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

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