Course Description

Biology in the 21st century is increasingly an interdisciplinary science where the major breakthroughs will be achieved with a combination of computation and high-throughput experiments. This way we may be able to (1) find all "parts" such as genes that constitute a functional organism; (2) see how those "parts" connect to modules such as biomolecular processes and whole cells, and develop elaborate dynamic models of those modules; (3) precisely associate genotype (our DNA) with phenotype (how we look, diseases) and design personalized health care; (4) reconstruct ancestral genomes and clone ancestral organisms (Jurassic park).

Genomics is the area of biology most infused with computer science today. This course will cover the main algorithms and systems in genomic research. We will look at how we obtain DNA sequences such as the human genome, how we compare those sequences among organisms to study evolution, how we find genes and gene-regulation elements ("parts") within DNA, and how we start to connect those to model functional modules.

The course will be primarily an algorithms course, as well as a gentle introduction to biological concepts for the computer scientist. People with a primarily biological background who have familiarity/interest in computation are encouraged to take the course. All assignments are done in groups, so that people of different backgrounds will have the opportunity to form teams.

Prerequisites

CS161, Design and Analysis of Algorithms, or equivalent familiarity with algorithmic and data structure concepts. Basic knowledge of genetics and biology is helpful, but not required.

Requirements and Grading

The course will have four challenging problem sets of equal size and grading weight. These must be handed in at the beginning of class on the due date, which will usually be two weeks after they are handed out. Collaboration is allowed on the homework, in groups of 2 or 3 students.

Recognizing that students may face unusual circumstances and require some flexibility in the course of the quarter, each student will have a total of three free late days to use as s/he sees fit. Once these late days are exhausted, any homework turned in late will be penalized at the rate of 20% per late day (or fraction thereof). Under no circumstances will a homework be accepted more than three days after its due date.

Late homework should be turned in to a member of the course staff, or, if none are available, placed under the door of S266 Clark Center (Serafim's office). You must write the time and date of submission on the assignment.

Optionally, a student can scribe one lecture.  Lecture notes will be due one week after the lecture date, and the grade on the lecture notes will substitute the two lowest-scoring problems in the homeworks. To ensure even coverage of the lectures, please sign up to scribe beforehand with one of the course staff.

Collaboration and Honor Code

Students may discuss and work on problems in groups but must write up their own solutions. When writing up the solutions, students should write the names of people with whom they discussed the assignment.