MedWorm.com provides a medical RSS filtering service. Over 5000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'RNA Bioinformatics' source. Sat, 16 Aug 2008 14:47:05 +0100 http://www.rnabioinformatics.com/2007/10/website_of_my_lab.html The website of my lab at University of Iowa is up. Please click here. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=961624 Fri, 19 Oct 2007 00:36:53 +0100 961624 http://www.rnabioinformatics.com/2007/10/alternative_splicing_differenc.html 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=956048 Tue, 16 Oct 2007 15:51:27 +0100 956048 http://www.rnabioinformatics.com/2007/08/efficient_genomic_interval_ove.html 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=793684 Sat, 11 Aug 2007 20:08:56 +0100 793684 http://www.rnabioinformatics.com/2007/08/dr_wing_wongs_web_seminar_on_e.html 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=778572 Sat, 04 Aug 2007 06:39:21 +0100 778572 http://www.rnabioinformatics.com/2007/07/new_alternative_splicing_revie.html 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=764715 Sun, 29 Jul 2007 07:02:06 +0100 764715 http://www.rnabioinformatics.com/2007/07/postdoc_positions_available.html 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=735489 Sun, 15 Jul 2007 18:58:37 +0100 735489 http://www.rnabioinformatics.com/2007/07/alternative_splicing_in_the_po.html 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=735072 Sun, 15 Jul 2007 10:09:51 +0100 735072 http://www.rnabioinformatics.com/2007/06/csb2007_workshop_in_alternativ.html A one-day workshop on alternative splicing during Computational Systems Biology (CSB) 2007. Details here. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=674713 Wed, 13 Jun 2007 08:18:35 +0100 674713 http://www.rnabioinformatics.com/2007/05/genebase.html 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=637752 Fri, 25 May 2007 07:29:17 +0100 637752 http://www.rnabioinformatics.com/2007/05/umnima_rna_workshop.html RNA in Biology, Bioengineering and Nanotechnology, part of UMN-IMA's year-long program on Mathematics of Molecular and Cellular Biology. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=637753 Fri, 25 May 2007 05:18:55 +0100 637753 http://www.rnabioinformatics.com/2007/04/affymetrix_gene_array.html a new expression array platform - Gene Array. It uses a subset of probes from Affymetrix Exon Arrays. Each gene has 26 probes on average. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=528771 Sun, 08 Apr 2007 00:51:23 +0100 528771 http://www.rnabioinformatics.com/2007/03/studying_evolution_of_gene_exp.html This is a simple study with very interesting implications for evolutionary genomics and microarray analysis. See the title and abstract below. I'll write more about it within the next several days. 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485498 Mon, 19 Mar 2007 08:56:16 +0100 485498 http://www.rnabioinformatics.com/2007/03/assig_2007_at_ismb.html ISMB will continue to hold a 2day SIG meeting on alternative splicing in 2007. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485499 Fri, 16 Mar 2007 06:57:41 +0100 485499 http://www.rnabioinformatics.com/2007/03/beyond_genome_2007_alternative.html 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... (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485500 Wed, 14 Mar 2007 07:29:36 +0100 485500 http://www.rnabioinformatics.com/2007/03/crossspecies_microarray_hybrid.html 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 a second (closely related) species (such as chimpanzees), for which a standard microarray platform is not available. There are a few nice reviews on this topic. Here is one from 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. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485501 Thu, 08 Mar 2007 21:05:38 +0100 485501 http://www.rnabioinformatics.com/2007/02/gene_ontology_tools.html I am wondering if someone can recommend a convenient webserver or software program to calculate the enrichment of GO terms in one gene list over another gene list. If only one gene list is provided, the program should be able to use a 'background" gene list containing all genes in a particular species. Ideally, it could also handle various types of identifiers (e.g. refseq, entrez id, UniGene,etc) in the input gene lists. I know there are a lot of tools out there for a simple GO enrichment analysis, but I haven't found one that I particularly like.... Fatigo cannot calculate enrichment score if only one gene list is provided. I also tried GOStat, but the links to AmiGO from individual GO terms on the result page seem broken... (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485502 Wed, 28 Feb 2007 04:45:27 +0100 485502 http://www.rnabioinformatics.com/2007/02/an_id_converter.html This one looks good. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485503 Fri, 23 Feb 2007 22:00:51 +0100 485503 http://www.rnabioinformatics.com/2007/02/affymetrix_lowlevel_analysis_w.html Click here for more info. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485504 Wed, 14 Feb 2007 08:34:51 +0100 485504 http://www.rnabioinformatics.com/2007/02/our_book_chapter_on_alternativ.html Alternative splicing in the post-genomic era (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485505 Sat, 10 Feb 2007 21:37:58 +0100 485505 http://www.rnabioinformatics.com/2007/01/statistics_courses.html Courses Winter 2007 of Stanford Statistics (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485506 Wed, 03 Jan 2007 09:52:45 +0100 485506 http://www.rnabioinformatics.com/2006/12/plos_one_is_launched.html Download our manuscript on Exon Arrays (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485507 Thu, 21 Dec 2006 05:27:31 +0100 485507 http://www.rnabioinformatics.com/2006/12/nih_study_sections.html Roster Index of NIH Study Sections (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485508 Sun, 17 Dec 2006 12:07:32 +0100 485508 http://www.rnabioinformatics.com/2006/12/ai_rna_editing.html a review (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485509 Sat, 09 Dec 2006 08:35:43 +0100 485509 http://www.rnabioinformatics.com/2006/11/depolarization_and_cam_kinase.html Lee , JA., Xing, Y., Nguyen, D., Xie, J., Lee, C., Black, DL. (2006) Depolarization and CaM Kinase IV Modulate NMDA Receptor Splicing through Two Essential RNA Elements. PLoS Biology. Accepted. Details soon. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485510 Wed, 22 Nov 2006 19:21:55 +0100 485510 http://www.rnabioinformatics.com/2006/11/asap_ii.html ASAP database version II (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485511 Thu, 16 Nov 2006 07:40:01 +0100 485511 http://www.rnabioinformatics.com/2006/11/postdocphd_student_positions_a.html Click here for details. (Source: RNA Bioinformatics) RNA Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485512 Wed, 15 Nov 2006 05:49:35 +0100 485512