Q'BIC Capstone Workshop 2010
Bioinformatics Component

• Jul 20: Homework #2 is ready. See below.
• Jul 16: The list of semester projects is ready. See below. You need to pick one that interests you and email me your choice. You can form groups of one or two. The choices are on a first-come-first-served basis. I need your choices by Monday or Tuesday. Also note that the earlier you work on your homework and your project, the better it is. The homework needs a lot of time and ifyou start on Monday, you may not finish on time.
• Jul 15: Homework #1 is ready. See below.

• Summer Workshop

• Bioinformatics and Functional Genomics, by Jonathan Pevsner, Wiley-Blackwell, Paperback, 2nd Edition, ISBN 978-0-470-08585-1
• [REFERENCE] Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• [REFERENCE] Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.
• [REFERENCE] Understanding Bioinformatics, by Zvelebil & Baum, ISBN: 0-815-34024-9.

• Homework 1: Click here: Due Jul 20, 2010.
• Projects List: Click here: Choices due Jul 20, 2010
• Homework 2: Click here: Due Jul 26, 2010.

• Jul 12: Lec 1[pdf] [Introduction & Biological preliminaries]; Reading: [Chapters 1, 2 (from JP); Extra]
• Jul 13: Lec 2[pdf] [BLAST, Global Sequence Alignment]; Reading: [Chapters 2, 3, 4 (from JP); Extra]
• Jul 14: Lec 3[pdf] [Sequence Alignment, Multiple Sequence Alignment, Hidden Markov Models];
• Jul 15: Lec 4[pdf] [Applications of HMMs, Patterns and Pattern Discovery, Motif Detection, Gene Expression and Microarrays];
• Jul 19: Lec 5[pdf] [Microarray Analysis and normalization, Clustering, Classification, PCR];
• Jul 20: Lec 6[pdf] [Sanger Sequencing, Shotgun Sequencing, Next Generation Sequencing];
• Jul 21: Lec 7[pdf] [Protein Structure, Proteomics];
• Jul 22: Lec 8[pdf] [Phylogenetics];

• Popular California Sea urchin genome sequenced, Nov 2006.
• Popular Time, Love, Memory, by Jonathan Weiner, 1999.