Jason E Stajich

Summary

Affiliation: Duke University Medical Center
Country: USA

Publications

  1. pmc Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins
    Jay R Hesselberth
    Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
    Genome Biol 7:R30. 2006
  2. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
  3. ncbi request reprint Open source tools and toolkits for bioinformatics: significance, and where are we?
    Jason E Stajich
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
    Brief Bioinform 7:287-96. 2006
  4. ncbi request reprint Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus
    Robert A Cramer
    Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, NC 27710, USA
    Gene 383:24-32. 2006
  5. ncbi request reprint Reconstructing the early evolution of Fungi using a six-gene phylogeny
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708 0338, USA
    Nature 443:818-22. 2006
  6. ncbi request reprint An Introduction to BioPerl
    Jason E Stajich
    Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
    Methods Mol Biol 406:535-48. 2007
  7. pmc Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
    Jason E Stajich
    Department of Molecular Genetics and Microbiology, Center for Genome Technology, Institute for Genome Science and Policy, Duke University, Durham, NC 27710, USA
    Genome Biol 8:R223. 2007
  8. pmc Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii
    James A Fraser
    Department of Molecular Genetics and Microbiology, 322 CARL Building, Research Drive, Duke University Medical Center, Durham, NC 27710, USA
    Eukaryot Cell 6:622-9. 2007
  9. ncbi request reprint Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak
    James A Fraser
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nature 437:1360-4. 2005
  10. pmc Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis
    Erica Bree Rosenblum
    Departments of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 105:17034-9. 2008

Detail Information

Publications24

  1. pmc Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins
    Jay R Hesselberth
    Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
    Genome Biol 7:R30. 2006
    ..WW domains bind proline-rich protein and peptide ligands, but the protein interaction partners of many WW domain-containing proteins in Saccharomyces cerevisiae are largely unknown...
  2. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  3. ncbi request reprint Open source tools and toolkits for bioinformatics: significance, and where are we?
    Jason E Stajich
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
    Brief Bioinform 7:287-96. 2006
    ....
  4. ncbi request reprint Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus
    Robert A Cramer
    Duke University Medical Center, Department of Molecular Genetics and Microbiology, Durham, NC 27710, USA
    Gene 383:24-32. 2006
    ..Further analysis of these genes and their peptide products may identify important roles for secondary metabolites produced by NRPS in Aspergillus physiology, ecology, and fungal pathogenicity...
  5. ncbi request reprint Reconstructing the early evolution of Fungi using a six-gene phylogeny
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708 0338, USA
    Nature 443:818-22. 2006
    ..The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree...
  6. ncbi request reprint An Introduction to BioPerl
    Jason E Stajich
    Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
    Methods Mol Biol 406:535-48. 2007
    ..This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record...
  7. pmc Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
    Jason E Stajich
    Department of Molecular Genetics and Microbiology, Center for Genome Technology, Institute for Genome Science and Policy, Duke University, Durham, NC 27710, USA
    Genome Biol 8:R223. 2007
    ..Genome sequencing and comparative analysis has made possible whole genome analysis of intron evolution to address these questions...
  8. pmc Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii
    James A Fraser
    Department of Molecular Genetics and Microbiology, 322 CARL Building, Research Drive, Duke University Medical Center, Durham, NC 27710, USA
    Eukaryot Cell 6:622-9. 2007
    ....
  9. ncbi request reprint Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak
    James A Fraser
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nature 437:1360-4. 2005
    ..This has implications for the emergence of other microbial pathogens and inbreeding in host range expansion in the fungal and other kingdoms...
  10. pmc Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis
    Erica Bree Rosenblum
    Departments of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 105:17034-9. 2008
    ..Finally we discuss the challenges inherent in developing a molecular toolkit for chytrids, a basal fungal lineage separated by vast phylogenetic distance from other well characterized fungi...
  11. pmc The Cryptococcus neoformans catalase gene family and its role in antioxidant defense
    Steven S Giles
    Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
    Eukaryot Cell 5:1447-59. 2006
    ..neoformans possesses a robust antioxidant system, composed of functionally overlapping and compensatory components that provide protection against endogenous and exogenous oxidative stresses...
  12. pmc Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
    Thomas J Sharpton
    Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
    Genome Res 19:1722-31. 2009
    ....
  13. pmc Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray
    Peter R Kraus
    Department of Molecular Genetics and Microbiology, 322 CARL Building, Box 3546, Research Dr, Duke University Medical Center, Durham, NC 27710, USA
    Eukaryot Cell 3:1249-60. 2004
    ..Our findings demonstrate the utility of even partial-genome microarrays for delineating regulatory cascades that contribute to microbial pathogenesis...
  14. ncbi request reprint Disentangling the effects of demography and selection in human history
    Jason E Stajich
    Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
    Mol Biol Evol 22:63-73. 2005
    ..These results are consistent with repeated selective sweeps in non-African populations, in agreement with recent reports using microsatellite data...
  15. ncbi request reprint Evolution of budding yeast prion-determinant sequences across diverse fungi
    Luke B Harrison
    Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, Canada H3A 1B1
    J Mol Biol 368:273-82. 2007
    ..Our findings on yeast prion evolution provide further support for the functional significance of these molecules...
  16. pmc BASC: an integrated bioinformatics system for Brassica research
    Timothy A Erwin
    Plant Biotechnology Centre, Victorian AgriBiosciences Centre, 1 Park Drive, Bundoora, Victoria 3083, Australia
    Nucleic Acids Res 35:D870-3. 2007
    ..The database is accessible at http://bioinformatics.pbcbasc.latrobe.edu.au...
  17. pmc A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    David A Fitzpatrick
    School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
    BMC Evol Biol 6:99. 2006
    ..As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available...
  18. pmc The generic genome browser: a building block for a model organism system database
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
    Genome Res 12:1599-610. 2002
    ..GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org...
  19. ncbi request reprint Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
    Jörg Kämper
    Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse, D 35043 Marburg, Germany
    Nature 444:97-101. 2006
    ..Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens...
  20. pmc Estimating the tempo and mode of gene family evolution from comparative genomic data
    Matthew W Hahn
    Center for Population Biology, University of California, Davis, California 95616, USA
    Genome Res 15:1153-60. 2005
    ..We apply our method to data from the genomes of five yeast species to show its applicability...
  21. pmc Investigating hookworm genomes by comparative analysis of two Ancylostoma species
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    BMC Genomics 6:58. 2005
    ..Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum...
  22. doi request reprint An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea
    Walt W Lilly
    Department of Biology, Southeast Missouri State University, Cape Girardeau, MO 63701, USA
    Mycol Res 112:389-98. 2008
    ..The proximity of these genes to telomeres and/or to transposable elements may have contributed to the expansion of this gene family in C. cinereus...
  23. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
    ..elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes...
  24. ncbi request reprint Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species
    Avril Coghlan
    Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
    Methods Mol Biol 351:13-29. 2006
    ..elegans and C. briggsae genomes to those of Caenorhabditis remanei, C. n. sp. represented by strains PB2801 and CB5161, among others (1), and Caenorhabditis japonica, which are currently being sequenced...