Ahmad (Mo) Khalil, PhD

Dorf-Ebner Distinguished Associate Professor, Department of Biomedical Engineering

Associate Director, Biological Design Center
Boston University
Visiting Scholar, Wyss Institute for Biologically Inspired Engineering
Harvard University

Contact
Mail: 610 Commonwealth Ave, Rm 405C, Boston, MA 02215
Telephone: +1 617-358-6957, Email: khalil@bu.edu, Lab: www.bu.edu/khalillab

Education
2009 PhD, Mechanical Engineering, MIT (Advisor: Dr. Angela M. Belcher)
2004 MSc, Mechanical Engineering, MIT (Advisor: Dr. Roger D. Kamm)
2002 BSc, Mechanical Engineering (Chemistry Minor), Stanford University

Postdoctoral Training
2008–11 HHMI Postdoctoral Fellow, Boston University (Advisor: Dr. James J. Collins)

Professional Experience
2019– Associate Professor, Department of Biomedical Engineering, Boston University
2019– Co-Director, Synthetic Biology & Biotechnology (SB2) NIH/NIGMS T32 PhD Training Program
2015– Associate Director and Founding Member, Biological Design Center, Boston University
2014– Visiting Scholar, Wyss Institute for Biologically Inspired Engineering, Harvard University
2012–2018 Assistant Professor, Department of Biomedical Engineering, Boston University
2012– Faculty, Molecular Biology, Cell Biology & Biochemistry Program, Boston University
Faculty, Bioinformatics Program, Boston University

Extramural Appointments
2019– Co-Founder, K2 Biotechnologies, Inc.
2018– Co-Founder, Fynch Bio, Inc.
2018– Scientific Advisory Board, Senti Biosciences, Inc.
2018– Consultant, Merck & Co., Inc.
2017– Scientific Advisor, Sigilon Therapeutics, Inc.
2015– Member, Scientific Advisory Board, Warwick Integrative Synthetic Biology Centre

Awards & Honors (selected)

2020 DoD Vannevar Bush Faculty Fellowship (VBFF)
2019 Dorf-Ebner Distinguished Faculty Fellow
2018 National Academy of Engineering (NAE) Frontiers of Engineering Invitee
2017 Presidential Early Career Award for Scientists and Engineers (PECASE)
2017 Boston University Early Career Research Excellence Award
2016 NIH New Innovator Award
2016 DARPA Young Faculty Award
2016 Outstanding Professor of the Year, College of Engineering, Boston University
2016 Award for Teaching Excellence, Biomedical Engineering Dept., Boston University
2015 Hartwell Foundation Individual Biomedical Research Award (Hartwell Investigator)
2015 Award for Teaching Excellence, Biomedical Engineering Dept., Boston University
2014 National Academy of Engineering (NAE) Frontiers of Engineering Education Invitee
2014 NSF CAREER Award
2014 GenomeWeb Young Investigator Award
2013–2016 Innovation Career Development Professorship, Boston University
2013 Kern Faculty Fellow, Boston University
2013 Award for Teaching Excellence, Biomedical Engineering Dept., Boston University
2013 Institut Mérieux Research Grant Award
2012 Wallace H. Coulter Foundation Translational Research Partnership Award
2012 College of Engineering Dean’s Catalyst Award, Boston University
2005 Charles Stark Draper Laboratory Graduate Fellowship, MIT
2002 Graduated with Distinction, Stanford University
2002 Phi Beta Kappa Liberal Arts & Sciences Honors Society, Stanford University
2002 Tau Beta Pi Engineering Honors Society, Stanford University

Research Statement
My research is interested in gene regulatory “circuits” and how they enable complex cellular functions, such as
signal processing, computation, and epigenetic memory. My team develops and applies two complementary
approaches to discover the design principles of genetic circuits, and to enable their purposeful manipulation for
biomedical applications, such as cell-based therapies and devices. First, we use rational design approaches, in which
we build regulatory circuits in eukaryotic cells from the bottom-up. This allows us to re-design existing circuits with
precisely tailored biochemical parameters and establish functional sufficiency in a native cellular context. We have
pioneered this synthetic biology approach to design and study regulatory circuits that control gene regulation and
epigenetic memory in eukaryotes, with important implications for biotechnology and therapeutics. While this first
principles-based approach enables unhindered exploration of biological design principles, deciphering which
regulatory designs persist depends on 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 large-scale automation of growth, testing, and evolution of cellular systems in precisely-
controlled conditions. These synergistic approaches can accelerate discovery of fundamental principles of genetic
and epigenetic regulatory mechanisms, and provide a powerful foundation for the purposeful manipulation of
regulatory circuits to combat disease and program new traits in engineered cells and tissues. Additionally, we
believe strongly in the principle of cooperativity as a mediator of new ideas, tools, and science. eVOLVER has been
adopted by labs across the world. To facilitate cooperative interactions based upon eVOLVER, we have developed
online forums (www.evolver.bio) for open sharing of documentation, ideas, protocols, and data. We envisage that
this decentralized approach and the cooperative principles we have established will allow eVOLVER to evolve and
advance over time to carry out studies across broad fields well beyond the original scope of conception.

