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. Mo is co-founder of K2 Biotechnologies and Fynch Biosciences, serves on the Scientific Advisory Board for Chroma Medicine and Senti Biosciences, and consults for numerous other biotechnology and therapeutics companies. His personal interests include taking his dog (Eloise) to the park and attempting to make the perfect cappuccino with his Nespresso machine.

Selected Awards:
2022 Schmidt Science Polymath Award
2022 W. M. Keck Foundation Medical Research Award
2021 AIMBE College of Fellows
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)

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

Heidi Klumpe
Postdoctoral Fellow
(*Co-advised with Mary Dunlop)
PhD Chemical Eng., Caltech (2021)
BA English, North Carolina State Univ. (2014)
BA Chemical Eng., North Carolina State Univ. (2013)

In her PhD, Heidi worked to untangle the combinatorial logic of BMP (Bone Morphogenetic Protein) signaling, whose diverse combinations of ligands pattern a wide array of tissues. Inspired and somewhat cowed by the beautiful complexity of development, she hopes to combine yeast synthetic biology and evolution experiments to understand the design principles of simple multicellularity. Outside of lab, she enjoys activities that pair well with podcasts, mostly running and cooking.

Selected Awards:
2022 Damon Runyon 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.
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

Nikit Patel
Postdoctoral Fellow
(*Co-advised with Chang Liu)
PhD Biomedical Eng., Boston University (2018)
BS Bioengineering, UC Berkeley (2011)

During graduate school, Nikit engineered cooperative transcription factor complexes in yeast to enable highly specific and tunable multi-input transcriptional logic. He also developed a thermodynamic model of protein assemblies in order to guide the construction of novel spatiotemporal regulatory behaviors in cells. For his postdoc, Nikit is building genetic circuits that enable high-throughput antibody discovery for multi-pass membrane proteins.

Selected Awards:
2020 Damon Runyon 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.
Mike Raymond
Postdoctoral Fellow
PhD Neuroscience, University of Virginia (2022)
BS Biological Sciences, Univ. of South Carolina (2010)

Mike received his BS in Biological Sciences from the University of South Carolina and his PhD in Neuroscience from the University of Virginia. During his PhD work in Dr. Kodi Ravichandran’s lab, Mike developed tools for tracking cell death and cell clearance in vivo. He is now interested in engineering synthetic circuits and immune cell behavior. When not in the lab, he enjoys hiking, cycling, making bad puns, and spending time with his wife and dog Murphy.

Selected Awards:
2018 EMBO Workshop Poster Award
2016 NIH Neuroscience Training Grant
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.

Selected Awards:
2021 EMBO Postdoctoral Fellowship

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
Nathaniel Borders
PhD Student, Bioinformatics
BS Biological Sciences, University of Delaware (2017)

At University of Delaware, Nate perturbed the genetics of mouse eye development in Dr. Salil Lachke's lab. Post-graduation, he developed synthetic cell-cell adhesion proteins and adapted the eVOLVER platform for growth of photosynthetic organisms in Dr. George Church’s lab. Currently, he adapts the eVOLVER for growth of bacteriophage in phage-assisted continuous evolution (PACE). He dreams of reversing man-made climate change, using biology to grow everything we need, and other utopian nonsense. His hobbies change rapidly but he could use suggestions for good fantasy series.
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.
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.
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.

Selected Awards:
2019 NIH SB2 Training Grant

Hanrong (Belle) Ye
PhD Student, Biomedical Eng.
(*Co-advised with Joyce Wong)
BS Biomedical Eng. & Chemical Eng., Vanderbilt University (2017)

Belle obtained her BS with a double major in Biomedical Engineering and Chemical Engineering from Vanderbilt University. Her undergraduate research focused on developing in vitro assays for a reactive oxygen species (ROS)-scavenging microparticle system. Currently she is working on an interdisciplinary project that combines nanoparticles-based drug delivery and immune cell engineering. Outside the lab, Belle enjoys playing the cello, napping, and any food-related activity.

