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, 25 August 2011	Getting Started Preliminary surveys. Discuss Wired article. Course expectations. Using the MathLAN. Getting started with Python.	Ratliff 2009
02	Tuesday, 30 August 2011	What is Bioinformatics? Discuss Science articles on dinosaur DNA. Studying interdisciplinary fields. Web exploration: Favism.	Chapter 1. Asara et al. 2007. Pevzner et al. 2008. Schweitzer et al. 2009.	Reading response to Science articles. RISC survey. Introductory survey.
03	Thursday, 1 September 2011	Programming Bioinformatics Programming exercises.		Write up of Web exploration 1
04	Tuesday, 6 September 2011	The Central Dogma (1) Introduction to the Central Dogma. Related computational problems. Guided project 2.5 - Web Exploration.	Chapter 2
05	Thursday, 8 September 2011	Gene Alignments (1) Aligning Genes, A Biological Perspective. Guided project 2.5 - Programming Project.	Chapter 3
06	Tuesday, 13 September 2011	Gene Alignments (2) Discussion: Altschul et al. (BLAST). The Needleman-Wunsch algorithm. Web exploration and other fun with BLAST.	Altschul et al. 1990	Response to Altschul et al.
07	Thursday, 15 September 2011	Gene Alignments (3) Experiments with Needleman-Wunsch. Start HIV analysis.		On your own project (2.6)
08	Tuesday, 20 September 2011	Protein Alignments (1) What's the difference? Why protein alignment is not gene alignment. Constructing similarity matrices.	Chapter 4
09	Thursday, 22 September 2011	Protein Alignments (2) Discussion of HIV data and paper. Introduce Biology Lab.	Markham et al. al. 1998.	Reading Response: Markham et al.; Exploration of HIV Data
10	Tuesday, 27 September 2011	Sequence Assembly (1) Constructing Similarity Matricies. Chapter 4 programming project.	Chapter 5
11	Thursday, 29 September 2011	Lab Day! Lab stuff (safety, using the tools, DNA digestion)	Lab instructions
12	Tuesday, 4 October 2011	Sequence Assembly (2) Biology lab: DNA ligation; The Biology of Sequence Assembly		Shotgun Fragmentation (Optional)
13	Thursday, 6 October 2011	Gene Prediction (1) Computational Issues in Sequence Assembly ;	Chapter 6 ; Kellis et al. 2003
14	Tuesday, 11 October 2011	Gene Prediction (2) Remaining topics from Chapter 6; Discussion of Kellis et al. ; Review for Midsem	Chapter 6	Reading response: Kellis et al. 2003
15	Thursday, 13 October 2011	Mid-Semester Examination
Fall Break!
16	Tuesday, 25 October 2011	Structure Prediction (1) About protein folding. PCR Reactions I & II	Chapter 7	Set up second PCR on Wednesday!
17	Thursday, 27 October 2011	Structure Prediction (2) Run gels; TA Clone (warning! may go late)
18	Tuesday, 1 November 2011	Microarrays (1) Dealing with quantitative data. Intro to microarrays	Chapter 9; Baggerly 2010	Web Exploration 7.5
19	Thursday, 3 November 2011	Microarrays (2) Exams returned. Project planning. Programming Lab.		Chou-Fasman Programming Project
20	Tuesday, 8 November 2011	Phylogenetics (1) Intro to Phylogenetics	Chapter 8;
21	Thursday, 10 November 2011	Phylogenetics (2) More project planning	Krings et al. 1997.	Reading response: Krings et al. 1997; Project proposals
22	Tuesday, 15 November 2011	Project Kickoff		Peer reviews of project proposals
23	Thursday, 17 November 2011	Guest Lecture Guest lecture (Jillian Goetz); Short presentations of project proposals
24	Tuesday, 22 November 2011	Time for work on projects		Revised project proposals; Lab data analysis results section
25	Tuesday, 29 November 2011	Time for work on projects
26	Thursday, 1 December 2011	Time for work on projects Status Reports; Guest Lecture by Paul Tymann
27	Tuesday, 6 December 2011	Project Presentations (1)
28	Thursday, 8 December 2011	Wrapup Project postmortem; What is bioinformatics?, revisited. Course evaluation. Review for final. Final comments.		Project Writeups; (Portfolios due at final)

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