Ahmad Khalil | Profiles RNS

Ahmad (Mo) Khalil, PhD

Research Professor

Boston University College of Engineering

Biomedical Engineering

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

Websites

	College of Engineering Faculty
	Khalil Lab
	BU Rajen Kilachand Center for Integrated Life Sciences & Engineering
	Twitter
	LinkedIn
	AIChE Profile
	Google Scholar
	EBRC Profile

ORCID : 0000-0002-8214-0546

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.

BU Research
NIH RePORTER Research

Synthetic Biology and Biotechnology (SB2) Predoctoral Training Program
08/13/2025 - 06/30/2030 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
NIH/National Institute of General Medical Sciences
1T32GM154655-01

A self-amplifying RNA-based synthetic nanobody platform for next-generation therapeutics
08/01/2025 - 04/30/2029 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
NIH/National Institute of Biomedical Imaging & Bioengineering
1R01EB038005-01

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

Synthetic circuit technologies for precision control and signal processing in mammalian cells
08/12/2024 - 04/30/2028 (PI)
NIH/National Institute of Biomedical Imaging & Bioengineering
5R01EB029483-06

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

ROGUE-Rx On-site generation Using Electronics
09/16/2024 - 09/15/2027 (Multi-PI)
PI: Ahmad (Mo) Khalil, PhD
Carnegie Mellon University ARPA-H

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
5R01EB033821-03

Synthetic ecology of mixed aerobic/anaerobic microbial consortia
07/01/2024 - 06/30/2027 (Subcontract PI)
Northeastern University National Science Fdn
MCB-2345872

Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiome
06/01/2025 - 05/31/2027 (PI)
NIH/National Institute of Allergy & Infectious Diseases
4R01AI171100-04

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
5R01EB027793-07

Showing 10 of 61 results. Show All Results

Title

Yr	Title	Project-Sub Proj
2025	Synthetic Biology and Biotechnology (SB2) Predoctoral Training Program	1T32GM154655-01
2025	A self-amplifying RNA-based synthetic nanobody platform for next-generation therapeutics	1R01EB038005-01
2025	Synthetic vascularization and regeneration in engineered tissues	5R01EB033821-03
2025	Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiome	4R01AI171100-04
2025	Synthetic circuit technologies for precision control and signal processing in mammalian cells	5R01EB029483-06
2025	ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential	5R01EB027793-07
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

Showing 10 of 29 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.

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Hoyt KO, Zhou G, Gasparrini W, Sliter PJ, Hart DJ, Khalil AS, Woolston BM. Exploring C1 substrate cofeeding in Eubacterium limosum with AneVO, a low-cost anaerobic parallel bioreactor platform. bioRxiv. 2025 May 02. PMID: 40654738; PMCID: PMC12247781; DOI: 10.1101/2025.05.02.651948;

Tong K, Datta S, Cheng V, Haas DJ, Gourisetti S, Yopp HL, Day TC, Lac DT, Khalil AS, Conlin PL, Bozdag GO, Ratcliff WC. Genome duplication in a long-term multicellularity evolution experiment. Nature. 2025 Mar; 639(8055):691-699.View Related Profiles.

Khalil, Ahmad
Tong, Kai

PMID: 40044858; PMCID: PMC12256070; DOI: 10.1038/s41586-025-08689-6;

Tycko J, Van MV, Aradhana, DelRosso N, Ye H, Yao D, Valbuena R, Vaughan-Jackson A, Xu X, Ludwig C, Spees K, Liu K, Gu M, Khare V, Mukund AX, Suzuki PH, Arana S, Zhang C, Du PP, Ornstein TS, Hess GT, Kamber RA, Qi LS, Khalil AS, Bintu L, Bassik MC. Development of compact transcriptional effectors using high-throughput measurements in diverse contexts. Nat Biotechnol. 2025 Sep; 43(9):1525-1538. PMID: 39487265; PMCID: PMC12043968; DOI: 10.1038/s41587-024-02442-6;

Larkin A, Kunze C, Seman M, Levashkevich A, Curran J, Morris-Evans D, Lemieux S, Khalil AS, Ragunathan K. Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation. Dev Cell. 2024 Aug 19; 59(16):2222-2238.e4. PMID: 39094565; PMCID: PMC11338711; DOI: 10.1016/j.devcel.2024.07.006;

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.View Related Profiles.

