BCB 410 Applied Bioinformatics
Fall 2009 - Course Webpage

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** NOTE: Readings are only available from on campus. **

Lecture 1: Course Intro, Biology Review, Problems in Computational Biology

Readings Assigned:

• "Molecular Biology for Computer Scientists", Hunter (pdf)  <-- long, don't wait to start reading
• "A Field Guide To Computational Biology", Haslinger (pdf)
• "Can a Biologist Fix a Radio?", Lazebnik (pdf)
  

Lecture Notes:

• Notes for Lecture 1 (here)

Readings Assigned:

• Eidhammer Text Chapters 1 and 2
• Optional Historic: Original BLAST paper (pdf)
• Optional Historic: Original Smith-Waterman paper (pdf)
  

Lecture Notes:

• Notes for Lecture 2 (here)

Readings Assigned:

• Eidhammer Text Chapter 3
• "Genome Sequence Assembly: Algorithms and Issues", Pop, Salzberg, Shumway (pdf)
• Optional: Eidhammer Text Chapter 5
• Optional Historic: Human Genome Paper (pdf)
  

Lecture Notes:

• Notes for Lecture 3 (here)

Lecture 4: Multiple Sequence Alignment / Phylogenetic Trees / Profiles

Readings Assigned:

• Eidhammer Text Chapters 4 and 6

Lecture Notes:

• Notes for Lecture 4 (here)

Lecture 5: Structure Intro, Secondary Structure Prediction

• Eidhammer Text Chapter 8
• "Predicting Protein Secondary and Supersecondary Structure" [pages 29-1 to 29-14] (pdf)

Lecture Notes:

• Notes for Lecture 5 (here)

Lecture 6: Structure Representation, Structure Alignment

• Eidhammer Text Chapter 9

Lecture Notes:

• Notes for Lecture 6 (Part1: here and Part2: here)

Lecture 7: Structure Alignment, Structure Databases

• (no new readings)

Lecture Notes:

• Notes for Lecture 7 (here)

• Eidhammer Text Chapter 14 and 15

Lecture Notes:

• Notes for Lecture 8 (here)

• "Protein-Ligand Docking: Current Status and Future Challenges" Sousa, Fernandes, Ramos (pdf)
• "Microarray Analysis", Gibson (pdf)
• "Cluster Analysis and Display of Genome-Wide Expression Patterns", Eisen, Spellman, Brown, Botstein (pdf)
• (Optional) "Genomics, Gene Expression, and DNA Arrays", Lockhart, Winzeler (pdf)

Lecture Notes:

• Notes for Lecture 9 (here)

• "Systematic Interpretation of Genetic Interactions Using Protein Networks", Kelley, Ideker (pdf)
• "Network-Based Prediction of Protein Function", Sharan, Ulitsky, Shamir (pdf)

Lecture Notes:

• Notes for Lecture 10 (here)