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)|
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 Tue Nov 29 12:46:30 2011.
The source to the document was last modified on Wed Aug 24 09:18:26 2011.
This document may be found at
You may wish to validate this document's HTML ; ;Samuel A. Rebelsky, email@example.com
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.