Publications (*equal)
1. Mancuso, C.P., Lee, H., Abreu, C.I., Gore, J. & Khalil, A.S. Environmental fluctuations reshape and
unexpected diversity-disturbance relationship in a microbial community. bioRxiv, doi:
10.1101/2020.07.28.225987.
2. Sun, Q., Vega, N.M., Cervantes, B., Mancuso, C.P., Mao, N., Taylor, M., Collins, J.J., Khalil, A.S.,
Gore, J. & Lu, T.K. Colonization with heterologous bacteria reprograms a Caenorhabditis elegans
nutritional phenotype. bioRxiv, doi: 10.1101/2020.03.01.972349.
3. Zhong, Z.*, Wong, B.G.*, Ravikumar, A., Arzumanyan, G.A., Khalil, A.S.† & Liu, C.C.† Automated
continuous evolution of proteins in vivo. ACS Synthetic Biology, 9: 1270-1276 (2020).
4. Qian, J.*, Lu, Z.X.*, Mancuso, C.P.*, Jhuang, H.Y.*, Del Carmen Barajas-Ornelas, R.*, Boswell,
S.A.*, Ramírez-Guadiana, F.H., Jones, V., Sonti, A., Sedlack, K., Artzi, L., Jung, G., Arammash, M.,
Pettit, M.E., Melfi, M., Lyon, L., Owen, S.V., Baym, M., Khalil, A.S., Silver, P.A., Rudner, D.Z. &
Springer, M. Barcoded microbial system for high-resolution object provenance. Science, 368: 1135-
1140 (2020).
• Perspective: Nivala J. Follow the barcoded microbes. Science, 368 (2020).
5. Chiesa, G.*, Kiriakov, S.* & Khalil, A.S. Protein assembly systems in natural and synthetic biology.
BMC Biology, 18: 35 (2020).
6. Tanner, K., Mancuso, C.P., Peretó, J., Khalil, A.S., Vilanova, C. & Pascual, J. Sphingomonas solaris
sp. nov., isolated from a solar panel in Boston, Massachusetts. International Journal of Systematic
and Evolutionary Microbiology, 70: 1814-1821 (2020).
7. Bashor, C.J.*, Patel, N.*, Beyzavi, A., Choubey, S., Kondev, J., Collins, J.J. & Khalil, A.S. Complex
signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science, 364:
593-597 (2019).
• Perspective: Ng A.H. and El-Samad H. Synthetic transcriptional synergy. Science, 364 (2019).
• News & Views: Cloney R. Cooperating on synthetic gene circuits. Nat. Biotechnol. 37 (2019).
8. Heins, Z.J., Mancuso, C.M., Kiriakov, S., Wong, B.G., Bashor, C.J. & Khalil, A.S. Designing
automated, high-throughput continuous cell growth experiments using eVOLVER. Journal of
Visualized Experiments, 147: e59652 (2019).
9. Lee, H.H., Ostrov, N., Wong, B.G., Gold, M.A., Khalil, A.S. & Church, G.M. Functional genomics of
the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nature Microbiology, 4: 1105-1113
(2019).
• Journal Cover
• News & Views: D’Gama J.D. and Waldor M.K. An ‘I’ for ingenuity. Nat. Microbiol., 4 (2019).
10. Park, M., Patel, N., Keung, A.J. & Khalil, A.S. Engineering epigenetic regulation using synthetic read-
write modules. Cell, 176: 227-238 (2019).
• Faculty of 1000.
• Research Highlight: Trenkmann M. Synthetic readers and writers for mammalian chromatin. Nat. Rev.
Genet., 20 (2019).
• Research Highlight: Rusk N. Creating epigenetic memory. Nat. Methods, 16 (2019).
• Viewpoint: Loveless T.B. and Liu C.C. Synthetic epigenetics to engineer regulation. Biochemistry, 58 (2019).
• Spotlight: Chang T.Z., Kuo J. and Silver P.A. Beyond the four bases: a home run for synthetic epigenetic
control? Mol. Cell, 74 (2019).
• Research Highlight: Song Y. Pass it along. Nat. Chem. Biol., 15 (2019).
11. Weinstein, Z.B., Kuru, N., Kiriakov, S., Palmer, A.C., Khalil, A.S., Clemons, P.A., Zaman, M.H.,
Roth, F.P. & Cokol, M. Modeling the impact of drug interactions on therapeutic selectivity. Nature
Communications, 9: 3452 (2018).
12. Wong, B.G.*, Mancuso, C.P.*, Kiriakov, S., Bashor, C.J. & Khalil, A.S. Precise, automated control of
conditions for high-throughput growth of yeast and bacteria with eVOLVER. Nature Biotechnology,
36: 614-623 (2018).
• Journal Cover
• Technology Feature: May M. Automated science on a shoestring. Nature, 569 (2019).
13. Zheng, X.*, Beyzavi, A.*, Krakowiak, J., Patel, N., Khalil, A.S.† & Pincus, D.† Hsf1 phosphorylation
generates cell-to-cell variation in Hsp90 levels and promotes phenotypic plasticity. Cell Reports, 22:
3099-3106 (2018).
14. Krakowiak, J.*, Zheng, X.*, Patel, N.*, Feder, Z.A., Anandhakumar, J., Valerius, K., Gross, D.S.†,
Khalil, A.S.† & Pincus, D.† Hsf1 and Hsp70 constitute a two-component feedback loop that regulates
the yeast heat shock response. eLife, 7: e31668 (2018).
15. Newby, G.A.*, Kiriakov, S.*, Hallacli, E.*, Kayatekin, C., Tsvetkov, P., Mancuso, C.P., Bonner, J.M.,
Hesse, W.R., Chakrabortee, S., Manogaran, A.L., Liebman, S.W., Lindquist, S. & Khalil, A.S. A
genetic tool to track protein aggregates and control prion inheritance. Cell, 171: 966-979 (2017).
• Journal Cover
• Faculty of 1000.
• Modus Operandi: Williams R. Detecting protein clumps. The Scientist. Feb 1, 2018.
16. Hawkins, F., Kramer, P., Jacob, A., Driver, I., Thomas, D.C., McCauley, K.B., Skvir, N., Crane, A.M.,
Kurmann, A.A., Hollenberg, A.N., Nguyen, S., Wong, B.G., Khalil, A.S., Huang, S.X., Guttentag, S.,
Rock, J.R., Shannon, J.M., Davis, B.R. & Kotton, D.N. Prospective isolation of NKX2-1-expressing
human lung progenitors from pluripotent stem cells. The Journal of Clinical Investigation, 127: 2277-
2294 (2016).
17. Pincus, D. & Khalil, A.S. Heat shock signaling, fast and slow (In: Principles of systems biology, no.
12). Cell Systems, 3: 504-506 (2016).
18. Zheng, X.*, Krakowiak, J.*, Patel, N., Beyzavi, A., Ezike, J., Khalil, A.S.† & Pincus, D.† Dynamic
 control of Hsf1 during heat shock by a chaperone switch and phosphorylation. eLife, 5: e18638 (2016).
• Insight: Breton L. and Mayer M. A model for handling cell stress. eLife, 5 (2016).
19. Park, M., Keung, A.J. & Khalil, A.S. The epigenome: the next substrate for engineering. Genome
Biology, 17: 183 (2016).
20. Mancuso, C.P., Kiriakov, S. & Khalil, A.S. Cellular advantages to signaling in a digital world
(Preview). Cell Systems, 3: 114-115 (2016).
21. Garcia-Ojalvo, J., Khalil, A.S. & McCarthy, J. Biological insights from synthetic biology (Editorial).
Integrative Biology, 8: 380-382 (2016).
22. Keung, A.J. & Khalil, A.S. A unifying model of epigenetic regulation (Perspective). Science, 351:
661-662 (2016).
23. Lobritz, M.A., Belenky, P., Porter, C.B.M., Gutierrez, A., Yang, J.H., Schwartz, E.G., Dwyer, D.J.,
Khalil, A.S.† & Collins, J.J.†. Antibiotic efficacy is linked to bacterial cellular respiration. Proc Natl
Acad Sci USA, 112: 8173-8180 (2015).
24. Keung, A.J., Joung, J.K., Khalil, A.S. & Collins, J.J. Chromatin regulation at the frontier of synthetic
biology. Nature Reviews Genetics, 16: 159-171 (2015).
25. Keung, A.J., Bashor, C.J., Kiriakov, S., Collins, J.J. & Khalil, A.S. Using targeted chromatin
regulators to engineer combinatorial and spatial transcriptional regulation. Cell, 158: 110-120 (2014).
• Journal Cover
• Research Highlight: Burgess D.J. Gene regulation: a chromatin-based recruitment drive. Nat. Rev. Genet., 15
(2014).
26. Dwyer, D.J., Belenky, P., Yang, J.H., MacDonald, I.C., Martell, J.D., Takahashi, N., Chan, C.T.Y.,
Lobritz, M.A., Braff, D., Schwartz, E.G., Ye, J.D., Pati, M., Vercuysse, M., Ralifo, P.S., Allison, K.R.,
Khalil, A.S., Ting, A.Y., Walker, G.C. & Collins, J.J. Antibiotics induce redox-related physiological
alterations as part of their lethality. Proc Natl Acad Sci USA, 111: E2100-9 (2014).
27. Litcofsky, K.D., Afeyan, R.B., Krom, R.J., Khalil, A.S.† & Collins, J.J.† Iterative plug-and-play
methodology for constructing and modifying synthetic gene networks. Nature Methods, 9: 1077–1080
(2012).
• News & Views: Tabor J.J. Modular gene-circuit design takes two steps forward. Nat. Methods, 9 (2012).
28. Khalil, A.S.*, Lu, T.K.*, Bashor, C.J.*, Ramirez, C.L., Pyenson, N.C., Joung, J.K. & Collins, J.J. A
synthetic biology framework for programming eukaryotic transcription functions. Cell, 150: 647–658
(2012).
• Research Highlight: Jones S. Expanding the engineer’s toolkit. Nat. Biotechnol., 30 (2012).
• Research Highlight: Programming transcription. Nat. Methods, 9 (2012).
• Highlighted in Genetic Engineering & Biotechnology News and MIT News.
29. Vega, N.M., Allison, K.R., Khalil, A.S. & Collins, J.J. Signaling-mediated bacterial persister
formation. Nature Chemical Biology, 8: 431–433 (2012).
• Journal Cover
• Research Highlight: Microbiology: bacteria signal to survive. Nature, 483 (2012).
• Editor’s Choice: Microbiology: bacteria hedge their bets. Science, 336 (2012).
• Research Highlight: Jermy A. From indolence to persistence. Nat. Rev. Microbiol. 10 (2012).
• Research Highlight: Signaling-mediated bacterial persister formation. Nat. Med., 18 (2012).
• Highlighted in Chemical & Engineering News.
30. Khalil, A.S. & Collins, J.J. Synthetic biology: applications come of age. Nature Reviews Genetics, 11:
367–379 (2010).
• Journal Cover
• Highlighted in The New York Times and Folha de S. Paulo.
31. Borenstein, J.T., Tupper, M.M., Mack, P.J., Weinberg, E.J., Khalil, A.S., Hsiao, J. & Garcia-Cardena,
G. Functionalized endothelialized microvascular networks with circular cross sections in a tissue
culture substrate. Biomedical Microdevices, 12: 71–79 (2010).
32. Lu, T.K., Khalil, A.S. & Collins, J.J. Next-generation synthetic gene networks. Nature Biotechnology,
27: 1139–1150 (2009).
33. Khalil, A.S., Appleyard, D.C., Labno, A.K., Georges, A., Karplus, M., Belcher, A.M., Hwang, W. &
Lang, M.J. Kinesin’s cover-neck bundle folds forward to generate force. Proc Natl Acad Sci USA,
105: 19247–19252 (2008).
34. Khalil, A.S., Ferrer, J.M., Brau, R.R., Kottmann, S.T., Noren, C.J., Lang, M.J. & Belcher, A.M. Single
M13 bacteriophage tethering and stretching. Proc Natl Acad Sci USA, 104: 4892–4897 (2007).
• Journal Cover
35. Khalil, A.S., Bouma, B.E. & Kaazempur-Mofrad, M.R. A combined FEM/genetic algorithm for
vascular soft tissue elasticity estimation. Cardiovascular Engineering, 6: 93–102 (2006).
36. Khalil, A.S., Chan, R.C., Chau, A.H., Bouma, B.E. & Kaazempur-Mofrad, M.R. Tissue elasticity
estimation with optical coherence elastography: toward complete mechanical characterization of in
vivo soft tissue. Annals of Biomedical Engineering, 33: 1631–1639 (2005).
37. Chan, R.C., Chau, A.H., Karl, W.C., Nadkarni, S., Khalil, A.S., Iftimia, N., Shishkov, M., Tearney,
G.J., Kaazempur-Mofrad, M.R. & Bouma, B.E. OCT-based arterial elastography: robust estimation
exploiting tissue biomechanics. Optics Express, 12: 4532–4572 (2004).

