Jeffrey P Townsend

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae
    Andrea Hodgins-Davis
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Genome Biol Evol 4:1061-79. 2012
  2. pmc Resampling QTL effects in the QTL sign test leads to incongruous sensitivity to variance in effect size
    Daniel P Rice
    Department of Ecology and Evolutionary Biology and Program in Computational Biology and Bioinformatics, YaleUniversity, New Haven, CT 06520, USA
    G3 (Bethesda) 2:905-11. 2012
  3. pmc Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi
    Kristiina Nygren
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, SE 752 36, Uppsala, Sweden
    BMC Evol Biol 12:229. 2012
  4. doi request reprint Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 61:835-49. 2012
  5. pmc Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
    Zhang Zhang
    Computational Bioscience Research Center CBRC, King Abdullah Universitof Science and Technology KAUST, Thuwal 23955 6900, Kingdom of Saudi Arabia
    BMC Bioinformatics 13:43. 2012
  6. doi request reprint The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    J Mol Evol 67:437-47. 2008
  7. 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
  8. ncbi request reprint Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 59:446-57. 2010
  9. pmc Evolving gene expression: from G to E to GxE
    Andrea Hodgins-Davis
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Trends Ecol Evol 24:649-58. 2009
  10. ncbi 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

Detail Information

Publications45

  1. pmc Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae
    Andrea Hodgins-Davis
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Genome Biol Evol 4:1061-79. 2012
    ....
  2. pmc Resampling QTL effects in the QTL sign test leads to incongruous sensitivity to variance in effect size
    Daniel P Rice
    Department of Ecology and Evolutionary Biology and Program in Computational Biology and Bioinformatics, YaleUniversity, New Haven, CT 06520, USA
    G3 (Bethesda) 2:905-11. 2012
    ....
  3. pmc Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi
    Kristiina Nygren
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, SE 752 36, Uppsala, Sweden
    BMC Evol Biol 12:229. 2012
    ..In fungi, genes involved in mate recognition have been found to evolve rapidly. However, the examples are too few to draw conclusions on a genome scale...
  4. doi request reprint Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 61:835-49. 2012
    ..The predicted power of resolution for the loci analyzed is consistent with the historic use of the genes in phylogenetics...
  5. pmc Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
    Zhang Zhang
    Computational Bioscience Research Center CBRC, King Abdullah Universitof Science and Technology KAUST, Thuwal 23955 6900, Kingdom of Saudi Arabia
    BMC Bioinformatics 13:43. 2012
    ..However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis...
  6. doi request reprint The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    J Mol Evol 67:437-47. 2008
    ....
  7. 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...
  8. ncbi request reprint Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships
    Jeffrey P Townsend
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 59:446-57. 2010
    ..Gene and taxon sampling according to the theory herein and following a "deepest ingroup" heuristic are shown to provide significantly improved resolution of specified deep internodes...
  9. pmc Evolving gene expression: from G to E to GxE
    Andrea Hodgins-Davis
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Trends Ecol Evol 24:649-58. 2009
    ..We review the literature on the evolution of gene expression in terms of genetics (G), environmental response (E) and GxE interactions to make this conceptual point...
  10. ncbi 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...
  11. pmc The filamentous fungal gene expression database (FFGED)
    Zhang Zhang
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
    Fungal Genet Biol 47:199-204. 2010
    ..A clear and efficient web interface is provided with enhancement by AJAX (Asynchronous JavaScript and XML) and through a collection of tools to effectively facilitate data submission, sharing, retrieval and visualization...
  12. pmc Multi-targeted priming for genome-wide gene expression assays
    Aleksandra B Adomas
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    BMC Genomics 11:477. 2010
    ..We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays...
  13. pmc Potential cost-effectiveness of schistosomiasis treatment for reducing HIV transmission in Africa--the case of Zimbabwean women
    Martial L Ndeffo Mbah
    School of Public Health, Yale University, New Haven, Connecticut, USA
    PLoS Negl Trop Dis 7:e2346. 2013
    ..Here we assess the potential cost-effectiveness of praziquantel as a novel intervention strategy against HIV infection...
  14. pmc LOX: inferring Level Of eXpression from diverse methods of census sequencing
    Zhang Zhang
    Department of Ecology and Evolutionary Biology and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 26:1918-9. 2010
    ..LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals...
  15. pmc Evolution of reproductive morphology in leaf endophytes
    Zheng Wang
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
    PLoS ONE 4:e4246. 2009
    ..Intriguingly, resemblance between asexual conidiomata and sexual ascomata in some leotiomycetes implicates some common developmental pathways for sexual and asexual development in these fungi...
  16. pmc Sex-specific gene expression during asexual development of Neurospora crassa
    Zheng Wang
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
    Fungal Genet Biol 49:533-43. 2012
    ..Further investigation of the impact of light and the roles of light response genes in asexual development of both mating types are warranted...
  17. pmc Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets
    Francesc Lopez-Giraldez
    Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
    Biomed Res Int 2013:621604. 2013
    ..Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed. ..