Khalil, Ahmad
Yin, Jiaze

PMID: 38880765; PMCID: PMC11781839; DOI: 10.1002/anie.202408163;

Khalil A, Stone D, Dysart J, Taqatqa A. Bicuspid Aortic Valve Function and Aortopathy on Presentation and Progression in Children: Does Sex Difference Have Any Implications? Pediatr Cardiol. 2025 Aug; 46(6):1600-1607. PMID: 38987442

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; PMCID: PMC11875203; DOI: 10.1126/science.ado7082;

Larkin A, Kunze C, Seman M, Levashkevich A, Curran J, Morris-Evans D, Lemieux S, Khalil AS, Ragunathan K. Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation. bioRxiv. 2024 Apr 05. PMID: 37503217; PMCID: PMC10369875; DOI: 10.1101/2023.07.10.548368;

D'Amato R, Taxiarchi C, Galardini M, Trusso A, Minuz RL, Grilli S, Somerville AGT, Shittu D, Khalil AS, Galizi R, Crisanti A, Simoni A, Müller R. Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages. Nat Commun. 2024 Feb 01; 15(1):952. PMID: 38296981; PMCID: PMC10830555; DOI: 10.1038/s41467-024-44907-x;

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; PMCID: PMC10661031; DOI: 10.1021/acssynbio.3c00423;

Showing 10 of 71 results. Show More

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.

Khalil, Ahmad
Wolozin, Benjamin
Van Der Spek, Sophie

PMID: 37522762; PMCID: PMC10549787; DOI: 10.1093/hmg/ddad122;

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; PMCID: PMC10528910; DOI: 10.1016/j.cell.2023.07.012;

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; PMCID: PMC10369027; DOI: 10.1098/rsob.230118;

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.

Khalil, Ahmad
Klumpe, Heidi
Dunlop, Mary

PMID: 37467372; PMCID: PMC11976981; DOI: 10.1021/acssynbio.3c00203;

Khalil A, Huang S, Ratnasamy C. Ablation of ventricular tachycardia from coronary sinus in congenitally corrected transposition of great arteries. Am J Cardiovasc Dis. 2023; 13(3):202-206. PMID: 37469532; PMCID: PMC10352817

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.

Khalil, Ahmad
Sutradhar, Indorica
Zaman, Muhammad

PMID: 37179426; PMCID: PMC10183007; DOI: 10.1038/s41598-023-34935-w;

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;

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; PMCID: PMC10472254; DOI: 10.1016/j.cels.2023.02.003;

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.

Khalil, Ahmad
Sutradhar, Indorica
Zaman, Muhammad

PMID: 36798199; PMCID: PMC9934683; DOI: 10.1101/2023.02.10.528009;

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.View Related Profiles.

Khalil, Ahmad
Segre, Daniel

PMID: 36756210; PMCID: PMC9900623; DOI: 10.1016/j.mtbio.2023.100560;

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;

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;

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.View Related Profiles.

Khalil, Ahmad
Wong, Wilson

PMID: 36395726; PMCID: PMC9681026; DOI: 10.1016/j.cels.2022.09.006;

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;

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;

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;

Huang TP, Heins ZJ, Miller SM, Wong BG, Balivada PA, Wang T, Khalil AS, Liu DR. High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs. Nat Biotechnol. 2023 Jan; 41(1):96-107. PMID: 36076084; PMCID: PMC9849140; DOI: 10.1038/s41587-022-01410-2;

Li HS, Wong NM, Tague E, Ngo JT, Khalil AS, Wong WW. High-performance multiplex drug-gated CAR circuits. Cancer Cell. 2022 Nov 14; 40(11):1294-1305.e4.View Related Profiles.