Invited Talks and Seminars

1. Invited Talk: Synthetic Biology CSHL Course, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY, USA, 2021.
2. Invited Talk: Yeast Genetics & Genomics CSHL Course, Cold Spring Harbor Laboratory, Cold
Spring Harbor, NY, USA, 2021.
3. Invited Talk: Quantitative Biology Series (QBS), Harvard Quantitative Biology Initiative, Harvard
University, Cambridge, MA, USA, 2021.
4. Invited Talk: Department of Microbiology, University of Massachusetts, Amherst, MA, USA, 2020.
5. Invited Talk: Institute for Systems Genetics, NYY Langone Health, New York University, New York,
NY, USA, 2020.
6. Invited Talk: 4th International Conference on Epigenetics and Bioengineering (EpiBio 2020), North
Carolina State University, Raleigh, NC, USA, 2020.
7. Invited Talk: q-Bio 2020: A Virtual Conference on Quantitative Biology, 2020.
8. Invited Talk: BME Higher Education and Research in a Pandemic-Challenged Environment, 2020
BME Council of Chairs Online Mini-Summit, 2020.
9. Invited Talk: BBC Seminar Series, Biophysics / Bioinformatics / Chemistry & Chemical Biology
Graduate Programs, UCSF, San Francisco, CA, USA, 2019.
10. Invited Talk: BMG Seminar Series, Department of Biochemistry and Molecular Genetics, Feinberg
School of Medicine, Northwestern University, Chicago, IL, USA, 2019.
11. Invited Talk: Molecular Engineering & Sciences (MolES) Seminar Series, University of Washington,
Seattle, WA, USA, 2019.
12. Invited Talk: Department of Chemical and Biological Engineering, Tufts University, Medford, MA,
USA, 2019.
13. Invited Talk: The Future of Quantitative Biology Symposium, NSF-Simons Center for Mathematical
& Statistical Analysis of Biology, Harvard University, Cambridge, MA, USA, 2019.
14. Invited Talk: Bioengineering Seminar Series, University of Illinois at Urbana-Champaign, Urbana,
IL, USA, 2019.
15. Invited Talk: Network Biology Meeting, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
USA, 2019.
16. Invited Talk: Bioengineering Lecture Series (BELS), Division of Biology and Biological Engineering,
Caltech, Pasadena, CA, USA, 2019.
17. Invited Talk: Department of Biomedical Engineering, University of California, Irvine, CA, USA,
2019.
18. Invited Talk: 9th International Conference on Biomolecular Engineering (9th ICBE), Newport Beach,
CA, USA, 2019.
19. Invited Talk: Sterling Drug Lecture. Pharmacological Sciences Seminar Series, Program in
Biomolecular Pharmacology, Department of Pharmacology & Experimental Therapeutics, Boston
University School of Medicine, Boston, MA, USA, 2018.
20. Invited Talk: BioEngineering Seminar, Center for Biomolecular and Tissue Engineering, Duke
University, Durham, NC, USA, 2018.
21. Invited Talk: 2nd International Conference on Epigenetics and Bioengineering (EpiBio 2018), UCSF,
San Francisco, CA, USA, 2018.
22. Invited Talk: Department of Biomedical Engineering, Boston University, Boston, MA, USA, 2018.
23. Invited Talk: Department of Chemical & Biological Engineering, Northwestern University, Evanston,
IL, USA, 2018.
24. Invited Talk: Biotechnology Training Program (BTP) Seminar Series, Advances in Biotechnology,
Northwestern University, Evanston, IL, USA, 2018.
25. Invited Talk: Engineering Biology Research Consortium (EBRC) Spring Retreat, University of
Washington, Seattle, WA, USA, 2018.
26. Invited Talk: Center for Molecular Discovery, Boston University, Boston, MA, USA, 2018.
27. Invited Talk: Department of Genetics & Development, Columbia University Medical Center, New
York, NY, USA, 2018.
28. Keynote Talk: Quantitative Biology Boot Camp, Quantitative Biology Program, Brandeis University,
Waltham, MA, USA, 2018.
29. Invited Talk: Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA, 2017.
30. Invited Talk: The BioTechnology Institute Seminar Series, University of Minnesota, St Paul, MN,
USA, 2017.
31. Invited Talk: Gene Expression and RNA Series (GEARS), Harvard Medical School, Boston, MA,
USA, 2017.
32. Invited Talk: The Hartwell Foundation 10th Annual Meeting, Duke University, Durham, NC, USA,
2017.
33. Invited Talk: Synthetic Biology at Molecular, Cellular and Multicellular Levels (International
Workshop Organized by WISB), Venice, Italy, 2017.
34. Invited Talk: Draper Laboratory, Cambridge, MA, USA, 2017.
35. Invited Talk: Green Center for Systems Biology Seminar, UT Southwestern Medical Center, Dallas,
TX, USA, 2017.
36. Invited Talk: Gordon Research Conference (GRC) on Synthetic Biology, Stowe, VT, USA, 2017.
37. Invited Talk: Synthetic Biology: Engineering, Evolution & Design (SEED), Vancouver, British
Columbia, Canada, 2017.
38. Invited Talk: Integrative BioSystems Institute Seminar Series, Department of Biomedical
Engineering, Georgia Institute of Technology, Atlanta, GA, USA, 2017.
39. Invited Talk: Center for Engineering in Medicine (CEM) Seminar Series, Massachusetts General
Hospital, Harvard Medical School, Boston, MA, USA, 2017.
40. Invited Talk: Genome Editing and Advances in Transgenic Technology USA Congress, Harvard
Medical School, Boston, MA, 2017.
41. Invited Talk: Department of Chemical and Systems Biology, Stanford University School of Medicine,
Stanford, CA, USA, 2017.
42. Invited Talk: Department of Bioengineering, University of California, Berkeley, CA, USA, 2017.
43. Invited Talk: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA,
2017.
44. Invited Talk: School of Biological and Health Systems Engineering, Arizona State University,
Tempe, AZ, USA, 2017.
45. Invited Talk: The Hartwell Foundation 9th Annual Meeting, Cleveland Clinic / Case Western
University, Cleveland, OH, USA, 2016.
46. Invited Talk: Physiology: Modern Cell Biology Using Microscopic, Biochemical and Computational
Approaches, Marine Biological Laboratory, Woods Hole, MA, USA, 2016.
47. Invited Talk: Warwick Integrative Synthetic Biology Centre Launch Event, University of Warwick,
Coventry, UK, 2016.
48. Invited Talk: LabLinks: Gene Circuits, Co-sponsored by Cell Press and the Center for Cell Circuits,
Broad Institute, Cambridge, MA, USA, 2016.
49. Invited Talk: Theory Lunch, Department of Systems Biology, Harvard Medical School, Boston, MA,
USA, 2016.
50. Invited Talk: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD,
USA, 2015.
51. Invited Talk: Department of Molecular Microbiology and Immunology, Brown University,
Providence, RI, USA, 2015.
52. Invited Talk: Lab-on-a-chip, Microfluidics & Microarrays World Congress, San Diego, CA, USA,
2015.
53. Invited Talk: Synthetic Biology: From Standard Biological Parts to Artificial Life, B-Debate
International Center for Scientific Debate, Barcelona, Spain, 2015.
54. Invited Talk: Synthetic Biology CSHL Course, Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY, USA, 2015.
55. Invited Talk: EpiCongress 2015, Boston, MA, USA, 2015.
56. Invited Talk: Gene Regulation by the Numbers, Radcliffe Institute for Advanced Study, Harvard
University, Cambridge, MA, USA, 2015.
57. Invited Talk: Department of Physiology & Biophysics, Boston University School of Medicine,
Boston, MA, USA, 2015.
58. Guest Lecture: MCB 187: Genome Editing – Progress and Frontiers (Spring 2015), Department of
Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA, 2015.
59. Invited Talk: Biophysics Seminar Series, MIT, Cambridge, MA, USA, 2014.
60. Invited Talk: Bioengineering Lecture Series, California Institute of Technology, Pasadena, CA, USA,
2014.
61. Invited Talk: Cell Circuits & Epigenomics Seminar, Broad Institute, Cambridge, MA, USA, 2014.
62. Invited Talk: Meeting for the Mérieux Research Grants, Annecy, France, 2014.
63. Invited Talk: Departments of Biology and Biochemistry, Genetics Training Grant Symposium
(Synthetic Biology: Insights and Applications), Brandeis University, Waltham, MA, USA, 2014.
64. Invited Talk: 7th World Congress of Biomechanics, Boston, MA, USA, 2014.
65. Invited Talk: Towards Next Generation Synthetic Biology, University of Warwick, Coventry, UK,
2013.
66. Invited Talk: Materials Research Science and Engineering Center (MRSEC) Seminar, Brandeis
University, Waltham, MA, USA, 2013.
67. Invited Talk: Precision Genome Engineering and Synthetic Biology, Keystone Symposia,
Breckenridge, CO, USA, 2013.
68. Invited Talk: Department of Molecular & Cell Biology, Boston University School of Dental
Medicine, Boston, MA, USA, 2013.
69. Invited Talk: Department of Biology and Program in Molecular Biology, Cell Biology &
Biochemistry, Biomolecular Seminar Series, Boston University, Boston, MA, USA, 2012.
70. Invited Talk: Synthetic Biology Working Group, Harvard Medical School, Boston, MA, USA, 2012.
71. Invited Plenary Talk: Italian Federation of Life Sciences (FISV) 12th Congress, Rome, Italy, 2012.
72. Invited Talk: Department of Biomedical Engineering, Boston University, Boston University, Boston,
MA, USA, 2011.
73. Invited Talk: Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA, 2011.
74. Invited Talk: Departments of Chemical Engineering, Biomedical Engineering, and Cell Biology, Yale
University, New Haven, CT, USA, 2011.
75. Platform Presentation: NASA Ames Research Center, Moffett Field, CA, USA, 2010.
76. Invited Talk: Center for Excellence in Vascular Biology Seminar Series, Harvard Medical School,
Brigham & Women’s Hospital, Boston, MA, USA, 2010.
77. Invited Talk: Harvard Single Molecule Discussion Group, Cambridge, MA, USA, 2008.
78. Invited Talk: Mechanics: Modeling, Experimentation, Computation Seminar Series, Department of
Mechanical Engineering, MIT, Cambridge, MA, USA, 2008.
79. Invited Talk: Biomechanical Engineering Seminar Series, Department of Mechanical Engineering,
Stanford University, Stanford, CA, USA, 2008.
80. Platform Presentation: Biophysical Society Annual Meeting, Long Beach, CA, USA, 2008.
81. Platform Presentation: Biophysical Society Annual Meeting, Salt Lake City, UT, USA, 2006.

