Choudhury A., Fankhauser R. G., Freed E. F., Oh E. J., Morgenthaler A. B., Bassalo M. C., Copley S. D., Kaar J. L., Gill R. T. "Determinants for efficient editing with Cas9-mediated recombineering in Escherichia coli", ACS Synthetic Biology, 2020.

Morgenthaler, A. B., Kinney, W. R., Ebmeier, C. C., Walsh, C. M., Snyder, D. J., Cooper, V. S., Old, W. M., Copley, S. D. “Mutations that improve the efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome", eLife, 2019.

Kim, J., Flood, J. J., Kristofich, M., Gidfar, C., Morgenthaler, A. B., Fuhrer, T., Sauer, U., Snyder, D. J., Cooper, V. S., Ebmeier, C. C., Old, W. M., and Copley, S. D. "Hidden resources in the E. coli genome restore PLP synthesis and robust growth after deletion of the 'essential' gene pdxB", PNAS, 2019.

Flood, J. J. and Copley, S. D. “Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum”, mSystems, 2018.

Kristofich, J., Morgenthaler, A. B., Kinney, W., Ebmeier, C. C., Snyder, D. J., Old, W. M., Cooper, V. S., and Copley, S. D. “Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme”, PLoS Genetics, 2018.

Copley, S. D. "Shining a light on enzyme promiscuity", Current Opinion in Structural Biology, 2017.

Kershner, J. P., Yu McLoughlin, S., Kim, J., Morgenthaler, A., Ebmeier, C. C., Old, W. M., Copley, S. D. “A synonymous mutation upstream of the gene encoding a weak-link enzyme causes an ultrasensitive response in growth rate”, Journal of Bacteriology, 2016.

Thiaville J.J., Flood J., Yurgel S., Prunetti L., Elbadawi-Sidhu M., Hutinet G., Forouhar F., Zhang X., Ganesan V., Reddy P., Fiehn O., Gerlt J.A., Hunt J.F., Copley S.D., de Crécy-Lagard V. "Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite", ACS Chemical Biology, 2016.

Copley, S. D. "An evolutionary biochemist's perspective on promiscuity", Trends in Biochemical Science, 2015.

Copley, S. D. "An evolutionary perspective on protein moonlighting", Biochemical Society Transactions, 2014

Kim J., Webb A.M., Kershner J.P., Blaskowski S., Copley S.D. "A versatile and highly efficient method for scarless genome editing in Escherichia coli and Salmonella enterica", BMC Biotechnology, 2014.

Khanal A., Yu McLoughlin S., Kershner J.P., Copley S.D. "Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution", Molecular Biology and Evolution, 2014.

Rudolph J., Erbse A.H., Behlen L.S., Copley S.D. "A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum", Biochemistry, 2014.

Rokicki J., Knox D., Dowell R.D., Copley S.D. "CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes", BMC Genomics, 2014.

Novikov Y., Copley S.D. "Reactivity landscape of pyruvate under simulated hydrothermal vent conditions", PNAS, 2013.

Yadid I., Rudolph J., Hlouchova K., Copley S.D. "Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol", PNAS, 2013.

Kim J., Copley S.D. "The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family", Biochemistry, 2013.

Kim J., Copley S.D. "Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network", PNAS, 2012.

Hlouchova K., Rudolph J., Pietari J.M., Behlen L.S., Copley S.D. "Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum", Biochemistry, 2012.

Copley, S. D. “Paradigm adjustment required: Moonlighting is mainstream”, Bioessays, 2012.

Copley, S. D. and Summons, R. E. “Terran Metabolism: The First Billion Years”, in Frontiers of Astrobiology, C. Impey, J. Lunine and J. Funes, Eds., Cambridge University Press, 2012.

Copley S.D., Rokicki J., Turner P., Daligault H., Nolan M., Land M. "The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway", Genome Biology and Evolution, 2011.

