publications

Bibliography via PubMed

Fitzgerald, P. R., Cochrane, W. G., & Paegel, B. M. Dose-Response Activity-Based DNA-Encoded Library Screening (2023, submitted)

 

Burdick, J. P., Hackler, A. L., Fitzgerald, P. R., FitzGerald, F. G., & Paegel, B. M. Off-DNA DNA-Encoded Library Screening of a Nucleic Acid-Binding Enzyme. (2023, submitted)

 

Cavett, V., Chan, A. I., Cunningham, C. N., & Paegel, B. M. Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening. (2023, submitted)

 

  1. 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. J Med Chem (2023).

 

  1. Dixit, A., Barhoosh, H. & Paegel, B. M. Translating the Genome into Drugs. Accounts Chem Res 56, 489–499 (2023).

 

  1. Gibaut, Q. M. R., Akahori, Y., Bush, J. A., Taghavi, A., Tanaka, T., Aikawa, H., Ryan, L. S., Paegel, B. M. & Disney, M. D. Study of an RNA-Focused DNA-Encoded Library Informs Design of a Degrader of a r(CUG) Repeat Expansion. J Am Chem Soc 144, 21972–21979 (2022).

 

  1. Benhamou, R. I., Suresh, B. M., Tong, Y., Cochrane, W. G., Cavett, V., Vezina-Dawod, S., Abegg, D., Childs-Disney, J. L., Adibekian, A., Paegel, B. M. & Disney, M. D. DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor. Proc Natl Acad Sci U.S.A. 119, e2114971119 (2022).

 

  1. Cochrane, W. G., Fitzgerald, P. R., & Paegel, B. M. Antibacterial Discovery via Phenotypic DNA-Encoded Library Screening. ACS Chem Biol 16, 2752–2756 (2021)

 

  1. Hu, J., Cochrane, W. G., Jones, A. X., Blackmond, D. G. & Paegel, B. M. Chiral Lipid Bilayers are Enantioselectively Permeable. Nat Chem 13, 786–791 (2021).

 

  1. Fitzgerald, P. R. & Paegel, B. M. DNA-Encoded Chemistry: Drug Discovery from a Few Good Reactions. Chem Rev 121, 7155–7177 (2021).

 

  1. Cavett, V. & Paegel, B. M. Activity-Based Probe Hybridization Display. ACS Comb Sci 11, 579-585 (2020). 

 

  1. Price, A. K. & Paegel, B. M. Considerations for Achieving Maximized DNA Recovery in Solid-Phase DNA-Encoded Library Synthesis. ACS Comb Sci 11, 649-655 (2020).

 

  1. Matos, J., Green, S., Chun, Y., Dang, V., Dushin, R., Richardson, P., Chen, J., Piotrowski, D., Paegel, B. M., & Shenvi, R. A. Cycloisomerization of Olefins in Water. Angew Chem Int Ed 31. 12998-13003 (2020).

 

  1. Hackler, A. L., Fitzgerald, F. G., Dang, V. Q., Satz, A. L., & Paegel, B. M. Off-DNA DNA-Encoded Library Screening. ACS Comb Sci 1, 25-34 (2020).

 

  1. Ratnayake, A. S., Flanagan, M. E., Foley, T. L., Smith, J. D., Johnson, J. G., Montgomery, J. I., & Paegel, B. M. A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis. ACS Comb Sci 21, 650-655 (2019).

 

  1. Vallejo, D., Nikoomanzar, A., Paegel, B. M., & Chaput, J. C. Fluorescence-Activated Droplet Sorting for Single-Cell Directed Evolution. ACS Synth Biol 8, 6, 1430-1440 (2019). 

 

  1. 31. Cochrane, W. G., Malone, M. L., Dang, V. Q., Cavett, V., Satz, A. L., & Paegel, B. M. Activity-Based DNA-Encoded Library Screening. ACS Comb Sci 21, 425 (2019). 

 

  1. Cochrane, W. G., Hackler, A. L., Cavett, V. J., Price, A. K., Paegel, B. M. Integrated, Continuous Emulsion Creamer. Anal Chem 89, 13227- 13234 (2017). 

 

  1. MacConnell, A. B. & Paegel, B. M. The Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening. ACS Comb 19, 524-532 (2017). 

 

  1. MacConnell, A. B., Price, A. K., & Paegel, B. M. An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening. ACS Comb Sci, 19, 181-192 (2017).

 

  1. Malone, M. L., Cavett, V. J., & Paegel, B. M. Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction. ACS Comb Sci 19, 9-14. (2017). 

 

  1. Malone*, M. L., Cavett, V. J. MacConnell, A. B., McEnaney, P. J., Doran, T., Walzl, G., Paegel*, B. M., & Kodadek*, T. High-throughput Identification of DNA-Encoded Ligands that Differentiate Active and Latent Mycobacterium Tuberculosis Infections. ACS Chem Biol 118, 234-243. (2017). 

 

  1. Tran, D. T., Cavett, V. J., Dang, V. Q., Torres, H. L., & Paegel, B. M. Evolution of a Mass Spectrometry-Grade Protease with PTM-Directed Specificity. Proc Natl Acad Sci U.S.A. 113, 14686- 14691 (2016).

