Ahmad (Mo) Khalil, PhD
Professor
Boston University College of Engineering
Biomedical Engineering

PhD, Massachusetts Institute of Technology
MS, Massachusetts Institute of Technology
BS, Stanford University



My research is interested in how molecular “circuits” enable core 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 apply synthetic biology approaches, in which we design and build regulatory circuits in living cells. This bottom-up approach allows us to test many different circuit designs and identify which circuits are sufficient to program cellular function. We have pioneered this approach to design and study molecular circuits that control gene regulation and epigenetic memory in eukaryotic cells, with important implications for biotechnology and therapeutics. Second, we apply evolutionary approaches, in which we develop methods for prospective evolution of biological systems in the laboratory. A central pillar of this effort is “eVOLVER”, a highly-flexible continuous culture system we invented that enables large-scale automation of growth, testing, and evolution of cellular systems in precisely-controlled conditions.


NRT-URoL: A Convergent Training Program on Biological Control
08/01/2023 - 07/31/2028 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
National Science Foundation
DGE-2244366

Schmidt Science Polymath Award
12/01/2022 - 10/31/2027 (PI)
The Eric and Wendy Schmidt Fund For Strategic Innovation


Synthetic vascularization and regeneration in engineered tissues
09/01/2023 - 08/31/2027 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
NIH/National Institute of Biomedical Imaging & Bioengineering
5R01EB033821-02

Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiome
06/10/2022 - 05/31/2027 (PI)
NIH/National Institute of Allergy & Infectious Diseases
5R01AI171100-03

ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential
07/01/2023 - 03/31/2027 (PI)
NIH/National Institute of Biomedical Imaging & Bioengineering
5R01EB027793-06

Damon Runyon Postdoctoral Fellowship Award
10/01/2022 - 09/30/2026 (Key Person / Mentor)
PI: Heidi Klumpe
Damon Runyon Cancer Research Foundation


Automated Nanobody Selection Collaboration
08/15/2023 - 02/14/2026 (PI)
Merck, Sharp & Dohme LLC


Semi-continuous evolution of DNMT3A/L-binding nanobodies for targeted epigenome editing
09/01/2021 - 08/31/2025 (PI)
Chroma Medicine, Inc.


Epigenetically Programmed Biological Materials
08/12/2020 - 08/11/2025 (PI)
Department of Defense/ONR


Billing Agreement: W. Shaw
07/15/2024 - 07/14/2025 (PI)
Whitehead Institute for Biomedical Research


Showing 10 of 52 results. Show All Results


Title


Yr Title Project-Sub Proj Pubs
2024 Synthetic vascularization and regeneration in engineered tissues 5R01EB033821-02
2024 Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiome 5R01AI171100-03
2024 Synthetic circuit technologies for precision control and signal processing in mammalian cells 2R01EB029483-05
2024 ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential 5R01EB027793-06
2023 Synthetic vascularization and regeneration in engineered tissues 1R01EB033821-01
2023 2023 Synthetic Biology Gordon Research Conference and Gordon Research Seminar 1R13EB035034-01
2023 Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiome 5R01AI171100-02
2023 Synthetic toolkit for precision gene expression control and signal processing in mammalian cells 5R01EB029483-04
2023 Synthetic Biology and Biotechnology (SB2) Predoctoral Training Program 5T32GM130546-05
2023 ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential 2R01EB027793-05
Showing 10 of 23 results. Show All Results

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis       Copy PMIDs To Clipboard

  1. Guo Z, Chiesa G, Yin J, Sanford A, Meier S, Khalil AS, Cheng JX. Structural Mapping of Protein Aggregates in Live Cells Modeling Huntington's Disease. Angew Chem Int Ed Engl. 2024 Aug 26; 63(35):e202408163. PMID: 38880765
     
  2. Neumann EN, Bertozzi TM, Wu E, Serack F, Harvey JW, Brauer PP, Pirtle CP, Coffey A, Howard M, Kamath N, Lenz K, Guzman K, Raymond MH, Khalil AS, Deverman BE, Minikel EV, Vallabh SM, Weissman JS. Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor. Science. 2024 Jun 28; 384(6703):ado7082. PMID: 38935715
     
