CPS 160: Introduction to Computational Genomics

Overview

A computational perspective on the exploration and analysis of genomic and genome-scale information. Provides an integrated introduction to genome biology, algorithm design and analysis, and probabilistic and statistical modeling. Topics include genome sequencing, genome sequence assembly, local and global sequence alignment, sequence database search, gene and motif finding, phylogenetic tree building, and gene expression analysis. Methods include dynamic programming, indexing and hashing, hidden Markov models, and elementary machine learning. Development of practical experience with handling, analyzing, and visualizing genomic data using the scripting language Perl.

The course will require students to program in Perl. Students coming in to the course should know how to program in some computer language, but it need not be Perl. Students should also have had some exposure to basic probability, statistics, and molecular or cellular biology; however, the course has no formal course prerequisites, and significant background will be provided. Please speak to the instructor if you are unsure about your background. This course is a valid elective in both biology and computer science.

Instructor

Professor Alex Hartemink

Webpage: http://www.cs.duke.edu/~amink
Email: amink at cs.duke.edu
Office Location: LSRC D239
Office Phone: (919) 660-6514

Office hours

Alex Hartemink

Email: amink at cs.duke.edu
Office Hours: Monday 3:00PM-4:00PM in LSRC D239.

Michael Mayhew

Email: michael.mayhew at duke.edu
Office Hours: Wednesday 11:30AM-12:30PM in LSRC D227.

Daphne Ezer

Email: daphne.ezer at gmail.com
Office Hours: Wednesday 8:30PM-9:30PM (new time) in the Link (map).

If these office hours do not work for you, please post questions via Piazza, or send any of us an email to schedule an alternate time.

Logistics

The class meets on Wednesdays and Fridays from 10:05 until 11:20 in LSRC, Room D243.