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"Self consistent analysis of the Micro-Array Quality Control (MAQC) data,
using the titration samples as quality indicators, reveals the high level
of splice regulation of the human transcriptome"
Who: Jean Thierry-Mieg and Danielle Thierry-Mieg (National Center for Biotechnology Information)
Abstract: The MAQC project compared expresion measures across six platforms and several labs using the same set of RNA samples. We propose an iterative self-consistent normalization of the MAQC microarrays, which takes advantage of the existence of titration samples. To compare platforms, one needs to identify the specific gene measured by each probe. We map the probes to genes and alternative variants in AceView, a manually curated comprehensive and non-redundant assembly of the GenBank, dbEST and RefSeq cDNAs. We identify 14,000 genes coherently seen as differentially expressed across multiple platforms. For these genes, considered as known titrators, we observe that 71% of the probes measure the expected result (between 49% and 89% depending on the platform), while only 3% see the opposite, but 26% (including 24% of the TaqMan assays) fail to see a titrating signal when they should. We identify some of the problems affecting the design of those probes. Many differentially expressed genes are not annotated in the RefSeq collection. We conclude that many inter-platform apparent contradictions are actually biological and measure the alternative regulation of promoters, splicing and polyadenylation.
"How do you describe
the taste of marzipan?"
Who: Jeff Elhai, Ph.D. (Department of Biology and the Center of the Study for Biological Complexity)
"Novel functions of axoneme central apparatus proteins: regulation of motility and control of gene expression"
Who: Zhibing Zhang, M.D., Ph.D. (Assistant Professor of Obstetrics & Gynecology, VCU Medical Center)
Refreshments will be served at 3:45 p.m.
"Estimation Under Model Uncertainty: Select the Best One or Average Over Many?"
Who: Nitai D. Mukhopadhyay, Ph.D. (Eli Lilly and Company, Indianapolis, IN)
Abstract: In case of prediction following model selection, the selection procedure and the parameter estimates have a lot of influence on predictive performance. One of the most popular model selection criteria, Akaike Information Criterion (AIC), can be shown to be approximately Bayes under a specific choice of parameter estimates. Using Bayes estimates for the parameters improves predictive performance even further. However, both these methods ignore the model uncertainty during prediction. Post model selection estimations that ignore model uncertainty pose many problems relevant to finite sample inference. These problems and comparative advantage of Bayesian model averaging, along with applications, will be discussed.
Refreshments will be served at 2:30 p.m. in Sanger Hall, B1-066C
"Biochemical Basis for Non-alcoholic Fatty Liver Disease"
Who: Arun Sanyal, M.D. (Chair, Division of Gastroenterology, Hepatology & NutritionVCU Medical Center)
To learn about Dr. Sanyal see: http://www.gastro.vcu.edu/faculty/sanyal/. Refreshments will be served at 3:45 p.m.
"Identification of Regulatory Sequences, Expression Activity, and Essential Risk Factors in the Cancer Genome "
Who: Vladimir Kutnetsov, Ph.D., Sci.D. (Senior Group Leader and Head, Computational Genomics and Systems Biology, & Genome Institute of Singapore)
Please see Danail Bonchev if you would like to speak with Dr. Kutnetsov.
|| NCBI Software Tutorial ||
On March 12, 13 and 14, the National Center for Biotechnology Information (NCBI), a branch of the National Library of Medicine at the NIH, will present a series of workshops and hands-on sessions related to the Molecular Biology Resources available on the NCBI Web site. Sessions will include an updated version of the overview or "Field Guide" and well as more specific workshops on various aspects of applications of the information in this key resource.
The schedule is given below: all lectures will be in Rm. 1-044 Sanger Hall and the Hands-on sessions in Rm B1-020 Sanger Hall. Registration for the lectures and hands-on sessions is required as we are limited for space and need to have advance information to adequately plan. To register, please go to the VCU online course registration site at http://www.pubinfo.vcu.edu/training/it/ and enter the keyword NCBI to see all lectures and hands-on sessions. Thanks for your attention.
The program for the three days appears below:
NCBI Field Guide Update