Call for Papers, Posters and Demonstrations

Session on Alternative Splicing

at the Pacific Symposium on Biocomputing 2004

Alternative splicing is an essential yet complicated biological process, often controlled by developmental or tissue-specific factors. More than one alternatively spliced mRNA from the same gene may be expressed in the same tissue, sometimes simultaneously yielding an extensive set of proteins with distinct functions. In humans, it is estimated that approximately 30-60% of genes undergo alternative splicing, and many human diseases are associated with aberrant splicing. However, until recent times, the complexity of alternative splicing has eluded detailed analysis. Bolstered by genomic data and new experimental approaches, bioinformatics is emerging as an important tool for studying this phenomenon.

This session, the first for PSB, will bring together researchers from the biological, computational and statistical fields with the goal of sharing efforts in alternative splicing research. We are soliciting papers in topics including the following:

· Computational study of alternative splicing mechanisms. This includes computational methods for identifying cis-acting elements and trans-acting factors, understanding their functions as well as their regulatory mechanisms.

· Computational analysis of mis-splicing and disease association. This includes identifying the cause of the aberrant splicing and it physiological effect.

· Computational study of alternative promoters and their effect in alternative splicing.

· Gene predictions/gene structure identification that incorporate alternative splicing events.

· Genome-scale alternative splicing data mining using public databases, including EST and SAGE analysis.

· Knowledge-based annotation and curation of known splice variants, identification of novel variants, and splice variant-based analysis of functional pathways.

· Understanding the functions of splice variants in protein space, including functional domains and protein structures.

· Large-scale analysis of differential expression analysis such as identifying tissue specific splice variants.

· Splice variant-related measurement technologies, such as novel instrumentation platforms, laboratory protocols, or splice-variant specific microarray designs.

· Computational algorithms for monitoring splice variant expression.

Session co-chairs

· Hui Wang

Affymetrix Inc.

hui_wang@affymetrix.com

· Ueng-Cheng Yang

National Yang-Ming University, Taiwan

yang@ym.edu.tw

· Christopher Lee

University of California, LA

leec@mbi.ucla.edu