• Landry, C.R., J.P. Townsend, D.L. Hartl and D. Cavalieri, 2006. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 15: 575-591.
  
  
• Townsend, J.P., and J.W. Taylor, 2005. Designing experiments using spotted microarrays to detect gene regulation differences within and among species. In “Methods in molecular evolution: producing the biochemical data, Part B”, Zimmer,  E., and Roalson, E., eds., Academic Press: Methods in Enzymology, Volume 395: 597-617.
  
  
• Gogarten, J.P. and J.P. Townsend, 2005. Horizontal gene transfer, genome innovation, and evolution. Nature Reviews Microbiology 3(9): 679-687.
  
  
• Meiklejohn, C.D. and J.P. Townsend, 2005. A Bayesian method for analysing spotted microarray data. Briefings in Bioinformatics 6(4): 318-330.
  
  
• Kasuga, T., J.P. Townsend, C. Tian, L.B. Gilbert, G. Mannhaupt, J.W. Taylor, and L.N. Glass, 2005. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 33(20): 6469-6485.
  
  
• Johannesson, H., J.P. Townsend, C.-Y. Hung, G.T. Cole, J.W. Taylor, 2005.  Concerted evolution of the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii.  Genetics 171:109-117.
  
  
• Townsend, J.P. 2004. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 5: 54.
  
  
• Townsend, J.P., and D.M. Rand. 2004. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity 93 (1): 98-103.
  
  
• Nielsen, K.M., and J.P. Townsend, 2004. Monitoring and modeling horizontal gene transfer. Nature Biotechnology 22: 1110-1114.
  -Correspondence
  'Informative' horizontal gene transfer
  Monitoring horizontal gene transfer
  Reply to 'Monitoring horizontal gene transfer'
  
  
• Hartl, D.L., C.D. Meiklejohn, C.I. Castillo-Davis, D. Cavalieri, J.M. Ranz and J.P. Townsend. 2004. Expression Profiling in Evolutionary Genetics. In The Evolution of Population Biology, R. Singh, M. Uyenoyama, eds. Cambridge University Press.
  
  
• Townsend, J.P., D. Cavalieri, and D.L. Hartl. 2003. Population genetic variation in genome-wide gene expression in wine yeasts. Molecular Biology and Evolution 20 (6): 955-963.
  *Editor's Top 10 Paper*
  
  
• Townsend J.P. 2003. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 4:41.
  
  
• Townsend, J.P., K.M. Neilsen, D.S. Fisher, and D.L. Hartl. 2003. Horizontal acquisition of divergent chromosomal DNA: consequences of mutator phenotypes. Genetics 164 (5): 13-21.
  
  
• Townsend, J.P., and D.L. Hartl. 2002. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 3 (12): research0071.1-0071.16.
  
  
• Grosu, P., J.P. Townsend, D.L. Hartl and D. Cavalieri. 2002. Pathway processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Research 12: 1121-1126.
  
  
• Townsend, J.P., D. Cavalieri, and D.L. Hartl. 2001. Population genomics: gene expression in a vineyard yeast from Tuscany. Biology International 41: 91-98.
  
  
• Nielsen, K.M. and J.P. Townsend. 2001. Environmental exposure, horizontal transfer, and selection of transgenes in bacterial populations. In Enhancing biocontrol agents and handling risks. Vurro, M., J. Gressel, Butts, T., Harman, G., Pilgeram, A., St.-Leger, R., and Nuss, D., eds., IOS Press, Amsterdam: 145-158.
  
  
• Cavalieri, D., J.P. Townsend, and D.L. Hartl, 2000. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings of the National Academy of Sciences 97: 12369-12374.
  
  
• Townsend, J.P. and D.L. Hartl, 2000. The kinetics of transposable element autoregulation. Genetica 108: 229-237.
  
  
• Bustamante, C.D., J.P. Townsend, D.L. Hartl, 2000. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Molecular Biology and Evolution 17(2): 301-308.
  
  
• Townsend, J.P., 1998. A model of resource harvesting along a linear trail: The leaf-cutter ant Atta cephalotes. OTS Tropical Biodiversity 98-10: 87-91.
  
  
• Townsend, J.P., 1998. Bird diversity in pastoral and restoration habitats. OTS Tropical Biodiversity 98-10: 64-68.
  

Department of Molecular and Cell Biology
354 Mansfield Rd., U-2131
Storrs, CT 06269

(860) 486-1899