Publications

Recent Publications

 

A complete collection of Josh Leonard’s publications can be found at Pubmed or Google Scholar.

2024

Jung JK, Dreyer KS, Dray KE, Muldoon JJ, George J, Shirman S, Cabezas MD, d’Aquino AE, Verosloff MS, Seki K, Rybnicky GA, Alam KK, Bagheri N, Jewett MC, Leonard JN*, Mangan NM*, and Lucks JB* (2024). Developing, characterizing, and modeling CRISPR-based point-of-use pathogen diagnostics. ACS Synthetic Biology. *co-corresponding authors. e-pub.

Corcoran WK, Cosio A, Edelstein HI, and Leonard JN. Exploring structure-function relationships in engineered receptor performance using computational structure prediction. bioRxiv. e-pub.

Dreyer KS*,  Donahue PS*, Boucher JD, Chambers KM, Ornelas MY, Edelstein HI, Leibowitz BD, Zhu KJ, Dray KE, Muldoon JJ, and Leonard JN. Engineered feedback employing natural hypoxia-responsive factors enhances synthetic hypoxia biosensors. bioRxiv. *co-first authorship. e-pub.

Mitrut RE, Stranford DM*, DiBiase BN*, Chan JM, Bailey MD, Luo M, Harper CS, Meade TJ, Wang M, and Leonard JN (2024). HaloTag display enables quantitative single-particle characterisation and functionalisation of engineered extracellular vesicles. Journal of Extracellular Vesicles. *co-second authorship. e-pub.
Peruzzi JA, Gunnels TF, Edelstein HI, Lu P, Baker D, Leonard JN*, and Kamat NP* (2024). Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions. Nature Communications. *co-corresponding authors. e-pub.
Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, and Leonard JN (2024). Building synthetic biosensors using red blood cell proteins. ACS Synthetic Biology. e-pub.
Edelstein HI, Cosio A, Ezekiel ML, Corcoran WK, Morris AH, and Leonard JN (2024). Conversion of natural cytokine receptors into orthogonal synthetic biosensors. bioRxiv. e-pub.

2023

Stranford DM, Simons LM, Berman KE, Cheng L, DiBiase BN, Hung ME, Lucks JB, Hultquist JF, and Leonard JN (2023). Genetically encoding multiple functionalities into extracellular vesicles for the targeted delivery of biologics to T cells. Nature Biomedical Engineering. e-pub.
Stranford DM and Leonard JN (2023). Engineering cell-derived extracellular vesicles for gene therapy. Nature Biomedical Engineering. e-pub.

Dray KE, Dreyer KS, Lucks JB, and Leonard JN (2023). Teaching systematic, reproducible model development using synthetic biology. Chemical Engineering Education. e-pub.

Deol S, Donahue PS, Mitrut RE, Hammit-Kess IJ, Ahn J, Zhang B, and Leonard JN (2023). Comparative evaluation of synthetic cytokines for enhancing production and performance of NK92 cell-based therapies. GEN Biotechnology. e-pub.

2022

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,  and Deans TL (2022). The sound of silence: Transgene silencing in mammalian cell engineering. Cell Systems. e-pub.
Prybutok AN, Yu JS, Leonard JN*, and Bagheri N* (2022). Mapping CAR T-cell design space using agent-based models. Frontiers in Molecular Biosciences. *co-corresponding authors. e-pub.
Edelstein HI*, Bora GG*, and Leonard JN (2022). Engineering Mammalian Cells to Communicate Using a Language from Plants. GEN Biotechnology. *co-first authorship. e-pub.
Gunnels TF, Stranford DM, Mitrut RE, Kamat N*, and Leonard JN* (2021). Elucidating design principles for engineering cell-derived vesicles to inhibit SARS-CoV-2 infection. Small. *co-corresponding authors. e-pub.
Prybutok AN*, Cain JY*, Leonard JN^, and Bagheri N^ (2022). Fighting fire with fire: deploying complexity in computational modeling to effectively characterize complex biological systems. Current Opinion in Biotechnology. *co-first authors. ^co-corresponding authors. e-pub.
Manhas J*, Edelstein HI*, Leonard JN, and Morsut L (2022). The evolution of synthetic receptor systems. Nature Chemical Biology. *co-first authors. e-pub.
Dray KE, Muldoon JJ, Mangan N, Bagheri N*, and Leonard JN* (2022). GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems. ACS Synthetic Biology. *co-corresponding authors. e-pub.

