Jeffrey P Townsend

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
    Genome Biol 3:RESEARCH0071. 2002
  2. ncbi request reprint Population genetic variation in genome-wide gene expression
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 20:955-63. 2003
  3. pmc Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 164:13-21. 2003
  4. pmc Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays
    Jeffrey P Townsend
    Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA
    BMC Genomics 4:41. 2003
  5. pmc Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays
    Jeffrey P Townsend
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 5:54. 2004
  6. ncbi request reprint Ecological and evolutionary genomics of Saccharomyces cerevisiae
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Ecol 15:575-91. 2006
  7. pmc Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination
    Takao Kasuga
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Nucleic Acids Res 33:6469-85. 2005
  8. pmc Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks
    Paul Grosu
    Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 12:1121-6. 2002
  9. ncbi request reprint Designing experiments using spotted microarrays to detect gene regulation differences within and among species
    Jeffrey P Townsend
    Plant and Microbial Biology Department, University of California, Berkeley, California 94720, USA
    Methods Enzymol 395:597-617. 2005
  10. pmc Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi
    John W Taylor
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Philos Trans R Soc Lond B Biol Sci 361:1947-63. 2006

Detail Information

Publications19

  1. pmc Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
    Genome Biol 3:RESEARCH0071. 2002
    ..This framework can be used to analyze normalized microarray data acquired by any replicated experimental design in which any number of treatments, genotypes, or developmental states are studied using a continuous chain of comparisons...
  2. ncbi request reprint Population genetic variation in genome-wide gene expression
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 20:955-63. 2003
    ..Genetic variation in gene expression among isolates from a natural population is present on a genomic scale. It remains to be determined what role differential gene expression may play in adaptation to new or changing environments...
  3. pmc Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 164:13-21. 2003
    ..We conclude that mutators can accelerate bacterial adaptation when desired genetic variability is present within DNA fragments of up to approximately 30% divergence...
  4. pmc Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays
    Jeffrey P Townsend
    Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA
    BMC Genomics 4:41. 2003
    ..Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored...
  5. pmc Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays
    Jeffrey P Townsend
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 5:54. 2004
    ..Meeting this challenge requires careful examination of the performance of a range of statistical models, as well as empirical examination of the effect of replication on the power to resolve these differences...
  6. ncbi request reprint Ecological and evolutionary genomics of Saccharomyces cerevisiae
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Ecol 15:575-91. 2006
    ....
  7. pmc Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination
    Takao Kasuga
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Nucleic Acids Res 33:6469-85. 2005
    ....
  8. pmc Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks
    Paul Grosu
    Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 12:1121-6. 2002
    ..This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned...
  9. ncbi request reprint Designing experiments using spotted microarrays to detect gene regulation differences within and among species
    Jeffrey P Townsend
    Plant and Microbial Biology Department, University of California, Berkeley, California 94720, USA
    Methods Enzymol 395:597-617. 2005
    ..We conclude with a discussion of experimental protocols that are designed for investigations of differential gene expression and their pitfalls...
  10. pmc Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi
    John W Taylor
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Philos Trans R Soc Lond B Biol Sci 361:1947-63. 2006
    ..The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change...
  11. ncbi request reprint Population structure and gene evolution in Saccharomyces cerevisiae
    Erlend Aa
    Department of Pharmacy, University of Tromsø, Tromsø, Norway
    FEMS Yeast Res 6:702-15. 2006
    ..cerevisiae, is the first study to demonstrate population structure within S. cerevisiae, and the first study to detect historical selection on a locus important to the natural history of wine yeast...
  12. pmc Enabling a community to dissect an organism: overview of the Neurospora functional genomics project
    Jay C Dunlap
    Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
    Adv Genet 57:49-96. 2007
    ..In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes...
  13. ncbi request reprint A Bayesian method for analysing spotted microarray data
    Colin D Meiklejohn
    Brown University, USA
    Brief Bioinform 6:318-30. 2005
    ..The focus is on a Bayesian analysis method, BAGEL, which is easy to implement and produces easily interpreted results...
  14. ncbi request reprint Horizontal gene transfer, genome innovation and evolution
    J Peter Gogarten
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 3125, USA
    Nat Rev Microbiol 3:679-87. 2005
    ....
  15. pmc Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii
    Hanna Johannesson
    Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Sweden
    Genetics 171:109-17. 2005
    ....
  16. doi request reprint Sleuthing the difference a nucleotide can make
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
    Mol Ecol 17:2793-5. 2008
    ..The finding also calls for further data, clarifying the kinds of genetic variation that constitute gene expression polymorphism between individuals in natural populations...
  17. ncbi request reprint Monitoring and modeling horizontal gene transfer
    Kaare M Nielsen
    Department of Pharmacy, Faculty of Medicine, University of Tromsø, N9037 Tromsø, Norway
    Nat Biotechnol 22:1110-4. 2004
    ....
  18. ncbi request reprint Profiling phylogenetic informativeness
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Syst Biol 56:222-31. 2007
    ..Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies...
  19. ncbi request reprint Quantifying variation in gene expression
    Travis A Clark
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Mol Ecol 16:2613-6. 2007