BIO/CSC 295 2011F Bioinformatics : Handouts

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)

Disclaimer: 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.

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