Allan, C. M.; Hill, S.; Morvaridi, S.; Saiki, R.; Johnson, J. S.; Liau, W-S.; Hirano, K.; Kawashima, T.; Ji, Z.; Loo, J. A.; Shepherd, J. N.; Clarke, C. F. "A conserved START domain coenzyme Q-binding polypeptide is required for efficient Q biosynthesis, respiratory electron transport, and antioxidant function in Saccharomyces cerevisiae," Biochim. Biophys. Acta 2013, 1831, 776-791.

Lonjers, Z. T.*; Dickson, E. L.*; Chu, T-P T.*; Kreutz, J. E.*; Neacsu, F. A.; Anders, K. R.; Shepherd, J. N. "Identification of a New Gene Required for the Biosynthesis of Rhodoquinone in Rhodospirillum rubrum,"  J. Bacteriol. 2012, 194, 965-971.

Murphy, K.; Kubin, Z. J.*; Shepherd, J. N.; Ettinger, R. H. "Valeriana officinalis Root Extracts have Potent Anxiolytic Effects in Laboratory Rats," Phytomedicine 2010, 17, 674-678.

Brajcich, B. C.*; Iarocci, A. L.*; Johnstone, L. A. G.*; Morgan, R. K.*; Lonjers, Z. T.*; Hotchko, M. J.*; Muhs, J. D.*; Kieffer, A.*; Reynolds, B. J.*; Mandel, S. M.; Marbois, B. N.; Clarke, C. F.; Shepherd, J. N. "Evidence that Ubiquinone is a Required Intermediate for Rhodoquinone Biosynthesis in Rhodospirillum rubrum," J. Bacteriol. 2010, 192, 436-445.

Paddock, M. L.; Flores, M.; Isaacson, R.; Shepherd, J. N.; Okamura, M. Y. "EPR and ENDOR Investigation of Rhodosemiquinone in Bacterial Reaction Centers Formed by B-branch Electron Transfer," Appl. Magn. Reson. 2010, 37, 39-48.

Shepherd, J. N.; Stenzel, J. R. "Synthesis of Unsymmetrical Alkynes via the Alkylation of Sodium Acetylides: An Introduction to Synthetic Design for Organic Chemistry Students," J. Chem. Educ. 2006, 83, 424-428.

Cape, J. L.; Strahan, J. R.; Lenaeus, M. J.; Yuknis, B. A.; Le, T. T.; Shepherd, J. N.; Bowman, M. K.; Kramer, D. M. "The Respiratory Substrate Rhodoquinol Induces Q-Cycle Bypass Reactions in the Yeast Cytochrome bc1 Complex: Mechanistic and Physiological Implications," J. Biol. Chem. 2005, 280, 34654-34660.

Marbois, B.; Gin,P.; Faull, K. M.; Poon, W. W.; Lee, P. T.; Strahan, J.; Shepherd, J. N.; Clarke, C. F. "Coq3 and Coq4 Define a Polypeptide Complex in Yeast Mitochondria for the Biosynthesis of Coenzyme Q," J. Biol. Chem. 2005, 280, 20231-20238.

Baba, S. W.; Belogrudov, G. I.; Lee, J. C.; Lee, P. T.; Strahan, J.; Shepherd, J. N.; Clarke, C. F. "Yeast Coq5 C-methyltransferase is required for stability of other polypeptides involved in coenzyme Q biosynthesis," J. Biol. Chem. 2004 , 279, 10052-10059.

Shepherd, J. N.; Myles, D. C. "Synthesis of Polyketides via Diastereoselective Acetalization," Organic Letters 2003, 5, 1027-1030.

W. W. Poon, R. J. Barkovich, A. Y. Hsu, A. Frankel, P. T. Lee, J. N. Shepherd, D. C. Myles and C. F. Clarke, “Yeast Coq3 and E. coli UbiG Polypeptides Catalyze Both O-Methyltransferase Steps in Coenzyme Q Biosynthesis,” J. Biol. Chem. 274, 21665-21672, 1999.

J. N. Shepherd, J. Na and D. C. Myles, “Diastereoselective Acetalization of Pseudo-C2-Symmetric 1,3,5-Triols: A New Strategy for the Synthesis of Polyacetates and Polypropionates,” J. Org. Chem. 62, 4558-4559, 1997.

R. J. Barkovich, A. Shtanko, J. A. Shepherd, P. T. Lee, D. C. Myles, A. Tzagoloff and C. F. Clarke, “Characterization of the COQ5 Gene from Saccharomyces cerevisiae, Evidence for a C-Methyltransferase in Ubiquinone Biosynthesis,” J. Biol. Chem. 272, 9182-9188, 1997.

A. Y. Hsu, W. W. Poon, J. A. Shepherd, D. C. Myles and C. F. Clarke, “Complementation of coq3 Mutant Yeast by Mitochondrial Targeting of the Escherichia coli UbiG Polypeptide: Evidence That UbiG Catalyzes Both O-Methylation Steps in Ubiquinone Biosynthesis,” Biochemistry 35, 9797-9808, 1996.

J. A. Shepherd, W. W. Poon, D. C. Myles and C. F. Clarke, “The Biosynthesis of Ubiquinone: Synthesis and Enzymatic Modification of Biosynthetic Precursors,” Tetrahedron Lett. 37, 2395-2398, 1996.