nodalpoint.org

HI HexiRPA000010
DN (Velculescu VE, 1997) Characterization of the Yeast Transcriptome @Cell #20060730
DA 2006.07.30
CP Cell. 1997 Jan 24;88(2):243-51.
TI Characterization of the yeast transcriptome.
AU Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW.
IN Program in Human Genetics and Molecular Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA.
AB We have analyzed the set of genes expressed from the yeast genome, herein called the transcriptome, using serial analysis of gene expression. Analysis of 60,633 transcripts revealed 4,665 genes, with expression levels ranging from 0.3 to over 200 transcripts per cell. Of these genes, 1981 had known functions, while 2684 were previously uncharacterized. The integration of positional information with gene expression data allowed for the generation of chromosomal expression maps identifying physical regions of transcriptional activity and identified genes that had not been predicted by sequence information alone. These studies provide insight into global patterns of gene expression in yeast and demonstrate the feasibility of genome-wide expression studies in eukaryotes.

Last reminder for Bio::Blogs #2.

Send your submissions to bioblogs <at> gmail.com. Same address if you'd like to host a future edition. We have 7 submissions so far (all from non-Nodal regulars!) and a volunteer for October, I'm pleased to say. I've also been keeping an eye on the blogs and have a few posts to add. See previous post for guidelines.

update: edition 2 is now online - thanks to all contributors.

update #2: note that the link above changed, as I just moved my blog to its new home. The old site is no more.

'Tis the season to be conferenced...

ISMB 2006 is almost upon us. Are there any nodalpointers going who fancy blogging (here or elsewhere) the conference for those of us who won't be sunning ourselves on Brazlian beaches? I'd love to know how the Robot Scientist and Ontology of Function presentations are received.

Hexi Reading Professional Articles (HexiRPA):

Readme for the docment:

for Each entry, there are 5 sections:Paper Tag (Line 1-2), Read Date (Line 3), PubMed Citation (Line 4-9), MyNotes (Line 10-12) and End Tag (Line 13)
Line 1 : Paper No. --(HI:HexiRRA Idendifier)
Line 2 : Document Name on myPC --(DN: Document Name)
Line 3 : Date read the paper --(DA:Date)
LIne 4 : Citation of PubMed Format (CP: Citation of PubMed)
Line 5 : Title (TI: Title)
LIne 6 : Authors (AU : Author)
Line 7 : Institutes [one or more lines] (IN : INstitutes)
Line 8 : Abstract (AB : ABstract)
Line 9 : PubMed ID (PM : PubMed ID)

Based on the comparison of different sequencing strategies in six small marine microbial genome, the paper evaluated the utility and cost-effectiveness of a hybrid sequencing approach using 3730xl Sanger sequecing and 454 run to generate higher-quality lower-quality lower-cost assemblies compared to current Sanger sequencing strategies alone. For the genome more than 3Mb with many sequencing gaps and hard stops, the sequence strategy of 5.3X Sanger sequencing plus two 454 runs is the best choice.

Proc Natl Acad Sci U S A. 2006 Jul 13; [Epub ahead of print] Books, LinkOut

A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.