2021

Dray KE*, Edelstein HI*, Dreyer KS*, and Leonard JN (2021). Control of mammalian cell-based devices with genetic programming. Current Opinion in Systems Biology. *co-first authors. e-pub.
Cable J, Leonard JN, Lu TK, Xie Z, Chang MW, Fernández LÁ, Lora JM, Kaufman HL, Quintana FJ, Geiger R, Lesser CF, Lynch JP, Hava DL, Cornish VW, Lee GK, DiAndreth B, Fero M, Srivastava R, De Coster T, Roybal KT, Rackham OJL, Kiani S, Zhu I, Hernandez-Lopez RA, Guo T, and Chen WCW (2021). Synthetic biology: at the crossroads of genetic engineering and human therapeutics–a Keystone Symposia report. Annals of The New York Academy of Sciences. e-pub.
Verosloff MS, Corcoran WK, Dolberg TD, Bushhouse DZ, Leonard JN, and Lucks JB (2020). RNA sequence and structure determinants of Pol III transcriptional termination in human cells. Journal of Molecular Biology. e-pub.
Muldoon JJ, Kandula V, Hong M, Donahue PS, Boucher JD, Bagheri N, and Leonard JN (2021). Model-guided design of mammalian genetic programs. Science Advances. e-pub.

*Dolberg TB, *Meger AT, Boucher JD, Corcoran WK, Schauer EE, Prybutok AN, Raman S, and Leonard JN (2021). Computation-guided optimization of split protein systems. Nature Chemical Biology. *co-first authors. e-pub.

2020

Edelstein HI, Donahue PS, Muldoon JJ, Kang AK, Dolberg TB, Battaglia LM, Allchin ER, Hong M, Leonard JN (2020). Elucidation and refinement of synthetic receptor mechanisms. Synthetic Biology. e-pub.

 

Nathamgari SSP, Pathak N, Lemaitre V, Mukherjee P, Muldoon JJ, Peng C, McGuire T, Leonard JN, Kessler JA, Espinosa HD (2020). Nano Fountain Probe Electroporation Enables Versatile Single-Cell Intracellular Delivery and Investigation of Post-Pulse Electro-pore Dynamics. Small. e-pub.

 

Muldoon JJ, Chuang Y, Bagheri N, and Leonard JN (2020). Macrophages employ quorum licensing to regulate collective activation. Nature Communications. e-pub.

 

 

 

 

Donahue PS, *Draut JW, *Muldoon JJ, *Edelstein HI, Bagheri N, and Leonard JN (2020). The COMET toolkit for composing customizable genetic programs in mammalian cells. Nature Communications. *co-second authors.  e-pub.

 

 

2018

Kang Li, Rodosthenous RS, Kashanchi F, Gingeras T, Gould SJ, Kuo LS, Kurre P, Lee H, Leonard JN, Liu H, Lombo TB, Momma S, Nolan JP, Ochocinska MJ, Pegtel DM, Sadovsky Y,  Sánchez-Madrid F, Valdes KM, Vickers KC, Weaver AM, Witwer KW, Zeng Y, Das S, Raffai RL, and Howcroft TK (2018). Advances, challenges, and opportunities in extracellular RNA biology: insights from the NIH exRNA Strategic Workshop. JCI Insight. e-pub.

 

Dolberg TB, Donahue PS, Leonard JN (2018). Synthetic biology: Reframing cell therapy for cancer. Nature Chemical Biology. e-pub

 

Hung ME, Lenzini SB, Stranford DM, Leonard JN (2018). Enrichment of Extracellular Vesicle Subpopulations Via Affinity Chromatography. Methods in Molecular Biology. Pubmed
Hong BJ, Iscen A, Chipre A, Li MM, Lee OS, Leonard JN, Schatz G, Nguyen SB (2018). Highly Stable, Ultra-Small Polymer-Grafted Nanobins (usPGNs) with Stimuli-Responsive Capability. Journal of Physical Chemistry. Pubmed

 

Younger AKD, Su PY, Shepard AJ, Udani SV, Cybulski TR, Tyo KE, Leonard JN (2018). Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion. Protein Engineering, Design, and Selection. Pubmed

2017

Nut C, Rodriguez E, Donahue PS, Stranford DM, Leonard JN (2017). An investigation of petty theft of beach decorations at American universities. Journal Criminal Justice. Read more
Muldoon JJ, Donahue PS, Dolberg TB, Leonard JN (2017). Building with intent: Technologies and principles for engineering mammalian cell-based therapies to sense and respond. Current Opinion in Biomedical Engineering. Epub ahead of print
Xiao X, Wang Y, Leonard JN, Hall CK (2017). Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm. Journal of Chemical Theory and Computation. Pubmed

 

Stranford DM, Leonard JN (2017). Delivery of Biomolecules via Extracellular Vesicles: A Budding Therapeutic Strategy. Advances in Genetics. Pubmed
Hartfield RM, Schwarz KA, Muldoon JJ, Bagheri N, Leonard JN (2017). Multiplexing engineered receptors for multiparametric evaluation of environmental ligands. ACS Synthetic Biology. Pubmed
Stranford DM, Hung ME, Gargus ES, Shah RN, Leonard JN (2017). A systematic evaluation of factors affecting extracellular vesicle uptake by breast cancer cells. Tissue Engineering Part A. Pubmed (Invited contribution to special issue)

 

leonard-graphical-abstract-01Schwarz KA, Daringer NM, Dolberg TB, Leonard JN (2017). Rewiring human cellular input–output using modular extracellular sensors. Nature Chemical Biology. Pubmed

 

2016

abstract-graphicYounger AKD, Dalvie NC, Rottinghaus AG, Leonard JN (2016). Engineering modular biosensors to confer metabolite-responsive regulation of transcription. ACS Synthetic Biology. Pubmed

