Cochliobolus genome released
Posted on July 17th, 2008 by Jason Stajich · No Comments
Categories: pezizomycota
AAM Releases "The Fungal Kingdom" Report
Posted on July 9th, 2008 by Jason Stajich · 2 Comments
The American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research.
Categories: news · science policy
Basidiomycete genomes galore
Posted on June 1st, 2008 by Jason Stajich · Comments Off
Just finished attending Genetics and Cell Biology of Basidiomycetes in Cape Girardeau, MO which was an intimate gathering of basidiomycetaphiles. I learned about systems that are used for studying fruiting body development, genetic mapping, pheromone and mating genes, kinesin dynamics, meoitic gene regulation, and a host of topics. I'm happy I got a chance to meet more folks in the community and learned about where informatics is needed
Categories: conferences
Lest you think annotation is easy
Posted on April 12th, 2008 by Jason Stajich · No Comments
Ewan Birney and Ensembl (the other/original genome browser depending on if you are a UCSC junkie) have started blogging a bit more about what is going on under the proverbial hood over there in Hinxton. There are some great nuggets talking about what are some of the current problems. These bite-sized comments should be a great glimpse into how Ensembl works
Categories: bioinformatics · comparative · database · genome
Fungal Genetics 2007 details
Posted on March 28th, 2007 by Jason Stajich · 2 Comments
Categories: bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete
Whole genome tiling arrays
Posted on February 1st, 2007 by Jason Stajich · No Comments
Whole genome tiling arrays have also been employed in other fungi. For example, Anita Sil’s group at UCSF constructed a random tiling array for Histoplasma capsulatum and used it to identify genes responding to reactive nitrogen species. A similar approach was used in Cryptococcus neoformans to investigate temperature regulated genes using random sequencing clones.
As the technology has become cheaper, it may become sensible to use a tiling array to detect transcripts rather than ESTs when attempting to annotate a genome. In the Histoplasma work transcriptional units could be identified from hybridization alone. Some of the algorithms will need some work to correct incorporate this information, and the sensitivity and density of the array will influence this. These techniques can be part of a resequencing approaches or fast genotyping progeny from QTL experiments when the sequence from both parents is known (or at least enough of the polymorphims for the genetic map).
What is superior about the current Affymetrix yeast tiling array is the inclusion of both strands. This allows detection of transcripts from both strands. Several anti-sense transcripts in yeast have been discovered recently including in the IME4 locus through more classical approaches, but perhaps many more await discovery with high resolution transcriptional data from whole genome tiling arrays.
Categories: microarray · saccharomyces · tiling array · transcription
