By Jason Stajich, on June 29th, 2010
I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus. You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some [...]
By Jason Stajich, on June 23rd, 2010
There are several databases that include orthology prediction for fungi. These all have pros and cons. Some are more comprehensive and have many more species. Some are curated orthologies and paralogy which should be pretty stable. Some are automated and groupings and ortholog group IDs change at each iteration.
A phylogenetic approach from a Saccharomyces perspective is [...]
By Jason Stajich, on April 30th, 2010
Another result from the analysis of the recently published genome of the pea aphid, Acyrthosiphon pisum. Nancy Moran and Tyler Jarvik present a study of the origin of the carotenoid production gene in pea aphid. Animals typically cannot make carotenoids so they sought to discover how this is possible. They find that it is [...]
By Jason Stajich, on September 14th, 2009
A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation sequencing [...]
By Jason Stajich, on March 1st, 2009
I cheered the Sanger-Wellcome SGRP group work to generate multiple Saccharomyces cerevisiae and S. paradoxus strain genome sequences. They submitted a version of the manuscript to Nature precedings and it is now published in Nature AOP showing that submitting to a preprint server doesn’t necessarily hurt your manuscript getting published in this instance. The research groups explored the impact of domestication (as was also recently done for the sake and soy sauce worker fungus, Aspergillus oryzae) on the Saccharomyces genome by comparing individuals from wild strains of S. paradoxus. [...]
By Jason Stajich, on October 31st, 2008
Genome Technology highlights the very cool thing about next-gen sequencing – it puts the power in the hands of the researchers to explore genome sequence and doesn’t limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke’s Institute for Genome Sciences and Policy through their next-gen sequencing program. [...]
By Jason Stajich, on August 24th, 2008
A quick post of some recent comparative genomics papers on our desk that are worth a look.
Khaldi N, Wolfe KH (2008) Elusive Origins of the Extra Genes in Aspergillus oryzae. PLoS ONE 3(8): e3036. doi:10.1371/journal.pone.0003036. This was a cool but somewhat controversal finding [...]
By Jason Stajich, on May 26th, 2008
This month’s Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae [[Chlamydomonas reinhardtii]]. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include:
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By Jason Stajich, on May 11th, 2008
The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings. The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons [...]
By Jason Stajich, on April 12th, 2008
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
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