Scholars@Duke

• Background
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  Education, Training, & Certifications

  • Ph.D., Tokyo Institute of Technology (Japan) 2008
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  Previous Appointments & Affiliations

  • Associate Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2019 - 2021
  • Assistant Professor of Biochemistry, Biochemistry, Basic Science Departments 2011 - 2019
  • Assistant Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2011 - 2019
• Expertise
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  Subject Headings

  • Muser Mentor
• Research
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  Selected Grants

  • Medical Scientist Training Program awarded by National Institutes of Health 2022 - 2027
  • Catalysis and inhibition of chitin synthesis from pathogenic fungi awarded by National Institutes of Health 2022 - 2027
  • Cell and Molecular Biology Training Program awarded by National Institutes of Health 2021 - 2026
  • MRI: Acquisition of a Microscale Thermophoresis System awarded by  National Science Foundation 2022 - 2025
  • Biosynthesis of antifungal nucleoside antibiotics awarded by National Institutes of Health 2015 - 2024
  • Mechanism of carbon skeleton formation in molybdenum cofactor biosynthesis awarded by National Institutes of Health 2020 - 2024
  • Medical Scientist Training Program awarded by National Institutes of Health 1997 - 2022
  • Organization and Function of Cellular Structure awarded by National Institutes of Health 1975 - 2020
  • Biochemistry and Structure of Lipid A Enzymes awarded by National Institutes of Health 2016 - 2020
  • Structural Biology and Biophysics Training Program awarded by National Institutes of Health 1994 - 2015
  • High sensitivity multi-purpose electron paramagnetic resonance spectroscopy for biotechnological and biomedical research awarded by North Carolina Biotechnology Center 2014 - 2015
• Publications & Artistic Works
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  Selected Publications

