Ahmad (Mo) Khalil
Principal Investigator, CV
Dorf-Ebner Distinguished Faculty Fellow
Associate Professor, Dept. of Biomedical Engineering
Associate Director, Biological Design Center
Co-Director, SB2 NIH/NIGMS T32 Training Program
Visiting Scholar, Wyss Institute at Harvard University
Faculty, Molecular Biology, Cell Biology & Biochemistry
Faculty, Bioinformatics

Mo is the Dorf-Ebner Distinguished Associate Professor of Biomedical Engineering and Founding Associate Director of the Biological Design Center at Boston University. He is also a Visiting Scholar at the Wyss Institute for Biologically Inspired Engineering at Harvard University, and Co-Director of a NIH/NIGMS T32 PhD Training Program in synthetic biology. 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. Angela 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:
2020 DoD Vannevar Bush Faculty Fellowship
2017 PECASE Award
2017 BU Early Career Research Excellence Award
2016 NIH New Innovator Award
2016 DARPA Young Faculty Award
2015 Hartwell Foundation Investigator
2014 NSF CAREER Award
2013 Innovation Career Development Professorship
2012 Wallace H. Coulter Foundation Research 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)
James Angstman
Postdoctoral Fellow
PhD Biochemistry, Harvard University (2020)
BS Genetics, Cell Biology, and Development / Biochemistry, University of Minnesota (2010)

During his PhD work in Keith Joung's lab, James worked on genome and epigenome editing technologies with a particular interest in CRIPSR Base Editing. He is interested in using continuous evolution to both expand the genome editing toolkit and upon current targeted editing technologies. James enjoys Boda Borg, is bad at chess, and has mined several dollars worth of Bitcoin on his home computer.

Selected Awards:
2014 DoD NDSEG Fellowship
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
Allison Drain
Postdoctoral Fellow
(*Co-advised with Chris Chen)
PhD Bioengineering, UC Berkeley-UCSF Graduate Program (2020)
BS Chemical Eng., University of Nebraska-Lincoln (2013)

Allison completed a BS in Chemical Engineering at the University of Nebraska-Lincoln in 2013 and a PhD in Bioengineering from the UC Berkeley-UCSF Graduate Program in Bioengineering in 2020. Her PhD work focused on understanding extracellular matrix remodeling in breast cancer progression and its impact on cells in the tumor. As a co-advised postdoc with Chris Chen's lab, Allison is excited about using synthetic biology tools to dissect cellular contributions to tissue-level phenotypes in regeneration and disease and to develop cell-based therapeutics. When not working, Allison loves running, backpacking, and live music.
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.
Hagar F. Moussa
Postdoctoral Fellow
Postdoc IST Austria (2020)
PhD Molecular Biology, University of Vienna/IMBA (2018)
MS Molecular & Cellular Biology, Heidelberg Univ. (2013)
BS Biotechnology, The German University in Cairo (2009)

Hagar received her MS in Molecular and Cellular Biology from Heidelberg University while working in Bruce Edgar’s Lab on the growth and proliferation of stem cells in the fly midgut. As a graduate student in Oliver Bell’s Lab at IMBA, she worked on deconstructing epigenetic inheritance mediated by the Polycomb group of Proteins in mammalian stem cells. Among her interests is delving deeper into the basics of epigenetic memory to engineer elaborate layers of artificial epigenetic control into cells, to see how far we can go and for potential applications in industrial settings. Outside the lab, Hagar enjoys long runs, following F1 racing, hunting for new music, and reading. There is also a sewing machine sitting somewhere in a corner, but we haven’t gotten there yet.

Selected Awards:
2010 HBIGS MSc/PhD Fellowship
Arjun Ravikumar
Postdoctoral Fellow
(*Co-advised with Chang Liu)
PhD Biomedical Eng., UC Irvine (2019)
BS Bioengineering, Caltech (2011)

As a graduate student in Chang Liu’s lab at UC Irvine, Arjun developed OrthoRep, a system for continuous evolution of genes in yeast. Currently, he is applying OrthoRep towards therapeutic and industrially relevant problems, including antibody discovery. In his spare time, Arjun suffers from a debilitating Youtube addiction, and occasionally musters the willpower to read a book.
Will Shaw
Postdoctoral Fellow
(*Co-advised with Mary Gehring)
PhD Bioengineering, Imperial College London (2019)
MBiolSci Biochemistry, Sheffield University (2014)

As a graduate student in Tom Ellis' group at Imperial College London, Will pioneered novel approaches for refactoring signal transduction pathways in yeast. He is now interested in applying a synthetic genomics approach for deciphering gene regulation over large regions of the eukaryotic genome, using plant metabolic gene clusters as a model system. Outside of the lab, Will is passionate about cycling, fly fishing, gardening, and of course, a nice cuppa tea.
Brandon Wong
Postdoctoral Fellow
(*Co-advised with Chang Liu)
PhD Biomedical Eng., Boston University (2018)
BS Biomedical Eng., UC Irvine (2012)

