Ahmad 'Mo' Khalil
Principal Investigator, CV
Assistant Professor, Dept. of Biomedical Engineering
Associate Director, Biological Design Center
Visiting Scholar, Wyss Institute at Harvard University
Faculty, Molecular Biology, Cell Biology & Biochemistry
Faculty, Bioinformatics

Mo is the Innovation Career Development Assistant Professor of Biomedical Engineering at Boston University. He is the Associate Director and a Founding Core Member of the Biological Design Center, and is also a Visiting Scholar at the Wyss Institute for Biologically Inspired Engineering at Harvard University. He was an HHMI Postdoctoral Fellow with Dr. Jim Collins at BU working in systems & synthetic biology. He completed his PhD at MIT with Drs. Angie Belcher and Matt Lang in molecular biophysics & engineering. His personal interests include taking his dog (Eloise) to the park and attempting to make the perfect cappuccino with his Nespresso machine.

Selected Awards:
2017 PECASE Award
2016 NIH New Innovator Award
2016 DARPA Young Faculty Award
2015 Hartwell Foundation Investigator
2014 NSF CAREER Award
2014 GenomeWeb Young Investigator Award
2013 Innovation Career Development Professorship
2013 Kern Faculty Fellow
2012 Wallace H. Coulter Foundation Research Award
2012 Dean's Catalyst Award

Teaching Awards:
2016 Outstanding Professor of the Year (College)
2016 Award for Teaching Excellence (Department)
2015 Award for Teaching Excellence (Department)
2014 NAE Frontiers of Engineering Education Invitee
2013 Award for Teaching Excellence (Department)
Phi Beta Kappa Honors Society (2002)
Zehua Bao
Postdoctoral Fellow
PhD Biochemistry, UIUC (2017)
BS Biological Sciences & Biotechnology, Tsinghua University (2010)

As a graduate student in Huimin Zhao's group at UIUC, Zehua worked on developing genome engineering technologies in yeast and gene regulation tools in mammalian cells. His long-lasting research interests include understanding how DNA packaging affects gene regulatory networks, as well as hijacking and engineering single cells or cell communities for applications in biomanufacturing and novel therapies. Outside the lab he enjoys sports, hiking, and practicing archery.

Selected Awards:
2011 Predoctoral Fellowship (UIUC)
2009 Zeng Xianzi Scholarship
Phi Beta Kappa Honors Society
Guilio Chiesa
Postdoctoral Fellow
PhD Biomedicine, IRB Barcelona (2015)
MS Molecular Biology & Genetics, Univ. of Pavia (2010)
BS Biotechnology, Univ. of Pavia (2008)

After completing his undergraduate studies at the University of Pavia (Italy), Giulio pursued his PhD at the Institute of Research in Biomedicine (IRB) Barcelona under the direction of Prof. Xavier Salvatella. There, he studied the biophysics and mechanisms of aggregation of a polyglutamine protein, in an attempt to better understand the role of polyglutamine tracts in Nature. His current scientific interests are exploiting and engineering disordered proteins in synthetic protein interaction networks. In his spare time, he is a wannabe fiction writer and a Sunday blogger; also, he pretends to do sport and, no, he can’t play guitar.

Selected Awards:
2011 FI-DGR Predoctoral Fellowship
2010 Predoctoral Fellowship (IRB Barcelona)
2009 iGEM Gold Medal & "Best Food and Energy Track"           Special Prize
Phi Beta Kappa Honors Society
Szilvia Kiriakov
Postdoctoral Fellow
PhD MCBB, Boston University (2018)
MS Bioeng., Budapest Univ. of Tech. & Econ. (2011)
BS Bioeng., Budapest Univ. of Tech. & Econ. (2009)

After completing her BS and MS in Biochemical Engineering in Budapest, Hungary, Szilvia pursued her PhD in the MCBB Program at Boston University, where she worked at the intersection of synthetic biology & yeast prions in Mo Khalil's lab. Her interests involve learning and improving the latest molecular biology methods, cooking, meeting with people, talking about science, and nurturing her Neolamprologus leleupi.