Academic Service at the Departmental, College and Campus Levels

2019– Co-Director, Synthetic Biology & Biotechnology (SB2) NIH/NIGMS T32 PhD Training Program
2018–19 Chair, Biological Design Center Faculty Search Committee, Boston University
2018–19 Member, Biomedical Engineering Undergraduate Committee, Boston University
2017–18 Member, Biomedical Engineering Undergraduate Committee, Boston University
2016–17 Member, Biomedical Engineering Faculty Search Committee, Boston University
2016–17 Member, Biomedical Engineering Undergraduate Committee, Boston University
2015– Associate Director and Founding Member, Biological Design Center, Boston University
2015–16 Member, Biomedical Engineering Faculty Search Committee, Boston University
2014–15 Member, Biomedical Engineering Faculty Search Committee, Boston University
2014–15 Member, Biomedical Engineering Undergraduate Committee, Boston University
2014–15 Faculty Adviser, Society of Asian Scientists & Engineers, Boston University
2013–14 Member, Biomedical Engineering Undergraduate Committee, Boston University
2013–14 Faculty Adviser, Society of Asian Scientists & Engineers, Boston University
2012–13 Member, Biomedical Engineering Undergraduate Committee, Boston University
2012 Member, Biomedical Engineering Graduate Admissions Committee, Boston University

Professional Service at the National and International Levels

2021 Chair, Gordon Research Conference (GRC) on Synthetic Biology
2021 Organizing Committee, 11th International Conference on Biomolecular Engineering, Santa Barbara,
CA, USA
2020 Co-Chair, Mammalian Synthetic Biology Workshop 7.0, Edinburgh, UK
2020 NIH Study Section Cellular and Molecular Technologies (CMT) (Ad-hoc member)
2019 Steering Committee, The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction:
Prospects and Challenges (Alfred P. Sloan Foundation), Boston University, Boston, MA USA
2019 Co-Author, EBRC Engineering Biology Roadmap (A Research Roadmap for the Next-Generation
Bioeconomy)
2019 Vice Chair, Gordon Research Conference (GRC) on Synthetic Biology
2019 NSF Advisory Panelist, Panel 191842, EFRI: Chromatin and Epigenetic Engineering
2019 Co-Chair, Mammalian Synthetic Biology Workshop 6.0, Northwestern University, Evanston, IL,
USA
2018 Organizing Committee, Synthetic Biology: Engineering, Evolution & Design (SEED), Scottsdale,
AZ, USA
2018 Chair, Mammalian Synthetic Biology Workshop 5.0, Harvard Medical School, Boston, MA, USA
2018– Academic Member, Engineering Biology Research Consortium (EBRC)
2018 Organizing Committee, 2nd International Conference on Epigenetics and Bioengineering (EpiBio
2018), UCSF, San Francisco, CA, USA
2017 Chair, Mammalian Synthetic Biology Workshop 4.0, Boston University, Boston, MA USA
2017 Chair, 1st International Conference on Epigenetics and Bioengineering (EpiBio 2017), Miami, FL,
USA
2016 Co-Chair, Mammalian Synthetic Biology Workshop 3.0, MIT, Cambridge, MA, USA
2016 Instructor, Cold Spring Harbor Laboratory Course on Synthetic Biology, Cold Spring Harbor, NY,
USA
2016 Guest Editor, Integrative Biology special themed issue on Synthetic Biology (8: 380-382 (2016))
2015 Workshop Invitee, “Gene Regulation by the Numbers”, Radcliffe Institute for Advanced Study,
Harvard University, Cambridge, MA, USA
2015 Organizing Committee, Mammalian Synthetic Biology Workshop 2.0, MIT, Cambridge, MA, USA.
2015 Organizing Committee, B-Debate International Center for Scientific Debate Meeting on Synthetic
Biology, Barcelona, Spain
2014 NIH/NIGMS Review Panelist, Special Emphasis Panel ZGM1 PPBC-Y(GN)
2014 Organizing Committee, Synthetic Biology Boston (SB2), Boston University, Boston, MA, USA
2014 NSF Advisory Panelist, Panel P140678, Division of Molecular and Cellular Biosciences
2013 Organizing Committee, Towards Next Generation Synthetic Biology, University of Warwick, UK
2013 Organizing Committee, Synthetic Biology Research & Innovation Partnership Campaign (US-UK
Partnerships in Synthetic Biology), Boston University & UK Consulate, Boston, MA, USA
2013 NIH/NIGMS Review Panelist, Special Emphasis Panel ZGM1 PPBC-A(NP).
2013 Organizing Committee & Session Chair, 4th International Conference on Biomolecular Engineering,
Fort Lauderdale, FL, USA
2010 Workshop Invitee, “What Are the Potential Roles for Synthetic Biology in NASA’s Mission?” NASA
Ames Research Center, Moffett Field, CA, USA

