20th Annual International Conference on
Intelligent Systems for Molecular Biology

ISMB 2012 - Tutorials

ISMB 2012 features two (2) half-day tutorial sessions on Saturday, July 14, 2012 one day prior to the conference scientific program. Tutorials are held on the same day as the second day of the SIG and Satellite meetings.
Tutorial attendees should register using the on-line registration system when registration opens on March 19, 2012. Tutorial participants must be registered for the ISMB conference to attend a tutorial. Attendees will receive a Tutorial Entry Pass (ticket) at the time they register on site. Tutorial handouts and electronic notes can be picked up at on-site registration at the Long Beach Convention Center. Lunch is included in the registration fee for attendees registering for two tutorials. Those attending one tutorial only have the option to purchase a lunch ticket during on-line registration.
Tutorials: Saturday, July 14
Location: Hyatt Regency Long Beach Hotel (adjacent to Long Beach Convention Center)
Room: Regency Ballroom E/F
Morning Tutorial (AMTUT):¬†8:30 a.m. ‚Äď 12:30 p.m.
Analyzing RNA-seq data
Ali Mortazavi, University of California Irvine, United States
Rabi Murad, University of California Irvine, United States
The rapid adoption of RNA-seq for transcriptome profiling has led to the development of a variety of computational approaches to maximize the twin benefits of the technology, namely discovery and quatitation. We will review the impact of the different RNA-seq experimental protocols on downstream analyses and discuss the latest advances in the analysis of RNA-seq data with respect to various topics such as de novo transcript assembly, reference-assisted transcript assembly, allele-specific expression and differential expression using the current generation of publicly available packages and discuss where the next generation of tools are likely to head as a new generation of sequencers with longer read lengths become more readily available.
Level:  General to intermediate
Afternoon Tutorial (PMTUT):¬†1:30 p.m. ‚Äď 5:30 p.m.
From GWAS to Personal Genomes:  The Fundamentals of Analysis of Genetic Variation
Russell Schwartz, Carnegie Mellon University, Pittsburgh, United States
Eleazar Eskin, University of California, Los Angeles, United States
This tutorial will provide a general overview of genetic variations and their computational analysis aimed at an audience with minimal prior training in computational biology. We will initially survey the biology and technology behind genetic variation studies, covering the major types of genetic variation studied, the technologies used to discover and type them, and major efforts to assess variation in populations.  We will examine some of the major computational tools for analyzing genetic variations and applying them to basic research into population structure, dynamics, and phylogenetics.  We will then turn to the problem of associating genotype and phenotype. There, we will review statistical methods for association, building from basic statistical concepts to practical application and some current questions in association study design.  We will then survey machine learning approaches to the association problem and current directions in structured association.  The full tutorial is intended to give the attendee a broad understanding of the major concepts, efforts, tools, and current research problems underlying the computational and statistical analysis of genetic variations.
Level:  General