Selected Awards:
2012 Boehringer Ingelheim Fonds PhD Fellowship
Hui-Shan Li
Postdoctoral Fellow
(*Co-advised with Wilson Wong)
PhD Animal Cell & Biotech., Seoul National (2016)
BS Bioengineering, Tianjin University (2010)

After completing her Bachelor’s in Bioengineering at Tianjin University of Commerce (TJCU), Huishan pursued her PhD in Animal Cell Biotechnology at Seoul National University, where she worked on developing delivery systems for oral and nasal vaccines. She is now a joint postdoc with Wilson Wong’s lab. Her scientific interests center around applying synthetic biology to enhance cell immunotherapy applications. She loves to watch TV shows and enjoys walks around Boston area parks on the weekends.
Nikit Patel
Postdoctoral Fellow
PhD Biomedical Eng., Boston University (2018)
BS Bioengineering, UC Berkeley (2011)

As a graduate student in Mo Khalil's lab at Boston University, Nikit applied synthetic biology and modeling to study and engineer cooperativity in genetic networks. His broad research interest involves engineering cells in order to systematically explore the relationship between network structure and function. He also enjoys the use of single cell analysis tools to investigate cellular heterogeneity. In his free time, Nikit likes to play basketball & soccer, rock climb, and slackline. He also enjoys sleeping, feeding squirrels, and thinking about the universe.

Selected Awards:
2012 NIH Quantitative Biology & Physiology Training Grant
Abdul Bhuiya
Master's Student, Biomedical Eng.
BS Molecular & Cellular Biology, and Chemistry (Minor), UIUC (2017)

Abdul completed his Bachelor's degree in Molecular & Cellular Biology with a minor in Chemistry at University of Illinois at Urbana-Champaign (UIUC). At UIUC, he worked on developing point-of-care diagnostic devices for infectious diseases. Currently as a MS student, Abdul is interested in developing a rapid antibiotic susceptibility test to detect transcriptional biomarkers using nano-optics. Outside of lab, Abdul enjoys watching and playing soccer, tennis and listening to TED talks.
Meghan Bragdon
Graduate Student, Mol. Biology, Cell Biology & Biochem.
BA Fine Arts and English, Stonehill College (2001)
Post-Baccalaureate Studies in Biology, NYU (2006)

Meghan completed her Bachelor’s degree in Fine Arts and English at Stonehill College and performed post-baccalaureate studies in Biology and Chemistry at NYU. She mapped expression of global transcription networks in the DePace Lab in Systems Biology at HMS. She seeks to further probe the mechanisms underlying gene regulation and evolution by building new regulatory architectures with synthetic tools. Meghan enjoys long runs, short bike rides and natural history museum dioramas.
Emma Briars
Graduate Student, Bioinformatics Program
BA Biochem. & Mol. Biology, and Mathematics, BU (2013)

Emma graduated from Boston University with a B.A. in Biochemistry and Molecular Biology, and Mathematics. She complemented her undergraduate research in bioinformatics with post-graduate research in experimental cancer biology at Massachusetts General Hospital and Merrimack Pharmaceuticals. Now as a PhD student in the Bioinformatics Program, Emma is interested in how we can use the intersection between computational and experimental approaches to understand and combat antibiotic resistance. Her hobbies outside of the lab include running, yoga, evaluating restaurants based off their nachos, and petting dogs she sees on the street.
Keith Gagnon
MD/PhD Student, Biomedical Eng.
(*Co-advised with Chris Chen)
BS Biomedical Engineering, WPI (2015)

Keith graduated from WPI with a B.S. in Biomedical Engineering. His undergraduate research focused on skeletal tissue engineering using fibrin scaffolds and scaffold vascularization. Now, completing the PhD portion of his MD/PhD, Keith is interested in working at the interface of tissue engineering and synthetic biology, combining the two to generate physiologically relevant models of cancer and tumor angiogenesis. Outside of lab, Keith enjoys running, swimming, photography, traveling and hiking.

