BIO/CSC 295 2009F Bioinformatics : Handouts

Course Schedule

This handout is also available in PDF.

Unless otherwise specified, readings are taken from,

St. Clair, Caroline & Visick, Jonathan (2010). Exploring Bioinformatics: A Project-Based Approach. Sudbury, MA: Jones and Bartlett.

  Date Topic Reading Work Due
01 Thursday, 27 August 2009 What is Bioinformatics? (1)
Preliminary Survey. Discuss Wired article. Course Expectations. Using the MathLAN. Getting started with Python.
Ratliff 2009  
02 Tuesday, 1 September 2009 What is Bioinformatics? (2)
Discuss Science articles on dinosaur DNA. What is bioinformatics?, revisited. Studying interdisciplinary fields. Web exploration.
Chapter 1. Asara et al. 2007. Pevzner et al. 2008. Schweitzer et al. 2009. Reading response to Science articles
03 Thursday, 3 September 2009 What is Bioinformatics? (3)
Web exploration, continued. Programming exercises.
   
04 Tuesday, 8 September 2009 The Central Dogma (1)
Introduction to the Central Dogma. Related computational problems. Web exploration.
Chapter 2 Writeup of Web exploration
05 Thursday, 10 September 2009 The Central Dogma (2)
Begin guided project.
   
06 Tuesday, 15 September 2009 Gene Alignments (1)
Continue guided project 2.5; Aligning Genes, A Biological Perspective
Chapter 3  
07 Thursday, 17 September 2009 Gene Alignments (2)
Discussion: BLAST Paper. Web exploration and other fun with BLAST.
Altschul et al. 1990: Basic local alignment search tool. Response to Altschul et al.
08 Tuesday, 22 September 2009 Gene Alignments (3)
Approximate pattern matching and the Needleman-Wunsch algorithm.
  On your own project (2.6)
09 Thursday, 24 September 2009 Gene Alignments (4)
Continue guided project; Start HIV analysis project
  On your own project (2.6) [extended deadline]
10 Tuesday, 29 September 2009 Protein Alignments (1)
What's the difference? Why protein alignment is not gene alignment. Constructing similarity matrices.
Chapter 4  
11 Thursday, 1 October 2009 Protein Alignments (2)
Discussion of HIV data and paper. Chapter 4 programming project.
  Exploration of HIV Data
12 Tuesday, 6 October 2009 Sequence Assembly (1)
Sanger-style sequencing, Basics of sequence assembly.
Chapter 5; Markham et al. al. 1998. Reading Response: Markham et al.
13 Thursday, 8 October 2009 Sequence Assembly (2)
   
14 Tuesday, 13 October 2009 Gene Prediction (1)
Chapter 6  
15 Thursday, 15 October 2009 Gene Prediction (2)
Kellis et al. 2003 Reflection on Kelis et al. 2003
Fall Break!
16 Tuesday, 27 October 2009 Pause for Breath
Review for mid-semester examination
   
17 Thursday, 29 October 2009 Mid-Semester Examination
   
18 Tuesday, 3 November 2009 Structure Prediction (1)
About protein folding; Web exploration
Chapter 7  
19 Thursday, 5 November 2009 Structure Prediction (2)
Project planning; Programming project
   
20 Tuesday, 10 November 2009 Phylogenetics (1)
Exams returned
Chapter 8 Response to Neanderthal and Mitochondrial DNA paper
21 Thursday, 12 November 2009 Phylogenetics (2)
Paper on Neanderthals and Mitochondrial DNA Project proposals; Chou-Fasman Programming Project
22 Tuesday, 17 November 2009 Microarrays (1)
Chapter 9 Peer reviews of project proposals
23 Thursday, 19 November 2009 Project Kickoff
Short presentations of project proposals; Discussion of Tuggle article
Tuggle article Response to Tuggle article
24 Tuesday, 24 November 2009 Time for work on projects
   
25 Tuesday, 1 December 2009 Time for work on projects
   
26 Thursday, 3 December 2009 Time for work on projects
   
27 Tuesday, 8 December 2009 Project Presentations (1)
   
28 Thursday, 10 December 2009 Wrapup
Project postmortem; What is bioinformatics?, revisited. Course evaluation. Review for final. Final comments.
  Project Writeups; Portfolios

Disclaimer: I usually create these pages on the fly, which means that I rarely proofread them and they may contain bad grammar and incorrect details. It also means that I tend to update them regularly (see the history for more details). Feel free to contact me with any suggestions for changes.

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