Prospective Isolation of NKX2-1–Expressing Human Lung Progenitors Derived From Pluripotent Stem Cells
Finn Hawkins, Philipp Kramer, Anjali Jacob, Ian Driver, Dylan C. Thomas, Katherine B. McCauley, Nicholas Skvir, Ana M. Crane, Anita A. Kurmann, Anthony N. Hollenberg, Sinead Nguyen, Brandon G. Wong, Ahmad S. Khalil, Sarah X.L. Huang, Susan Guttentag, Jason R. Rock, John M. Shannon, Brian R. Davis and Darrell N. Kotton
The Journal of Clinical Investigation, doi:10.1172/JCI89950 (2016).
Dynamic Control of Hsf1 During Heat Shock By a Chaperone Switch and Phosphorylation
Xu Zheng, Joanna Krakowiak, Nikit Patel, Ali Beyzavi, Jideofor Ezike, Ahmad S. Khalil* and David Pincus* (*Co-corresponding)
eLife, 5: e18638 (2016)

  Commentary in eLife by Laura Le Breton & Matthias P. Mayer (PDF); in Cell Systems by David Pincus & Ahmad S. Khalil (PDF)
The Epigenome: The Next Substrate for Engineering
Minhee Park, Albert J. Keung and Ahmad S. Khalil
Genome Biology, 17: 183 (2016)
Cellular Advantages to Signaling in a Digital World (Preview)
Christopher P. Mancuso, Szilvia Kiriakov and Ahmad S. Khalil
Cell Systems, 3: 114-115 (2016)
Biological Insights From Synthetic Biology (Editorial)
Jordi Garcia-Ojalvo, Ahmad S. Khalil and John McCarthy
Integrative Biology, 8: 380-382 (2016)
A Unifying Model of Epigenetic Regulation (Perspective)
Albert J. Keung and Ahmad S. Khalil
Science, 351: 661-662 (2016)
Antibiotic Efficacy is Linked to Bacterial Cellular Respiration
Michael A. Lobritz*, Peter Belenky, Caroline B.M. Porter, Arnaud Gutierrez, Jason H. Yang, Eric G. Schwarz, Daniel J. Dwyer, Ahmad S. Khalil* and James J. Collins* (*Co-corresponding)
Proc. Natl. Acad. Sci. USA, 112: 8173-8180 (2015)
Chromatin Regulation at the Frontier of Synthetic Biology
Albert J. Keung, J. Keith Joung, Ahmad S. Khalil and James J. Collins
Nature Reviews Genetics, 16: 159-171 (2015)
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)

  Commentary in Nature Reviews Genetics by Darren J. Burgess (PDF).
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)

  Commentary in Nature Methods by Jeffrey J. Tabor (PDF)
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)

  Commentary in Nature Biotechnology by Susan Jones (PDF); in Nature Methods (PDF)
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)

  Commentary in Nature (PDF); in Science (PDF); in Nature Medicine (PDF); in Nat. Rev. Microbiol. (PDF)
Synthetic Biology: Applications Come of Age
Ahmad S. Khalil and James J. Collins
Nature Reviews Genetics, 11: 367-370 (2010)

  Highlighted in The New York Times by Olivia Judson (link); in Folha de S. Paulo (PDF)
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)

Cells are the ultimate computational devices. Cells use genetically-encoded molecular networks to monitor their environment, make sophisticated decisions, and execute diverse tasks. We are fundamentally interested in the function and evolution of these complex networks. Using synthetic biology, we build artificial versions of these circuits from genetic “parts” to understand the molecular basis by which cells solve computational and information-processing problems. In turn, we use these tools and insights to create genetic programming languages that allow us to engineer cells for a range of therapeutic and diagnostic applications. Complementing these molecular approaches, we develop novel fluidic technologies to manipulate and analyze cells in dynamic environments that mimic those in Nature, e.g. in the wild or human body. These platforms provide new capabilities and resolution for studying how cellular systems – single cells and populations – behave and evolve in diverse environments.

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