RNA Bioinformatics

The website of my lab at University of Iowa is up. Please click here.

A new paper will come out on Genes and Development on Nov 15:

Calarco, JA.*, Xing, Y.*, Caceres, M.*, Calarco, JP., Xiao, X., Pan, Q., Lee, C.,, Preuss, T. and Blencowe, B. (2007) Global analysis of alternative splicing differences between humans and chimpanzees. Genes and Development.

Found this python script for quick computation of overlapping features in genomic interval databases. The script can be downloaded from the author's FTP site indicated in this paper. It's a small script and very easy to use. It works with standard GFF format.

Dr. Wong will give a web seminar on August 9 for Exon Array analysis.

PS: I am adding new features to the probe selection algorithm. We will allow users to initiate iterative probe selection from a pre-defined probe list. This could be probes that are selected from a high-quality and diverse exon array dataset, or probes that do not have cross-match to any other transcripts. We will provide such pre-defined probe lists from our GeneBASE website soon.

Gelfand and colleagues wrote a comprehensive review concerning the evolution of alternative splicing. They covered lots of materials, explained some important subtleties in the published work, and presented different opinions in a balanced way. A pleasure to read.

I am setting up my lab in University of Iowa. I am looking for postdocs to work on RNA splicing and microRNA related projects. The successful candidates should have a proven record in genome sequence analysis or microarray analysis. Send me an email for details if you are interested.

Brenton Graveley and Ben Blencowe edited a book on alternative splicing - "Alternative splicing in the postgenomic era". Click this link for a list of chapters. Chris and I contributed a chapter "Relating Alternative Splicing to Proteome Complexity and Genome Evolution". This book is scheduled to come out in November.

A one-day workshop on alternative splicing during Computational Systems Biology (CSB) 2007. Details here.

Another Exon array paper is published! See Kapur, Xing, Ouyang and Wong, Genome Biology, 5:R82

The probe selection algorithm in the PLOS One 2006 paper is replaced by a more robust algorithm, which performs an initial cut of the clustering dendrogram, followed by iterative probe selection and fitting to the Li-Wong model.

RNA in Biology, Bioengineering and Nanotechnology, part of UMN-IMA's year-long program on Mathematics of Molecular and Cellular Biology.