Foundations of Computational Genomics
November 29 - December 6, 2017
Application Deadline: September 1, 2017
Aaron Mackey, HemoShear LLC, Charlottesville
William Pearson, University of Virginia, Charlottesville
Lisa Stubbs, University of Illinois, Urbana
James Taylor, Johns Hopkins University
Please note special application instructions:
Only ONE letter of reference is required along with your application and Statement/Essay
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 & analysis of "next-gen"; sequencing data, with applications from metagenomic, RNA-Seq, & CHiP-Seq experiments
- The Galaxy environment for high-throughput analysis
- Regulatory element and motif identification from conserved signals in aligned and unaligned sequences
- Integration of genetic and sequence information in biological databases
- Genome Browsers and Genome Features
2016 Lecturers include:
Gary Stormo, Washington University
Ross Hardison, Pennsylvania State University
David Hawkins, University of Washington, Seattle
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 individuals in other disciplines (e.g., computer science) who wish to survey current research problems in biological sequence analysis. Advanced programming skills are not required.
The primary focus of the Computational & Comparative Genomics course is the theory and practice of algorithms in computational biology, with the goals of using current methods more effectively for biological discovery and developing new algorithms. The schedule and lectures for last year's Computational & Comparative Genomics course can be found at: fasta.bioch.virginia.edu/cshl/. Students more interested in the practical aspects of software development are encouraged to apply to the course on Programming for Biology. 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. Applicants interested in statistical training in genomics, including R/BioConductor programming, should apply to the course on Statistical Methods for Functional Genomics.
Support & Stipends
Major support provided by the National Human Genome Research Institute
Stipends are available to offset tuition costs as follows:
US applicants (National Human Genome Research Institute)
Interdisciplinary Fellowships (transitioning from outside biology) & Scholarships (transitioning from other biological disciplines) (Helmsley Charitable Trust)
International applicants (Howard Hughes Medical Institute)
Please indicate your eligibility for funding in your stipend request submitted when you apply to the course. Stipend requests do not affect selection decisions made by the instructors.
Cost (including board and lodging): $3,000
This button links to a short form which confirms your interest in the course. No fees are due until you have completed the full application process and are accepted into the course.
Students accepted into the course should plan to arrive by early evening on November 28 and plan to depart after lunch on December 6.