User Profile


Jeffrey Townsend
New Haven, CT
Research Interests:
# Ongoing experimental research includes work characterizing genome-wide gene expression variation in the model microbes Saccharomyces cerevisiae (the wine and bread yeast) and Neurospora crassa (the filamentous fireburn saprobe). # Theoretical work includes modeling of the evolution of gene expression, bioinformatics and statistics for the analysis of DNA microarrays, phylogenetics and evolutionary biology, and novel theoretical approaches for the analysis of microbial communities when horizontal gene transfer belies traditional species concepts.
Yale University
Publications in PubMed
  1. Zhang Z, Townsend JP. Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS computational biology 2009 5(6). DOI:10.1371/journal.pcbi.1000421.
  2. Johnsen PJ, Townsend JP, Bøhn T, Simonsen GS, Sundsfjord A, Nielsen KM. Factors affecting the reversal of antimicrobial-drug resistance. The Lancet infectious diseases 2009 9(6). DOI:10.1016/S1473-3099(09)70105-7.
  3. Wang Z, Johnston PR, Yang ZL, Townsend JP. Evolution of reproductive morphology in leaf endophytes. PloS one 2009 4(1). DOI:10.1371/journal.pone.0004246.
  4. Zhang Z, Cheung KH, Townsend JP. Bringing Web 2.0 to bioinformatics. Briefings in bioinformatics 2009 10(1). DOI:10.1093/bib/bbn041.
  5. Townsend JP, López-Giráldez F, Friedman R. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. Journal of molecular evolution 2008 67(5). DOI:10.1007/s00239-008-9142-0.
  6. Townsend JP. Sleuthing the difference a nucleotide can make. Molecular ecology 2008 17(12). DOI:10.1111/j.1365-294X.2008.03824.x.
  7. Cheung KH, Yip KY, Townsend JP, Scotch M. HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0. Journal of biomedical informatics 2008 41(5). DOI:10.1016/j.jbi.2008.04.001.
  8. Clark TA, Townsend JP. Quantifying variation in gene expression. Molecular ecology 2007 16(13). DOI:10.1111/j.1365-294X.2007.03354.x.
  9. Townsend JP. Profiling phylogenetic informativeness. Systematic biology 2007 56(2). DOI:10.1080/10635150701311362.
  10. Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Ba?türkmen M, Altamirano L, Xu J. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in genetics 2007 57. DOI:10.1016/S0065-2660(06)57002-6.
  11. Taylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006 361(1475). DOI:10.1098/rstb.2006.1923.
  12. Aa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS yeast research 2006 6(5). DOI:10.1111/j.1567-1364.2006.00059.x.
  13. Johannesson H, Kasuga T, Schaller RA, Good B, Gardner MJ, Townsend JP, Cole GT, Taylor JW. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal genetics and biology : FGB 2006 43(8). DOI:10.1016/j.fgb.2006.02.003.
  14. Landry CR, Townsend JP, Hartl DL, Cavalieri D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular ecology 2006 15(3). DOI:10.1111/j.1365-294X.2006.02778.x.
  15. Meiklejohn CD, Townsend JP. A Bayesian method for analysing spotted microarray data. Briefings in bioinformatics 2005 6(4). DOI:10.1111/j.1365-294X.2006.02778.x.
  16. Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass NL. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic acids research 2005 33(20). DOI:10.1093/nar/gki953.
  17. Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature reviews. Microbiology 2005 3(9). DOI:10.1038/nrmicro1204.
  18. Johannesson H, Townsend JP, Hung CY, Cole GT, Taylor JW. Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii. Genetics 2005 171(1). DOI:10.1534/genetics.105.040923.
  19. Townsend JP, Taylor JW. Designing experiments using spotted microarrays to detect gene regulation differences within and among species. Methods in enzymology 2005 395. DOI:10.1016/S0076-6879(05)95031-3.
  20. Nielsen KM, Townsend JP. Monitoring and modeling horizontal gene transfer. Nature biotechnology 2004 22(9). DOI:10.1038/nbt1006.
  21. Townsend JP, Rand DM. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity 2004 93(1). DOI:10.1038/sj.hdy.6800484.
  22. Townsend JP. 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 2004 5. DOI:10.1186/1471-2105-5-54.
  23. Townsend JP. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC genomics 2003 4(1). DOI:10.1186/1471-2164-4-41.
  24. Townsend JP, Nielsen KM, Fisher DS, Hartl DL. Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes. Genetics 2003 164(1). DOI:10.1186/1471-2164-4-41.
  25. Townsend JP, Cavalieri D, Hartl DL. Population genetic variation in genome-wide gene expression. Molecular biology and evolution 2003 20(6). DOI:10.1093/molbev/msg106.
  26. Townsend JP, Hartl DL. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome biology 2002 3(12). DOI:10.1093/molbev/msg106.
  27. Grosu P, Townsend JP, Hartl DL, Cavalieri D. Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome research 2002 12(7). DOI:10.1101/gr.226602.
  28. Townsend JP, Hartl DL. The kinetics of transposable element autoregulation. Genetica 2000 108(3). DOI:10.1101/gr.226602.
  29. Cavalieri D, Townsend JP, Hartl DL. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings of the National Academy of Sciences of the United States of America 2000 97(22). DOI:10.1073/pnas.210395297.
  30. Bustamante CD, Townsend JP, Hartl DL. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Molecular biology and evolution 2000 17(2). DOI:10.1073/pnas.210395297.
History of Education and Employment
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