Jason E Stajich
Affiliation: Duke University Medical Center
- Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteinsJay 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...
- The Bioperl toolkit: Perl modules for the life sciencesJason 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...
- 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....
- Phylogenomic analysis of non-ribosomal peptide synthetases in the genus AspergillusRobert 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...
- Reconstructing the early evolution of Fungi using a six-gene phylogenyTimothy 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...
- An Introduction to BioPerlJason 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...
- Comparative genomic analysis of fungal genomes reveals intron-rich ancestorsJason 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...
- Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasiiJames 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....
- Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreakJames 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...
- Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidisErica 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...
- The Cryptococcus neoformans catalase gene family and its role in antioxidant defenseSteven 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...
- Comparative genomic analyses of the human fungal pathogens Coccidioides and their relativesThomas J Sharpton
Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
Genome Res 19:1722-31. 2009....
- Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarrayPeter 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...
- Disentangling the effects of demography and selection in human historyJason 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...
- Evolution of budding yeast prion-determinant sequences across diverse fungiLuke 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...
- BASC: an integrated bioinformatics system for Brassica researchTimothy 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...
- A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysisDavid 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...
- The generic genome browser: a building block for a model organism system databaseLincoln 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...
- Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydisJörg 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...
- Estimating the tempo and mode of gene family evolution from comparative genomic dataMatthew 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...
- Investigating hookworm genomes by comparative analysis of two Ancylostoma speciesMakedonka 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...
- An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinereaWalt 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...
- The genome sequence of Caenorhabditis briggsae: a platform for comparative genomicsLincoln 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...
- Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis speciesAvril 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...