Software

	CGI by Example
	Oregon Bioinformatics ToolSet
ntdiffs	Software for analyzing nucleotide substitutions
GSL	Genetic Simulation Library

 

Data

 

Papers

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	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.
	Conery, J.S. Continuation based control for parallel logic programs. Lisp and Symbolic Computation 7 (1), Jan. 1994, pp. 111-133.
	Sundararajan, R. and Conery, J.S. An abstract interpretation scheme for groundness, freeness, and sharing analysis of logic programs. In Proc. 12th. Conf. Foundations of Software Technology and Theoretical Computer Science (New Delhi, Dec. 18-20), 1992, pp. 203-216.
	Conery, J.S. Parallel logic programs on the Mayfly. Lisp and Symbolic Computation 5 (1), May 1992, pp. 49-72.
	Conery, J.S. The OPAL Machine. In Implementations of Distributed Prolog, P. Kacsuk and M. Wise, eds, John Wiley and Sons Ltd., 1992, pp. 159-185.
	Conery, J.S. Binding environments for parallel logic programs in non-shared memory multiprocessors. Int. Journal of Parallel Programming 17 (2), Apr 1988, pp. 125-152.