[Bioperl-l] Application Deadline - 2012 CSHL Computational and Comparative Genomics Course

William Pearson wrp at virginia.edu
Mon Jul 2 10:31:40 EDT 2012

Course announcement - Application deadline, July 15, 2012


Oct 31 - Nov 6, 2011
Application Deadline: July 15, 2012


William Pearson, University of Virginia, Charlottesville, VA
Lisa Stubbs, University of Illinois, Urbana, IL
This course presents a comprehensive overview of the theory and practice of computational methods for the identification and characterization of functional elements from DNA sequence data. The course focuses on approaches for extracting the maximum amount of information from protein and DNA sequence similarity through sequence database searches, statistical analysis, and multiple sequence alignment. Additional topics include:

Alignment and analysis of "Next-Gen" sequencing data
The Galaxy environment for high-throughput analysis
Identification of conserved signals in aligned and unaligned sequences
Regulatory element and motif recognition
Integration of genetic and sequence information in biological databases
The ENSEMBL genome browser and BioMart
Function/phenotype prediction for sequence variants
The course combines lectures with hands-on exercises; students are encouraged to pose challenging sequence analysis problems using their own data. The course is designed for biologists seeking advanced training in biological sequence and genome analysis, computational biology core resource directors and staff, and for scientists in other disciplines, such as computer science, who wish to survey current research problems in biological sequence analysis. Advanced programming skills are not required.

The lecture/lab schedule for the 2011 course can be found at fasta.bioch.virginia.edu/cshl

Speakers in the 2011 course included:
Aaron Mackey, U. of Virginia, Next-Gen analysis pipelines
Bert Overduin, European Bioinformatics Institute, UK, ENSEMBL and BioMart
Francis Ouellette, Ontario Institute for Cancer Research, Databases for Biological Function
William Pearson, U. of Virginia, Similarity Searching, Multiple Alignment
Lisa Stubbs, U. of Illinois, Urbana, ChIP, Transcription Factors, and Comparative Genomics
James Taylor, Emory, Galaxy and genome analysis pipelines
The primary focus of the computational and comparative genomics course is the theory and practice of algorithms used in computational biology, with the goal of using current methods more effectively and evaluating new approaches. Students who wish to learn Perl programming for Bioinformatics are encouraged to apply to the Programming for Biology course. Students who would like in-depth training in the analysis of next-generation sequencing data (e.g., SNP calling and the detection of structural variants) should apply to the course on Advanced Sequencing Technologies & Applications. This Computational and Comparative Genomics course will discuss methods for phenotype prediction from variation data.

To apply to the course, fill out and send in the form at:


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