  3. Shaw WM, Khalil AS, Ellis T. A Multiplex MoClo Toolkit for Extensive and Flexible Engineering of Saccharomyces cerevisiae. ACS Synth Biol. 2023 Nov 17; 12(11):3393-3405. PMID: 37930278; DOI: 10.1021/acssynbio.3c00423;
     
  4. Webber CJ, Murphy CN, Rondón-Ortiz AN, van der Spek SJF, Kelly EX, Lampl NM, Chiesa G, Khalil AS, Emili A, Wolozin B. Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways. Hum Mol Genet. 2023 Oct 04; 32(20):2966-2980.View Related Profiles. PMID: 37522762; DOI: 10.1093/hmg/ddad122;
     
  5. Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ, Khalil AS. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell. 2023 Aug 31; 186(18):3810-3825.e18. PMID: 37552983; DOI: 10.1016/j.cell.2023.07.012;
     
  6. García-Ruano D, Jain A, Heins ZJ, Wong BG, Yimer Wolle E, Khalil AS, Coudreuse D. Long-term evolution of proliferating cells using the eVOLVER platform. Open Biol. 2023 Jul; 13(7):230118. PMID: 37491941; DOI: 10.1098/rsob.230118;
     
  7. Klumpe HE, Lugagne JB, Khalil AS, Dunlop MJ. Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes. ACS Synth Biol. 2023 Aug 18; 12(8):2367-2381.View Related Profiles. PMID: 37467372
     
  8. Sutradhar I, Ching C, Desai D, Heins Z, Khalil AS, Zaman MH. Effects of antibiotic interaction on antimicrobial resistance development in wastewater. Sci Rep. 2023 May 13; 13(1):7801.View Related Profiles. PMID: 37179426; DOI: 10.1038/s41598-023-34935-w;
     
  9. Martinez-Corral R, Park M, Biette KM, Friedrich D, Scholes C, Khalil AS, Gunawardena J, DePace AH. Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology. Cell Syst. 2023 Apr 19; 14(4):324-339.e7. PMID: 37080164; DOI: 10.1016/j.cels.2023.02.003;
     
  10. Garc A-Ruano D, Jain A, Heins ZJ, Wong BG, Wolle EY, Khalil AS, Coudreuse D. Long-term evolution of proliferating cells using the eVOLVER platform. bioRxiv. 2023 Apr 19. PMID: 37034650; DOI: 10.1101/2023.03.28.534552;
     
Showing 10 of 60 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 60 publications over 18 distinct years, with a maximum of 11 publications in 2022

YearPublications
20051
20061
20071
20081
20091
20102
20123
20142
20152
20165
20172
20185
20193
20204
20214
202211
202310
20242

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2021 AIMBE College of Fellows
2020 DoD Vannevar Bush Faculty Fellowship
2019 Dorf-Ebner Distinguished Faculty Fellow
2018 National Academy of Engineering: Frontiers of Engineering Invitee
2017 Presidential Early Career Award for Scientists and Engineers
2017 Boston University: Early Career Research Excellence Award
2016 National Institute of Health: New Innovator Award
2016 DARPA Young Faculty Award
2016 College of Engineering, Boston University: Outstanding Professor of the Year
2016 Biomedical Engineering Dept., Boston University: Award for Teaching Excellence
2015 Hartwell Foundation: Individual Biomedical Research Award
2015 Biomedical Engineering Dept., Boston University: Award for Teaching Excellence
2014 National Academy of Engineering: Frontiers of Engineering Education Invitee
2014 National Science Foundation: CAREER Award
2013-2016 Boston University: Innovation Career Development Professorship
2013 Biomedical Engineering Dept., Boston University: Award for Teaching Excellence
2013 Institut Mérieux: Research Grant Award
2012 Wallace H. Coulter Foundation: Translational Research Partnership Award
2005 Charles Stark Draper Laboratory, Massachusetts Institute of Technology: Graduate Fellowship
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610 Commonwealth Ave
Boston MA 02215
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