Professional Societies
Biophysical Society (BPS)
Engineering Biology Research Consortium (EBRC)
Editorial Board
iScience (Cell Press), Scientific Reports (Nature)

Archival Journals Refereed (selected)

ACS Synthetic Biology, APL Bioengineering, Biophysical Journal, Biotechnology Journal, Cell, Cell Reports, Cell
Systems, eLife, Frontiers in Antimicrobials, G3: Genes Genomes Genetics, Journal of Biological Engineering,
Journal of Visualized Experiments, Molecular Biosystems, Molecular Cell, Nature Biomedical Engineering, Nature
Biotechnology, Nature Chemical Biology, Nature Communications, Nature Methods, Nature Nanotechnology,
Nucleic Acids Research, PNAS, Resistance and Chemotherapy, Science

Patent Applications
1. “Notch Receptors with Zinc Finger-Containing Transcriptional Effector.” Provisional Patent
Application No. US 63/007,795 (April 9, 2020).
2. “Parathyroid Hormone (PTH) Expression Vectors and Uses Thereof.” Provisional Patent Application
No. US 62/889,223 (August 20, 2019).
3. “NS3-Regulated Synthetic Gene Expression Systems.” Provisional Patent Application No. US
62/848,850 (May 16, 2019).
4. “Systems and Methods for Control of Gene Expression.” Patent Application Publication No. US
2020/0002710 A1 (January 2, 2020) and WO 2020/006409 A1 (January 2, 2020).
5. “Methods for Experimental Evolution of Natural and Synthetic Microbes.” Patent Application
Publication No. US 16/081,975 (February 17, 2017) and WO 2018/152442 A1 (August 23, 2018).

Patents Issued
6. “An Integrated System for Programmable DNA Methylation.” Patent No. US 10,465,187 B2
(November 5, 2019) and WO 2018/145068 A1 (August 9, 2018).
7. “Synthetic Transcriptional and Epigenetic Regulators Based on Engineered, Orthogonal, Zinc Finger
Proteins.” Patent No. US 10,138,493 B2 (November 27, 2018) and WO 2018/039471 A2 (March 1,
2018).
8. “Method of Fabricating Microfluidic Structures for Biomedical Applications.” Patent No. US
8,266,791 B2 (September 18, 2012), WO 2009/039378 A2 (March 26, 2009), and EP 2 200 931 B1
(June 7, 2017).
9. “High-Throughput Biological Screening.” Patent No. US 9,006,149 B2 (April 14, 2015), WO
2010/083282 A1 (July 22, 2010), and EP 2 382 305 B1 (July 24, 2014).

Training, Education, and Outreach

I have a strong record and passion for training, education, and outreach. I have trained 20 graduate students (9
former, 11 current) and 12 postdoctoral associates (5 former). Former group members have gone on to a wide range
of academic and industrial positions, and 4 former trainees have gone on to establish independent labs in academia. I
am the Founding Associate Director of the Biological Design Center at Boston University, where I oversee research
and training programs in synthetic biology and biological engineering. I am proud to have led the successful
application and currently serve as Co-Director for the nation’s first NIH/NIGMS T32 PhD Training Program in
synthetic biology, which aims to recruit and train a new generation of diverse synthetic biology research leaders.
Unique components of our program include: (1) curriculum and research environments designed for a highly
interdisciplinary field; (2) hands-on exposure to biotechnology and training in the principles of commercialization
and entrepreneurship; (3) extensive professional skills development, including communication, leadership,
entrepreneurship, and working in multidisciplinary teams.
My teaching activities at the undergraduate and graduate student levels have spanned a wide variety of new and
existing courses. Altogether, I have taught 714 undergraduate and 61 graduate students in the classroom and
received one of the highest average evaluation scores in our department’s history (4.75 / 5.00). I have been fortunate
to receive the Department Award for Teaching Excellence three times (2016, 2015, 2013), the Outstanding
Professor of the Year for the College of Engineering (2016), and to be invited to both National Academy of
Engineering (NAE) Frontiers in Engineering Education (2014) and NAE Frontiers in Engineering (2018) Symposia.

Students from underrepresented groups leave STEM careers disproportionately often. How can we help these
students persist in STEM careers? Research experience in engaging and diverse labs is key, where students gain
confidence and learn to identify themselves as scientists (Graham et al, Science 2013). I have embraced this model
in my outreach activities. Our lab has hosted undergraduate summer interns, providing students from
underrepresented and disadvantaged backgrounds meaningful mentored lab experiences. I have established a
summer bootcamp for high school students to gain experiential training in synthetic biology. Alumni consistently
express a desire to pursue degrees in engineering and life sciences, and one female alumnus was awarded the
Mitchell Scholarship and will pursue a PhD at Harvard University. Other outreach activities include serving as
organizer and instructor for the Cold Spring Harbor Laboratory Course on synthetic biology (2016), and serving as
Faculty Mentor for award-winning undergraduate iGEM (International Genetically Engineered Machine) teams, a
synthetic biology research competition with immense global reach.

Teaching
Boston University, Department of Biomedical Engineering
Term Subject Number Title Role (Evaluation) Type / # of Students
Thermodynamics & Instructor (4.82/5.00)
Fall 2012 EK424 Lecture / 78 Ugrad
Statistical Mechanics AWARD
Thermodynamics &
Spring 2014 EK424 Instructor (4.92/5.00) Lecture / 81 Ugrad
Statistical Mechanics
Methods and Logic in Instructor (N/A)
Fall 2014 BE700 Discussion / 11 Grad
Quantitative Biology NEW COURSE
Thermodynamics &
Fall 2014 EK424 Instructor (4.85/5.00) Lecture / 87 Ugrad
Statistical Mechanics
Control Systems in Instructor (4.84/5.00)
Spring 2015 BE402 Lecture / 130 Ugrad
Biomedical Eng. AWARD
Thermodynamics & Instructor (4.73/5.00)
Spring 2016 EK424 Lecture / 74 Ugrad
Statistical Mechanics AWARD
Control Systems in Instructor (4.54/5.00)
Spring 2016 BE402 Lecture / 110 Ugrad
Biomedical Eng. AWARD
Control Systems in
Spring 2017 BE402 Instructor (4.49/5.00) Lecture / 154 Ugrad
Biomedical Eng.
Methods and Logic in
Spring 2018 BE700 Instructor (4.95/5.00) Discussion / 22 Grad
Quantitative Biology
Biomedical Signals and Co-Instructor
Fall 2018 BE403 Lecture / 142 Ugrad
Controls (4.23/5.00)
Methods and Logic in
Spring 2020 BE700 Instructor (4.95/5.00) Discussion / 26 Grad
Quantitative Biology

Current & Past Postdoctoral Fellows Advised

Name Prior Universities Training Period Current Position
Current Postdoctoral Fellows
Giulio Chiesa IRB Barcelona (PhD) 2016–
University of Pavia (BS, MS)
Hui-Shan Li Seoul National (PhD) 2016–
Tianjin University (BS)
Brandon Wong Boston University (PhD) 2019–
 UC Irvine (BS)
Arjun UC Irvine (PhD) 2019–
Ravikumar Caltech (BS)
James Harvard University (PhD) 2020–
Angstman University of Minnesota (BS)
William Shaw Imperial College London (PhD) 2020–
University of Sheffield (BS)
Hagar Moussa Universität Wien, IMBA (PhD) 2020–
Universität Heidelberg (MS)
German University Cairo (BS)
Past Postdoctoral Fellows
Albert Keung UC Berkeley (PhD) 2012–2015 Assistant Professor, Chemical & Biomolecular
Stanford University (BS) Engineering, NC State University
Derin Sevenler Boston University (PhD) 2017–2018 Postdoc, MGH / Harvard Medical School (Lab of
Cornell University (BS) Mehmet Toner)
Zehua Bao University of Illinois Urbana- 2018–2020 Assistant Professor, Institute of Bioengineering,
Champaign (PhD) College of Chemical and Biological Engineering,
Tsinghua University (BS) Zhejiang University
Marco Galardini EMBL-EBI (Postdoc) 2019–2020 Associate Professor in Systems Biology of
University of Florence (PhD, Microbial Communities, Helmholtz Centre for
BS) Infection Research, Hannover Medical School
Sungho Jang POSTECH (Postdoc) 2019–2020 Assistant Professor, Division of Bioengineering,
POSTECH (PhD, BS) Incheon National University, Korea