  • Academic Articles

    • Nguyen, Hai, I Dewa Made Kresna, Nils Böhringer, Jeremie Ruel, Eugenio de la Mora, Jil-Christine Kramer, Kim Lewis, Yvain Nicolet, Till F. Schäberle, and Kenichi Yokoyama. “Characterization of a Radical SAM Oxygenase for the Ether Crosslinking in Darobactin Biosynthesis.” J Am Chem Soc 144, no. 41 (October 19, 2022): 18876–86. https://doi.org/10.1021/jacs.2c05565.
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    • Ren, Zhenning, Abhishek Chhetri, Ziqiang Guan, Yang Suo, Kenichi Yokoyama, and Seok-Yong Lee. “Structural basis for inhibition and regulation of a chitin synthase from Candida albicans.” Nat Struct Mol Biol 29, no. 7 (July 2022): 653–64. https://doi.org/10.1038/s41594-022-00791-x.
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    • Yokoyama, Kenichi, Di Li, and Haoran Pang. “Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems.” Acs Bio Med Chem Au 2, no. 2 (April 20, 2022): 94–108. https://doi.org/10.1021/acsbiomedchemau.1c00046.
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    • Draelos, Matthew M., Anyarat Thanapipatsiri, Yanan Du, and Kenichi Yokoyama. “Cryptic Phosphorylation-Mediated Divergent Biosynthesis of High-Carbon Sugar Nucleoside Antifungals.” Acs Chem Biol 17, no. 4 (April 15, 2022): 898–907. https://doi.org/10.1021/acschembio.1c00971.
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    • Draelos, Matthew M., Anyarat Thanapipatsiri, Hilda Sucipto, and Kenichi Yokoyama. “Addendum: Cryptic phosphorylation in nucleoside natural product biosynthesis.” Nat Chem Biol 17, no. 10 (October 2021): 1111–12. https://doi.org/10.1038/s41589-021-00867-7.
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    • Pang, Haoran, Lindsey M. Walker, Alexey Silakov, Pan Zhang, Weitao Yang, Sean J. Elliott, and Kenichi Yokoyama. “Mechanism of Reduction of an Aminyl Radical Intermediate in the Radical SAM GTP 3',8-Cyclase MoaA.” J Am Chem Soc 143, no. 34 (September 1, 2021): 13835–44. https://doi.org/10.1021/jacs.1c06268.
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    • Draelos, Matthew M., Anyarat Thanapipatsiri, and Kenichi Yokoyama. “Conserved Mechanism of 2'-Phosphorylation-Aided Amide Ligation in Peptidyl Nucleoside Biosynthesis.” Biochemistry 60, no. 28 (July 20, 2021): 2231–35. https://doi.org/10.1021/acs.biochem.1c00327.
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    • Chhetri, Abhishek, Anna Loksztejn, and Kenichi Yokoyama. “Quantitative Characterization of the Amount and Length of (1,3)-β-d-glucan for Functional and Mechanistic Analysis of Fungal (1,3)-β-d-glucan Synthase.” Bio Protocol 11, no. 8 (April 2021): e3995. https://doi.org/10.21769/bioprotoc.3995.
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    • Draelos, Matthew M., Anyarat Thanapipatsiri, Hilda Sucipto, and Kenichi Yokoyama. “Cryptic phosphorylation in nucleoside natural product biosynthesis.” Nat Chem Biol 17, no. 2 (February 2021): 213–21. https://doi.org/10.1038/s41589-020-00656-8.
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    • Pang, Haoran, Edward A. Lilla, Pan Zhang, Du Zhang, Thomas P. Shields, Lincoln G. Scott, Weitao Yang, and Kenichi Yokoyama. “Mechanism of Rate Acceleration of Radical C-C Bond Formation Reaction by a Radical SAM GTP 3',8-Cyclase.” J Am Chem Soc 142, no. 20 (May 20, 2020): 9314–26. https://doi.org/10.1021/jacs.0c01200.
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    • Chhetri, Abhishek, Anna Loksztejn, Hai Nguyen, Kaila M. Pianalto, Mi Jung Kim, Jiyong Hong, J Andrew Alspaugh, and Kenichi Yokoyama. “Length Specificity and Polymerization Mechanism of (1,3)-β-d-Glucan Synthase in Fungal Cell Wall Biosynthesis.” Biochemistry 59, no. 5 (February 11, 2020): 682–93. https://doi.org/10.1021/acs.biochem.9b00896.
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    • Yang, Hao, Elizabeth C. McDaniel, Stella Impano, Amanda S. Byer, Richard J. Jodts, Kenichi Yokoyama, William E. Broderick, Joan B. Broderick, and Brian M. Hoffman. “The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Spectroscopies.” J Am Chem Soc 141, no. 30 (July 31, 2019): 12139–46. https://doi.org/10.1021/jacs.9b05926.
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    • Nguyen, Hai P., and Kenichi Yokoyama. “Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C Biosynthesis.” Biochemistry 58, no. 25 (June 25, 2019): 2804–8. https://doi.org/10.1021/acs.biochem.9b00379.
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    • Yang, Hao, Elizabeth McDaniel, Stella Impano, Amanda Byer, Richard Jodts, Kenichi Yokoyama, William Broderick, Joan Broderick, and Brian Hoffman. “The Elusive 5′-Deoxyadenosyl Radical: Captured and Characterized by EPR and ENDOR Spectroscopies,” June 10, 2019. https://doi.org/10.26434/chemrxiv.8244596.v1.
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    • Kuhnert, Eric, Yan Li, Nan Lan, Qun Yue, Li Chen, Russell J. Cox, Zhiqiang An, Kenichi Yokoyama, and Gerald F. Bills. “Enfumafungin synthase represents a novel lineage of fungal triterpene cyclases.” Environ Microbiol 20, no. 9 (September 2018): 3325–42. https://doi.org/10.1111/1462-2920.14333.
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    • Byer, Amanda S., Hao Yang, Elizabeth C. McDaniel, Venkatesan Kathiresan, Stella Impano, Adrien Pagnier, Hope Watts, et al. “Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis.” J Am Chem Soc 140, no. 28 (July 18, 2018): 8634–38. https://doi.org/10.1021/jacs.8b04061.
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    • Yokoyama, Kenichi, and Edward A. Lilla. “C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products.” Nat Prod Rep 35, no. 7 (July 18, 2018): 660–94. https://doi.org/10.1039/c8np00006a.
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    • Yokoyama, Kenichi. “Radical Breakthroughs in Natural Product and Cofactor Biosynthesis.” Biochemistry 57, no. 4 (January 30, 2018): 390–402. https://doi.org/10.1021/acs.biochem.7b00878.
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    • Pang, Haoran, and Kenichi Yokoyama. “Lessons From the Studies of a CC Bond Forming Radical SAM Enzyme in Molybdenum Cofactor Biosynthesis.” Methods Enzymol 606 (2018): 485–522. https://doi.org/10.1016/bs.mie.2018.04.014.
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    • Ravichandran, Kanchana, Ellen C. Minnihan, Qinghui Lin, Kenichi Yokoyama, Alexander T. Taguchi, Jimin Shao, Daniel G. Nocera, and JoAnne Stubbe. “Glutamate 350 Plays an Essential Role in Conformational Gating of Long-Range Radical Transport in Escherichia coli Class Ia Ribonucleotide Reductase.” Biochemistry 56, no. 6 (February 14, 2017): 856–68. https://doi.org/10.1021/acs.biochem.6b01145.
