Genomes are the ultimate biological information medium, carrying the key instructions for every organism's development, life-cycle, and reproduction. In this course we will study genomes from a bioinformatics perspective. We will cover advances in our understanding of biology that have resulted from recent sequencing of the human and dozens of related organisms. Topics will include: (1) genome sequencing: technologies, assembly, personalized sequencing; (2) functional landscape: genes, regulatory modules, repeats, RNA genes, epigenetics; (3) genome evolution: evolutionary processes, comparative genomics, ultraconservation, exaptation. As time permits, we may cover population genetics and personalized genomics, ancient DNA, metagenomics, or other current topics.

Beginning in Autumn 2008, there are no biological or computational prerequisites for CS273a. 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 BMI273A, 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: ude.drofnats@mifares (written backwards to avoid spam)

Gill Bejerano
Office: Beckman Center B321
Office hours: Email for appointment
Phone: (650) 723-7666
Email: ude.drofnats@onarejeb (written backwards to avoid spam)

Aaron Wenger
Office: Beckman Center B319
Office hours: Monday 10AM-11AM
Email: ude.drofnats@regnewa (written backwards to avoid spam)

Konstantinos (Gus) Katsiapis
Office: Gates B24A (Tuesday), Gates B26A (Thursday)
Office hours: Tuesday 11AM-1PM, Thursday 2:15PM-4:15PM
Email: ude.drofnats@paistakk (written backwards to avoid spam)

Questions should be sent to ude.drofnats.stsil@ffats-0190tua-a372sc (written backwards to avoid spam), 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.

   Homework should be completed individually.

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 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-200 (one floor directly below the lecture room) from 10:00am-11:00am.

Date	Subject
9/25	Introductory Biology Primer
10/2	Introduction to Text Processing
10/9	UCSC Genome Browser Tools

As the quarter progresses, the following schedule will be updated accordingly. Please check back often for the latest material.

	Date	Title	HW
		Related Material
1	9/21	Introduction (Gill)
2	9/23	The Human Genome, Human Variation, Somatic Mutations, and Cancer (Gill)
3	9/28	Genome Content: Repetitive Sequences and Genes (Gill)
4	9/30	DNA Sequencing (Serafim)	HW1 HW1 FAQ HW1 Solutions HW1 CA Feedback HW1 Statistics
		Modelling the recent common ancestry of all living humans
5	10/5	Sequence Assembly (Serafim)
6	10/7	Genome Evolution, Chromosomal Mutations, Paralogy & Orthology, Chains & Nets (Gill)
7	10/12	Genome Reconstruction, Chains & Nets, Conservation & Function (Gill)
8	10/14	Sequencing Technologies (Serafim)	HW2 HW2 FAQ HW2 Solutions HW2 CA Feedback HW2 Statistics
9	10/19	Multiple Sequence Alignment (Serafim)
10	10/21	Multiple Sequence Alignment Continued (Serafim)
11	10/26	Non-coding RNAs (Gill)	Halfway Feedback
12	10/28	Cis-regulation and Cellular Signalling (Gill)
13	11/2	Conservation (Serafim)	Project out
14	11/4	(Guest)
15	11/9	Human Population Genetics (Serafim)
16	11/11	(Guest)
17	11/16	Ultraconservation (Gill)	Project milestone
18	11/18	(Guest)
19	11/30	(Serafim)
20	12/2	Project presentations