Selected Publications

Bioinformatics and Computational Biology

	Catchen, J. M., Conery, J. S., and Postlethwait, J. H. Automated identification of conserved synteny after whole-genome duplication. Genome Res 19(8):1497–1505, 2009.
	Catchen, J., Conery, J. S., and Postlethwait, J. H. Inferring ancestral gene order. Methods in Molecular Biology 452 (3), 365-383, 2008
	Conery, J. S. Aligning sequences by minimum description length. EURASIP Journal on Bioinformatics and Systems Biology. doi:10.1155/2007/72936, 2007.
	Dunn, N. A., Conery, J. S., and Lockery, S. R. Circuit motifs for spatial orientation behaviors identified by neural network optimization. J Neurophysiol 98(2):888–897, 2007.
	Saks, M. E. and Conery, J. S. Anticodon-dependent conservation of bacterial tRNA gene sequences. RNA 13(5):651–660, 2007.
	Dunn, N. A., Pierce-Shimomura, J. T., Conery, J. S., and Lockery, S. R. Clustered neural dynamics identify motifs for chemotaxis in Caenorhabditis elegans. International Joint Conference on Neural Networks, pp. 547–554, 2006.
	Conery, J.S., Catchen, J.M., and Lynch, M. Rule-based workflow management for bioinformatics. VLDB Journal 14(3): 318-329, 2005.
	Dunn, N.A., Lockery, S.R., Pierce-Shimomura, J.T., and Conery, J.S. A neural network model of chemotaxis predicts functions of synaptic connections in the nematode Caenorhabditis elegans. Journal of Computational Neuroscience 17:137-147, 2004.
	Dunn, N.A., Conery, J.S., and Lockery, S.R. Circuit optimization predicts dynamic network for chemosensory orientation in the nematode C. elegans. Advances in Neural Information Processing Systems 16, MIT Press, 2004.
	Lynch, M. and Conery, J.S. The origins of genomic complexity. Science 302 (5649), 2003, pp. 1401-04. [Supporting On-Line Material]
	May, H.K. and Conery, J.S. FOREST: A system for developing and evaluating ecosystem simulation models. Proc. Summer Computer Simulation Conference, 2003.
	Dunn, N.A., Conery, J.S., and Lockery, S.R. A neural network model for chemotaxis in Caenorhabditis elegans. Proc. Int. Joint Conf. on Neural Networks, IEEE, 2003.
	Lynch, M. and Conery, J.S. Evolutionary demography of duplicate genes. Journal of Structural and Functional Genomics 3 (1), 2003, pp. 35-44.
	Conery, J.S. and Lynch, M. Nucleotide substitutions and the evolution of duplicate genes. Pacific Symposium on Biocomputing 6, 2001, pp. 167-178.
	Lynch, M. and Conery, J.S. The evolutionary fate and consequences of duplicate genes. Science 290 (5494), 2000, pp. 1151-55. [On-line Supplement]
	Conery, J.S., and Lynch, M. The Genetic Simulation Library. Bioinformatics 15 (1), 1999, pp. 85-86.
	Glass, K., Livingston, M., and Conery, J.S. Distributed simulation of spatially explicit ecological models. Proc. 11th Workshop on Parallel and Distributed Simulation (PADS'97), (Vienna, June 10-13), 1997, pp. 60-63.
	Lynch, M., Conery, J.S., and Bürger, R. Mutation accumulation and the extinction of small populations. American Naturalist 146 (4), 1995, pp. 489-518.
	Lynch, M., Conery, J.S., and Bürger, R. Mutational meltdowns in sexual populations. Evolution 49 (6), 1995, pp. 1067-1080.
	Conery, J.S., Lynch, M., and Hovland, T. Optimizing irregular computations on SIMD machines: A case study. In Proc. Fifth Symposium on Frontiers of Massively Parallel Computation, (MacLean, VA, Feb. 6-9), 1995, pp. 222-230.
	Conery, J.S., Peticolas, W., Rush, T., Shanmugam, K., and Dominguez, J. A parallel algorithm for calculating the free energy in DNA. Proc. Hawaii International Conference on System Sciences, Vol. V (Biotechnology), (Maui, Jan. 3-6), 1995, pp. 123-131.

Computer Science

	Conery, J.S. Computation is symbol manipulation. Computer Journal 55:814–816, 2012.
	Conery, J.S. Continuation based control in the implementation of parallel logic programs. LISP and Symbolic Computing 7(1):111-133, 1994.
	Conery, J.S. The OPAL machine. In Implementations of Distributed Prolog, John Wiley and Sons, 1992.
	Conery, J.S. Parallel logic programs on the Mayfly. LISP and Symbolic Computing 5(1):49-72, 1992.
	Conery, J.S. Binding environments for parallel logic programs in non-shared memory multiprocessors. Int. J. Parallel Programming 17:125-152, 1988.
	Conery, J.S. Parallel Execution of Logic Programs. Kluwer Academic Press, 1987.
	Conery, J.S., and Kibler, D.F. Parallel interpretation of logic programs. In Conference on Functional Programming and Computer Architecture (Manchester, NH), ACM, pp. 163-170, 1981.