Research Summary
The Bashor lab uses synthetic biology approaches to reprogram the behavior of human cells. We engineer synthetic regulatory networks, including gene regulatory and signal transduction circuits, to enable cells to sense, compute, and respond to their environment, thereby reshaping cellular phenotype to support the development of transformative cell-based therapies.
Our engineering approach integrates theory and computational modeling with high-throughput experimental platforms that enable the building and testing of synthetic regulatory circuits at scale. We use machine learning and artificial intelligence models to map regulatory circuit design-to-function relationships, enabling faster and more predictive genetic design, with the long-term objective of developing models that enable the generative design of synthetic regulatory systems.
We are applying these capabilities to discover new mechanistic principles for establishing synthetic control of diverse cellular processes, such as decision-making, cell-state control, migration/localization, and secretion. Working across multiple human cell types, including immune effector cells (e.g., T cells and macrophages) and stem cells (iPSCs and MSCs) we focus on converting these principles into broadly deployable biotechnology tools for engineering human cells to function reliably in complex environments.
Our ultimate goal is to translate these technologies into safer, more effective therapies for indications spanning inflammatory disorders, trauma, and cancer. Efforts include sense-and-response programs that sharpen adoptive cell therapy specificity and multi-gene regulatory systems that boost therapeutic bioproduction or direct cell differentiation. We collaborate closely with translational and clinical researchers to ensure our designs meet real-world constraints and move efficiently toward therapeutic impact.
Selected Recent Publications
Rai K*, O'Connell RW*, Piepergerdes TC, Wang Y, Brown LBC, Samra KD, Wilson JA, Lin S, Zhang TH, Ramos EM, Sun A, Kille B, Curry KD, Rocks JW, Treangen TJ, Mehta P, Bashor CJ. (2026) Ultra-high-throughput mapping of genetic design space. Nature, 650, 1035-1044
Yang X, Rocks JW, Jiang K, Walters AJ, Rai K, Liu J, Nguyen J, Olson SD, Mehta P, Collins JJ, Daringer NM, Bashor CJ (2025) Engineering synthetic phosphorylation networks in human cells. Science, 387(6729): 74-81
Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ*, Khalil AS* (2023) Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell, 186 (18): 3810-25
Bashor CJ*, Hilton IB*, Bandukwala H*, Smith DH*, Veiseh* (2022) Engineering the next generation of cell-based therapeutics. Nature Reviews Drug Discovery, 21(9): 655-75
Bashor CJ*, Patel N*, Choubey S, Beyzavi A, Kondev J, Collins JJ, Khalil AS (2019) Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science, 364(6440): 593-7