Current & Past Graduate Students Advised

Name Prior Universities Degree / Dept / Yr Current Position
Current PhD Students
Divya Israni UC Berkeley (BS) PhD / BME / 2020
Meghan Bragdon Stonehill College (BA) PhD / MCBB / -
NYU (Post-bac)
Emma Briars Boston University (BA) PhD /
Bioinformatics / -
Keith Gagnon Worcester Polytechnic Institute MD-PhD / BME / -
Kok Ann (Sam) Illinois Tech PhD / MCBB / -
Gan UW Madison
Zachary Heins Georgetown (MS) PhD / BME / -
UT Dallas (BS)
Colin Kunze USC (BS) PhD / BME / -
Daniel Hart Stanford University (BS) PhD / BME / -
Adam Sanford Northeastern University (BS) PhD / BME / -
Ezira Yimer Boston University (BS) PhD / BME / -
Wolle
Charles Jo Boston University (MS) PhD / BME / -
Duke University (BS)
Past PhD Students
Ali Beyzavi Nanyang University (MS) PhD / ME / 2016 Postdoc, Chemical Engineering, MIT (Lab of Robert
Azad University (BS) Langer)
Saloni Jain MIT (BS) PhD / BME / 2017 Associate Consultant, QuintilesIMS
Gregory Newby Carnegie Mellon (BS) PhD (MIT) / Postdoc, Broad Institute / Harvard (Lab of David Liu)
Biology / 2017
Dana Braff MIT (BS) PhD / BME / 2017 Principal Scientist, GRO Biosciences
Szilvia Kiriakov Budapest University of Technol. PhD / MCBB / 2018 Automation & Data Scientist, Axcella Health Inc.
& Econ. (MS, BS)
Brandon Wong UC Irvine (BS) PhD / BME / 2018 Co-Founder, Fynch Bio, Inc.;
Postdoc, Biomedical Engineering, BU (Lab of Mo Khalil)
Nikit Patel UC Berkeley (BS) PhD / BME / 2018 Postdoc, Systems Biology, HMS (Lab of Allon Klein)
Minhee Park Rice University (BS) PhD / BME / 2019 Postdoc, Developmental Biology, Stanford (Lab of
Alistair Boettiger)
Christopher Cornell University (BS) PhD / BME / 2020 Postdoc, Systems Biology, HMS (Lab of Michael
Mancuso Springer)

Current & Past Undergraduate & High School Students Advised

Current Students
Name School Years / Distinction Name School Years / Distinction
Akhila Sonti Boston University 2018– / UROP Pallavi Balivada Boston University 2018–
Leen Arnaout Boston University 2019– / UROP, Lutchen Jack Cardini Boston University 2019– / UROP
Distinguished Fellow
Shuwen (Eric) Boston University 2019– / UROP Matthew Boston University 2019–
Lee Reynolds-Tejeda
Paarth Patel Boston University 2020– Blaire Smith Boston University 2020– / UROP

Past Students
Name School Years / Distinction Name School Years / Distinction
Nora Pyenson Boston University 2012 Max Cotler Boston University 2012–2014 / Presidential
Scholarship, UROP
Cathryn Hart Boston University 2012–2014 / HS Thesis Davis Borucki Boston University 2013–2014 / Trustee
Academy (HS) Scholarship, UROP
Madeleine Joung Boston University 2014–2016 / HS Thesis Rachel William G. Enloe 2014 / RISE Program
Academy (HS) Petherbridge HS (Raleigh, NC)
Samantha Pipe Boston University 2014–2015 / UROP, Amir Boston University 2014–2016 / UROP
Lutchen Distinguished Soltanianzadeh
Fellow
Rishi Jain Boston University 2014–2015 / Presidential Andrew Caltech 2015 / Caltech SURF
Scholar., UROP Montequin Program
Hannah Boston University 2015–2016 / Presidential Aditya Cavale Boston University 2015–2017 / UROP,
Vanbenschoten Scholar., UROP STARS
Alexander Sun Boston University 2015–2018 / UROP Maxime French-American 2016
Fouilleron School of NY
Rachel Boston University 2016–2019 / Presidential Michelle Rose Boston University 2016–2017
Petherbridge Scholarship, Goldwater
Scholarship, Harvard
Amgen Scholar, Lutchen
Fellow, Mitchell Scholar
Teja Karri Boston University 2017 Grace Qian Dover-Sherborn HS 2017
Shaan Bhandarkar Phillips Exeter 2017 Benjamin Chew Boston University 2016–2018 / UROP
Academy HS
Kevin Lorch Boston University 2017–2019 Erdene Boston University 2017–2019 / UROP
Galbadrakh
Louisa University of 2018 Connor (Cass) Boston University 2019
Brenninkmeijer Birmingham (UK) Leach

Boston University Senior Design Project Teams Mentored

2013–2014 “A universal system for high-throughput loading of microfluidic devices”
Rami Barghout, Traci Kent, Oussama Benjelloun Touimi
2014–2015 “A modular system for optical measurement of pH in a continuous culture turbidostat”
 Alan Pacheco, Juliann Tefft, Hallie Thorp
2014–2015 “Fluorescence measurement in a high throughput turbidostat platform”
Zhi Jiao, Harsh Patel, Jean-Marc Tsang
2017–2018 “Ergonomic design and prototype of next generation culture devices”
Henok Haile, Jakov Kendes, John Le, Mark Viteri
2019–2020 “AnaeVOLVER: Developing high-throughput fluidic and gas control modules to grow, evolve and
study anaerobic microbiomes”
Gordon Ellis, Katherine Hastie, Griffen Larkin, Christopher LaRoche, Jai Singh
2019–2020 “Developing a 4OHT inducible therapeutic genetic circuit for reversing tauopathy in Alzheimer
disease model”
Nouf Alharbi, Zhonghao Dai, Shuwen (Eric) Lei

International Genetically Engineered Machine (iGEM) Teams Mentored

2015 Jeffrey Chen, Abha Patil, Shaheer Piracha, Kate Ryan, Nicholas Salvador, John Viola
2016 William Benman, Kami Drezek, Jeffrey Marano, Marisa Mendes, Rachel Petherbridge
2018 Connor (Cass) Leach, Kevin Lorch, Linda Luo

Doctoral Theses
2020 Thesis Advisor: Divya V. Israni, “Advanced Gene Expression Control in Therapeutic Human Cells
Using Synthetic Transcriptional Programs,” Department of Biomedical Engineering, Boston
University.

2020 Thesis Committee Member: Bernardo Cervantes, “Tool Development for the Rapid Identification of
Microbiome Manipulating Agents,” Microbiology Graduate Program, MIT. (Advisors: Drs. James J.
Collins and Kristala Prather).

2020 Thesis Committee Member: Ross D. Jones, “Genetic Devices for Robust, Context-Independent Control
of Gene Expression Levels in Mammalian Cells,” Department of Biological Engineering, MIT.
(Advisors: Drs. Ron Weiss and Domitilla Del Vecchio).

2020 Thesis Committee Chair: David B. Bernstein, “Probabilistic Metabolic Modeling of Microbial
Communities,” Department of Biomedical Engineering, Boston University. (Advisor: Dr. Daniel
Segré).

2020 Thesis Committee Member: Isaak E. Müller, “Engineering Probiotic Microbes for In Vivo
Applications,” Microbiology Graduate Program, MIT. (Advisor: Dr. Timothy K. Lu).

