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. [...]
By Jason Stajich, on March 11th, 2008
Estimating divergence times is notorious difficult and the field can be downright rancorous with some being accused of reading tea leaves and chicken entrails – interesting reading for personalities as much as the different scientific approaches. There are several different approaches to trying to estimate a divergence time among species, using [...]
By Jason Stajich, on March 6th, 2008
The following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad [...]
By Jason Stajich, on April 19th, 2007
A paper in PLoS One, Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, reports a new approach to assess the performance of automated orthology detection. These authors also wrote the OrthoMCL (2006 DB paper, 2003 algorithm paper) which uses MCL to build orthologous gene families. [...]
By Jason Stajich, on March 28th, 2007
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome [...]
By sharpton, on February 6th, 2007
Your eye contains the same genetic content as your fingernail, but these two tissues look nothing alike. One significant cause of this difference is the tissue specific regulation of the genes in the genome. In some tissues in your body, a gene may be expressed (transcribed) while that same gene may be silent in another tissue type. [...]