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    • Lilla, Edward A., and Kenichi Yokoyama. “Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes.” Nat Chem Biol 12, no. 11 (November 2016): 905–7. https://doi.org/10.1038/nchembio.2187.
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    • Chen, Li, Yan Li, Qun Yue, Anna Loksztejn, Kenichi Yokoyama, Edd A. Felix, Xingzhong Liu, Ningyan Zhang, Zhiqiang An, and Gerald F. Bills. “Engineering of New Pneumocandin Side-Chain Analogues from Glarea lozoyensis by Mutasynthesis and Evaluation of Their Antifungal Activity.” Acs Chem Biol 11, no. 10 (October 21, 2016): 2724–33. https://doi.org/10.1021/acschembio.6b00604.
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    • Hover, Bradley M., Edward A. Lilla, and Kenichi Yokoyama. “Mechanistic Investigation of cPMP Synthase in Molybdenum Cofactor Biosynthesis Using an Uncleavable Substrate Analogue.” Biochemistry 54, no. 49 (December 15, 2015): 7229–36. https://doi.org/10.1021/acs.biochem.5b00857.
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    • Yokoyama, Kenichi, and Silke Leimkühler. “The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria.” Biochim Biophys Acta 1853, no. 6 (June 2015): 1335–49. https://doi.org/10.1016/j.bbamcr.2014.09.021.
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    • Hover, Bradley M., Nam K. Tonthat, Maria A. Schumacher, and Kenichi Yokoyama. “Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis.” Proc Natl Acad Sci U S A 112, no. 20 (May 19, 2015): 6347–52. https://doi.org/10.1073/pnas.1500697112.
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    • Hover, Bradley M., and Kenichi Yokoyama. “C-Terminal glycine-gated radical initiation by GTP 3',8-cyclase in the molybdenum cofactor biosynthesis.” J Am Chem Soc 137, no. 9 (March 11, 2015): 3352–59. https://doi.org/10.1021/ja512997j.
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    • Wei, Yifeng, Guinevere Mathies, Kenichi Yokoyama, Jiahao Chen, Robert G. Griffin, and JoAnne Stubbe. “A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase.” J Am Chem Soc 136, no. 25 (June 25, 2014): 9001–13. https://doi.org/10.1021/ja5030194.
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    • Wörsdörfer, Bigna, Denise A. Conner, Kenichi Yokoyama, Jovan Livada, Mohammad Seyedsayamdost, Wei Jiang, Alexey Silakov, JoAnne Stubbe, J Martin Bollinger, and Carsten Krebs. “Function of the diiron cluster of Escherichia coli class Ia ribonucleotide reductase in proton-coupled electron transfer.” J Am Chem Soc 135, no. 23 (June 12, 2013): 8585–93. https://doi.org/10.1021/ja401342s.
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    • Hover, Bradley M., Anna Loksztejn, Anthony A. Ribeiro, and Kenichi Yokoyama. “Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis.” J Am Chem Soc 135, no. 18 (May 8, 2013): 7019–32. https://doi.org/10.1021/ja401781t.
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    • Ando, Nozomi, Edward J. Brignole, Christina M. Zimanyi, Michael A. Funk, Kenichi Yokoyama, Francisco J. Asturias, Joanne Stubbe, and Catherine L. Drennan. “Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase.” Proc Natl Acad Sci U S A 108, no. 52 (December 27, 2011): 21046–51. https://doi.org/10.1073/pnas.1112715108.
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    • Yokoyama, Kenichi, Albert A. Smith, Björn Corzilius, Robert G. Griffin, and Joanne Stubbe. “Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the Escherichia coli class Ia ribonucleotide reductase.” J Am Chem Soc 133, no. 45 (November 16, 2011): 18420–32. https://doi.org/10.1021/ja207455k.
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    • Yokoyama, Kenichi, Ulla Uhlin, and JoAnne Stubbe. “A hot oxidant, 3-NO2Y122 radical, unmasks conformational gating in ribonucleotide reductase.” J Am Chem Soc 132, no. 43 (November 3, 2010): 15368–79. https://doi.org/10.1021/ja1069344.
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    • Yokoyama, Kenichi, Ulla Uhlin, and Joanne Stubbe. “Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-active tyrosines in ribonucleotide reductase.” J Am Chem Soc 132, no. 24 (June 23, 2010): 8385–97. https://doi.org/10.1021/ja101097p.
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    • Artin, Erin, Jun Wang, Gregory J. S. Lohman, Kenichi Yokoyama, Guixue Yu, Robert G. Griffin, Galit Bar, and JoAnne Stubbe. “Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5'-diphosphate in the presence or absence of reductant.” Biochemistry 48, no. 49 (December 15, 2009): 11622–29. https://doi.org/10.1021/bi901590q.
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    • Minnihan, Ellen C., Kenichi Yokoyama, and JoAnne Stubbe. “Unnatural amino acids: better than the real things?” F1000 Biology Reports 1 (November 26, 2009). https://doi.org/10.3410/b1-88.
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    • Kudo, Fumitaka, Taiki Kawashima, Kenichi Yokoyama, and Tadashi Eguchi. “Enzymatic preparation of neomycin C from ribostamycin.” J Antibiot (Tokyo) 62, no. 11 (November 2009): 643–46. https://doi.org/10.1038/ja.2009.88.
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    • Yokoyama, Kenichi, Daijiro Ohmori, Fumitaka Kudo, and Tadashi Eguchi. “Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy.” Biochemistry 47, no. 34 (August 26, 2008): 8950–60. https://doi.org/10.1021/bi800509x.
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    • Yokoyama, Kenichi, Yasuhito Yamamoto, Fumitaka Kudo, and Tadashi Eguchi. “Involvement of two distinct N-acetylglucosaminyltransferases and a dual-function deacetylase in neomycin biosynthesis.” Chembiochem 9, no. 6 (April 14, 2008): 865–69. https://doi.org/10.1002/cbic.200700717.
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    • Yokoyama, Kenichi, Mario Numakura, Fumitaka Kudo, Daijiro Ohmori, and Tadashi Eguchi. “Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin.” J Am Chem Soc 129, no. 49 (December 12, 2007): 15147–55. https://doi.org/10.1021/ja072481t.
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    • Kudo, Fumitaka, Yasuhito Yamamoto, Kenichi Yokoyama, Tadashi Eguchi, and Katsumi Kakinuma. “Biosynthesis of 2-deoxystreptamine by three crucial enzymes in Streptomyces fradiae NBRC 12773.” J Antibiot (Tokyo) 58, no. 12 (December 2005): 766–74. https://doi.org/10.1038/ja.2005.104.
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    • Yokoyama, Kenichi, Fumitaka Kudo, Mieko Kuwahara, Kousuke Inomata, Hideyuki Tamegai, Tadashi Eguchi, and Katsumi Kakinuma. “Stereochemical recognition of doubly functional aminotransferase in 2-deoxystreptamine biosynthesis.” J Am Chem Soc 127, no. 16 (April 27, 2005): 5869–74. https://doi.org/10.1021/ja0445948.
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  • Book Sections