 

abstractgraphic-01Du Lac M, Scarpelli AH, Younger AKD, Bates DG, Leonard JN (2016). Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes. ACS Synthetic Biology. Pubmed

 

Chuang_II_Fig4Chuang YC, Hung ME, Cangelose BK, Leonard JN (2016). Regulation of the IL-10-driven macrophage phenotype under incoherent stimuli. Innate Immunity. Pubmed

 

hungXaio-and-HungXaio X, Hung ME, Leonard JN, Hall CK (2016). Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA. Journal of Computational Chemistry. Pubmed

 

 

schwarz-reveiwAbstractFigureSchwarz KA, Leonard JN. (2016) Engineering cell-based therapies to interface robustly with host physiology. Advanced Drug Delivery Reviews. Pubmed

 

Figure 1 16-0316Hung ME, Leonard JN (2016). A platform for actively loading cargo RNA to elucidate limiting steps in EV-mediated delivery. Journal Extracellular Vesicles. Pubmed

 

gowerGower 2016Liu JM, Zhang J, Zhang X, Hlavaty KA, Ricci CF, Leonard JN, Shea LD, Gower RM. (2016) Transforming growth factor-beta 1 delivery from microporous scaffolds decreases inflammation post-implant and enhances function of transplanted islets. Biomaterials. Pubmed

Other Publications

 

Jelinek I, Leonard JN, Price G, Brown K, Meyer-Manlapat A, Goldsmith PK, Wang Y, Venzon D, Epstein SL, Segal DM. TLR3-specific dsRNA oligonucleotide adjuvants induce dendritic cell cross-presentation, CTL responses, and antiviral protection. Journal of Immunology. 2011 186 (4): 2422-9. Pubmed

Leonard JN, Bell JK, Segal DM. Predicting TLR structures and characterizing ligand binding. Methods in Molecular Biology. 2009 517:55-67. Pubmed

Leonard JN, Ghirlando R, Askins J, Bell JK, Margulies DH, Davies DR, Segal DM. The TLR3 signaling complex forms by cooperative receptor dimerization. Proceedings of the National Academy of Sciences USA. 2008 105(1):258-63. Pubmed

Liu L, Botos I, Wang Y, Leonard JN, Shiloach J, Segal DM, Davies DR. Structural basis of toll-like receptor 3 signaling with double-stranded RNA. Science. 2008 320(5874):379-81. Pubmed

Leonard JN*, Shah PS*, Burnett JC, Schaffer DV. HIV evades RNA interference directed at TAR by an indirect compensatory mechanism. Cell Host & Microbe. 2008 4(5):484-94. *co-first authors. Pubmed

Ricci C, Pastukh V, Leonard JN, Turrens J, Wilson G, Schaffer DV, Schaffer SW. Mitochondrial DNA damage triggers mitochondrial-superoxide generation and apoptosis. American Journal of Physiology. 2008 294, C413-22. Pubmed

Zhang SY, Jouanguy E, Ugolini S, Smahi A, Elain G, Romero P, Segal D, Sancho-Shimizu V, Lorenzo L, Puel A, Picard C, Chapgier A, Plancoulaine S, Titeux M, Cognet C, von Bernuth H, Ku CL, Casrouge A, Zhang XX, Barreiro L, Leonard J, Hamilton C, Lebon P, Héron B, Vallée L, Quintana-Murci L, Hovnanian A, Rozenberg F, Vivier E, Geissmann F, Tardieu M, Abel L, Casanova JL. TLR3 deficiency in patients with herpes simplex encephalitis. Science. 2007 317:1522-7. Pubmed

Ashton RS, Peltier J, Fasano CA, O’neill A, Leonard J, Temple S, Schaffer DV, Kane R. High-throughput screening of gene function in stem cells using clonal microarrays. Stem Cells. 2007 25:2928-35. Pubmed

Leonard JN, Ferstl P, Delgado A, Schaffer DV. Enhanced preparation of adeno-associated viral vectors by using high hydrostatic pressure to selectively inactivate helper adenovirus. Biotechnology and Bioengineering. 2007  97:1170-9. (Featured in a spotlight in this issue) Pubmed

Leonard JN, Schaffer DV. Antiviral RNAi therapy: emerging approaches for hitting a moving target. Gene Therapy. 2006 13(6):532-40. Pubmed

Leonard JN, Schaffer DV. Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape. Journal of Virology. 2005 79(3):1645-54. Pubmed

Patents

 

Leonard JN, Dudek RM, Daringer NM, inventors; 2012 Aug 3. Modular Extracellular Sensor Architecture for Cell-based Biosensors. United States Patent 9,732,392. Download

Schaffer DV, Leonard JN, inventors; 2010 Dec. 14. Methods for Purifying Adeno-Associated Virus Particles. United States Patent 7,851,196. Download

Schaffer DV, Leonard JN, inventors; 2009 Dec. 1. Methods for Purifying Adeno-Associated Virus. United States Patent 7,625,570. Download

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