Brian M Paegel

•Chair, Department of Pharmaceutical Sciences, University of California, Irvine

•Professor (Step IV), Department of Pharmaceutical Sciences (primary), Chemistry, Biomedical Engineering, University of California, Irvine

Biography

Brian M. Paegel, Ph.D., is Professor and Chair of the Department of Pharmaceutical Sciences, with courtesy appointments in Chemistry and Biomedical Engineering at the University of California, Irvine. He earned his Ph.D. in Chemistry from the University of California, Berkeley, where he contributed to the Human Genome Project through work on DNA sequencing technology. He subsequently trained as an NIH NRSA Postdoctoral Fellow at Scripps Research, where he developed microfluidic automated systems for the continuous directed evolution of catalytic RNAs under the mentorship of Gerald F. Joyce.

Paegel joined the chemistry faculty at Scripps Research in 2009, where he was recognized with the NIH Director's New Innovator Award and an NSF CAREER Award for his work in reaction miniaturization. Scripps granted him tenure in 2017 in recognition of his contributions to DNA-encoded library synthesis and analysis technology. In 2019, he joined the University of California, Irvine, where his laboratory develops synthesis and screening platforms aimed at supporting translational research and democratizing drug discovery. He has co-founded five biotechnology companies.

Paegel's research centers on DNA-encoded chemical library technology and microfluidic approaches to drug discovery. His laboratory has received sustained NIH support for this work, including a current NIH MIRA award. He has been invited to present his research at universities, pharmaceutical companies, and international symposia across North America, Europe, and Asia, and has served on scientific advisory boards for multiple biotechnology companies and the Novartis Institute of Biomedical Research.

Education

Ph.D. in Chemistry, University of California, Berkeley, 2003
B.S. in Chemistry, Duke University, 1998

Distinctions

NIH MIRA, 2021, 2026
NIH Director's New Innovator Award, 2011
NIH Ruth L. Kirschstein National Research Service Award, 2005
NSF CAREER Award, 2013
NIH Pathway to Independence Award, 2007
NIH Program in Genomics Fellow, 2000
ACS Division of Analytical Chemistry Fellow, 2000
Athalie Clarke Achievement Award, 2022
Dean's Honoree Teaching Award, 2022-2023
Hypercube Scholar, 1998

Areas of Expertise

Drug discovery
Chemical biology
DNA-encoded libraries
Combinatorial synthesis
Miniaturization
Automation
Solid-phase synthesis

Recent Publications

Burdick J. P., Cerna Arroyo E. M., Levine S. R., Paegel B. M., “Automated DNA-Encoded Library Synthesis and Activity-Based Screening at the Attomole Scale” (opens in new tab), Journal of Medicinal Chemistry, vol. 69, pp. 19005-19017, 2026.
Nguyen, A. A., Paegel, B. M., “Hydrogel-Bead Particles Enable Activity-Based Identification of Nucleic Acid Aptamer Enzyme Inhibitors” (opens in new tab), Analytical Chemistry, vol. 97, pp. 21003–21011, 2025.
Dixit, A., Paegel, B. M., “Solid-phase DNA-encoded library synthesis: a master builder's instructions” (opens in new tab), Nature Protocols, vol. 21, pp. 1–40, 2025.
Barhoosh, H., Dixit, A., Cochrane, W. G., Cavett, V., Prince, R. N., Blair, B. O., Ward, F. R., McClure, K. F., Patten, P. A., Paulick, M. G., Paegel, B. M., “Activity-Based DNA-Encoded Library Screening for Selective Inhibitors of Eukaryotic Translation” (opens in new tab), ACS Central Science, vol. 10, pp. 1960–1968, 2024.
Fitzgerald, P. R., Dixit, A., Zhang, C., Mobley, D. L., Paegel, B. M., “Building Block-Centric Approach to DNA-Encoded Library Design” (opens in new tab), Journal of Chemical Information and Modeling, vol. 64, pp. 4661–4672, 2024.
Fitzgerald, P. R., Cochrane, W. G., Paegel, B. M., “Dose–Response Activity-Based DNA-Encoded Library Screening” (opens in new tab), ACS Medicinal Chemistry Letters, vol. 14, pp. 1295–1303, 2023.
Cavett, V., Chan, A. I., Cunningham, C. N., Paegel, B. M., “Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening” (opens in new tab), ACS Central Science, vol. 9, pp. 1603–1610, 2023.
Yang, X., Childs‐Disney, J. L., Paegel, B. M., Disney, M. D., “DNA‐Encoded Libraries and Their Application to RNA” (opens in new tab), Israel Journal of Chemistry, vol. 63, 2023.
Yik, E. J., Medina, E., Paegel, B. M., Chaput, J. C., “Highly Parallelized Screening of Functionally Enhanced XNA Aptamers in Uniform Hydrogel Particles” (opens in new tab), ACS Synthetic Biology, vol. 12, pp. 2127–2134, 2023.
Hu, J., Chan, A. I., Adaligil, E., Kekessie, I., Takahashi, M., Song, A., Cunningham, C. N., Paegel, B. M., “Liposomal Permeation Assay for Droplet-Scale Pharmacokinetic Screening” (opens in new tab), Journal of Medicinal Chemistry, vol. 66, pp. 6288–6296, 2023.
Dixit, A., Barhoosh, H., Paegel, B. M., “Translating the Genome into Drugs” (opens in new tab), Accounts of Chemical Research, vol. 56, pp. 489–499, 2023.
Cochrane, W. G., Fitzgerald, P. R., Paegel, B. M., “Antibacterial Discovery via Phenotypic DNA-Encoded Library Screening” (opens in new tab), ACS Chemical Biology, vol. 16, pp. 2752–2756, 2021.
Hu, J., Cochrane, W. G., Jones, A. X., Blackmond, D. G., Paegel, B. M., “Chiral Lipid Bilayers are Enantioselectively Permeable” (opens in new tab), Nature Chemistry, vol. 13, pp. 786–791, 2021.

