http://www.rnabioinformatics.com/ en Copyright 2007 Thu, 18 Oct 2007 17:20:11 -0800 http://www.sixapart.com/movabletype/ http://blogs.law.harvard.edu/tech/rss click here.]]> http://www.rnabioinformatics.com/2007/10/website_of_my_lab.html http://www.rnabioinformatics.com/2007/10/website_of_my_lab.html Thu, 18 Oct 2007 17:20:11 -0800 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. ]]> http://www.rnabioinformatics.com/2007/10/alternative_splicing_differenc.html http://www.rnabioinformatics.com/2007/10/alternative_splicing_differenc.html Tue, 16 Oct 2007 07:51:27 -0800 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. ]]> http://www.rnabioinformatics.com/2007/08/efficient_genomic_interval_ove.html http://www.rnabioinformatics.com/2007/08/efficient_genomic_interval_ove.html Sat, 11 Aug 2007 12:08:56 -0800 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. ]]> http://www.rnabioinformatics.com/2007/08/dr_wing_wongs_web_seminar_on_e.html http://www.rnabioinformatics.com/2007/08/dr_wing_wongs_web_seminar_on_e.html Fri, 03 Aug 2007 22:39:21 -0800 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. ]]> http://www.rnabioinformatics.com/2007/07/new_alternative_splicing_revie.html http://www.rnabioinformatics.com/2007/07/new_alternative_splicing_revie.html Sat, 28 Jul 2007 23:02:06 -0800 Send me an email for details if you are interested. ]]> http://www.rnabioinformatics.com/2007/07/postdoc_positions_available.html http://www.rnabioinformatics.com/2007/07/postdoc_positions_available.html Sun, 15 Jul 2007 10:58:37 -0800 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. ]]> http://www.rnabioinformatics.com/2007/07/alternative_splicing_in_the_po.html http://www.rnabioinformatics.com/2007/07/alternative_splicing_in_the_po.html Sun, 15 Jul 2007 02:09:51 -0800 here.]]> http://www.rnabioinformatics.com/2007/06/csb2007_workshop_in_alternativ.html http://www.rnabioinformatics.com/2007/06/csb2007_workshop_in_alternativ.html Wed, 13 Jun 2007 00:18:35 -0800 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. ]]> http://www.rnabioinformatics.com/2007/05/genebase.html http://www.rnabioinformatics.com/2007/05/genebase.html Thu, 24 May 2007 23:29:17 -0800 RNA in Biology, Bioengineering and Nanotechnology, part of UMN-IMA's year-long program on Mathematics of Molecular and Cellular Biology. ]]> http://www.rnabioinformatics.com/2007/05/umnima_rna_workshop.html http://www.rnabioinformatics.com/2007/05/umnima_rna_workshop.html Thu, 24 May 2007 21:18:55 -0800 Gene Array. It uses a subset of probes from Affymetrix Exon Arrays. Each gene has 26 probes on average. ]]> http://www.rnabioinformatics.com/2007/04/affymetrix_gene_array.html http://www.rnabioinformatics.com/2007/04/affymetrix_gene_array.html Sat, 07 Apr 2007 16:51:23 -0800 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. ]]> http://www.rnabioinformatics.com/2007/03/studying_evolution_of_gene_exp.html http://www.rnabioinformatics.com/2007/03/studying_evolution_of_gene_exp.html Mon, 19 Mar 2007 00:56:16 -0800 2day SIG meeting on alternative splicing in 2007. ]]> http://www.rnabioinformatics.com/2007/03/assig_2007_at_ismb.html http://www.rnabioinformatics.com/2007/03/assig_2007_at_ismb.html Thu, 15 Mar 2007 22:57:41 -0800 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...]]> http://www.rnabioinformatics.com/2007/03/beyond_genome_2007_alternative.html http://www.rnabioinformatics.com/2007/03/beyond_genome_2007_alternative.html Tue, 13 Mar 2007 23:29:36 -0800 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. ]]> http://www.rnabioinformatics.com/2007/03/crossspecies_microarray_hybrid.html http://www.rnabioinformatics.com/2007/03/crossspecies_microarray_hybrid.html Thu, 08 Mar 2007 13:05:38 -0800