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.


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
1R01AI171100-01

Schmidt Science Polymath Award
12/01/2022 - 10/31/2026 (PI)
The Eric and Wendy Schmidt Fund For Strategic Innovation


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


Scalable and automatable nanobody discovery and affinity maturation in yeast
07/13/2022 - 07/13/2025 (PI)
FTX Philanthropy, Inc.


Deciphering a new dimension of GPCR biology through the continuous evolution of biased modulators
07/01/2022 - 06/30/2025 (Subcontract PI)
University of California, Irvine Keck Foundation


URoL: Epigenetics 2: Robustness and Adaptability of the Dynamic Epigenome: A Multiscale Approach
10/01/2022 - 08/31/2024 (Subcontract PI)
Brandeis University National Science Fdn


Semi-continuous evolution of DNMT3A/L-binding nanobodies for targeted epigenome editing
09/01/2021 - 08/31/2024 (PI)
Chroma Medicine, Inc.


Schmidt Futures "Modular Biofilm Reactors to Convert Waste-Based Feedstocks to Vitamin A"
03/01/2023 - 08/30/2024 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
BioMADE Schmidt Futures


Synthetic Biology and Biotechnology (SB2) Predoctoral Training Program
07/01/2019 - 06/30/2024 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
NIH/National Institute of General Medical Sciences
5T32GM130546-04

Synthetic toolkit for precision gene expression control and signal processing in mammalian cells
05/01/2020 - 01/31/2024 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
NIH/National Institute of Biomedical Imaging & Bioengineering
5R01EB029483-04

Showing 10 of 44 results. Show All Results


Title


Yr Title Project-Sub Proj Pubs
2023 Synthetic toolkit for precision gene expression control and signal processing in mammalian cells 5R01EB029483-04
2022 Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiome 1R01AI171100-01
2022 Synthetic toolkit for precision gene expression control and signal processing in mammalian cells 5R01EB029483-03
2022 Synthetic Biology and Biotechnology (SB2) Predoctoral Training Program 5T32GM130546-04
2022 ePACE: an automated system for high-throughput, closed-loop control of continuous molecular evolution to enable novel therapeutics 5R01EB027793-04
2021 Synthetic toolkit for precision gene expression control and signal processing in mammalian cells 5R01EB029483-02
2021 Synthetic Biology and Biotechnology (SB2) Predoctoral Training Program 5T32GM130546-03
2021 ePACE: an automated system for high-throughput, closed-loop control of continuous molecular evolution to enable novel therapeutics 5R01EB027793-03
2020 Synthetic toolkit for precision gene expression control and signal processing in mammalian cells 1R01EB029483-01
2020 Synthetic Biology and Biotechnology (SB2) Predoctoral Training Program 5T32GM130546-02
Showing 10 of 14 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. 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; PMCID: PMC10081182; DOI: 10.1101/2023.03.28.534552;
     
  2. 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
     
  3. Sutradhar I, Ching C, Desai D, Heins Z, Khalil AS, Zaman MH. Effects of Antibiotic Interaction on Antimicrobial Resistance Development in Wastewater. bioRxiv. 2023 Feb 10.View Related Profiles. PMID: 36798199; PMCID: PMC9934683; DOI: 10.1101/2023.02.10.528009;
     
  4. Jo C, Zhang J, Tam JM, Church GM, Khalil AS, Segrè D, Tang TC. Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio. 2023 Apr; 19:100560. PMID: 36756210; PMCID: PMC9900623; DOI: 10.1016/j.mtbio.2023.100560;
     
  5. Cabrera A, Edelstein HI, Glykofrydis F, Love KS, Palacios S, Tycko J, Zhang M, Lensch S, Shields CE, Livingston M, Weiss R, Zhao H, Haynes KA, Morsut L, Chen YY, Khalil AS, Wong WW, Collins JJ, Rosser SJ, Polizzi K, Elowitz MB, Fussenegger M, Hilton IB, Leonard JN, Bintu L, Galloway KE, Deans TL. The sound of silence: Transgene silencing in mammalian cell engineering. Cell Syst. 2022 Dec 21; 13(12):950-973. PMID: 36549273; PMCID: PMC9880859; DOI: 10.1016/j.cels.2022.11.005;
     
  6. Li HS, Israni DV, Gagnon KA, Gan KA, Raymond MH, Sander JD, Roybal KT, Joung JK, Wong WW, Khalil AS. Multidimensional control of therapeutic human cell function with synthetic gene circuits. Science. 2022 Dec 16; 378(6625):1227-1234. PMID: 36520914; PMCID: PMC10054295; DOI: 10.1126/science.ade0156;
     
  7. Lee S, Khalil AS, Wong WW. Recent progress of gene circuit designs in immune cell therapies. Cell Syst. 2022 Nov 16; 13(11):864-873. PMID: 36395726; PMCID: PMC9681026; DOI: 10.1016/j.cels.2022.09.006;
     
  8. Sanford A, Kiriakov S, Khalil AS. A Toolkit for Precise, Multigene Control in Saccharomyces cerevisiae. ACS Synth Biol. 2022 Dec 16; 11(12):3912-3920. PMID: 36367334; PMCID: PMC9764411; DOI: 10.1021/acssynbio.2c00423;
     
  9. Sun Q, Vega NM, Cervantes B, Mancuso CP, Mao N, Taylor MN, Collins JJ, Khalil AS, Gore J, Lu TK. Enhancing nutritional niche and host defenses by modifying the gut microbiome. Mol Syst Biol. 2022 Nov; 18(11):e9933. PMID: 36377768; PMCID: PMC9664710; DOI: 10.15252/msb.20209933;
     
  10. Shaw WM, Zhang Y, Lu X, Khalil AS, Ladds G, Luo X, Ellis T. Screening microbially produced ?9-tetrahydrocannabinol using a yeast biosensor workflow. Nat Commun. 2022 Sep 20; 13(1):5509. PMID: 36127350; PMCID: PMC9489785; DOI: 10.1038/s41467-022-33207-x;
     
Showing 10 of 52 results. Show More

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

Bar chart showing 52 publications over 17 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
20234

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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