 

  1. Malone, M. L. & Paegel, B. M. What is a ‘DNA-Compatible’ Reaction? ACS Comb 18, 182-187 (2016). 

 

  1. Price, A. K., MacConnell, A. B., & Paegel, B. M. hvSABR: Photochemical Dose-Response Bead Screening in Droplets. Anal Chem 88, 2904-2911 (2016).

 

  1. Price, A. K. & Paegel, B. M. Discovery in Droplets. Anal Chem 88, 339-353 (2016). 

 

  1. 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. ACS Comb Sci 17, 518-534 (2015).

 

  1. Price, A. K., MacConnell, A. B., & Paegel, B. M. Microfluidic Bead Suspension Hopper. Anal Chem 86, 5039-5044 (2014). 

 

  1. Matosevic, S. & Paegel, B. M. Layer-by-Layer Cell Membrane Assembly. Nat. Chem 5, 958-963 (2013).

 

  1. Matosevic, S. & Paegel, B. M. Stepwise Synthesis of Giant Unilamellar Vesicles on a Microfluidic Assembly Line. J Am Chem Soc 133, 2798-2800 (2011).

 

  1. B. M. Paegel. “Microfluidic Landscapes for Evolution.” Curr. Opin. Chem. Biol., 2010, 14, 568.

 

  1. B.M. Paegel, G. F. Joyce. “Microfluidic Compartmentalized Directed Evolution.” Chem. Biol., 2010, 17, 717. 

 

  1. B.M. Paegel, G. F. Joyce. “Darwinian Evolution on a Chip.” PLoS Biol., 2008, 6, 900. 

 

  1. B. M. Paegel, W. H. Grover, A. M. Skelley, R. A. Mathies, G. F. Joyce. “Microfluidic Serial Dilution Circuit.” Anal. Chem., 2006, 78, 7522.

 

  1. E. A. S. Doherty, C. Kan, B. M. Paegel, S. H. I. Yeung, S. Cao, R. A. Mathies, A. E. Barron “Sparsely Cross-Linked ‘Nanogel’ Matrixes as Fluid, Mechanically Stabilized Polymer Networks for High-Throughput Microchannel DNA Sequencing.” Anal. Chem., 2004, 76, 5249.

 

  1. T. Kamei, B. M. Paegel, J. R. Scherer, A. M. Skelley, R. A. Street, R. A. Mathies. “Integrated Hydrogenated Amorphous Si Photodiode Detector for Microfluidic Bioanalytical Devices.” Anal. Chem., 2003, 75, 5300.

 

  1. T. Kamei, B.M. Paegel, J. R. Scherer, A.M. Skelley, R.A. Street, R.A. Mathies. “Fusion of a-Si:H Sensor Technology with Microfluidic Bioanalytical Devices.” J. Non-Cryst. Solids, 2004, 338–340, 715–719.

 

  1. B. M. Paegel, R. G. Blazej, R. A. Mathies. “Microfluidic Devices for DNA Sequencing Sample Preparation and Electrophoretic Analysis.” Curr. Opin. Biotechnol., 2003, 14, 42.

 

  1. R. G. Blazej, B. M. Paegel, R. A. Mathies. “SNP Discovery and Screening by Polymorphism Ratio Sequencing.” Genome Res., 2003, 13, 287.

 

  1. B. M. Paegel, S. H. I. Yeung, R. A. Mathies. “Microchip Bioprocessor for Integrated Nanovolume Sample Purification and DNA Sequencing.” Anal. Chem., 2002, 74, 5092.

 

  1. B. M. Paegel, C. A. Emrich, G. J. Wedemayer, J. R. Scherer, R. A. Mathies. “High-Throughput DNA Sequencing with a Microfabricated 96-Lane Capillary Array Electrophoresis Bioprocessor.” Proc. Natl. Acad. Sci. U. S. A., 2002, 99, 574.

 

  1. J. R. Scherer, B. M. Paegel, G. J. Wedemayer, C. A. Emrich, J. Lo, I. L. Medintz, R. A. Mathies. “High-Pressure Gel Loader for Capillary Array Electrophoresis Microchannel Plates.” Biotechniques, 2001, 31, 1150.

 

  1. I. L. Medintz, B. M. Paegel, R. G. Blazej, C. A. Emrich, L. Berti, J. R. Scherer, R. A. Mathies. “High-Performance Genetic Analysis Using Microfabricated Capillary Array Electrophoresis.” Electrophoresis, 2001, 22, 3845.

 

  1. I. L. Medintz, B. M. Paegel, R. A. Mathies. “Microfabricated Capillary Array Electrophoresis DNA Analysis Systems.” J. Chromatogr. A, 2001, 924, 265.

 

1. B. M. Paegel, L. D. Hutt, P. C. Simpson, R. A. Mathies. “Turn Geometry for Minimizing Band Broadening in Microfabricated Capillary Electrophoresis Channels.” Anal. Chem., 2000, 72, 3030.