This complete list is also available on the zotero website of the group.


Davies, Jamie, and Michael Levin. “Synthetic Morphology with Agential Materials.” Nature Reviews Bioengineering 1, no. 1 (January 19, 2023): 46–59. 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. Download
Pleyer, Jonas, and Christian Fleck. “Agent-Based Models in Cellular Systems.” Frontiers in Physics 10 (January 4, 2023): 968409. 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. 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). 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. 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. 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. 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. 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. 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. 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. Download
Christie, John M., and Matias D. Zurbriggen. “Optogenetics in Plants.” New Phytologist 229, no. 6 (2021): 3108–15. 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. 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. Download
Davies, Jamie A., and Fokion Glykofrydis. “Engineering Pattern Formation and Morphogenesis.” Biochemical Society Transactions 48, no. 3 (June 30, 2020): 1177–85. 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. 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. Download
Davies, Jamie A, Patricia Murray, and Bettina Wilm. “Regenerative Medicine Therapies: Lessons from the Kidney.” Current Opinion in Physiology 14 (2020): 41–47. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Download
Davies, Jamie. “Using Synthetic Biology to Explore Principles of Development.” Development 144, no. 7 (April 1, 2017): 1146–58. 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. 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. 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. Download
Davies, Jamie A., and Elise Cachat. “Synthetic Biology Meets Tissue Engineering.” Biochemical Society Transactions 44, no. 3 (June 15, 2016): 696–701. 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. 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. Download