Novikov Y., Copley S.D., Eaton B.E. "A Simple Route for Synthesis of 4-Phospho-D-Erythronate", Tetrahedron Letters, 2011.

Copley S.D., "Toward a systems biology perspective on enzyme evolution", Journal of Biological Chemistry, 2011.

Chumachenko N., Novikov Y., Shoemaker R.K., Copley S.D. "A dimethyl ketal-protected benzoin-based linker suitable for photolytic release of unprotected peptides", Journal of Organic Chemistry, 2011.

Kim J., Kershner J.P., Novikov Y., Shoemaker R.K., Copley S.D. "Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis", Molecular Systems Biology, 2010.

Rudolph J., Kim J., Copley S.D. "Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates", Biochemistry, 2010.

Copley, S. D. “Evolution and the Enzyme”, in Comprehensive Natural Products Chemistry, vol. 8, (Enzymes and Enzyme Mechanisms), Elsevier, pp 9-46; L. Mander and H.-W. Liu, Eds., 2010.

Copley, S. D., Smith, E. and Morowitz, H. J. “How life began: The emergence of sparse metabolic networks”, Journal of Cosmology, 2010.

Copley, S. D. “Prediction of function in enzyme superfamilies”, F1000 Biology Reports, 1, Report 91, 2009.

Copley, S. D. “Evolution of efficient pathways for degradation of anthropogenic chemicals”, Nature Chem. Biol., 2009.

Smith, E., Morowitz, H. J., and Copley, S. D. “Core metabolism as a self-organized system”, in Protocells: Bridging Nonliving and Living Matter, edited by Rasmussen, S. et al., MIT Press, 2009.

Yu McLoughlin, S. and Copley, S. D. “A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities”, PNAS, 2008.

Hamady, M., Widmann, J., Copley, S. D., and Knight, R. “MotifCluster: An interactive online tool for clustering and visualizing sequences using shared motifs”, Genome Biology, 2008.

Warner, J. R., Behlen, L. S. and Copley, S. D. “A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase”, Biochemistry, 2008.

Kim, J. and Copley, S. D. “Why metabolic enzymes are essential or non-essential for growth of Escherichia coli K12 on glucose”, Biochemistry, 2007.

Warner, J. R. and Copley, S. D.  “Pre-steady state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase”, Biochemistry, 2007.

Copley, S. D., Smith, E. and Morowitz, H. J. “The origin of the RNA world: Co-evolution of genes and metabolism”, Bioorganic Chemistry, 2007.

Warner, J. R. and Copley, S. D. “Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates”, Biochemistry, 2007.

Copley, Shelley D. “Glutathione transferases”, in Redox Biology, R. Banarjee, Ed., Wiley, 2007.

Cleland, C. E., and Copley, S. D. “The possibility of alternative microbial life on earth”, International Journal of Astrobiology, 2005.

Warner, J. P., Lawson, S. L., and Copley, S. D. "A mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase", Biochemistry, 2005.

Copley, S. D., Smith, D. E., and Morowitz, H. G. “A mechanism for the association of amino acids with their codons and the origin of the genetic code”, Proc. Natl. Acad. Sciences, 2005.

Dai, M. H., Gill, R. T., and Copley, S. D. “Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli”, Metabolic Engineering, 2005.

Copley, S. D., Novak, W., and Babbitt, P. C. “Divergence of function in the thioredoxin-fold suprafamily: Evidence for evolution of peroxiredoxins from thioredoxins”, Biochemistry, 2004.

Dai, M.-H. and Copley, S. D. “Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723”, Appl. Env. Microbiol., 2004.

Copley, S.D. "Enzymes with extra talents: moonlighting functions and catalytic promiscuity", Current Opinion in Chemical Biology, 2003.

Dai, M.H., Rogers, J. B., Warner, J. P., and Copley, S. D. “A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD)”, Journal of Bacteriology, 2003.

