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)
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
HuiShan 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.
Derin Sevenler
Postdoctoral Fellow
(*Co-advised with M. Selim Ünlü)
PhD Biomedical Engineering, Boston University (2017)
BS Mechanical & Aerospace Eng, Cornell (2011)

As a graduate student in Selim Ünlü's group at Boston University, Derin worked on developing new nano-optics techniques for detecting and measuring single biological molecules and viruses. His current work is focused on applying these techniques to develop sensitive tests for medical diagnosis of infectious disease. Outside the lab he enjoys reading, hiking, and playing guitar.

Selected Awards:
2015 NIH Cross-Training Program
2013 NSF Graduate Assistance in Areas of National Need
2012 NIH Quantitative Biology & Physiology Training Grant
Dana Braff
Graduate Student, Biomedical Eng.
(*Co-advised with Jim Collins)
BS Biological Engineering, MIT (2012)

Dana completed her Bachelor’s in Biological Engineering at MIT. She is interested in various applications of systems and synthetic biology and is currently working to study the effects of antibiotics on bacterial systems. Dana’s personal interests revolve primarily around food, though she also enjoys taking her dog, Scout, on adventures throughout Boston. Dana was voted “most likely to complain about the cold or wear five layers” by her undergraduate peers. She lives up to this reputation quite spectacularly.

Selected Awards:
2012 NIH Quantitative Biology & Physiology Training Grant
Meghan Bragdon
Graduate Student, Mol. Biology, Cell Biology & Biochem.
BA Fine Arts and English, Stonehill College (2001)
Post-Baccalaureate Studies in Biology, NYU

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.
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.
Szilvia Kiriakov
Graduate Student, Mol. Biology, Cell Biology & Biochem.
MS Bioeng., Budapest Univ. of Tech. & Econ. (2011)
BS Bioeng., Budapest Univ. of Tech. & Econ. (2009)

Szilvia completed her Bachelor’s and Master’s degrees in Biochemical Engineering in Budapest, Hungary. Her interests involve learning and improving the latest
molecular biology, cell biology and biochemical methods, as well as designing new experiments to interrogate Mother Nature. Currently, she is studying transcriptional master regulation in yeast and mammalian cells. Szilvia likes cooking, meeting with people, talking about science, and nurturing her Neolamprologus leleupi.

Selected Awards:
2012 Boehringer Ingelheim Fonds PhD Fellowship
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.
Nikit Patel
Graduate Student, Biomedical Eng.
BS Bioengineering, UC Berkeley (2011)

Nikit graduated UC Berkeley with a Bioengineering degree. His main 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
Brandon Wong
Graduate Student, Biomedical Eng.
BS Bioengineering, UC Irvine (2012)

Brandon completed his Bachelor’s in Biomedical Engineering at UC Irvine. His main research interests involve developing programmable microfluidic devices as a platform to study how complex environments drive and affect cellular function. Brandon is known for (and proud of) his loud and hearty laugh. Less importantly, his interests include swimming, biking, and just about any sport invented. 

Selected Awards:
2013 GAANN Fellowship
      Former Postdocs
Synthetic chromatin
Current Position
Assistant Professor of Chemical & Biomolecular Engineering, North Carolina State University
      Former Graduate Students
Ali Beyzavi

Saloni Jain
Gregory Newby

Microfluidics; yeast heat shock response
Antibiotic resistance
Yeast prions
Current Position
Postdoctoral Fellow, Langer Lab, MIT

Associate Consultant, QuintilesIMS
Postdoctoral Fellow, Liu Lab, Broad/Harvard
      Former Undergraduate & High School Students
Nora Pyenson
Max Cotler
Cathryn Hart
Davis Borucki
Madeleine Joung
Rachel Petherbridge
Amir Soltanianzadeh
Samantha Pipe
Rishi Jain
Maxime Fouilleron
Boston University
Boston University
BU Academy HS
Boston University
BU Academy HS
William G. Enloe HS
Boston University
Boston University
Boston University
Synthetic biology
Yeast prions
Molecular biology
Lab automation
Lab automation
Current Position
PhD Student, Cornell
PhD Student, MIT
Undergraduate, MIT
Undergraduate, BU
Undergraduate, Harvard
Undergraduate, BU
M.S. Student, JHU
Engineer, Epic Systems
Undergraduate, BU
Gap year

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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A Genetic Tool to Track Protein Aggregates and Control Prion Inheritance
Gregory A. Newby*, Szilvia Kiriakov*, Erinc Hallacli*, Can Kayatekin, Peter Tsvetkov, Christopher P. Mancuso, J. Maeve Bonner, William R. Hesse, Sohini Chakrabortee, Anita L. Manogaran, Susan W. Liebman, Susan Lindquist and Ahmad S. Khalil
Cell, 171: 966-979 (2017)

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)

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)

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