Jeffrey P. Townsend

Assistant Professor Department of Ecology and Evolutionary Biology Yale University Osborne Memorial Labs 165 Prospect Street P.O. Box 208106 New Haven, CT 06520-8106 (203) 432-4646 email: Jeffrey.Townsend (at) Yale.edu Townsend Lab web site

Assistant Professor, University of Connecticut, 2004-2006

Miller Research Fellow, 2002-2004, University of California, Berkeley, California

Ph.D. 2002, Harvard University, Cambridge, Massachusetts

B.A. 1994, Brown University, Providence, Rhode Island

• 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.
  
  
• Townsend, J.P., 2007. Profiling phylogenetic informativeness. Systematic Biology 56(2): 222-231.
  
  
• Clark, T.A., and J.P. Townsend, 2007. Quantifying variation in gene expression. Molecular Ecology 16: 2613-2616.
  
  
• Dunlap, J.C., K.A. Borkovich, M.R. Henn, G.E. Turner, M.S. Sachs, N.L. Glass, K. McCluskey, M. Plamann, J.E. Galagan, B.W. Birren, R.L. Weiss, J.P. Townsend, J.J. Loros, M.A. Nelson, R. Lambreghts, H.V. Colot, G. Park, P. Collopy, C. Ringelberg, C. Crew, L. Litvinkova, D. DeCaprio, H.M. Hood, S. Curilla, M. Shi, M. Crawford, M. Koerhsen, P. Montgomery, L. Larson, M. Pearson, T. Kasuga, C. Tian, M. Basturkmen, L. Altamirano, J. Xu, 2007. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in Genetics 57: 49-69.
  
  
• 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.
  
  
• 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.
  
  
• 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., 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.
  
  
• 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.
  
  
• 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.
  
  
• Nielsen, K.M., and J.P. Townsend, 2004. Monitoring and modeling horizontal gene transfer. Nature Biotechnology 22: 1110-1114.
  
  
• 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., 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.
  

• 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 1.9: 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