Copley, S. D. and Dhillon, J. K. “Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes”, Genome Biology, 2002.

Kiefer, P. M., Jr., McCarthy, D. L., and Copley, S. D. “The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution”, Biochemistry, 2002.

Kiefer, P. M., Jr., and Copley, S. D. “Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase”, Biochemistry, 2002.

Copley, S. D. “Aromatic dehalogenases: Insights into structures, mechanisms, and evolutionary origins”, Dehalogenation: Microbial Processes and Environmental Applications, Kluwer Academic Publishers, 2002.

Copley, S. D., Anandarajah, K, and Kiefer, P. M., Jr. “A tale of two enzymes – tetrachlorohydroquinone dehalogenase and maleylacetoacetate isomerase”, Chemico-Biological Interactions, 2001.

Copley, S. D. “Evolution of a metabolic pathway for degradation of a toxic xenobiotic: The patchwork approach”, Trends in Biochemical Sciences, 2000.

Anandarajah, K.; Kiefer, P. M.; Donohoe, B. S. and Copley, S. D. “Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol”, 2000.

Fall, R. and Copley, S. D. “Bacterial sources and sinks of isoprene, a reactive atmospheric hydrocarbon”, Environmental Microbiology, 2000.

Xu, L.; Resing, K.; Babbitt, P. C.; Lawson, S. L. and Copley, S. D. “Evidence that pcpA Encodes dichlorohydroquinone dioxygenase, the ring-cleavage enzyme required for degradation of pentachlorophenol in Sphingomonas chlorophenolica”, Biochemistry, 1999.

Copley, S. D. “Microbial dehalogenases”. In Enzymes, Enzyme Mechanisms, Proteins, and Aspects of NO Chemistry, C. D. Poulter, Ed., Vol. 5 of Comprehensive Natural Products Chemistry, D. Barton and K. Nakanishi, Eds., 1999.

Copley, S. D. “Microbial dehalogenases: Enzymes recruited to convert xenobiotic substrates”, Curr. Opin. Chem. Biol., 1998.

McCarthy, D. L.; Louie, D. F.; Copley, S. D. “Identification of a covalent intermediate between glutathione and Cys13 formed during catalysis by tetrachlorohydroquinone dehalogenase.” J. Am. Chem. Soc., 1997.

Copley, S. D. “Diverse mechanistic approaches to difficult chemical transformations: Microbial dehalogenation of chlorinated aromatic compounds.Chem. & Biol., 1997.

Plowman, D. L.; Copley, S. D. and Claude, A. “In vivo levels of chlorinated hydroquinones in a pentachlorophenol-degrading bacterium”, Appl. Env. Microbiol, 1997.

McCarthy, D.; Navarette, S.; Willett, W. S.; Babbitt, P. C. and Copley, S. D. “Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily”, Biochemistry , 1996.

Willett, W. S.; Copley, S. D. “Identification and localization of a stable sulfenic acid in peroxide-treated tetrachlorohydroquinone dehalogenase using electrospray mass spectrometry”, Chem. & Biol., 1996.

Crooks, G. P.; Xu, L.; Barkley, R. and Copley, S. D. "Exploration of possible mechanisms for 4-chlorobenzoyl CoA dehalogenase: Evidence for an aryl-enzyme intermediate.J. Am. Chem. Soc., 1995.

Crooks, G. P. and Copley, S. D. "Purification and characterization of 4-chlorobenzoyl CoA dehalogenase from Arthrobacter sp. 4CB-1" Biochemistry, 1994.

Crooks, G. P. and Copley, S. D. "A surprising effect of leaving group on the nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl CoA dehalogenase.J. Am. Chem. Soc., 1993.

Copley, S. D. and Crooks, G. P. "Enzymic dehalogenation of 4-chlorobenzoyl CoA in Acinetobacter sp. 4-CB1.Appl. Env. Microbiol., 1992.