CAP 5510 & CGS 5166: Spring 2015
Bioinformatics Course Homepage
Mon 1:00 - 3:50, ECS 235

• Apr 25: NOTE PRESENTATIONS WILL START AT NOON INSTEAD OF 1:00 PM ON MONDAY APR 27. Attendance is mandatory. No cell phones and laptops during the presentations. Class participation during the presentations is part of your evaluation.
• Apr 16: Attendance is mandatory. Missing even one presentation will be penalized. I want you to put aside your cell phones and your laptops and pay attention to your fellow-students' presentations. Class participation during the presentations is part of your evaluation.
• Apr 16: For those of presenting on April 20, I need to see your presentation by end of day tomorrow.
• Apr 16:Presentations are scheduled for April 20 and 27. The schedule is as follows:
  • Apr 20 Joana, Daniel, Andrius, and Juan
  • Apr 27 Fernand and German, Chunfei, Jorge, Srikanth, and Wenrui
• Apr 1:HW #2 is ready. Get started immediately.
• Mar 30: We agreed that the final project presentations will be on April 20 and 27. The exact schedule will be announced later. Your final project report is due on April 28.
• Feb 28:Some of you have not yet picked your project topic. I need to hear from you soon. Earlier, I had asked you to prepare a 5-minute presentation for the Mar 2 class. Instead, I want you to send me a presentation (about 6 slides) by noon on Wednesday, Mar 4. The slides should address problem statement, motivation, background, specific aims, approach, and expected conclusions (in any reasonable order) Once they are cleared by me, you will make presentations for the Mar 16 class. Plan to work very hard for your project over Spring Break!
• Feb 16:ProjectIdeas are now available in pdf form. You need to pick a project by next Monday.
• Feb 2:We will have a Bioinformatics professional visiting us as part of Panther Alumni Week.
• Feb 1:Homework 1 is ready and is due Feb 16. Get started immedaitely -- it's a fair bit of work.

• For CS Majors: CAP 5510
• For NON-CS Students: CGS 5166

• Apr 13: Lec X2 [pdf];
• Apr 6: Lec X1 [pdf];
• Mar 30: Lec X [pdf];
• Mar 23: Lec 9 [pdf];
• Mar 16: Lec 8 [pdf]; Lecture Notes by Tom Mitchell] [Machine Learning]
• Mar 16: First Round Presentations
• Mar 2: Lec 7 [pdf] [Proteins]
• Feb 23: Lec 6 [pdf] [Next Generation Sequencing; HMMs]
• Feb 16: Lec 5 [pdf] [Gene Expression studies]
• Feb 9: Lec 4 [pdf] [Patterns in DNA and Protein Sequences]
• Feb 2: Lec 3 [pdf] [Sequence Alignments]
• Jan 26: Lec 2 [pdf] [Mol Biol Preliminaries; Public Databases; Sequence Alignment]; [Lecture Slides by Pevsner pdf]
• Jan 12: Lec 1[pdf] [Introduction & Motivation]; Reading: [Chapters 1, 2 (from Pevsner); Also see section on "Additional Reading" below]; [ Statistical Preliminaries]; [ MIT Lectures on Computational Biology]
• Jan 19: MLK Holiday - No Class!

• HW 2 Due Apr 13, at the start of class.
• HW 1 Due Feb 16, at the start of class.

• Bioinformatics and Functional Genomics, by Jonathan Pevsner, Wiley-Blackwell Press, 2009, 2nd Edition, Paperback, ISBN: 978-0-470-08585-1

• Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.
• Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• Understanding Bioinformatics, by Zvelebil & Baum, ISBN: 0-815-34024-9.
• Introduction to Bioinformatics, by Arthur M. Lesk, 3rd Edition, Oxford University Press, 2008.

• News: Genome News Network. Online magazine covering important developments in genomics research.
• Popular: Virtual Cell Animation Collection. Find some great animations here, especially ones on Transcription and Regulated Transcription.
• Popular: Time, Love, Memory, by Jonathan Weiner, 1999.
• Useful Blurbs: What's a Genome (and also Chromosome, Gene, DNA, Sequencing, genome map, genome variations), by Sarah E. DeWeedt, 2003.
• Guide to Sequenced Genomes