Most Cited Publications

Paegel, B. M., Emrich, C. A., Wedemayer, G. J., Scherer, J. R., Mathies, R. A., “High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor” (opens in new tab), Proceedings of the National Academy of Sciences of the United States of America, vol. 99, pp. 574-579, 2002.
Matosevic, S., Paegel, B. M., “Stepwise Synthesis of Giant Unilamellar Vesicles on a Microfluidic Assembly Line” (opens in new tab), Journal of the American Chemical Society, vol. 133, pp. 2798-2800, 2011.
Paegel, B. M., Blazej, R. G., Mathies, R. A., “Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis” (opens in new tab), Current Opinion in Biotechnology, vol. 14, pp. 42-50, 2003.
Malone, M. L., Paegel, B. M., “What is a 'DNA-Compatible' Reaction?” (opens in new tab), ACS Combinatorial Science, vol. 18, pp. 182–187, 2016.
Fitzgerald, P. R., Paegel, B. M., “DNA-Encoded Chemistry: Drug Discovery from a Few Good Reactions” (opens in new tab), Chemical Reviews, vol. 121, pp. 7155–7177, 2021.
Paegel, B. M., Hutt, L. D., Simpson, P. C., Mathies, R. A., “Turn Geometry for Minimizing Band Broadening in Microfabricated Capillary Electrophoresis Channels” (opens in new tab), Analytical Chemistry, vol. 72, pp. 3030-3037, 2000.
Kamei, T., Paegel, B. M., Scherer, J. R., Skelley, A. M., Street, R. A., Mathies, R. A., “Integrated hydrogenated amorphous Si photodiode detector for microfluidic bioanalytical devices” (opens in new tab), Analytical Chemistry, vol. 75, pp. 5300-5305, 2003.
MacConnell, A. B., McEnaney, P. J., Cavett, V. J., Paegel, B. M., “DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis” (opens in new tab), ACS Combinatorial Science, vol. 17, pp. 518-534, 2015.
Matosevic, S., Paegel, B. M., “Layer-by-Layer Cell Membrane Assembly” (opens in new tab), Nature Chemistry, vol. 5, pp. 958-963, 2013.
Vallejo, D., Nikoomanzar, A., Paegel, B. M., Chaput, J. C., “Fluorescence-Activated Droplet Sorting for Single-Cell Directed Evolution” (opens in new tab), ACS Synthetic Biology, vol. 8, no. 6, pp. 1430–1440, 2019.

Contact Information

Email: bpaegel@uci.edu

Phone: (949) 824-9368

Address: 1107 Natural Sciences II

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Last updated on 9/11/2026.