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. Guest lectures from genomic researchers.

Beginning in Autumn 2008, 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 11:00am-12:15pm in Beckman B302 (nicer map here). Once inside Beckman, take elevator to third floor, make a left at the lobby, and B-302 is the second door on the right.

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. You are also encouraged to consult online resources such as Wikipedia.

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). There is also a bookmarklet that can do this for you on a push of a button.

The following book can be used as a general reference to the biological topics discussed in class: Human Molecular Genetics, 3rd edition. The 2nd edition is freely available online. You can also read the NCBI Primer to Genomics. 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:

Aaron Wenger
Office: B319 (Walking out of the elevators, turn left then left again into the first corrider. B319 is eventually on the left side of the hall.)
Office hours: Thursday 3:00 - 5:00 PM
Email:

Jim Notwell
Office: B319 (Walking out of the elevators, turn left then left again into the first corrider. B319 is eventually on the left side of the hall.)
Office hours: Wednesday 12:15 - 2:15 PM
Email:

Questions should be sent to or communicated to the course staff during office hours. To receive course emails as an auditor, request to be added to the course mailing list using the Mailman website.

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 of 3, 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 elaine 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 2010/2011, Autumn 2009/2010, Autumn 2008/2009, Autumn 2007/2008, and Spring 2006/2007 versions of the course.

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 B-302 (the lecture room) from 10:00am-11:00am.

Date	Subject
9/30	Introductory Biology Primer
10/7	Introduction to Text Processing
10/14	UCSC Genome Browser Tools

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	9/26	Gill: Introduction
2	9/28	Serafim: DNA Sequencing Part I
3	10/3	Serafim: DNA Sequencing Part II
4	10/5	Gill: Human Genomic Variation	HW1 out
5	10/10	Gill: Genome Size, Repeats & Genes
6	10/12	Gill: Genome Evolution, Chromosomal Mutations, Paralogy & Orthology, Chains & Nets
7	10/17	Gill: Chains & Nets, Genome Reconstruction, Conservation
8	10/19	Serafim: Human Population Genomics I	HW2 out
9	10/24	Serafim: Human Population Genomics II
10	10/26	Serafim: Cancer Genomics
11	10/31	Gill: Conservation & Non-Coding RNAs	Halfway Feedback
12	11/2	Gill: Gene Regulation	Project out HW2 Due 11/4
13	11/7	Gill: GREAT.stanford.edu & The search for what makes us human
14	11/9	Serafim: Sequencing extinct human ancestors I
15	11/14	Serafim: Sequencing extinct human ancestors II
16	11/16	Serafim: Batzoglou Lab Projects	Project milestone (Monday, 11/21)
17	11/28	Serafim/Gill: Guest #1
18	11/30	Serafim/Gill: Guest #2
19	12/5	Serafim/Gill: Guest #3
20	12/7	Serafim+Gill+CAs: Project Presentations