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, Yale University, 2006-present

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.S. 1994, Brown University, Providence, Rhode Island

• Lopez-Giraldez, F., and J.P. Townsend, 2011. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evolutionary Biology 11: 152.
  
  
• Townsend, J.P., and C. Leuenberger, 2011. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Systematic Biology 60(3): 358-365.
  
  
• Moeller, A.H., and J.P. Townsend, 2011. Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates. Molecular Phylogenetics and Evolution 60(2): 271-272.
  
  
• Wang, Z., R.H. Nilsson, F. Lopez-Giraldez, W.-y. Zhuang, Y.-c. Dai, P.R. Johnston, and J.P. Townsend, 2011. Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data. PLoS ONE 6(4): e19039.
  
  
• Guo, Z., A.B. Adomas, E.D. Jackson, H. Qin, and J.P. Townsend, 2011. SIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae. FEMS Yeast Res. 11(4): 345-55.
  
  
• Johnsen, P.J., J.P. Townsend,, T. Bøhn, G.S. Simonsen, A. Sundsfjord, and K.M. Nielsen, 2011. Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures. Journal of Antimicrobial Chemotherapy 66(3): 608-610.
  
  
• Zhang, Z., V.B. Bajic, J. Yu, K.-H. Cheung, and J.P. Townsend, 2011. Data integration in bioinformatics: current efforts and challenges. Bioinformatics - Trends and Methodologies, M.A. Mahdavi (Ed.), ISBN: 978-953-307-282-1.
  
  
• Mathioni, S.M., A. Beló, J.P. Townsend, and Nicole M. Donofrio, 2011. Getting the most out of your fungal microarray data: two cost- and time-effective methods. “Fungal Genomics: Methods and Protocols”, J.-R. Xu and B.H. Bluhm (eds.), Methods in Molecular Biology 722:61-77.
  
  
• Adomas, A.B., F. Lopez-Giraldez, T.A. Clark, Z. Wang and J.P. Townsend, 2010 Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 11: 477.
  
  
• Ohenoja, E., Z. Wang, J.P. Townsend, D. Mitchel and A. Voitk, 2010. Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia 102: 1089-1095.
  
  
• Zhang, Z., F. Lopez-Giraldez and J.P. Townsend, 2010. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics 26: 1918-1919.
  
  
• Townsend, J.P., F. Lopez-Giraldez, 2010. Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships. Systematic Biology 59(4):446-457.
  
  
• Zhang, Z. and J.P. Townsend, 2010. The filamentous fungal gene expression database (FFGED). Fungal Genetics and Biology 47(3):199-204.
  
  
• Tekle, Y.I., J.R. Grant, A.M. Kovner, J.P. Townsend, and L.A. Katz. 2010. Identification of new molecular markers for assembling the eukaryotic tree of life. Molecular Phylogenetics and Evolution 55(3): 1177-1182.


• Zhang, Z., and J.P. Townsend, 2009. Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Computational Biology 5(6): e1000421.
  
  
  
• Wang, Z., P.R. Johnston, Z.L. Yang, and J.P. Townsend, 2009. Evolution of reproductive morphology in leaf endophytes. PLoS ONE 4(1): e4246.
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• Hodgins-Davis, A. and J.P. Townsend, 2009. Evolving gene expression: from G to E to G x E. Trends in Ecology & Evolution 24(12):649-658.
  
  
• Wang, Z., F. López-Giráldez, and J.P. Townsend 2009. Snapshots of tree space. Evolutionary Bioinformatics 5 133-136.
  
  
• Zhang, Z., K.H. Cheung, and J.P. Townsend, 2009. Bringing Web 2.0 to bioinformatics. Briefings in Bioinformatics 10(1):1-10.
  
  
• Johnsen, P., J.P. Townsend, T. Behn, G.S. Simonsen, A. Sundsfjord, and K.M. Nielsen, 2009. Factors affecting the reversal of antimicrobial-drug resistance. The Lancet Infectious Diseases 9(6):357-364.
  
  
• Schoch, C.L., Z. Wang, J.P. Townsend, and J.W. Spatafora, 2009. Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life. Persoonia 22:129-138.
  
  
• Otto, W., P.F. Stadler, F. Lopez-Giraldez, J.P. Townsend, V.J. Lynch, and G.P. Wagner, 2009. Measuring transcription factor-binding site turnover: A maximum likelihood approach using phylogenies. Genome Biology and Evolution 85-98.
  
  
• Schoch, C.L., G-H Sung, F. Lopez-Giraldez, J.P. Townsend, (5 authors), Z. Wang, (53 authors), and J.W. Spatafora, 2009. The Ascomycota Tree of Life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology 58(2):224-239.
  
  
• Townsend, J.P., F. Lopez-Giraldez, and R. Friedman, 2008. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. Journal of Molecular Evolution 67(5): 437-447.
  
  
• 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.
  
  
• Cheung, K.-H., K.Y. Yip, J.P. Townsend, and M. Scotch, 2008. HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0. Journal of Biomedical Informatics 41: 694-705.
  
  
• 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, and 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, and 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