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D'Alessio, M., R. Nordeste, A.C. Doxey, and T.C. Charles, "Transcriptome analysis of polyhydroxybutyrate cycle mutants reveals discrete loci connecting nitrogen utilization and carbon storage in Sinorhizobium meliloti", mSystems. 2:e00035-17, 2017.
DasGupta, B., X. He, T. Jiang, M. Li, J. Tromp, L. Wang, and L. Zhang, "Computing distances between evolutionary trees", In Handbook in Combinatorial Optimization, 1999.
DasGupta, B., X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, "On distances between phylogenetic trees", Proc. 8th Ann. ACM-SIAM Symp. on Discrete Algorithms (SODA'97), New Orleans, 1997.
DasGupta, B., T. Jiang, S. Kannan, M. Li, and Z. Sweedyk, "On the complexity and approximation of syntenic distance", In Proc. 1st Symp. on Computational Molecular Biology (RECOMB'97) Santa Fe, 1997.
DasGupta, B., X. He, M. Li, J. Tromp, and L. Zhang, "Nearest neighbor interchange and related distances", Encyclopedia of Algorithms, Springer, 2014.
DasGupta, B., X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, "On computing the neares t neighbor interchange distance", in D.Z. Du, P.M. Pardalos and J. Wang (eds.), Proceedings of the DIMACS Workshop on Discrete Problems with Medical Applications, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, AmericanMathematical Society, Vol. 55, pp. 125-143, 2000.
DasGupta, B., X. He, T. Jiang, M. Li, and J. Tromp, "On the linear-cost subtree-transfer distance between phylogenetic trees", Algorithmica, 25, 176-195, 1999.
DasGupta, B., T. Jiang, S. Kannan, M. Li, and Z. Sweedyk, "On the complexity and approximation of syntenic distance", Discrete Applied Mathematics (special issue in computational biology), 88:1-3,59-82, 1998.
Deng, X., G. Li, Z. Li, B. Ma, and L. Wang, " Genetic Design of Drug without Side Effects", SIAM Journal on Computing 32(4): 1073-1090, 2003.
Deng, X., G. Li, Z. Li, B. Ma, and L. Wang, " A PTAS for Distinguishing (Sub)string Selection", The 29th International Colloquium on Automata, Languages, and Programming. 740-751, 2002.
Dexter, D., and D.G. Brown, "Fast half-sibling population reconstruction: theory and algorithms", Algorithms for Molecular Biology 8: 20, 2013.
Doxey, A.C., M.J. Mansfield, and B. Lobb, "Exploring the evolution of virulence factors through bioinformatic data mining", mSystems. 4:e00162-19, 2019.
Doxey, A.C., M.J. Mansfield, and C. Montecucco, "Discovery of novel bacterial toxins by genomics and computational biology", Toxicon. 147:2-12, 2018.
Doxey, A.C., D. Kurtz, L. Sauder, M.D.J. Lynch, and J.D. Neufeld, "Aquatic metagenomes implicate Thaumarchaeaota in global cobalamin production", ISME Journal. 9:461-71, 2015.
Doxey, A.C., and B.J. McConkey, "Prediction of molecular mimicry candidates in human pathogenic bacteria", Virulence. 4:453-66, 2013.
Doxey, A.C., Z. Cheng, B.A. Moffatt, and B.J. McConkey, "Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d", BMC Structural Biology. 10:23, 2010.
Doxey, A.C., M.D.J. Lynch, K.M. Muller, E.M. Meiering, and B.J. McConkey, "Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster", BMC evolutionary biology, 8:316, 2008.
Doxey, A.C., M.W. Yaish, B.A. Moffatt, M. Griffith, and B.J. McConkey, "Functional divergence in the Arabidopsis beta-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states", Doxey AC, Yaish MW, Moffatt BA, Griffith M, McConkey BJ, 2007.
Doxey, A.C., M.W. Yaish, M. Griffith, and B.J. McConkey, "Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions", Nature biotechnology, 24:852, 2006.
Duncker, B.P., I.N. Chesnokov, and B.J. McConkey, "The origin recognition complex protein family", Genome biology.10:214, 2009.

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