Selected Awards:
2014 Barry M. Goldwater Scholar
Sam Gan
Graduate Student, Mol. Biology, Cell Biology & Biochem.
BS Biology, Illinois Institute of Technology (2009)
MS Pharm Sci, UW-Madison (2013)

Upon graduating with his Bachelor’s from Illinois Institute of Technology, Sam obtained a Master’s degree in Pharmaceutical Sciences from University of Wisconsin-Madison where he studied neurodegenerative diseases. He is interested in unraveling how cells compartmentalize specific biochemical reactions in order to perform cellular functions. Current interests include regulation of transcription via liquid-liquid phase separation. When not spotted in the lab, he can be found imagining dragons, reading a good book, or photographing. He has a surprisingly good singing voice.
Zachary Heins
Graduate Student, Biomedical Eng.
MS Biochem. & Mol. Biology - Bioinformatics, Georgetown University (2015)
BS Computer Engineering, UT Dallas (2013)

Zack received his BS in Computer Engineering from UT Dallas and his MS in Bioinformatics from Georgetown University. As an undergraduate he worked in a power electronics lab and competed in combat robotics at the international level. He is now interested in probing and engineering cellular behavior. When not in the lab, he enjoys rock climbing, hiking, traveling, reading, enjoying fine wines, and baking great bread.

Selected Awards:
2017 NIH Quantitative Biology & Physiology Training Grant
Divya Israni
Graduate Student, Biomedical Eng.
BS Bioengineering, UC Berkeley (2013)

Divya completed her Bachelor's degree in Bioengineering at UC Berkeley. Her research interests involve engineering biomolecules and controlling fundamental processes to explore interesting cellular behaviors, with the goal of creating therapies for complex genetic diseases. Divya enjoys traveling, swimming, reading, talking about the Californian sunshine, and mentoring the next generation of scientists.

Selected Awards:
2013 NSF Graduate Fellowship
Haytham Khalil
Research Associate
MS Sys. & Syn. Biology, Université Paris Decartes (2015)
MS Microelectronics, University of Strasbourg (2011)
BS Applied Physics, University of Strasbourg (2009)

Haytham completed his Bachelor’s degree in Applied Physics & Electronics at the University of Strasbourg, and then performed post-baccalaureate studies in Systems & Synthetic Biology at the Université Paris Decartes. He used microfluidics and single-cell time lapse imaging to study stress response in bacteria in Johan Paulsson’s Lab in Systems Biology at Harvard Medical School. He seeks to develop programmable microfluidic technologies to study individual cells responding to time-varying environmental conditions. Haytham enjoys sleeping, reading, and food design.
Chris Mancuso
Graduate Student, Biomedical Eng.
BS Biological Engineering, Cornell University (2013)

Chris completed his Bachelor’s in biological engineering at Cornell University. He is interested in understanding and engineering how cells make decisions at both the individual and population-wide scales. Mixed populations of microbes are of particular interest to Chris. Other than working in the lab, he enjoys skiing, hiking, playing music, and making far too many puns.

Selected Awards:
2013 NIH Quantitative Biology & Physiology Training Grant
Minhee Park
Graduate Student, Biomedical Eng.
BS Bioengineering, Rice University (2012)

Minhee completed her Bachelor’s degree in Bioengineering at Rice University. She is interested in understanding how cells behave and respond to the environment. Also, she’s interested in engineering cells in order to control their gene expression and allow them to function accordingly. Minhee’s personal interests include playing the piano, coming up with her own simple recipe of her favorite foods, reading books and designing rooms.
      Former Postdocs
Albert Keung

Derin Sevenler

Synthetic biology;
chromatin regulation
Molecular diagnostics
Current Position
Assistant Professor of Chemical & Biomolecular Eng., NCSU
Postdoctoral Fellow, Toner Lab, MGH/HMS
      Former Graduate Students
Ali Beyzavi

