunner, 2026:121–33. New York, NY: Springer New York, 2019. http://link.springer.com/10.1007/978-1-4939-9612-4_9. Download

Hörner, Maximilian, Katrin Raute, Barbara Hummel, Josef Madl, Guido Creusen, Oliver S. Thomas, Erik H. Christen, et al. “Phytochrome-Based Extracellular Matrix with Reversibly Tunable Mechanical Properties.” Advanced Materials 31, no. 12 (2019): 1806727. https://doi.org/10.1002/adma.201806727. Download

Baaske, Julia, Patrick Gonschorek, Raphael Engesser, Alazne Dominguez-Monedero, Katrin Raute, Patrick Fischbach, Konrad Müller, et al. “Dual-Controlled Optogenetic System for the Rapid down-Regulation of Protein Levels in Mammalian Cells.” Scientific Reports 8, no. 1 (October 9, 2018): 15024. https://doi.org/10.1038/s41598-018-32929-7. Download

Benzinger, Dirk, and Mustafa Khammash. “Pulsatile Inputs Achieve Tunable Attenuation of Gene Expression Variability and Graded Multi-Gene Regulation.” Nature Communications 9, no. 1 (August 30, 2018): 3521. https://doi.org/10.1038/s41467-018-05882-2. Download

Rullan, Marc, Dirk Benzinger, Gregor W. Schmidt, Andreas Milias-Argeitis, and Mustafa Khammash. “An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation.” Molecular Cell 70, no. 4 (2018): 745-756.e6. https://doi.org/10.1016/j.molcel.2018.04.012. Download

Davies, Jamie A. “Adaptive Self-Organization in the Embryo: Its Importance to Adult Anatomy and to Tissue Engineering.” Journal of Anatomy 232, no. 4 (2018): 524–33. https://doi.org/10.1111/joa.12691. Download

Middleton, Alistair M., Cristina Dal Bosco, Phillip Chlap, Robert Bensch, Hartmann Harz, Fugang Ren, Stefan Bergmann, et al. “Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake.” Cell Reports 22, no. 11 (2018): 3044–57. https://doi.org/10.1016/j.celrep.2018.02.074. Download

Waites, William, Matteo Cavaliere, Elise Cachat, Vincent Danos, and Jamie A. Davies. “An Information-Theoretic Measure for Patterning in Epithelial Tissues.” IEEE Access 6 (2018): 40302–12. https://doi.org/10.1109/ACCESS.2018.2853624. Download

Baumschlager, Armin, Stephanie K. Aoki, and Mustafa Khammash. “Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control.” ACS Synthetic Biology 6, no. 11 (November 17, 2017): 2157–67. https://doi.org/10.1021/acssynbio.7b00169. Download

Mills, Christopher G., Melanie L. Lawrence, David A. D. Munro, Mona Elhendawi, John J. Mullins, and Jamie A. Davies. “Asymmetric BMP4 Signalling Improves the Realism of Kidney Organoids.” Scientific Reports 7, no. 1 (November 1, 2017): 14824. https://doi.org/10.1038/s41598-017-14809-8. Download

Davies, Jamie. “Using Synthetic Biology to Explore Principles of Development.” Development 144, no. 7 (April 1, 2017): 1146–58. https://doi.org/10.1242/dev.144196. Download

Cachat, Elise, Weijia Liu, and Jamie A. Davies. “Synthetic Self‐patterning and Morphogenesis in Mammalian Cells: A Proof‐of‐concept Step towards Synthetic Tissue Development.” Engineering Biology 1, no. 2 (2017): 71–76. https://doi.org/10.1049/enb.2017.0013. Download

Samodelov, Sophia L., Hannes M. Beyer, Xiujie Guo, Maximilian Augustin, Kun-Peng Jia, Lina Baz, Oliver Ebenhöh, et al. “StrigoQuant: A Genetically Encoded Biosensor for Quantifying Strigolactone Activity and Specificity.” Science Advances 2, no. 11 (November 4, 2016): e1601266. https://doi.org/10.1126/sciadv.1601266. Download

Milias-Argeitis, Andreas, Marc Rullan, Stephanie K. Aoki, Peter Buchmann, and Mustafa Khammash. “Automated Optogenetic Feedback Control for Precise and Robust Regulation of Gene Expression and Cell Growth.” Nature Communications 7, no. 1 (August 26, 2016): 12546. https://doi.org/10.1038/ncomms12546. Download

Davies, Jamie A., and Elise Cachat. “Synthetic Biology Meets Tissue Engineering.” Biochemical Society Transactions 44, no. 3 (June 15, 2016): 696–701. https://doi.org/10.1042/BST20150289. Download

Smith, Robert W., Britta Helwig, Adrie H. Westphal, Eran Pel, Maximilian Hörner, Hannes M. Beyer, Sophia L. Samodelov, et al. “Unearthing the Transition Rates between Photoreceptor Conformers.” BMC Systems Biology 10, no. 1 (2016): 110. https://doi.org/10.1186/s12918-016-0368-y. Download

Davies, Jamie A. “Machines for Living in: Connections and Contrasts between Designed Architecture and the Development of Living Forms.” Architectural Research Quarterly 20, no. 1 (2016): 45–50. https://doi.org/10.1017/S1359135516000154. Download