As a graduate student in Mo Khalil's lab, Brandon developed eVOLVER: a DIY, automated, high-throughput microbial cell growth platform. His current work is applying eVOLVER to various problems in molecular evolution and experimental evolution. 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
Meghan Bragdon
PhD 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
PhD 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
PhD 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.
Daniel Hart
PhD Student, Biomedical Eng.
BS Bioengineering, Stanford University (2017)

Daniel completed his Bachelor’s degree in Bioengineering at Stanford University. At Stanford, he developed genomic screens for validating cancer driver genes in organoids. His current research focus is adapting the Khalil Lab’s eVOLVER platform for novel applications in synthetic and evolutionary biology, including anaerobic microbial communities and biotherapeutics. Away from lab, Daniel likes to read nonfiction, cook potatoes, sail boats, and dodge Boston traffic on his bike.
Zachary Heins
PhD 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
PhD 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
Charles Jo
PhD Student, Biomedical Eng.
(*Co-advised with Seth Rakoff-Nahoum)
MS Biomedical Eng., Boston University (2019)
BS Biomedical Eng., Duke University (2017)

Charles graduated from Duke University with a BSE in Biomedical Engineering, before pursuing his MS in Biomedical Engineering at Boston University. There he discovered his passion for microbiome and synthetic biology research, developing a co-culture device that enables real-time growth measurements of interacting microbes. Charles is currently interested in developing novel tools to understand how ecological interactions drive the evolution of community members and structure, particularly in the human gut microbiome. You can usually find Charles laughing way too loud, tending to his pet fish, microgreens and Corgi-mix, and daydreaming about a day Pokémon are real.

Colin Kunze
PhD Student, Biomedical Eng.
BS Biomedical Engineering, USC (2017)

Colin graduated from the University of Southern California in 2017 with a BS in Biomedical Engineering and a minor in Computational Biology and Bioinformatics. At USC, he worked in a vision research lab studying retinitis pigmentosa. His current research interests involve engineering epigenetic regulatory systems and cellular memory. Outside of the lab, he enjoys swimming, eating everything, and competing in triathlons.
Adam Sanford
PhD Student, Biomedical Eng.
BS Biophysics, Northeastern University (2018)

Adam graduated from Northeastern University with a B.S. in Biomedical Physics and a keen interest in synthetic biology. His undergraduate work involved metabolic engineering in E. coli, creating genetic circuits in bugs to create living probiotic therapeutics that replace lost metabolic function in humans. Adam’s research interests now encompass exploring new ways to encode and drive cellular behavior and memory, both at the genetic and epigenetic level. Beyond the lab, Adam enjoys reading, hiking, skiing, and above all, tinkering with everything from Legos to airplanes.
Ezira Yimer Wolle
PhD Student, Biomedical Eng.
BS Biomedical Eng., Boston University (2019)

Ezira completed his Bachelor’s degree in Biomedical Engineering with a minor in Computer Engineering at Boston University in 2019. At BU he worked on research projects involving genetic circuit design and automation tool development for synthetic biology. Ezira’s current research interests involve developing technologies at the interface of biology, software, and hardware to engineer complex cellular phenotypes. In particular, he is interested in leveraging cellular adaption and memory encoded by epigenetic elements. Outside of the lab, Ezira is engaged with the greater synthetic biology community through iGEM and the Nona Research Foundation. For fun he enjoys listening to music, working out, biking, gaming, and discovering novel ways to efficiently kill time in silico.

Selected Awards:
2020 NIH SB2 Training Grant
      Former Postdocs
Albert Keung
Derin Sevenler
Marco Galardini
Zehua Bao
Sungho Jang
Synthetic chromatin biology
Antibiotic resistance diagnostics
Experimental evolution
Continuous directed evolution
Microbiome engineering
Current Position
Assistant Professor, NC State Univ.
Postdoctoral Fellow, Toner Lab, MGH/HMS
Associate Professor, Hannover Med. School
Assistant Professor, Zhejiang Univ.
Assistant Professor, Incheon National Univ.
      Former Graduate Students
Ali Beyzavi
Saloni Jain
Gregory Newby
Dana Braff
Szilvia Kiriakov
Brandon Wong
Nikit Patel
Abdul Bhuiya (MS)
Maria Simbirsky (MS)
Minhee Park
Chris Mancuso
Microfluidics; yeast heat shock
Antibiotic resistance
Yeast prions
Antibiotic resistance diagnostics
Yeast prions
Synthetic gene circuits
Antibiotic resistance diagnostics
Synthetic epigenetic regulation
Microbial ecology; eVOLVER
Current Position
Postdoctoral Fellow, Langer Lab, MIT
Associate Consultant, QuintilesIMS
Postdoctoral Fellow, Liu Lab, Broad/Harvard
Principal Scientist, GRO Biosciences
Automation & Data Scientist, Axcella
Co-Founder, Fynch Bio
Postdoctoral Fellow, Klein Lab, Harvard
PhD Student, Bioengineering, UC Berkeley
Bioinformatics Scientist, Inscripta Postdoctoral Fellow, Boettiger Lab, Stanford
Postdoctoral Fellow, Springer Lab, Harvard
      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 “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.

more >

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)

more >