Research

My archived Thesis with data and code.

Some resources pages for my research data.

Archived talks.

• Fungal Comparative Genomics
  • Fungal Intron evolution
    • Loss and gain among the fungi (submitted; with Scott Roy)
    • The mechanism of intron loss in Cryptococcus (Euk Cell)
  • Fungal gene family evolution (PhD thesis chapter; manuscript in prep)
  • Annotation and analysis of the basidiomycete mushroom Coprinus cinereus genome (in prep; with P.Pukkilla, A.Gathman, W. Lilly, Analysis pipelines for automated genome annotation
    • C. cinereus
    • C. neoformans
    • C. gattii
    • P. chrysosporium
    • H. capsulatum
  • Fungal species trees of sequenced genomes based on whole genome data - see my Fungal Comparative site. (BMC Evol Biology; tree of 42 fungal species from whole genome data with David Fitzpatrick and Geraldine Butler)
    • I also generated a Fungal species tree with animal, plant, and slime-mold outgroup from 50 random orthologous loci (using the whole set of 160+ also produces a consistent and well supported tree) [PDF] for a book chapter: Stajich JE and Dietrich FS, "Genomic perspectives on the fungal kingdom." In: Heitman J, Filler SG, Edwards JE, and Mitchell AP, editors. Principles of Molecular Pathogeneis. ASM Press; 2006. This is a ML tree using PHYML and the WAG model and 100 bootstrap replicates. 100% bootstrap support indicated by thickened branches.
  • WW-domain evolution (Stan Fields and Jay Hesselberth) (Genome Biology)
  • NRPS family evolution in Aspergillus (Gene; with Robert Cramer)
  • U.maydis intron analysis (Nature )
• Cryptococcus genome analysis
  • C. neoformans var grubii genome annotation and comparative analysis (Duke CGT, Broad Institute).
  • C. neoformans genomic microarray Kraus et al, 2004 Euk Cell
  • Phylogenomics of C. neoformans catalase gene family (Euk Cell; with S. Giles)
  • C. gattii Vancouver Island, BC outbreak strain MLST analysis (with J.Fraser, J.Heitman). (Nature)
• Assembling the Fungal Tree of Life (Nature; with Tim James, Rytas Vilgalys, Joey Spatafora, and others)
  
• Gene Family Evolution
  • Statistical framework for evalution of gene family size in Saccharomyces genomes (with Matt Hahn). (Genome Research)
  • Mammalian gene family evolution (PLoS One; Matt Hahn)
  
  
• Nematode Comparative Genomics
  • C. briggsae genome analysis (PLoS Biology) evaluating substitution rates, gene family, synteny with C. elegans
  • Overview of nematode comparative genomics (Comparative genomics in C. elegans, C. briggsae and other nematodes. In: Strange K, editor. C. elegans: methods and applications. Humana Press; 2006.)
  • Comparative genomics of Ancylostoma ESTs (BMC Genomics) evaluating substitution rates in two hookworm species.
  • C. remanei ; Development Gbrowse site. Gene family evolution, substitution rates, ortholog and paralog identification, gene phylogenies.
  
  
• Population Genetics
  • Perlymorphism: BioPerl modules for population genomics. Our paper (MBE) applying the modules to human polymorphism data.
    A HOWTO on using these Perl modules.
  • MLE methods for estimating population parameters from summary statistics (with M. Uyenoyama) (Genetics)
  
  
• Motif Bias
  • Chaos Game Representation of Genomes, Motif Bias in Bacteria (with Greg Wray, Matt Hahn) (Mol Biol Evol)
  • Motif Bias in fungi (with Matt Hahn)