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|
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.
This document was generated by
Siteweaver on Thu Feb 17 12:32:46 2011.
The source to the document was last modified on Thu Feb 17 12:32:42 2011.
This document may be found at
You may wish to validate this document's HTML ; ;Samuel A. Rebelsky, firstname.lastname@example.org
http://creativecommons.org/licenses/by-nc/2.5/or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.