THEORETICAL & COMPUTATIONAL
Clark, T.A., and J.P. Townsend, 2007. Quantifying variation in gene expression. Molecular Ecology 16: 2613-2616.
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.
Meiklejohn, C.D. and J.P. Townsend, 2005. A Bayesian method for analysing spotted microarray data. Briefings in Bioinformatics 6(4): 318-330.
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. 2003. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 4:41.
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.
LABORATORY EXPERIMENTAL
Townsend, J. P. 2008. Sleuthing the difference a nucleotide can make. Molecular Ecology 17:2793-2795.
Clark, T.A., J.M. Guilmette, D. Renstrom, and J.P. Townsend, 2008. RNA extraction, probe preparation, and competitive hybridization for transcriptional profiling using Neurospora crassa long-oligomer DNA microarrays. Fungal Genetics Reports 55:18-28.
Dunlap, J.C. and 35 additional authors, 2007. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in Genetics 57: 49-69.
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.
Johannesson, H., T. Kasuga, R.A. Schaller, B. Good, M.J. Gardner, J.P. Townsend, G.T. Cole and J.W. Taylor, 2006. Phase-specific genes expression underlying morphological adaptiations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology 43(8): 545-559.
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.
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., D. Cavalieri, and D.L. Hartl. 2001. Population genomics: gene expression in a vineyard yeast from Tuscany. Biology International 41: 91-98.
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.
Comparative Genomics and Population Genetics
Townsend, J. P, 2007. Profiling phylogenetic informativeness. Systematic Biology 56(2): 222-231.
Gogarten, J.P. and Townsend, J.P. 2005. Horizontal gene transfer, genome innovation, and evolution. Nature Reviews Microbiology 3(9): 679-687.
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'
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.
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.
Townsend, J.P. and D.L. Hartl. 2000. The kinetics of transposable element autoregulation. Genetica 108: 229-237.
Aa, E., Townsend, J.P., R.I. Adams, K.M. Nielsen, J.W. Taylor, 2006. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Research 6: 702-716.
Taylor, J.W., E. Turner, J. P. Townsend, J. R. Dettman, D. Jacobson, 2006. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions of the the Royal Society B: Biological Sciences 361: 1947-1963.
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., and D.M. Rand. 2004. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity 93 (1): 98-103.
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.