2020 Thesis Committee Member: Rebecca T. Cottman, “Engineering CTCF DNA-Binding Specificity to
Alter Gene Expression and Genome Topology in Human Cells,” Biological and Biomedical Sciences,
Division of Medical Sciences, Harvard U`niversity. (Advisor: Dr. J. Keith Joung).

2020 Thesis Committee Member: Gergana Shipkovenska, “Requirements for Epigenetic Inheritance of
Heterochromatin in Fission Yeast,” Biological and Biomedical Sciences, Division of Medical
Sciences, Harvard University. (Advisor: Dr. Danesh Moazed).

2020 Thesis Committee Member: Surojit Biswas, “Principles of Machine Learning-Guided Protein
Engineering,” Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard
University. (Advisor: Dr. George Church).

2020 Thesis Advisor: Christopher P. Mancuso, “Environmental Fluctuations Modulate Microbial

Competition, Diversity, and Persistence,” Department of Biomedical Engineering, Boston University.

2020 Thesis Committee Chair: Meghan Thommes, “Strategies for Engineering Microbial Communities,”
Department of Biomedical Engineering, Boston University. (Advisor: Dr. Daniel Segrè).
2020 Thesis Committee Member: Wei-Hsi Yeh, “In Vivo Delivery and Therapeutic Applications of Base
Editors,” Speech and Hearing Bioscience and Technology, Division of Medical Sciences, Harvard
University. (Advisor: Dr. David Liu).

2020 Thesis Committee Chair: Tiebin Wang, “Fitness Costs in Antibiotic Resistance and Metabolic
Engineering,” Molecular Biology, Cell Biology & Biochemistry Program, Boston University.
(Advisor: Dr. Mary Dunlop).

2019 Thesis Committee Member: James Angstman, “Characterizing and Reducing Spurious DNA Edits by
CRISPR Cytosine Base Editors,” Department of Molecular and Cellular Biology, Harvard University.
(Advisor: Dr. J. Keith Joung).

2019 Thesis Committee Member: Puting Dong, “Single-Cell Pump Probe Imaging of Intrinsic
Chromophores Identifies Diagnostic Marker and Therapeutic Target of Diseases,” Department of
Chemistry, Boston University. (Advisor: Dr. Ji-Xin Cheng).

2019 Thesis Committee Member: Robert J. Seager, “Toward a Quantitative Understanding of Cancer Cell
Signaling: Mathematical Models, Computational Tools, Applications, and Beyond,” Department of
Biomedical Engineering, Boston University. (Advisor: Dr. Muhammad Zaman).

2019 Thesis Committee Chair: Patricia Marie Aquino, “Genome-Wide Identification and Characterization of
Transcription Factor-DNA Binding Interactions in Bacteria,” Department of Biomedical Engineering,
Boston University. (Advisor: Dr. James Galagan).

2019 Thesis Committee Member: Demetrius DiMucci, “Machine Learning Applications for Synthetic
Microbial Ecology: Predicting Interactions and Identifying Their Putative Mechanisms,”
Bioinformatics Program, Boston University. (Advisor: Dr. Danel Segrè).

2019 Thesis Committee Chair: Jessica Keenan, “Characterizing Mechanisms of Regulatory Specificity in the
Nuclear Receptors and General Transcriptional Cofactors,” Bioinformatics Program, Boston
University. (Advisor: Dr. Trevor Siggers).

2019 Thesis Advisor: Minhee Park, “Engineering a Synthetic Epigenetic System,” Department of
Biomedical Engineering, Boston University.

2019 Thesis Committee Member (MS): Charles Jo, “A Co-Culture Microplate Platform to Quantify
Microbial Interactions and Growth Dynamics,” Department of Biomedical Engineering, Boston
University. (Advisor: Dr. Daniel Segrè).

2019 Thesis Co-Advisor (MS): Abdul Bhuiya, “Amplification-Free Detection of Transcriptional Biomarkers
of Antibiotic Resistance Using Interferometric Reflectance Imaging Sensor (IRIS),” Department of
Biomedical Engineering, Boston University.

2019 Thesis Committee Member: Pierce J. Ogden, “Dissecting Protein Fitness Landscapes Using DNA
Synthesis and Sequencing: Case Studies in AAV and Beyond,” Biological and Biomedical Sciences,
Division of Medical Sciences, Harvard University. (Advisor: Dr. George Church).

2019 Thesis Co-Advisor: James Chuang, “Genomic Analyses of Transcription Elongation Factors and
Intragenic Transcription,” Department of Biomedical Engineering, Boston University. (Advisor: Dr.
Fred Winston).

2019 Thesis Advisor (MS): Maria Simbirsky, “Continuous Culture of Bacteria Under Antibiotic Response,”
Department of Biomedical Engineering, Boston University.

2019 Thesis Committee Chair: James Needham, “Multiplexed Antibody Kinetics Using the Interferometric
Reflectance Imaging Sensor,” Department of Biomedical Engineering, Boston University. (Advisor:
Dr. M. Selim Ünlü).
2019 Thesis Committee Member: Jang Hwan Cho, “Synthetic Biology Approaches to Improve Cell-Based
Cancer Immunotherapy,” Department of Biomedical Engineering, Boston University. (Advisors: Drs.
Wilson Wong and James Collins).

2018 Thesis Committee Member: Nicholas Rossi, “Noise and Information in Bacterial Multigene Stress
Response Systems,” Molecular Biology, Cell Biology & Biochemistry Program, Boston University.
(Advisor: Dr. Mary Dunlop).

2018 Thesis Committee Member: Demarcus Briers, “Mathematical Modeling and Pattern Design in
Networks of Mammalian Cells,” Bioinformatics Program, Boston University. (Advisor: Dr. Calin
Belta).

2018 Thesis Committee Chair: Nitinun Bell Varongchayakul, “Protein Sensing Using Solid-State
Nanopore,” Department of Biomedical Engineering, Boston University. (Advisors: Dr. Mark Grinstaff,
Dr. Amit Meller).

2018 Thesis Committee Member: Andrew M. Shumaker, “Discovery and Characterization of an

Antimicrobial Toxin of the Gut Symbiont Bacteroides fragilis,” Chemical Biology PhD Program,
Harvard University. (Advisors: Dr. Pamela Silver, Dr. Laurie E. Comstock).

2018 Thesis Committee Member: Joshua E. Goldford, “Multi-Scale Metabolism: From the Origin of Life to
Microbial Ecology,” Bioinformatics Program, Boston University. (Advisor: Dr. Daniel Segrè).

2018 Thesis Advisor: Nikit Patel, “Engineering Biological Networks Using Cooperative Transcription
Factor Assembly,” Department of Biomedical Engineering, Boston University.

2018 Thesis Committee Member: Jason M. Gehrke, “Engineering High-Precision CRISPR-Cas9 Nuclease
and Base Editor Technologies,” Department of Molecular and Cellular Biology, Harvard University
(Advisor: Dr. J. Keith Joung).

2018 Thesis Advisor: Brandon G. Wong, “Design, Development and Application of an Automated
Framework for Cell Growth and Laboratory Evolution,” Department of Biomedical Engineering,
Boston University.

2018 Thesis Committee Member: Johnny H. Hu, “Directed Evolution of Cas9 for Mammmalian Genome
Editing,” Biological and Biomedical Sciences, Division of Medical Sciences, Harvard University.
(Advisor: Dr. David Liu).

2018 Thesis Committee Chair: Benjamin H. Weinberg, “Engineering Biocomputers in Mammalian Cells,”
Department of Biomedical Engineering, Boston University (Advisor: Dr. Wilson Wong).

2018 Thesis Advisor: Szilvia Kiriakov, “Synthetic Epigenetics in Yeast,” Molecular Biology, Cell Biology
& Biochemistry Program, Boston University.

2017 Thesis Committee Chair: Deboki Chakravarti, “Recombinase-Based Genetic Circuits in Human T
Cells for Cellular Immunotherapy,” Department of Biomedical Engineering, Boston University
(Advisor: Dr. Wilson Wong).

2017 Thesis Co-Advisor: Ning Mao, “Exploiting the Benefits of Probiotics for Intestinal Disease Diagnosis
and Therapy,” Department of Biomedical Engineering, Boston University (Advisor: Dr. James
Collins).