    • Cáceres, Juan Carlos, Clara A. Bailey, Kenichi Yokoyama, and Brandon L. Greene. “Selenocysteine substitutions in thiyl radical enzymes.,” 662:119–41, 2022. https://doi.org/10.1016/bs.mie.2021.10.014.
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    • Draelos, Matthew M., and Kenichi Yokoyama. “Biosynthesis and Mechanism of Action of Antifungal Peptidyl Nucleoside Natural Products.” In Comprehensive Natural Products III, 613–41. Elsevier, 2020. https://doi.org/10.1016/b978-0-12-409547-2.14680-3.
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    • Yokoyama, Kenichi. “Radical-Mediated Carbon Skeleton Formation in Cofactor and Natural Product Biosynthesis.” In Comprehensive Natural Products III, 70–95. Elsevier, 2020. https://doi.org/10.1016/b978-0-12-409547-2.14745-6.
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  • Conference Papers

    • Yokoyama, Kenichi, Bradley Hover, and Edward Lilla. “Radical-mediated C-C bond formation in natural product and cofactor biosynthesis.” In Abstracts of Papers of the American Chemical Society, Vol. 258. AMER CHEMICAL SOC, 2019.
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    • McDaniel, Elizabeth, Hao Yang, Amanda Byer, William Broderick, Kenichi Yokoyama, Brian Hoffman, and Joan Broderick. “Insights into the universal radical SAM organometallic intermediate, Omega.” In Abstracts of Papers of the American Chemical Society, Vol. 257. AMER CHEMICAL SOC, 2019.
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    • Yokoyama, Kenichi, Bradley M. Hover, Nam K. Tonthat, and Maria A. Schumacher. “Capturing a Cryptic Biosynthetic Intermediate Reveals Novel Enzyme Functions in Molybdenum Cofactor Biosynthesis.” In Faseb Journal, Vol. 30. FEDERATION AMER SOC EXP BIOL, 2016.
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    • Yokoyama, Kenichi, Bradley M. Hover, Nam K. Tonthat, and Maria A. Schumacher. “Capturing a Cryptic Biosynthetic Intermediate Reveals Novel Enzyme Functions in Molybdenum Cofactor Biosynthesis.” In Faseb Journal, Vol. 30. FEDERATION AMER SOC EXP BIOL, 2016.
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• Teaching & Mentoring
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  Recent Courses

  • BIOCHEM 393: Research Independent Study 2023
  • BIOCHEM 593: Research Independent Study 2023
  • BIOCHEM 393: Research Independent Study 2022
  • BIOCHEM 593: Research Independent Study 2022
  • BIOCHEM 393: Research Independent Study 2021
  • BIOCHEM 593: Research Independent Study 2021

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