CAP 5510 & CGS 5166: Spring 2011
Bioinformatics Course Homepage
Tue & Thu 9:30 - 10:45, ECS 134

• Mar 29: Homework #3 is now ready. See below. It is due on Apr 14 in class.
• Jan 27: Homework #2 is now ready. See below. It is due on Feb 15 in class. I have tried my best to guide you clearly. However, situations may change with browser and your personal settings. It is up to you explore and navigate and try to answer the questions therein.
• Jan 27: We will have a short quiz in class today.
• Jan 20: Take a look at the animation links provided below under "Additional Reading". Also make sure you look at specific extra "Reading" specified for each lecture below under "Lecture Transparencies".
• Jan 16: There is no need to submit the informal homework from Lecture 1 on finding the shortest and longest genomes known to mankind.
• Jan 16: I like the book by Pevsner. You can buy it from a variety of sources through Amazon.com for about $40.
• Jan 16: Homework 1 on writing Challenge Summaries is now ready. See below. It is due any time before Apr 1, 2011.
• Jan 16: If you are interested in research in this area, please visit the website for the Bioinformatics Research Group @ FIU.

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

• 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.

• Homework 3: Homework #3 (Due Apr 14, 2011);
• Homework 2: Homework #2 (Due Feb 15, 2011);
• Homework 1: Challenge Summaries (Due Apr 1, 2011);

• Needleman-Wunsch Method: click here
• Smith-Waterman Method: click here

• Mar 24: Lec 18[pdf] [GO Annotations, KEGG Pathways];
• Mar 22: Lec 17[pdf] [Microarray Analysis; Multiple Hypothesis Testing];
• Mar 10: Student presentations: 5-minute presentations introducing semester project
• Mar 8 & 10:< /b> Lec 15 & 16[pdf] [pdf] [Protein Structure];
• Mar 3: Lec 14[pdf] [Microarray Analysis];
• Mar 1: Lec 13[pdf] [Next Generation Sequencing and Assembly];
• Feb 24: Lec 12[pdf] [Sequencing];
• Feb 22: Lec 11[pdf] [Clustering; PCR];
• Feb 17: Lec 10[pdf] [Gene Expression; Microarray Technology];
• Feb 15: Lec 9[pdf] [Perl and BioPerl]
• Feb 10: Lec 8[pdf] [Applications of HMMs]
• Feb 8: Lec 7[pdf] [HMMs];
• Feb 1: Lec 6[pdf] [MSA, Patterns and Profiles];
• Jan 27: Lec 5[pdf] [BLAST];
• Jan 25: Lec 4[pdf] [Sequence Alignment];
• Jan 20: Lec 3[pdf] [Local and Global Sequence Alignment]; Reading: [Chapters 3, 4 (from Pevsner); Also see lecture slides by Pevsner: pdf and pdf ]
• Jan 18: Lec 2[pdf] [Molecular Biology Prelminaries]; Reading: [Lecture slides by Pevsner: pdf]
• Jan 13: Lec 1[pdf] [Introduction & Motivation]; Reading: [Chapters 1, 2 (from Pevsner); Additional Reading]
• Jan 11: No class