Introduction to computational biology through an informatic exploration of the human genome. Topics include: genome sequencing (technologies, assembly, personalized sequencing); functional landscape (genes, gene regulation, repeats, RNA genes, epigenetics); genome evolution (comparative genomics, ultraconservation, co-option). Additional topics may include population genetics, personalized genomics, and ancient DNA. Course includes primers on molecular biology, the UCSC Genome Browser, and text processing languages.

There are no biological or computational prerequisites for CS273a. While there are no official prerequisites, a background in programming is strongly encouraged. Optional introductory sections on molecular biology, text processing in UNIX, and the UCSC Genome Browser will be given early in the quarter (see schedule below).

This course is cross-listed within Developmental Biology and Biomedical Informatics as DBIO273A and BIOMEDIN273A, respectively.

Mon Wed 1:30pm-2:50pm in Clark Center S361. EXCEPTION: The lecture on October 05 is going to be in Beckman B302.

The course is mostly based on current or very recent literature. As such, it does not follow any textbook. Please use the papers mentioned at each lecture as pointers into the relevant literature (for more material, you can look at the papers' references, or at more recent publications that cite those papers). The easiest way to find a paper would be to search for its title and/or authors on Google Scholar or vanilla Google.

As a Stanford student you also have free access to many biomedical journals. In order to be granted access to them while you are off-campus you simply need to add ".laneproxy.stanford.edu" to the main URL and enter your Stanford credentials upon request (for example http://www.somejournal.com/other/stuff would become http://www.somejournal.com.laneproxy.stanford.edu/other/stuff).

The following book can be used as a general reference to the biological topics discussed in class: Human Molecular Genetics, 4th edition. The course may also use material from Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases.

Serafim Batzoglou
Office: Clark Center S266
Office hours: Email for appointment
Phone: (650) 723-3334
Email:

Gill Bejerano
Office: Beckman Center B321
Office hours: Email for appointment
Phone: (650) 723-7666
Email:

Johannes Birgmeier
Office: Beckman B383
Office hours: Thursdays 2-4pm (Beckman B383) starting on 10/08
Email:

Karthik Jagadeesh
Office: Beckman B381
Office hours: Tuesdays 10am-12pm (Beckman B302) starting on 10/06
Email:

All course communication will be handled via Piazza. Find our class page at Piazza and enroll to receive announcements and access to other private course resources.

There are three course requirements:

1. Homeworks. Throughout the class there will be two homework assignments, due at the beginning of class on their due dates. Three late days are awarded for the quarter. Once these late days are used up, homework turned in late will be penalized 20% per late day. The number of late days used is rounded up to the nearest day, so assignments turned in one hour late use one full late day. Late days cannot be applied to the project milestone or final project presentation.

   A link to frequently asked questions about each homework will be created on the schedule and updated as questions come in, so refresh and check the FAQ to see if your question has been addressed already.

   Because we reuse some problem set questions from previous years' homeworks, looking at previous years' solution sets is not permitted and is an honor code violation.

   Students may discuss homework problems in groups. However, each student must write down the solutions independently, and without referring to written notes from the joint session. In other words, each student must understand the solution well enough in order to reconstruct it by him/herself. In addition, each student should write on the problem set the set of people with whom s/he collaborated.

2. Project. Students will form groups, and each group will be assigned an individual project. Instead of a final exam, at the end of the class there will be a poster session where the groups will present their work.

3. Attendance. For this class, attendance is mandatory. You may miss up to 2 lectures without affecting your grade, with consideration given if you are not feeling well.

Grades will be determined by roughly the following breakdown: 20% HW1, 25% HW2, 5% Attendance, 50% Final Project.

The base course directory is located at /afs/ir.stanford.edu/class/cs273a, and is reachable from the cardinal and corn machines. Source tree executables are available within the bin directory, and are machine-dependent. If you add "/afs/ir.stanford.edu/class/cs273a/bin/@sys" to your PATH variable, the correct version of the executable will be executed.

There are course schedules and materials available from the Autumn 2013/2014, Autumn 2011/2012, Autumn 2010/2011, Autumn 2009/2010, Autumn 2008/2009, Autumn 2007/2008, and Spring 2006/2007 versions of the course. Also see the Winter 2012/13 class of CS173.

The following is a list of introductory sessions for students unfamiliar with (or just wanting a refresher lecture on) biology and computer science to the depth necessary to make the course enjoyable. All sessions will take place in Beckman B302 on Fridays from 2-3:30. Beckman B302: Enter Beckman, take the elevator to the 3rd floor, take a left in the lobby and B302 is going to be on your right.

Date	Subject
9/25	Introductory Biology Primer (!! Beckman B302 !!)
10/2	Introduction to Text Processing (!! Beckman B302 !!) Bash shell text processing commands Classic shell scripting (online book) SQL Introduction Learn Python the Hard Way
10/9	UCSC Genome Browser Tools (!! Beckman B302 !!)

As the quarter progresses, the following schedule will be updated accordingly. Please check back often for the latest material. Homework related materials require a SUNet ID and password for registered students. If you are auditing the class and want access to these materials, please email the staff mailing list.

	Date	Title	HW
		Related Material
1	9/21	Gill: Introduction
2	9/23	Gill: Protein Coding Genes
3	9/28	Gill: Non Coding Genes
4	9/30	Serafim: DNA Sequencing I	HW1 Out
5	10/05	Serafim: DNA Sequencing II
6	10/07	Gill: Genes Enrichment, Gene Regulation I
7	10/12	Gill: Gene Regulation II
8	10/14	Serafim: Human Population Genomics I
9	10/19	Serafim: Human Population Genomics II	HW2 Out
10	10/21	Serafim: Human Population Genomics III
11	10/26	Gill: Neutral Evolution: Repetitive Elements
12	10/28	Gill: Inferring Evolution: Chains & Nets
13	11/02	Serafim: Multiple Sequence Alignment
14	11/04	Serafim: Cancer Sequencing
15	11/09	Serafim: Cancer Sequencing
16	11/11	Gill
17	11/16	Serafim: Cancer Sequencing II
18	11/18	Serafim: Cancer Sequencing II
19	11/30	Gill
20	12/02	PROJECT PRESENTATIONS (!! Beckman B302 !!)