tag:www.rnabioinformatics.com,2007://6 2007-10-19T01:20:56Z Movable Type 3.31 tag:www.rnabioinformatics.com,2007://6.341 2007-10-19T01:20:11Z 2007-10-19T01:20:56Z

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

click here.]]> tag:www.rnabioinformatics.com,2007://6.340 2007-10-16T15:51:27Z 2007-10-16T15:53:46Z

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...

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. ]]> tag:www.rnabioinformatics.com,2007://6.339 2007-08-11T20:08:56Z 2007-08-11T20:11:15Z

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...

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. ]]> tag:www.rnabioinformatics.com,2007://6.338 2007-08-04T06:39:21Z 2007-08-04T19:36:37Z

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...

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. ]]> tag:www.rnabioinformatics.com,2007://6.337 2007-07-29T07:02:06Z 2007-07-29T07:15:09Z

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....

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. ]]> tag:www.rnabioinformatics.com,2007://6.336 2007-07-15T18:58:37Z 2007-07-15T19:04:46Z

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...

Send me an email for details if you are interested. ]]> tag:www.rnabioinformatics.com,2007://6.335 2007-07-15T10:09:51Z 2007-07-15T10:13:56Z

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...

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. ]]> tag:www.rnabioinformatics.com,2007://6.334 2007-06-13T08:18:35Z 2007-06-13T08:21:30Z

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

here.]]> tag:www.rnabioinformatics.com,2007://6.333 2007-05-25T07:29:17Z 2007-05-25T08:31:33Z

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...

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. ]]> tag:www.rnabioinformatics.com,2007://6.332 2007-05-25T05:18:55Z 2007-05-25T05:21:23Z

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

RNA in Biology, Bioengineering and Nanotechnology, part of UMN-IMA's year-long program on Mathematics of Molecular and Cellular Biology. ]]> tag:www.rnabioinformatics.com,2007://6.331 2007-04-08T00:51:23Z 2007-04-08T00:53:20Z

a new expression array platform - Gene Array. It uses a subset of probes from Affymetrix Exon Arrays. Each gene has 26 probes on average....

Gene Array. It uses a subset of probes from Affymetrix Exon Arrays. Each gene has 26 probes on average. ]]> tag:www.rnabioinformatics.com,2007://6.330 2007-03-19T08:56:16Z 2007-03-26T08:06:18Z

This is a simple study with interesting implications for evolutionary genomics and microarray analysis. Here is our paper and online supplemental material. Assessing the Conservation of Mammalian Gene Expression Using High-density Exon Arrays. Xing Y*, Ouyang Z, Kapur K, Scott...

our paper and online supplemental material. Assessing the Conservation of Mammalian Gene Expression Using High-density Exon Arrays. Xing Y*, Ouyang Z, Kapur K, Scott MP, Wong WH*. Molecular Biology and Evolution, 2007, In press. Microarray data from multiple species have been used to study evolutionary constraints on gene expression. Expression measurements from conventional microarray platforms such as the 3' expression arrays are strongly affected by platform-dependent probe effects that may introduce apparent, but misleading discrepancies between species. In this manuscript, we assess the conservation of mammalian gene expression in adult tissues using data from a high-density exon array platform. The exon arrays have more than six million probes on a single array targeting all exons in a genome. We find that, unlike 3' array data, gene expression measurements from exon arrays reveal patterns of gene expression that are highly conserved between humans and mice in multiple tissues. Our analysis provides strong evidence for widespread stabilizing selection pressure on transcript abundance during mammalian evolution. ]]> tag:www.rnabioinformatics.com,2007://6.329 2007-03-16T06:57:41Z 2007-03-16T06:59:27Z

ISMB will continue to hold a 2day SIG meeting on alternative splicing in 2007....

2day SIG meeting on alternative splicing in 2007. ]]> tag:www.rnabioinformatics.com,2007://6.328 2007-03-14T07:29:36Z 2007-03-14T07:34:00Z

Beyond Genome 2007 will have a 2-day symposium on alternative splicing. Click here for details. The list of speakers is excellent. Unfortunately I'll be in China for IBW2007 during the same week and cannot go to listen to these talks......

here for details. The list of speakers is excellent. Unfortunately I'll be in China for IBW2007 during the same week and cannot go to listen to these talks...]]> tag:www.rnabioinformatics.com,2007://6.327 2007-03-08T21:05:38Z 2007-03-14T07:29:27Z

Lately, cross-species microarray hybridization has become a popular approach for gene expression profiling in less-annotated genomes, in particular for comparative genomics analyses of gene expression. The idea is to use a microarray platform designed for one species (e.g. humans) on...

Gilad et.al; another one from Bar-Or et.al. A major issue with cross-species microarray hybridization is the effect of sequence divergence on probe affinity. It is common that a probe that perfectly matches its target in one species doesn't match the same region in the second species. Moreover, due to difference in sequence divergence rates, such effects are not uniform across all genes. For the moment, it's hard to correct for such effects during the analysis of microarray data. ]]>