Khalil, Ahmad
Ngo, John
Wong, Wilson

PMID: 36084652; PMCID: PMC9669166; DOI: 10.1016/j.ccell.2022.08.008;

Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. Nat Rev Methods Primers. 2022; 2. PMID: 37073402; PMCID: PMC10108624; DOI: 10.1038/s43586-022-00130-w;

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;

Kunze C, Khalil AS. One cell, many fates. Science. 2022 Jan 21; 375(6578):262-263. PMID: 35050646

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;

Acevedo Rua L, Mumme M, Manferdini C, Darwiche S, Khalil A, Hilpert M, Buchner DA, Lisignoli G, Occhetta P, von Rechenberg B, Haug M, Schaefer DJ, Jakob M, Caplan A, Martin I, Barbero A, Pelttari K. Engineered nasal cartilage for the repair of osteoarthritic knee cartilage defects. Sci Transl Med. 2021 Sep; 13(609):eaaz4499. PMID: 34516821

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.

Khalil, Ahmad
Sutradhar, Indorica
Zaman, Muhammad

PMID: 34100640; PMCID: PMC8579810; DOI: 10.1128/mSystems.00360-21;

Moussa HF, Angstman JF, Khalil AS. Here to stay: Writing lasting epigenetic memories. Cell. 2021 04 29; 184(9):2281-2283.View Related Profiles.

Khalil, Ahmad
Moussa, Hagar
Angstman, James

PMID: 33930295; DOI: 10.1016/j.cell.2021.04.007;

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.

Khalil, Ahmad
Annas, George

PMID: 33571044; PMCID: PMC7898401; DOI: 10.1089/crispr.2020.0096;

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

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.View Related Profiles.

Khalil, Ahmad
Ravikumar, Arjun

PMID: 32374988; PMCID: PMC7370864; DOI: 10.1021/acssynbio.0c00135;

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;

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;

Heins ZJ, Mancuso CP, Kiriakov S, Wong BG, Bashor CJ, Khalil AS. Designing Automated, High-throughput, Continuous Cell Growth Experiments Using eVOLVER. J Vis Exp. 2019 05 19; (147). PMID: 31157778; PMCID: PMC6738936; DOI: 10.3791/59652;

Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ, Khalil AS. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science. 2019 05 10; 364(6440):593-597. PMID: 31000590; PMCID: PMC6650298; DOI: 10.1126/science.aau8287;

Lee HH, Ostrov N, Wong BG, Gold MA, Khalil AS, Church GM. Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nat Microbiol. 2019 07; 4(7):1105-1113. PMID: 30962569; DOI: 10.1038/s41564-019-0423-8;

Park M, Patel N, Keung AJ, Khalil AS. Engineering Epigenetic Regulation Using Synthetic Read-Write Modules. Cell. 2019 Jan 10; 176(1-2):227-238.e20. PMID: 30528434; PMCID: PMC6329643; DOI: 10.1016/j.cell.2018.11.002;

Weinstein ZB, Kuru N, Kiriakov S, Palmer AC, Khalil AS, Clemons PA, Zaman MH, Roth FP, Cokol M. Modeling the impact of drug interactions on therapeutic selectivity. Nat Commun. 2018 08 27; 9(1):3452.View Related Profiles.

Khalil, Ahmad
Zaman, Muhammad
Weinstein, Zohar

PMID: 30150706; PMCID: PMC6110842; DOI: 10.1038/s41467-018-05954-3;

Wong BG, Mancuso CP, Kiriakov S, Bashor CJ, Khalil AS. Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER. Nat Biotechnol. 2018 08; 36(7):614-623. PMID: 29889214; PMCID: PMC6035058; DOI: 10.1038/nbt.4151;

Zheng X, Beyzavi A, Krakowiak J, Patel N, Khalil AS, Pincus D. Hsf1 Phosphorylation Generates Cell-to-Cell Variation in Hsp90 Levels and Promotes Phenotypic Plasticity. Cell Rep. 2018 03 20; 22(12):3099-3106. PMID: 29562166; PMCID: PMC5893160; DOI: 10.1016/j.celrep.2018.02.083;

Krakowiak J, Zheng X, Patel N, Feder ZA, Anandhakumar J, Valerius K, Gross DS, Khalil AS, Pincus D. Hsf1 and Hsp70 constitute a two-component feedback loop that regulates the yeast heat shock response. Elife. 2018 02 02; 7. PMID: 29393852; PMCID: PMC5809143; DOI: 10.7554/eLife.31668;

