CS 374 - Algorithms in Biology Fall 2004

• Course Description

This course will cover algorithms and computational models applied to molecular biology. Current, exciting algorithms from a variety of biological areas will be covered. The topics should be of interest to computer scientists and biologists alike. In Fall 2004 we will cover topics from genomics and evolution of DNA, such as sequence comparison methods, annotating DNA with genes and evolutionary important elements, genomic rearrangements, microarray analysis, and new sequencing technologies. We will also cover topics from protein structure, protein surface and interactions modeling, multiple alignment of proteins, phylogenetic trees, and DNA-based computation. The course will consist primarily of student presentations of topics in the syllabus, which will be prepared with the help of the instructor. Students will help forming the syllabus, by choosing the topics they would like to present.

• Class Schedule

          Lecture: TTh 11:00AM-12:15PM, Clark Center S361

• Staff and Office hours

  Instructor: Serafim Batzoglou
  Office: S266 Clark Center 
  Phone: (650) 723-3334 
  E m a il: serafim (at the address of) cs period stanford period edu (so as to avoid spam)
  Office hours: Tuesday 1:15-3:30PM.
  
  TA: Omkar Deshpande

  Office: S260 Clark Center 
  Phone: (650) 725-6094
  E m a il: omkard (at the address of) stanford period edu (so as to avoid spam)
  Office hours: Monday&Wednesday, 1:00-2:00PM

   

• Prerequisites
  These are recommended but will not be strictly enforced.

  • CS161, Design and Analysis of Algorithms, or equivalent familiarity with algorithmic and data structure concepts. 

  • CS262, Computational Genomics, or CS274, Representations and Algorithms for Computational Molecular Biology, or BIOCHEM218, Computational Molecular Biology; or equivalent familiarity with computational biology concepts, problems, and algorithms.

•  Course Requirements and Grading

1.     The main course requirement is to select a topic and prepare a presentation based on 2 papers on the topic. The instructor and TA will meet with each student to help with the preparation, and ensure that the resulting presentation will be interesting and accessible to students in the class who are not experts in the given topic. Most of the topics have a strong algorithmic flavor, but some topics are more geared towards biology. Please sign up for topics to present, on a first-come first-serve basis (see Topics below).

2.     The second requirement is scribing a lecture.  Lecture notes should provide students who are taking the class a useful resource for remembering the material presented. Ideally, lecture notes should be written up in a way so that they are readable by students of next year who did not necessarily read the papers that were presented. For formatting, here is a sample of how lecture notes should look like in terms of format and organization. We suggest that you use this as a template to prepare your lecture notes in Word. (Please do not read for content because we edited the original in ways that do not make sense in order to shorten it and put it in a specific format.)

Please sign up for scribing, on a first-come first-serve basis. To do so, please email both instructor and TA with subject "CS374, signing up for scribing". Lecture notes are due 1 week after the presentation.

3.    As a third requirement, you should select one of the first 10 lectures, and one of the rest. For this lecture, you should find one paper in addition to the 2 presented, which is related to the topic. It is preferable to find recent papers (2000-2004). Then, you should write a 1-page summary of what the paper presents and how it relates to the other two. The deadline for that summary is 1 week from the time of your selected lecture, and it will be distributed to class 2 weeks from that lecture, after we edit it together.  If you select a topic from the last week of class, then the edited version will not be distributed in class but will still be made available online.

Here is a sample structure of this short summary:

- Paper reference

- Abstract: in your own words (preferably simple description), what does the paper present

- Discussion: how do these results relate to the topic? Is it an advance over what was described, a different approach, and what are the main advantages/disadvantages?

4.    As this is a seminar-style class, attendance is mandatory, and each student can miss up to 2 classes without affecting his/her grade.

Taking the class for 2 units: If you take the class for 2 units, you can drop (2) or (3) above; or, in case enrollment is too high we will consider dropping (1) if you prefer.

• Communication

Questions should be sent to the instructor and TA directly with email, or communicated to course staff in person after lecture or during office hours.
 

Topics

Students will select topics from the following list. Also, they will sign up for a date of presentation. All this will be done on a first-come first-serve basis. Please email both instructor and TA with subject "CS374, signing up for presentation". Each lecture will cover 2 papers. Underlined topics have been assigned.

Schedule

The schedule will be filled-in as students sign up for topics. Click on the scribe's name for lecture notes.  (We try to make one set of lecture notes per talk, but due to some conflicts and problems with scheduling, there are some gaps while a lecture can have more than two scribed versions.)

Thanks to all students for a great class this year!  The material below will be kept online (disclaimer: we have not edited it, and even though students did a great job preparing presentations and lecture notes, there are, unavoidably, many errors).