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

PhD, Massachusetts Institute of Technology
MS, Massachusetts Institute of Technology




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.


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


URoL: Epigenetics 2: Robustness and Adaptability of the Dynamic Epigenome: A Multiscale Approach
09/01/2019 - 08/31/2024 (Subcontract PI)
University of Michigan National Science Fdn
EF-1921677

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
5T32GM130546-03

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
5R01EB029483-03

Design and in vivo comparison of alternative strategies for artificial Zinc Finger (aZnF) based regulatable gene therapies
03/04/2022 - 09/03/2023 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
Novartis Institutes for BioMedical Research


Automated semi-continuous evolution of therapeutic binding proteins and bioconjugation enzymes
06/18/2021 - 06/18/2023 (PI)
Merck, Sharp & Dohme LLC


Semi-continuous evolution of DNMT3A/L-binding nanobodies for targeted epigenome editing
09/01/2021 - 02/28/2023 (PI)
Chroma Medicine, Inc.


Development of synthetic gene feedback circuits to prevent tau aggregation
02/01/2020 - 01/31/2023 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
Bright Focus Foundation


ePACE: an automated system for high-throughput, closed-loop control of continuous molecular evolution to enable novel therapeutics
05/03/2019 - 01/31/2023 (PI)
NIH/National Institute of Biomedical Imaging & Bioengineering
5R01EB027793-04

Deciphering genetic and epigenetic regulation in eukaryotic gene clusters using synthetic genomics
01/01/2021 - 12/31/2022 (Key Person / Mentor)
European Molecular Biology Organization


Showing 10 of 38 results. Show All Results


Title


Yr Title Project-Sub Proj Pubs
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
2020 ePACE: an automated system for high-throughput, closed-loop control of continuous molecular evolution to enable novel therapeutics 5R01EB027793-02
Showing 10 of 13 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. Zhu I, Liu R, Garcia JM, Hyrenius-Wittsten A, Piraner DI, Alavi J, Israni DV, Liu B, Khalil AS, Roybal KT. Modular design of synthetic receptors for programmed gene regulation in cell therapies. Cell. 2022 Apr 14; 185(8):1431-1443.e16. PMID: 35427499; PMCID: PMC9108009; DOI: 10.1016/j.cell.2022.03.023;
     
  2. Kunze C, Khalil AS. One cell, many fates. Science. 2022 Jan 21; 375(6578):262-263. PMID: 35050646
     
  3. Mancuso CP, Lee H, Abreu CI, Gore J, Khalil AS. Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community. Elife. 2021 09 03; 10. PMID: 34477107; PMCID: PMC8460265; DOI: 10.7554/eLife.67175;
     
  4. Sutradhar I, Ching C, Desai D, Suprenant M, Briars E, Heins Z, Khalil AS, Zaman MH. Computational Model To Quantify the Growth of Antibiotic-Resistant Bacteria in Wastewater. mSystems. 2021 Jun 29; 6(3):e0036021.View Related Profiles. PMID: 34100640; PMCID: PMC8579810; DOI: 10.1128/mSystems.00360-21;
     
  5. Moussa HF, Angstman JF, Khalil AS. Here to stay: Writing lasting epigenetic memories. Cell. 2021 04 29; 184(9):2281-2283. PMID: 33930295; DOI: 10.1016/j.cell.2021.04.007;
     
  6. Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grünewald J, Immobile G, Khalil AS, Müller R, Pattanayak V, Petri K, Paul L, Pinello L, Simoni A, Taxiarchi C, Joung JK. A Code of Ethics for Gene Drive Research. CRISPR J. 2021 02; 4(1):19-24.View Related Profiles. PMID: 33571044; PMCID: PMC7898401; DOI: 10.1089/crispr.2020.0096;
     
  7. Qian J, Lu ZX, Mancuso CP, Jhuang HY, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. Barcoded microbial system for high-resolution object provenance. Science. 2020 06 05; 368(6495):1135-1140. PMID: 32499444
     
  8. Zhong Z, Wong BG, Ravikumar A, Arzumanyan GA, Khalil AS, Liu CC. Automated Continuous Evolution of Proteins in Vivo. ACS Synth Biol. 2020 06 19; 9(6):1270-1276. PMID: 32374988; PMCID: PMC7370864; DOI: 10.1021/acssynbio.0c00135;
     
  9. Chiesa G, Kiriakov S, Khalil AS. Protein assembly systems in natural and synthetic biology. BMC Biol. 2020 03 26; 18(1):35. PMID: 32216777; PMCID: PMC7099826; DOI: 10.1186/s12915-020-0751-4;
     
  10. Tanner K, Mancuso CP, Peretó J, Khalil AS, Vilanova C, Pascual J. Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts. Int J Syst Evol Microbiol. 2020 Mar; 70(3):1814-1821. PMID: 31951194; PMCID: PMC7539908; DOI: 10.1099/ijsem.0.003977;
     
Showing 10 of 39 results. Show More

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

Bar chart showing 39 publications over 16 distinct years, with a maximum of 5 publications in 2016 and 2018

YearPublications
20051
20061
20071
20081
20091
20102
20123
20142
20152
20165
20172
20185
20193
20204
20214
20222

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
Contact for Mentoring:

610 Commonwealth Ave
Boston MA 02215
Google Map


Khalil's Networks
Click the "See All" links for more information and interactive visualizations
Concepts
_
Media Mentions
_
Co-Authors
_
Similar People
_
Same Department