Newby GA, Kiriakov S, Hallacli E, Kayatekin C, Tsvetkov P, Mancuso CP, Bonner JM, Hesse WR, Chakrabortee S, Manogaran AL, Liebman SW, Lindquist S, Khalil AS. A Genetic Tool to Track Protein Aggregates and Control Prion Inheritance. Cell. 2017 Nov 02; 171(4):966-979.e18. PMID: 29056345; PMCID: PMC5675731; DOI: 10.1016/j.cell.2017.09.041;

Somoza RA, Correa D, Labat I, Sternberg H, Forrest ME, Khalil AM, West MD, Tesar P, Caplan AI. Transcriptome-Wide Analyses of Human Neonatal Articular Cartilage and Human Mesenchymal Stem Cell-Derived Cartilage Provide a New Molecular Target for Evaluating Engineered Cartilage. Tissue Eng Part A. 2018 Feb; 24(3-4):335-350. PMID: 28602122

Hawkins F, Kramer P, Jacob A, Driver I, Thomas DC, McCauley KB, Skvir N, Crane AM, Kurmann AA, Hollenberg AN, Nguyen S, Wong BG, Khalil AS, Huang SX, Guttentag S, Rock JR, Shannon JM, Davis BR, Kotton DN. Prospective isolation of NKX2-1-expressing human lung progenitors derived from pluripotent stem cells. J Clin Invest. 2017 Jun 01; 127(6):2277-2294.View Related Profiles.

Khalil, Ahmad
Jacob, Anjali
Hollenberg, Anthony
Kotton, Darrell
Hawkins, Finn
Rock, Jason

PMID: 28463226; PMCID: PMC5451263; DOI: 10.1172/JCI89950;

Zheng X, Krakowiak J, Patel N, Beyzavi A, Ezike J, Khalil AS, Pincus D. Dynamic control of Hsf1 during heat shock by a chaperone switch and phosphorylation. Elife. 2016 11 10; 5. PMID: 27831465; PMCID: PMC5127643; DOI: 10.7554/eLife.18638;

Park M, Keung AJ, Khalil AS. The epigenome: the next substrate for engineering. Genome Biol. 2016 08 31; 17(1):183. PMID: 27582168; PMCID: PMC5006378; DOI: 10.1186/s13059-016-1046-5;

Mancuso CP, Kiriakov S, Khalil AS. Cellular Advantages to Signaling in a Digital World. Cell Syst. 2016 Aug; 3(2):114-115. PMID: 27559921

Garcia-Ojalvo J, Khalil AS, McCarthy J. Biological Insights from Synthetic Biology. Integr Biol (Camb). 2016 Apr 18; 8(4):380-2. PMID: 27064018; DOI: 10.1039/c6ib90013e;

Keung AJ, Khalil AS. MOLECULAR BIOLOGY. A unifying model of epigenetic regulation. Science. 2016 Feb 12; 351(6274):661-2. PMID: 26912843; PMCID: PMC6124315; DOI: 10.1126/science.aaf1647;

Lobritz MA, Belenky P, Porter CB, Gutierrez A, Yang JH, Schwarz EG, Dwyer DJ, Khalil AS, Collins JJ. Antibiotic efficacy is linked to bacterial cellular respiration. Proc Natl Acad Sci U S A. 2015 Jul 07; 112(27):8173-80. PMID: 26100898

Keung AJ, Joung JK, Khalil AS, Collins JJ. Chromatin regulation at the frontier of synthetic biology. Nat Rev Genet. 2015 Mar; 16(3):159-71. PMID: 25668787

Keung AJ, Bashor CJ, Kiriakov S, Collins JJ, Khalil AS. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell. 2014 Jul 03; 158(1):110-20. PMID: 24995982

Dwyer DJ, Belenky PA, Yang JH, MacDonald IC, Martell JD, Takahashi N, Chan CT, Lobritz MA, Braff D, Schwarz EG, Ye JD, Pati M, Vercruysse M, Ralifo PS, Allison KR, Khalil AS, Ting AY, Walker GC, Collins JJ. Antibiotics induce redox-related physiological alterations as part of their lethality. Proc Natl Acad Sci U S A. 2014 May 20; 111(20):E2100-9. PMID: 24803433; PMCID: PMC4034191; DOI: 10.1073/pnas.1401876111;

Litcofsky KD, Afeyan RB, Krom RJ, Khalil AS, Collins JJ. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat Methods. 2012 Nov; 9(11):1077-80.View Related Profiles.