2017 Thesis Committee Member: Arion Stettner, “How Evolutionary Objectives and the Intracellular
Environment Shape Metabolic Fluxes,” Department of Biomedical Engineering, Boston University
(Advisor: Dr. Daniel Segrè).
2017 Thesis Committee Member: Derin Sevenler, “Development of a Digital Microarray with
Interferometric Reflectance Imaging,” Department of Biomedical Engineering, Boston University
(Advisor: Dr. M. Selim Ünlü).

2017 Thesis Advisor: Dana Braff, “Technological Advancements Towards Paper-Based Biomolecular
Diagnostics,” Department of Biomedical Engineering, Boston University.

2017 Thesis Advisor: Saloni Jain, “Quinolone Mechanism of Action: Sensitivity, Mutagenesis and
Tolerance,” Department of Biomedical Engineering, Boston University.

2017 Thesis Committee Member: Tyler E. Wagner, “Engineering a Regulatory Framework for Synthetic
Self-Amplifying RNA Circuits,” Department of Biomedical Engineering, Boston University. (Advisor:
Dr. Ron Weiss).

2016 Thesis Committee Member: William Hesse, “Quantitative Analysis of Proteotoxicity Associated with
Neurodegenerative Disease,” Department of Biological Engineering, MIT. (Advisor: Dr. Susan
Lindquist).

2016 Thesis Committee Chair: Swati Banerjee, “Reliable Gene Expression and Assembly for Synthetic
Biological Devices in E. coli Through Customized Promoter Insulator Elements and Automated DNA
Assembly,” Molecular Biology, Cell Biology & Biochemistry Program, Boston University. (Advisor:
Dr. Douglas Densmore).

2016 Thesis Advisor: Ali Beyzavi, “Investigation of the Heat Shock Response in Yeast: Quantitative
Modeling and Single-Cell Microfluidic Studies,” Department of Mechanical Engineering, Boston
University.

2016 Thesis Committee Member: Deepak Mishra, “Principles for the Design and Construction of Synthetic
Circuits Utilizing Protein-Protein Interactions in Saccharomyces cerevisiae,” Department of Biological
Engineering, MIT. (Advisor: Dr. Ron Weiss).

2015 Thesis Committee Member: Yu Sun, “Improving Recombineering Beyond Escherichia coli MG1655
Through the Broad Host-Range Expression of Metagenomic Libraries of Recombinases,” Department
of Biomedical Engineering, Boston University. (Advisor: Dr. George M. Church).

2015 Thesis Committee Member: Haiyao Huang, “Fluigi: An End-to-End Software Workflow for
Microfluidic Design,” Department of Electrical and Computer Engineering, Boston University.
(Advisor: Dr. Douglas Densmore).

2015 Thesis Committee Chair: Christopher Jacobs, “Functional and Evolutionary Implications of In Silico
Gene Deletion Studies,” Bioinformatics Program, Boston University. (Advisor: Dr. Daniel Segrè).

2015 Thesis Committee Member: Sonia V. Iverson, “Improved Modular Multipart Assembly, Development
of a DNA Part Toolkit for E. coli, and Applications in Traditional Biology and Bioelectronic Systems,”
Molecular Biology, Cell Biology & Biochemistry Program, Boston University. (Advisor: Dr. Douglas
Densmore).

2015 Thesis Committee Member: Evan Appleton, “A Design-Build-Test-Learn Tool for Synthetic Biology,”
Bioinformatics Program, Boston University. (Advisor: Dr. Douglas Densmore).

2015 Thesis Committee Member: Yasha Sharma, “Collective Cell Motility in 3-Dimensions: Dynamics,
Adhesions, and Emergence of Heterogeneity,” Department of Biomedical Engineering, Boston
University. (Advisor: Dr. Muhammad Zaman).

2015 Thesis Committee Chair: Elif Seymour, “Improvement of a Microarray-based Immunosensor for Rapid
and Robust Detection of Viral Pathogens,” Department of Biomedical Engineering, Boston University.
(Advisor: Dr. M. Selim Ünlü).
2015 Thesis Committee Member: James E. DiCarlo, “Engineering Yeast Genomes and Populations,”
Department of Biomedical Engineering, Boston University. (Advisor: Dr. George M. Church).

2015 Thesis Committee Member: Michael T. Mee, “Controlling Microbial Community Dynamics Through
Engineered Metabolic Dependencies,” Department of Biomedical Engineering, Boston University.
(Advisor: Dr. George M. Church).

2015 Thesis Committee Member: Russell-John Krom, “Bacteriophage Technologies and Their Application
to Synthetic Gene Networks,” MD/PhD Program, Boston University School of Medicine (Advisor: Dr.
James J. Collins).

2015 Thesis Committee Member: Tyler J. Ford, “Engineering Escherichia coli Fatty Acid Metabolism for
the Production of Biofuel Precursors,” Biological and Biomedical Sciences, Division of Medical
Sciences, Harvard University. (Advisor: Dr. Pamela A. Silver).

2014 Thesis Committee Member: Sandeep Choubey, “Biophysical Models of Transcription in Cells,”
Graduate Program in Physics, Brandeis University. (Advisor: Dr. Jané Kondev).

2014 Thesis Committee Member: Anna Lyubetskaya, “Transcription Factor Binding Distribution and
Properties in Prokaryotes,” Bioinformatics Program, Boston University. (Advisor: Dr. James Galagan).

2014 Thesis Committee Chair: Paul Iazzetti, “High-Throughput Binding Characterization of Bacterial
Transcription Factors,” Department of Biomedical Engineering, Boston University. (Advisor: Dr.
James Galagan).

2014 Thesis Committee Chair: Suma Jaini, “Methods for Functional Characterization of Transcription
Factor Binding Sites in Bacteria,” Department of Biomedical Engineering, Boston University.
(Advisor: Dr. James Galagan).

2014 Thesis Committee Chair: Jason P. Keller, “A Microfluidic Platform for Quantitative Analysis of Single
Mycobacteria Cells,” Department of Biomedical Engineering, Boston University. (Advisor: Dr. James
Galagan).

2014 Thesis Committee Member: Mara C. Inniss, “Tracking Cell Fate with Synthetic Memory and Pulse
Detecting Transcriptional Circuits,” Biological and Biomedical Sciences, Division of Medical
Sciences, Harvard University. (Advisor: Dr. Pamela A. Silver).

2014 Thesis Committee Member: Jun Li, “Towards Construction of Synthetic Ribosomes and a Self-
Replicating System,” Biological Sciences in Dental Medicine, Harvard University. (Advisor: Dr.
George M. Church).

2013 Thesis Committee Member: Wen-Han Yu, “Quantitative Studies of Mycobacterial Single Cell
Dynamics Using a Synthetic Gene Oscillator,” Bioinformatics Program, Boston University. (Advisor:
Dr. James Galagan).

2013 Thesis Committee Member: Irina Glotova, “Reconstruction of Lipid Metabolism Regulatory Network in
Mycobacterium Tuberculosis,” Bioinformatics Program, Boston University. (Advisor: Dr. James
Galagan).

2013 Thesis Committee Member: Antonio Gomes, “Computational Approaches to Deciphering Regulatory
Circuits in Mycobacterium tuberculosis From ChIP-Seq Data, and Developing Theoretical Strategies to
Combat Drug-Resistant Infections,” Bioinformatics Program, Boston University. (Advisor: Dr. James
Galagan).

2012 Thesis Committee Chair: Sheetal Modi, “Systems Biology Approaches to Mechanisms of Bacterial
Stress Adaptation,” Department of Biomedical Engineering, Boston University. (Advisor: Dr. James
J. Collins).
2012 Thesis Committee Member: Nicole M. Vega, “Induction of Antibiotic Tolerance in Bacteria by Self-
Produced and Inter-Species Signaling,” Molecular Biology, Cell Biology & Biochemistry Program,
Boston University. (Advisor: Dr. James J. Collins).

2012 Thesis Committee Chair: Jonathan A. Winkler, “Improving Antibiotic Activity by Manipulating
Bacterial Reactive Oxygen Species Metabolism,” Molecular Biology, Cell Biology & Biochemistry
Program, Boston University. (Advisor: Dr. James J. Collins).

2012 Thesis Committee Chair: Kyle R. Allison, “Engineering Solutions to Persistent Bacteria,” Department
of Biomedical Engineering, Boston University. (Advisor: Dr. James J. Collins).