Computational Genomics
Biochemistry 228
Biochemistry 228
Doug Brutlag
Course Description
Computational Genomics is a graduate level course targeted at graduate students or upper level undergraduates desiring an advanced knowledge of the application of computational genomic methods to biological problems. Topics to be covered include assembly of genomic sequences, genome databases, comparative genomics, gene discovery, gene expression analyses including gene clustering by expression, transcription factor binding site discovery, metabolic pathway discovery, functional genomics, gene and genome ontologies, and medical diagnostics using SNPs and gene expression. We will also cover gene regulation via epigenetic and port-transcriptional mechanisms. The course will be based on recent papers from the literature as well as practical hands-on use of these methods. Prerequisites include an introductory course in computational molecular biology or genomics such as Biochem 218, Biomedical Informatics 214, Genetics 211 or permission of instructor.
Course Requirements
Course Availability
Biochemistry 228 will be taught live, in the Spring quarter 2007-2008. The course will also be available online via the Stanford Center for Professional Development (SCPD). The course will be available to off campus students during all three quarters via SCPD.
Registration
Registration is limited to 50 students. On campus students must register with the registrar's office. Off campus students must register with the Stanford Center for Professional Development.
Auditors
Anyone on Stanford Campus or participating in Stanford Overseas Campus may audit the lectures on the Internet via Stanford Online during a quarter this course is being taught. All lectures are recorded and made available via streaming video (see below for instructions). There is no limit on the number of auditors. Stanford Online lectures are available 24 hours a day, 7 days a week. The only requirement is that the auditors must use a computer on campus (in the stanford.edu domain) and have a valid SUNET ID in order to view the lecture. Auditors will also be permitted to attend the classes as long as there are seats available. No homework will be permitted and no grade will be awarded for auditors.
Teaching Assistants and Staff
Lee Kozar (kozar@stanford.edu) is the Associate Director of the Bioinformatics Resource at Stanford and is in charge of the computing facilities including software and databases that will be used for the homework. Questions concerning the programs, databases and other computing resources used in the course should be addressed to him.
Kimberley Latta (klatta@stanford.edu) is the Administrator for the course. You should contact her for all administrative needs such as web page problems, student status, etc.
Lecture Syllabus
Date Topic Lecturer Genome assembly
Gene finding
Comparative genomics & gene regulatory regions Eddy Rubin Functional genomics
Non-coding RNA genes
Genome annotation
Clustering coordinately regulated genes
Discovering DNA regulatory motifs I
Discovering DNA regulatory motifs II
DNA methylation & epigenetic gene regulation
Translational regulation: siRNA and microRNA
Diseases and phenotypes
SNPS & STS markers and haplotype mapping
Ultraconserved regions
Metabolic pathways A
Metabolic pathways B
The ENCODE project
Copy number variation
Bioinformatics Week Videos
https://cmgm.stanford.edu/classes/EBI-NCBI/videos/
Bioinformatics Resource Courses
http://cmgm.stanford.edu/classes/
** Last Updated September 29, 2007**
