Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation
Albert J. Keung, Caleb J. Bashor, Szilvia Kiriakov, James J. Collins and Ahmad S. Khalil
Cell, 158: 110-120 (2014)
Antibiotics Induce Redox-Related Physiological Alterations as Part of Their Lethality
Daniel J. Dwyer, Peter A. Belenky, Jason H. Yang, I. Cody MacDonald, Jeffrey D. Martell, Noriko Takahashi, Clement T. Y. Chan, Michael A. Lobritz, Dana Braff, Eric G. Schwarz, Jonathan D. Ye, Mekhala Pati, Maarten Vercruysse, Paul S. Ralifo, Kyle R. Allison, Ahmad S. Khalil, Alice Y. Ting, Graham C. Walker and James J. Collins
Proc. Natl. Acad. Sci. USA, 111: E2100-E2109 (2014)
Engineering Life
Ahmad S. Khalil, Caleb J. Bashor, and Timothy K. Lu
The Scientist, August 1, 2013
Iterative Plug-and-Play Methodology for Constructing and Modifying Synthetic Gene Networks
Kevin D. Litcofsky, Raffi B. Afeyan, Russell J. Krom, Ahmad S. Khalil* and James J. Collins* (*Co-corresponding)
Nature Methods, 9: 1077-80 (2012)
A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions
Ahmad S. Khalil, Timothy K. Lu, Caleb J. Bashor, Cherie L. Ramirez, Nora C. Pyenson, J. Keith Joung and James J. Collins
Cell, 150: 647-658 (2012)
Signaling-Mediated Bacterial Persister Formation
Nicole M. Vega, Kyle R. Allison, Ahmad S. Khalil and James J. Collins
Nature Chemical Biology, 8: 431-433 (2012)
Synthetic Biology: Applications Come of Age
Ahmad S. Khalil and James J. Collins
Nature Reviews Genetics, 11: 367-370 (2010)
Functionalized Endothelialized Microvascular Networks with Circular Cross Sections in a Tissue Culture Substrate
Jeffrey T. Borenstein, Malinda M. Tupper, Peter J. Mack, Eli J. Weinberg, Ahmad S. Khalil, James Hsiao and Guillermo Garcia-Cardena
Biomedical Microdevices, 12: 71-79 (2010).
Next-Generation Synthetic Gene Networks
Timothy K. Lu, Ahmad S. Khalil and James J. Collins
Nature Biotechnology, 27: 1139-1150 (2009).
Kinesin's Cover-Neck Bundle Folds Forward to Generate Force
Ahmad S Khalil, David C Appleyard, Anna K. Labno, Adrien Georges, Martin Karplus, Angela M. Belcher, Wonmuk Hwang and Matthew J. Lang
Proc. Natl. Acad. Sci. USA, 105: 19247-19252 (2008).
Single M13 Bacteriophage Tethering and Stretching
Ahmad S. Khalil, Jorge M. Ferrer, Ricardo R. Brau, Stephen T. Kottmann, Christopher J. Noren, Matthew J. Lang and Angela M. Belcher
Proc. Natl. Acad. Sci. USA, 104: 4892-4897 (2007).
A Combined FEM/Genetic Algorithm for Vascular Soft Tissue Elasticity Estimation
Ahmad S. Khalil, Brett E. Bouma and Mohammad R. Kaazempur-Mofrad
Cardiovascular Engineering, 6: 93-102 (2006)
Tissue Elasticity Estimation with Optical Coherence Elastography: Toward Complete Mechanical Characterization of In Vivo Soft Tissue
Ahmad S. Khalil, Raymond C. Chan, Alexandra H. Chau, Brett E. Bouma and Mohammad R. Kaazempur-Mofrad
Annals of Biomedical Engineering, 33: 1631-1639 (2005)
OCT-Based Arterial Elastography: Robust Estimation Exploiting Tissue Biomechanics
Raymond C. Chan, Alexandra H. Chau, W. Clem Karl, Seemantini Nadkarni, Ahmad S. Khalil, Nicusor Iftimia, Milen Shishkov, Guillermo J. Tearney, Mohammad R. Kaazempur-Mofrad and Brett E. Bouma
Optics Express, 12: 4532-4572 (2004)

A unifying feature of living systems is the ability to store, process, and transmit information. We are fundamentally interested in molecular mechanisms and networks that control the flow of biological information, underlying how cells make decisions, develop, and evolve. We employ multidisciplinary approaches to identify and characterize these complex biological systems. A unique aspect of our research is the development of technologies and synthetic biology approaches to unlock new ways of probing biological systems, and frameworks for engineering them to reprogram cellular behavior for therapeutic and other benefit.

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