  18. pmc HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0
    Kei Hoi Cheung
    Center for Medical Informatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA
    J Biomed Inform 41:694-705. 2008
    ..We discuss the areas of intersection of Web 2.0 and Semantic Web, and describe the potential benefits that can be brought to HCLS research by combining these two sets of technologies...
  19. pmc Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa
    Zheng Wang
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Fungal Genet Biol 49:405-13. 2012
    ..This result facilitates comparative studies that will require different nutritional resources for sexual development in different fungi...
  20. pmc A test for selection employing quantitative trait locus and mutation accumulation data
    Daniel P Rice
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Genetics 190:1533-45. 2012
    ..Our test thus represents the first integration of population genetic theory and QTL data to measure the historical influence of selection...
  21. ncbi request reprint Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa
    Zheng Wang
    Department of Biostatistics, Yale University, New Haven, Connecticut, USA
    Eukaryot Cell 13:154-69. 2014
    ..Overall, our analysis provides a fine-scale transcriptomic landscape and novel inferences regarding the control of the multistage development process of sexual crossing and fruiting body development in N. crassa. ..
  22. pmc Optimal targeting of seasonal influenza vaccination toward younger ages is robust to parameter uncertainty
    Martial L Ndeffo Mbah
    School of Public Health, Yale University, New Haven, CT CT 06510, USA
    Vaccine 31:3079-89. 2013
    ....
  23. pmc Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data
    Zheng Wang
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 6:e19039. 2011
    ..Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit...
  24. doi request reprint Identification of new molecular markers for assembling the eukaryotic tree of life
    Yonas I Tekle
    Department of Biological Sciences, Smith College, Northampton, MA, USA
    Mol Phylogenet Evol 55:1177-82. 2010
    ..Finally, we present phylogenetic informativeness profiles for seven selected markers, revealing that the markers contain phylogenetic signal that spans the whole tree including the deeper branches...
  25. pmc Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences
    Zhang Zhang
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS Comput Biol 5:e1000421. 2009
    ....
  26. pmc PhyDesign: an online application for profiling phylogenetic informativeness
    Francesc Lopez-Giraldez
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
    BMC Evol Biol 11:152. 2011
    ..However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available...
  27. doi request reprint Probabilistic uncertainty analysis of epidemiological modeling to guide public health intervention policy
    Jennifer A Gilbert
    Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
    Epidemics 6:37-45. 2014
    ....
  28. ncbi request reprint Epidemiological mechanisms of genetic resistance to kuru
    Katherine E Atkins
    Yale School of Public Health, 135 College Street, New Haven, CT 06510, USA
    J R Soc Interface 10:20130331. 2013
    ..This work provides evidence for balancing selection acting on a human population and the mechanistic basis for the heterozygote resistance to kuru...
  29. pmc Cost-effectiveness of a community-based intervention for reducing the transmission of Schistosoma haematobium and HIV in Africa
    Martial L Ndeffo Mbah
    School of Public Health, and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 110:7952-7. 2013
    ..haematobium [corrected] is an economically attractive strategy for reducing schistosomiasis and HIV transmission in sub-Saharan Africa that would have a powerful impact on averting infections and saving lives...
  30. pmc Controlling antimicrobial resistance through targeted, vaccine-induced replacement of strains
    Yonas I Tekle
    Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America
    PLoS ONE 7:e50688. 2012
    ..The broader utility of vaccine-based resistance control strategies should be further explored taking into account population structure, and the resistance and transmission patterns of the pathogen considered...
  31. pmc Bringing Web 2.0 to bioinformatics
    Zhang Zhang
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Brief Bioinform 10:1-10. 2009
    ..We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies...
  32. doi request reprint Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection
    Robert C McBride
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    FEMS Yeast Res 13:162-79. 2013
    ....
  33. pmc Reevaluation of epidemiological data demonstrates that it is consistent with cross-immunity among human papillomavirus types
    David P Durham
    Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520 8034, USA
    J Infect Dis 206:1291-8. 2012
    ..Epidemiological data on HPV infections has been repeatedly interpreted as inconsistent with cross-immunity...
  34. doi request reprint RBE controls microRNA164 expression to effect floral organogenesis
    Tengbo Huang
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520 8104, USA
    Development 139:2161-9. 2012
    ..These results indicate that one role of RBE is to fine-tune miR164 expression to regulate the CUC1 and CUC2 effector genes, which, in turn, regulate developmental events required for sepal and petal organogenesis...
  35. 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
  36. 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...
  37. 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
    ....
  38. 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...
  39. 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
    ....
  40. 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
    ....
  41. 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...
  42. 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
    ....
  43. 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...
  44. 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...
  45. 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...