Saloni Jain
Gregory Newby
Dana Braff

Szilvia Kiriakov
Brandon Wong


yeast heat shock response
Antibiotic resistance
Yeast prions
Synthetic biology;
molecular diagnostics
Yeast prions
Current Position
Postdoctoral Fellow, Langer Lab, MIT

Associate Consultant, QuintilesIMS
Postdoctoral Fellow, Liu Lab, Broad/Harvard
Principal Scientist, GRO Biosciences

Postdoctoral Fellow, Khalil Lab, BU
Co-Founder and CEO, Fynch Bio
      Former Undergraduate & High School Students
Nora Pyenson
Cathryn Hart
Madeleine Joung
Amir Soltanianzadeh
Rishi Jain
Aditya Cavale
Maxime Fouilleron
Teja Karri
Shaan Bhandarkar
Boston University
BU Academy HS
BU Academy HS
Boston University
Boston University
Boston University
Boston University
Phillips Exeter HS
Max Cotler
Davis Borucki
Rachel Petherbridge
Samantha Pipe
Andrew Montequin
Hannah Vanbenschoten
Michelle Rose
Grace Qian

Boston University
Boston University
William Enloe HS
Boston University
Boston University

Boston University
Dover-Sherborn HS

Cells use networks of interacting regulatory molecules to process information, make memories, and execute computations. Our research is interested in the design, function, and evolution of these cellular regulatory systems. To examine them, we employ multidisciplinary approaches including synthetic biology, which allows us to construct artificial versions of these regulatory systems from components “parts” to systematically explore their design principles and functional properties. Our work has pioneered synthetic biology platforms for engineering a wide range of cellular systems, from eukaryotic transcriptional networks to chromatin/epigenetic regulation and functional protein aggregation systems. In parallel, we invent high-throughput technologies, such as the eVOLVER system for continuous cell growth, to help us experimentally interrogate cellular adaptation and to conduct continuous laboratory evolution of regulatory molecules and cells. Ultimately, with these tools and approaches, we aim to gain integrated, quantitative understanding of how cellular decisions and phenotypes emerge from underlying regulatory networks, and how these phenotypes are adapted to evolutionary selective pressures. We additionally seek to translate our synthetic tools to address unmet biomedical and therapeutic needs, such as development of gene expression control schemes for gene- and cell-based therapy, and cell-based models and platforms for neurodegenerative disease.

more >

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

Modeling the Impact of Drug Interactions on Therapeutic Selectivity
Zohar B. Weinstein, Nurdan Kuru, Szilvia Kiriakov, Adam C. Palmer, Ahmad S. Khalil, Paul A. Clemons, Muhammad H. Zaman, Frederick P. Roth and Murat Cokol
Nature Communications, 9: 3452 (2018)

Precise, Automated Control of Conditions for High-Throughput Growth of Yeast and Bacteria with eVOLVER
Brandon G. Wong*, Christopher P. Mancuso*, Szilvia Kiriakov, Caleb J. Bashor and Ahmad S. Khalil
Nature Biotechnology, 36: 614-623 (2018)

Hsf1 Phosphorylation Generates Cell-to-Cell Variation in Hsp90 Levels and Promotes Phenotypic Plasticity
Xu Zheng*, Ali Beyzavi*, Joanna Krakowiak, Nikit Patel, Ahmad S. Khalil and David Pincus
Cell Reports, 22: 3099-3106 (2018)

Hsf1 and Hsp70 Constitute a Two-Component Feedback Loop that Regulates the Yeast Heat Shock Response
Joanna Krakowiak*, Xu Zheng*, Nikit Patel*, Zoe A. Feder, Jayamani Anandhakumar, Kendra Valerius, David S. Gross, Ahmad S. Khalil and David Pincus
eLife, 7: e31668 (2018)

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