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
Allison Drain
Chromatin; synthetic biology
Antibiotic resistance
Experimental evolution
Continuous evolution
Microbiome engineering
Immune cell 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.
Scientist II, Affini-T Therapeutics
      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
Divya Israni
Emma Briars
Zachary Heins
Microfluidics; yeast heat shock
Antibiotic resistance
Yeast prions
Antibiotic resistance
Yeast prions
Gene circuits
Antibiotic resistance
Epigenetics; synthetic biology
Microbial ecology; eVOLVER
Mammalian synthetic biology
Antibiotic resistance
Continuous evolution; eVOLVER
Current Position
Postdoctoral Fellow, Langer Lab, MIT
Associate Consultant, QuintilesIMS
Postdoctoral Fellow, Liu Lab, Broad/Harvard
Principal Scientist, GRO Biosciences
Senior Computational Biologist, Asimov, Inc.
Co-Founder, Fynch Bio
Postdoctoral Fellow, Klein Lab, Harvard
PhD Student, Bioengineering, UC Berkeley
Bioinformatics Scientist, Inscripta
Assistant Professor, KAIST
Postdoctoral Fellow, Lieberman Lab, MIT
Scientist, Satellite Bio
Comp. Biologist, Day Zero Diagnostics
Bioreactor Engineer, Biosphere
      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

Cellular Innovation by Rational Design and Evolution

Living cells use circuits of interacting molecules to process signals, remember information, and interact in complex ways with their environments. Our laboratory is interested in creating artificial cellular systems that exceed the design and functional repertoire of nature. Through building these synthetic systems de novo, we are uncovering the design principles of natural cellular circuits and how they carry out specific biological functions. To address the most pressing human diseases, we also use these systems to program useful cellular behaviors in a broader quest to develop next-generation cellular therapeutics.

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Multidimensional Control of Therapeutic Human Cell Function with Synthetic Gene Circuits
Hui-Shan Li*, Divya V. Israni*, Keith A. Gagnon, Kok Ann Gan, Michael H. Raymond, Jeffry D. Sander, Kole T. Roybal, J. Keith Joung, Wilson W. Wong and Ahmad S. Khalil
Science, 378: 1227-1234 (2022)

A Toolkit for Precise, Multi-Gene Control in Saccharomyces cerevisiae
Adam Sanford, Szilvia Kiriakov and Ahmad S. Khalil
ACS Synthetic Biology, 11: 3912-3920 (2022)

Recent Progress of Gene Circuit Designs in Immune Cell Therapies
Seunghee Lee, Ahmad S. Khalil and Wilson W. Wong
Cell Systems, 13: 864-873 (2022)

High-Throughput Continuous Evolution of Compact Cas9 Variants Targeting Single-Nucleotide-Pyrimidine PAMs
Tony P. Huang*, Zachary J. Heins*, Shannon M. Miller, Brandon G. Wong, Pallavi A. Balivada, Tina Wang, Ahmad S. Khalil and David R. Liu
Nature Biotechnology, doi: 10.1038/s41587-022-01410-2 (2022)

High-Performance Multiplex Drug-Gated CAR Circuits
Hui-Shan Li*, Nicole M. Wong*, Elliot Tague, John T. Ngo, Ahmad S. Khalil and Wilson W. Wong
Cancer Cell, 40: 1-12 (2022)

Cooperative Assembly Confers Regulatory Specificity and Long-Term Genetic Circuit Stability
Meghan D. J. Bragdon*, Nikit Patel*, James Chuang, Ethan Levien, Caleb J. Bashor* and Ahmad S. Khalil*
bioRxiv, doi: 10.1101/2022.05.22.492993

In Vivo Hypermutation and Continuous Evolution
Rosana S. Molina, Gordon Rix, Amanuella A. Mengiste, Beatriz Alvarez, Daeje Seo, Haiqi Chen, Juan E. Hurtado, Qiong Zhang, Jorge Donato Garcia-Garcia, Zachary J. Heins, Patrick J. Almhjell, Frances H. Arnold, Ahmad S. Khalil, Andrew D. Hanson, John E. Dueber, David V. Schaffer, Fei Chen, Seokhee Kim, Luis Angel Fernandez, Matthew D. Shoulders, and Chang C. Liu
Nature Reviews Methods Primer, 2: 36 (2022)

Modular Design of Synthetic Receptors for Programmed Gene Regulation in Cell Therapies
Iowis Zhu, Raymond Liu, Julie M. Garcia, Axel Hyrenius-Wittsten, Dan I. Piraner, Josef Alavi, Divya V. Israni, Bin Liu, Ahmad S. Khalil and Kole T. Roybal
Cell, 185: 1431-1443 (2022)

Once Cell, Many Fates (Perspective)
Colin Kunze and Ahmad S. Khalil
Science, 375: 262-263 (2022)

Here to Stay: Writing Lasting Epigenetic Memories (Preview)
Hagar F. Moussa*, James F. Angstman* and Ahmad S. Khalil
Cell, 184: 2281-2283 (2021)

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