CAP 5510 & CGS 5166: Spring 2005
Bioinformatics Course Homepage
Tue & Thu 11:00 - 12:15, ECS 141

• Apr 22 : Note that there are 3 presentations scheduled for Thursday, Apr 28, at 9:30 AM (exam time). The final exam is replaced by your project report. You were sent feedback about your presentations so that you can fix your reports appropriately. Your reports are due in class on Apr 28.
• Apr 18 : Attendance for all the presentations is mandatory for student in the class. Since we have many presentations to listen to, do not be late for the class.
• Apr 18 : We will meet in the same room (ECS 141) for the presentations for both days, Tue (Apr 19) and Thu (Apr 21).
• Apr 18 : I am proposing replacing the final exam with the final project report. Please email me to indicate whether or not you are in favor of this proposal.
• Apr 16:
  • Talks for Tuesday, Apr 19: Camilo, Vicky, Wei, Javier
  • Talks for Thursday, Apr 21: Raquel, Sarah, Miaohua, Todd
  • Talks for Thursday, April 28: Rafael, Roman, Rob
• Apr 16 : Please email me your presentations the night before your presentation so that we do not waste time before your presentation. If you have a problem with the above schedule, email me before Monday.
• Apr 03: You cannot make a presentation unless your project and results have been approved by me. Please come and see me with your partial results. I am willing to accept the project report later (by Apr 25). Right now, focus on getting results for your project. The presentations will start from April 14. All students must be present for, and must participate in, all presentations.
• Mar 06: I have been down with the flu and have not been able to put up this announcement earlier. My apologies. Homework 1 has now been graded. You can collect them from me Monday. For the exam, read your classnotes and the text by Mount. In particular, read chapters 1, 2, 3, 5, 6, 9, 10, 12 and 13 from Mount. I also receommend trying out the exercise problems from Mount's text, wherever relevant. The exam will consist of lots of short questions. The students enrolled in CAP 5510 will be graded separately from those enrolled in CGS 5166, since the expectations in terms of computer science background are different.

• Apr 7 Lec 21[pdf] [Phylogeny] Reading: []
• Apr 5  Lec 20[pdf] [Phylogeny] Reading: []
• Mar 29 Lec 19[pdf] [PCR, Gels, 2D-Gels] Reading: [Chapters 13 (from DM)]
• Mar 08/10 Lec 17/18[pdf] [Clustering, SVMs, SOMs] Reading: [Chapters 13 (from DM)]
• Mar 01/03 Lec 15/16[pdf] [Microarray Technology and Microarray Data Analysis] Reading: [Chapters 13 (from DM)]
• Feb 24 No Lecture! Reading: [Chapters 10 (from DM)]
• Feb 22 Lec 13[pdf] [PSI-BLAST, PHI-BLAST; Protein Structure Prediction] Reading: [Chapters 10 (from DM)]
• Feb 17 Lec 12[pdf] [HMM Applications; Gene Prediction] Reading: [Chapters 5 & 9 (from DM)]
• Feb 10, 15 Lec 10, 11[pdf] [HMM Applications; Gene Prediction] Reading: [Chapters 5 & 9 (from DM)]
• Feb 8 Lec 9[pdf] [Protein Structures; Hidden Markov Models] Reading: [Chapters 10 & 5 (from DM)]
• Feb 3 Lec 8[pdf] [Multiple Sequence Alignment; Hidden Markov Models] Reading: [Chapter 5 (from DM); Extra]
• Feb 1: Lec 7[pdf] [BioPerl; Multiple Sequence Alignment; Profile Methods] Reading: [Chapter 5, 12 (from DM); Extra]
• Jan 27: Lec 6[pdf] [BioPerl] Reading: [Chapter 12 (from DM); Extra]
• Jan 25: Lec 5[pdf] [FASTA, BLAST]; More slides on BioPerl; Reading: [Chapters 3, 6, 12 (from DM); Extra]
• Jan 20: Lec 4[pdf] [Global & Local Sequence Alignment; String Matching] Reading: [Chapters 3, 6 (from DM); Extra]
• Jan 18: Lec 3[pdf] [Sequence Alignment; Accessing Genomic Databases] Reading: [Chapters 2, 3 (from DM); Extra]
• Jan 13: Lec 2[pdf] [Biological Preliminaries] Reading: [ Extra]
• Jan 11: Lec 1[pdf] [Introduction & Motivation]; Reading: [Chapters 1, 2 (from DM); Extra]

• Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.