Cells use “circuits” of interacting regulatory molecules to activate and control sophisticated gene expression programs, allowing organisms to process information and interact with their environments. We are interested in how these gene regulatory circuits function and how they evolve to generate phenotypic novelty. My team is pioneering the development of two complementary approaches to discover the design principles of gene regulatory circuits and to enable their purposeful manipulation, which could lead to breakthroughs in the development of cell-based devices for therapeutics and other biomedical applications. First, we use rational design approaches, in which we build regulatory circuits in eukaryotic cells from the bottom-up. This synthetic biology approach allows us to re-design existing circuits with precisely tailored biochemical parameters and establish functional sufficiency in a native cellular context. While this first-principles based approach can illuminate general principles of circuit design, deciphering which regulatory designs nature chooses depends on other factors, such as the types of selective pressures that organisms encounter. Thus, second, we develop new high-throughput methods for the evolution of biological circuits to recreate and identify drivers of regulatory change. A central pillar of this effort is eVOLVER, a DIY highly-flexible continuous culture system we invented that enables automated continuous growth and evolution of cellular systems in precisely-controlled conditions. We have used these synergistic approaches to accelerate discovery of fundamental principles governing genetic and epigenetic mechanisms of gene regulation, and to provide a powerful foundation for designing biological systems to program new traits in engineered cells and tissues and combat disease.

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Transcriptional Kinetic Synergy: A Complex Landscape Revealed by Integrating Modelling and Synthetic Biology
Rosa Martinez-Corral, Minhee Park, Kelly Biette, Dhana Friedrich, Clarrissa Scholes, Ahmad S. Khalil, Jeremy Gunawardena and Angela H. DePace
bioRxiv, doi: 10.1101/2020.08.31.276261

Environmental Fluctuations Reshape an Unexpected Diversity-Disturbance Relationship in a Microbial Community
Christopher P. Mancuso, Hyunseok Lee, Clare I. Abreu, Jeff Gore and Ahmad S. Khalil
bioRxiv, doi: 10.1101/2020.07.28.225987

Automated Continuous Evolution of Proteins In Vivo
Ziwei Zhong*, Brandon G. Wong*, Arjun Ravikumar, Garri A. Arzumanyan, Ahmad S. Khalil and Chang C. Liu
ACS Synthetic Biology, 9: 1270-1276 (2020)

Barcoded Microbial System for High-Resolution Object Provenance
Jason Qian*, Zhi-xiang Lu*, Christopher P. Mancuso*, Han-Ying Jhuang*, Rocío del Carmen Barajas-Ornelas*, Sarah A. Boswell*, Fernando H. Ramírez-Guadiana, Victoria Jones, Akhila Sonti, Kole Sedlack, Lior Artzi, Giyoung Jung, Mohammad Arammash, Mary E. Pettit, Michael Melfi, Lorena Lyon, Siân V. Owen, Michael Baym, Ahmad S. Khalil, Pamela A. Silver, David Z. Rudner and Michael Springer
Science, 368: 1135-1140 (2020)

Protein Assembly Systems in Natural and Synthetic Biology
Giulio Chiesa*, Szilvia Kiriakov and Ahmad S. Khalil
BMC Biology, 28: 35 (2020)

Designing Automated, High-Throughput Continuous Cell Growth Experiments Using eVOLVER
Zachary J. Heins, Christopher P. Mancuso, Szilvia Kiriakov, Brandon G. Wong, Caleb J. Bashor and Ahmad S. Khalil
Journal of Visualized Experiments, 147: e59652 (2019)

Complex Signal Processing in Synthetic Gene Circuits Using Cooperative Regulatory Assemblies
Caleb J. Bashor*, Nikit Patel*, Sandeep Choubey, Ali Beyzavi, Jane Kondev, James J. Collins and Ahmad S. Khalil
Science, 364: 593-597 (2019)

Functional Genomics of the Rapidly Replicating Bacterium Vibrio natriegens by CRISPRi
Henry H. Lee, Nili Ostrov, Brandon G. Wong, Michaela A. Gold, Ahmad S. Khalil and George M. Church
Nature Microbiology, 4: 1105-1113 (2019)

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules
Minhee Park, Nikit Patel, Albert J. Keung and Ahmad S. Khalil
Cell, 176: 227-238 (2019)

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