Computational Genomics
November 28 - December 5, 2018
Application Deadline: September 1, 2018


David Hawkins (@hawkinslab), University of Washington
William Pearson (@fastabill), University of Virginia
James Taylor (@jxtx), Johns Hopkins University

Please note special application instructions:
Only ONE letter of reference is required along with your application materials and personal statement/essay

See the roll of honor - who's taken the course in the past

This course presents a comprehensive overview of the theory and practice of computational methods for the characterization of functional elements in DNA and RNA sequence data. The course helps students achieve a deep, algorithmic understanding of the technologies and methods used to reveal genome function; the goal is to push beyond basic data analysis, and into experimental design and the development of new analysis strategies. The course enables students to extract the maximum amount of correct information from data by a developing a broad understanding of genomic analysis approaches and their shortcomings.

Topics include:
  • Protein & DNA sequence similarity, comparisons, multiple alignments, and database searches
  • Alignment & analysis of high-throughput sequencing data, with applications from RNA-Seq & ChIP-Seq experiments
  • Analysis environments including Galaxy, RStudio, and the UNIX command line, with a strong focus on reproducible research
  • Statistical considerations in the design and analysis of genomic experiments
  • 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 features
Invited lecturers for 2018 include:

Jeff Leek (@jtleek), Johns Hopkins University
Aaron Mackey (@ajmackey), HemoShear LLC
Shaun Mahoney (@mahonylab), Pennsylvania State University
Melissa Wilson Sayres (@sexchrlab), Arizona State University
Lisa Stubbs (@stubbslab), University of Illinois

The course combines lectures with hands-on exercises; students are encouraged to pose challenging problems using their own data. It is designed for biologists seeking advanced training in sequence and genome analysis, computational biology core resource directors and staff, and 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 schedule and lectures for last year's course can be found here.

The primary focus of the Computational Genomics course is the theory and practice of algorithms in computational biology, with the dual goals of 1) using current methods more effectively for biological discovery and 2) developing new algorithms. 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. Those interested in statistical training in genomics, including programming in R/BioConductor, should apply to the course on Statistical Methods for Functional Genomics.

Support & Financial Aid

Major support provided by the National Human Genome Research Institute

Financial aid is available to offset tuition costs as follows:


U.S. 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 the financial aid request that you submit when you apply to the course. Financial aid requests do not affect selection decisions made by the instructors.

Cost (including board and lodging): $3,060

No fees are due until you have completed the full application process and are accepted into the course. Accepted students should plan to arrive by early evening on November 27 and depart after lunch on December 5.

Before applying, ensure you have all of the following ready: 1) Personal statement/essay; 2) One letter of recommendation; 3) Curriculum vitae/resume (optional); 4) Financial aid request (optional). See this page for more details on application procedures, selection criteria, and financial aid.

If you are not yet ready to fully apply, but wish to express interest in the course and receive a reminder two weeks prior to the application deadline, click below: