Bioinformatics describes the computational analysis of gene sequences, protein structures, and expression datasets on a large scale. Specific topics include sequence alignment, biological database design, geometric analysis of protein structure, and macromolecular simulation.

Timing, Dates, & Location

Instructors

Prof Mark Gerstein

TFs : Sara Nichols, Xiaowei Zhu

General Information

The bioinformatics module will follow a very similar progression to the course offered last academic year.
Please see last year's site as a rough guide to lectures -- it has links to powerpoints -- and the readings.

Also, see other related on-line lectures.

Research Jobs in Bioinformatics

Use of Overheads and Other Course Materials

Class Requirements

Attendence, class participation

Reading

Papers will be assigned throughout the course. These papers will be discussed in weekly sections led by the TAs.

Quizzes

There will be 2 short quizzes (25 minutes) in class comprising SIMPLE questions that you should be able to answer from the lectures plus the main readings. The first quiz will cover the first part of the bioinformatics lectures. The second quiz will cover the rest of the material in the bioinformatics section.

Final Project Description

We will assign TWO papers in the last class on. And you can select ONE of them for your project. The final project should be 8 pages long, with the first half as a review and the second half as an extension for new ideas. Please carefully cite your references at the end of your project (not included in the 8 pages).

The review section will contain 1) a background introduction, 2) a summary of the general concepts and methods, 3) a new figure that helps to illustrate the basic schemes and 4) your comments on the paper including its advantages and disadvantages. 

In the second half, imagine you were a post-doc who wants to design a summer project to further investigate the work in the selected paper. You will write a simple proposal describing your thoughts and methods to test them. (We will give more details on this in one of the sections.)

You are expected to read relevant background to help you formulate your review and project proposal. This can come from the references in the reviewed paper itself and, more broadly, from literature mentioned in the class. You should explain your ideas on basis of the knowledge from the class and describe them with your own words. Please submit an electronic version of your project onto the classes server before the due date (see above). The project will make up 30% of your final grade, and we will put it on our public website after the grading. You can see previous projects below.

Final Projects Handed In

Projects done this year and previously: Spring 2005, 2003, 2002, 2001, 2000, 1999, 1998

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READINGS

Introduction Readings
Nicholas M Luscombe, Dov Greenbaum & Mark Gerstein (2001).
What is bioinformatics? A proposed definition and overview of the field
Methods Inf Med. 2001;40(4):346-58. REQUIRED FOR SECTION 6

D Greenbaum, N M Luscombe, R Jansen, J Qian, M Gerstein. (2001)
Interrelating Different Types of Whole-genome Data, from Proteome to Secretome: 'Oming in on Function
Genome Res. 2001 Sep;11(9):1463-8  REQUIRED FOR SECTION 6

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Sequence Readings
Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller and David J. Lipman (1997).
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Nucleic Acids Research. 1997;25(17):3389-3402. REQUIRED FOR SECTION 7&8

Michael Levitt and Mark Gerstein. (1998)
A unified statistical framework for sequence comparison and structure comparison
PNAS. 1998;95(11):5913-5920  REQUIRED FOR SECTION 7&8

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