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, 27 August 2009||What is Bioinformatics? (1) |
Preliminary Survey. Discuss Wired article. Course Expectations. Using the MathLAN. Getting started with Python.
|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
|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.
|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|
|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
|19||Thursday, 5 November 2009||Structure Prediction (2) |
Project planning; Programming project
|20||Tuesday, 10 November 2009||Phylogenetics (1) |
|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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