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.
|01||Thursday, 25 August 2011||Getting Started |
Preliminary surveys. Discuss Wired article. Course expectations. Using the MathLAN. Getting started with Python.
|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 |
|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.
|05||Thursday, 8 September 2011||Gene Alignments (1) |
Aligning Genes, A Biological Perspective. Guided project 2.5 - Programming Project.
|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.
|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.
|11||Thursday, 29 September 2011||Lab Day! |
Lab stuff (safety, using the tools, DNA digestion)
|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 |
|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
|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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