Khalil, Ahmad
Krom, Russell-John

PMID: 23042452; PMCID: PMC3492501; DOI: 10.1038/nmeth.2205;

Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ. A synthetic biology framework for programming eukaryotic transcription functions. Cell. 2012 Aug 03; 150(3):647-58. PMID: 22863014

Vega NM, Allison KR, Khalil AS, Collins JJ. Signaling-mediated bacterial persister formation. Nat Chem Biol. 2012 Mar 18; 8(5):431-3. PMID: 22426114; PMCID: PMC3329571; DOI: 10.1038/nchembio.915;

Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Semin Cell Dev Biol. 2011 Jun; 22(4):359-65. PMID: 21333748

Khalil AS, Collins JJ. Synthetic biology: applications come of age. Nat Rev Genet. 2010 May; 11(5):367-79. PMID: 20395970; PMCID: PMC2896386; DOI: 10.1038/nrg2775;

Borenstein JT, Tupper MM, Mack PJ, Weinberg EJ, Khalil AS, Hsiao J, García-Cardeña G. Functional endothelialized microvascular networks with circular cross-sections in a tissue culture substrate. Biomed Microdevices. 2010 Feb; 12(1):71-9. PMID: 19787455

Lu TK, Khalil AS, Collins JJ. Next-generation synthetic gene networks. Nat Biotechnol. 2009 Dec; 27(12):1139-50. PMID: 20010597; PMCID: PMC2796205; DOI: 10.1038/nbt.1591;

Khalil AS, Appleyard DC, Labno AK, Georges A, Karplus M, Belcher AM, Hwang W, Lang MJ. Kinesin's cover-neck bundle folds forward to generate force. Proc Natl Acad Sci U S A. 2008 Dec 09; 105(49):19247-52. PMID: 19047639; PMCID: PMC2592363; DOI: 10.1073/pnas.0805147105;

Khalil AS, Ferrer JM, Brau RR, Kottmann ST, Noren CJ, Lang MJ, Belcher AM. Single M13 bacteriophage tethering and stretching. Proc Natl Acad Sci U S A. 2007 Mar 20; 104(12):4892-7. PMID: 17360403; PMCID: PMC1829235; DOI: 10.1073/pnas.0605727104;

Khalil AS, Bouma BE, Kaazempur Mofrad MR. A combined FEM/genetic algorithm for vascular soft tissue elasticity estimation. Cardiovasc Eng. 2006 Sep; 6(3):93-102. PMID: 16967325; DOI: 10.1007/s10558-006-9013-5;

Khalil AS, Chan RC, Chau AH, Bouma BE, Mofrad MR. Tissue elasticity estimation with optical coherence elastography: toward mechanical characterization of in vivo soft tissue. Ann Biomed Eng. 2005 Nov; 33(11):1631-9. PMID: 16341928; DOI: 10.1007/s10439-005-6766-3;

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

Bar chart showing 71 publications over 20 distinct years, with a maximum of 11 publications in 2022 and 2023

Bar chart showing 71 publications over 20 distinct years, with a maximum of 11 publications in 2022 and 2023

Year	Publications
2005	1
2006	1
2007	1
2008	1
2009	1
2010	2
2011	1
2012	3
2014	2
2015	2
2016	5
2017	3
2018	5
2019	3
2020	4
2021	5
2022	11
2023	11
2024	7
2025	2

Media Mentions
Tweets

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Two synthetic biology experiments offer hope for future cancer treatments

El Pais 12/16/2022

Cancer treatments boosted by immune-cell hacking

Nature 12/15/2022

Designer Protein Acts as a Switch for Cellular Circuitry

The Scientist 7/25/2019

The ‘dawn’ of designer proteins: Biologists build a protein that turns cells on and off

The Washington Post 7/24/2019

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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