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The Bashor Lab

We use synthetic biology approaches to design, build, and test artificial regulatory programs in human cells. This not only provides insight into the design logic of natural regulation, but also allows us to predictively alter cellular phenotype to create powerful cell-based biotechnologies.

Synthetic Regulatory Circuits

Our work explores the fundamentals of gene expression control in mammalian cells. By leveraging multi-scale regulatory control, we can engineer stable, precise control over complex multi-gene expression programs that can both report on and reprogram cellular function.

Synthetic Signaling Networks

We engineer protein circuits that sense, compute, and respond to extracellular inputs. These circuits serve as model systems for understanding the molecular and biophysical determinants of signal transduction, and can be used to reshape how a cell interacts with its environment.

Data-driven Genetic Design

We are creating high-throughput experimental pipelines that enable building and testing of synthetic circuits at an unprecedented scale. The data we generate can be used to train AI algorithms that map genetic design space, dramatically increasing the pace of circuit engineering.

Engineering Cell-Based Therapeutics

Our ultimate goal is to use our work to create safer, more effective cell-based therapies for indications spanning inflammatory disorders, trauma, and cancer. We work closely with translational and clinical researchers to ensure our designs meet real-world constraints and move efficiently toward therapeutic impact.

PUBLICATIONS

Kshitij Rai, Ronan W. O'Connell, Trenton C. Piepergerdes, Yiduo Wang, Lucas B. C. Brown, Kian D. Samra, Jack A. Wilson, Shujian Lin, Thomas H. Zhang, Eduardo M. Ramos, Andrew Sun, Bryce Kille, Kristen D. Curry, Jason W. Rocks, Todd J. Treangen, Pankaj Mehta, Caleb J. Bashor (2026). Ultra-high-throughput mapping of genetic design space. Nature. 1-10.

Xiaoyu Yang, Jason W. Rocks, Kaiyi Jiang, Andrew J. Walters, Kshitij Rai, Jing Liu, Jason Nguyen, Scott D. Olson, Pankaj Mehta, Caleb J. Bashor (2025). Engineering synthetic phosphorylation signaling networks in human cells. Science. 387 (6729): 74-81.

◇Comment in Clinical and Translational Medicine 15(5):e70328

Kshitij Rai, Yiduo Wang, Ronan W. O'Connell, Ankit B. Patel, Caleb J. Bashor (2024). Using machine learning to enhance and accelerate synthetic biology. Current Opinion in Biomedical Engineering. 31: 100553.

Payam E. Farahani, Xiaoyu Yang, Emily V. Mesev, Kaylan A. Fomby, Ellen H. Brumbaugh-Reed, Caleb J. Bashor, Celeste M. Nelson, Jared E. Toettcher (2023). pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells. eLife.

Meghan D.J. Bragdon, Nikit Patel, James Chuang, Ethan Levien, Caleb J. Bashor, Ahmad S. Khalil (2023). Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell 186, no. 18. 1-16.

Caleb J. Bashor, Isaac B. Hilton, Hozefa Bandukwala, Devyn M. Smith, Omid Veiseh (2022). Engineering the next generation of cell-based therapeutics. Nature Reviews Drug Discovery 21, no. 9. 655-675.

Xiaoyu Yang, John Her, Caleb J. Bashor (2019). Mammalian signaling circuits from bacterial parts. Nature Chemical Biology 16 no. 2. 110-111.

Zachary J. Heins, Christopher P. Mancuso, Szilvia Kiriakov, Brandon G. Wong, Caleb J. Bashor, Ahmad S. Khalil (2019). Designing Automated, High-throughput, Continuous Cell Growth Experiments Using eVOLVER. Journal of Visualized Experiments (JoVE) . 147: 10-3791.

Ronan W. O'Connell, Caleb J. Bashor (2019). The Least Mating Pathway: Synthetically Refactoring a Familiar Signaling System for New Applications. Cell 177 no. 3. 521-523.

Caleb J. Bashor, Nikit Patel, Sandeep Choubey, Ali Beyzavi, Jané Kondev, James J. Collins, Ahmad S. Khalil (2019). Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science 364, no. 6440. 593-597.

Brandon G. Wong, Christopher P. Mancuso, Szilvia Kiriakov, Caleb J. Bashor, Ahmad S. Khalil (2018). Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER. Nature Biotechnology 36 no. 7. 614-623.

Caleb J. Bashor, James J. Collins (2018). Understanding Biological Regulation Through Synthetic Biology. Annual Review of Biophysics 47, no 21. 399-423.

Russell M. Gordley, Reid E. Williams, Caleb J. Bashor, Jared E. Toettcher, Shude Yan, Wendell A. Lim (2016). Engineering dynamical control of cell fate switching using synthetic phospho-regulons. Proceedings of the National Academy of Sciences (PNAS) 113 no. 47. 13528-13533.

Clement T.Y. Chan, Jeong Wook Lee, D. Ewen Cameron, Caleb J. Bashor, James J. Collins (2016). 'Deadman' and 'Passcode' microbial kill switches for bacterial containment. Nature Chemical Biology 12 no. 2. 82-86.

Albert J. Keung, Caleb J. Bashor, Szilvia Kiriakov, James J. Collins, Ahmad S. Khalil (2014). Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation. Cell 158. 110-120.

D. Ewen Cameron, Caleb J. Bashor, James J. Collins (2014). A brief history of synthetic biology. Nature Reviews Microbiology 12, no. 5. 381-390.

Caleb J. Bashor, James J. Collins (2012). Insulating gene circuits from context by RNA processing. Nature Biotechnology 30, no. 11. 1061-1062.

Ahmad S. Khalil, Timothy K. Lu, Caleb J. Bashor, Cherie L. Ramirez, Nora C. Pyenson, J. Keith Joung, James J. Collins (2012). A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions. Cell 150 no. 3. 647-658.

Caleb J. Bashor, Andrew A. Horwitz, Sergio G. Peisajovich, Wendell A. Lim (2010). Rewiring Cells: Synthetic Biology as a Tool to Interrogate the Organizational Principles of Living Systems. Annual Review of Biophysics 39. 515-537.

Caleb J. Bashor, Noah C. Helman, Shude Yan, Wendell A. Lim (2008). Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics. Science 319, no 5869. 1539-1543.