Jeff Townsend

Work Address: Jeffrey P. Townsend Department of Ecology and Evolutionary Biology Yale University Osborne Memorial Labs 165 Prospect Street P.O. Box 208106 New Haven, CT 06520-8106 phone: (203) 432 4646 email: Jeffrey.Townsend@yale.edu Townsend lab web site

Jeff joined the Taylor lab in August 2002. His research interest is whether evolutionarily relevant mutations are structural or regulatory in nature. If adaptation by regulatory evolution is common, there must be (1) population variation in the regulation of genes, (2) inheritance of that variation, and (3) differential reproductive success based on that regulatory variation. He is interested in the modeling, measurement, and analysis of population genetic variation in global gene expression in order to reveal the extent of variation in regulation of gene expression in natural populations.

Jeff left the Taylor lab in September 2004 and is currently an assistant professor in the Department of Ecology and Evolutionary Biology at Yale.

Software

• Bayesian Analysis of Gene Expression Levels (BAGEL): a program for the statistical analysis of spotted microarray data.
  
  • Download the archive for
    • Macintosh OS X
    • Macintosh OS 9
    • Windows
    • Ryan Weddle's compile for Linux
      
  • View some papers that have used the BAGEL software.
    
    
• Pathway Processor: A program that tests for overrepresentation of differentially expressed genes within known pathways of S. cerevisiae or B. subtilis.
  • Available in
    • Virtual-machine Java.
      
      
• SeqPop: A program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.
  
  • Download the archive for
    • Macintosh OS X
    • Macintosh OS 9
      
      
• Jeff's software page at Yale

Publications

• Taylor, John W.; Turner, Elizabeth; Townsend, Jeffrey P.; Dettman, Jeremy R.; Jacobson, David. 2006. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions of the Royal Society of London B Biological Sciences 361(1475): 1947-1963.
  
  
• H. Johannesson, T. Kasuga, R.A. Schaller, B. Good, M.J. Gardner, J.P. Townsend, G.T. Cole and J.W. Taylor. 2006. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology 43(8): 545-559.
  
  
• Takao Kasuga, Jeffrey P. Townsend, Chaoguang Tian, Luz B. Gilbert, Gertrud Mannhaupt, John W. Taylor and N. Louise 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.
  
  
• Jeffrey P. Townsend and John W. Taylor. 2005. Designing experiments using spotted microarrays to detect gene regulation differences within and among Species. Methods in Enzymology 395: 597-617.
  
  
• 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.
  
  
• 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., 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.
  
  
• 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.
  
  
• 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.
  

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