Fall06: CSE/BIMM/BENG 182: Biological Data Analysis

Instructor: Vineet Bafna

TA: Julio Ng

TR 2:00-3:20pm. SOLIS 111
Discussion:M3:00-3:50pm. CENTR201

Office hours:
Vineet Bafna: TR 3:30-4:30pm EBU3b(CSE building) 4218

TA Office hours: By appointment.

Course Information:

A class mailing list exists at cse182@cse.ucsd.edu .
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Final Exam Please find it here . I did send it out by email but have been told that not everyone had it.

Midterm 1 will be held in class October 26.

Assignment Due date Data
A1 (10pt) Thurs.,9/28 db
A2 (10pt) Tues. 10/10 Note: For problem 1, run with the following parameters: match:1, mismatch:-3, indel: -2
for Problem 1: human.seq and mouse.seq
for Problem 5: two sequences
A3 (10pt) Thurs. 10/19 F1 , F2 , Db , Matrix
A4 (10 pt) 12/7/06 S1.dta
Problem 3:data1
Problem 3:data2
Midterm 1 (15pt) Thurs. 10/26
project (updated 10/14)
Checkpoint I (3pt) Tues., 10/31
Project Checkpoint II (10pt) Tues. 11/14
Final project (17pt) Thurs. 11/30

There is no required text for the course. We will use Jones and Pevzner, "An Introduction To Bioinformatics Algorithms", MIT Press, as an optional book.
Future recommended reading is subject to change with little notice. Please note that the available manuscripts are copyright protected, and may be used only for educational purposes. The notes presented here are unedited, and may contain errors. Powerpoint slides are used only to illustrate examples in class, and are not intended to substitute lecture notes.

For Biology, the classic reference Molecular Biology of the Cell is now online, although a bit cumbersome to search. We will link to some of the chapters.

Lecture Topic Slides Suggested Reading
9/21 Course outline L1 Perl 5 guide
Bioinformatics Algorithms web-site
Chap 3 has a brief introduction to Molecular Biology
9/26 Overview of Hirudo (Prof. Macagno)
Sequence Alignment
L2 questions
Notes on DP
9/28 Dynamic programming variants
Local alignment
Affine gap costs
Linear Space
10/3 The Piegeonhole principle
Blast Statistics
Scoring Matrices
L4 Notes and questions on L4
Notes on Blast Statistics
10/5 Dictionary Matching
Regular expression matching
L5 Scoring matrices
Dictionary Matching Notes
ExPASy tools
10/10 Protein Sequence Analysis
Pattern matching (Regular expressions)
psi-blast (optional reading)
10/12 Protein Sequence Analysis (HMMs)
Transcription and Translation
EST sequencing, EST assembly
L7 questions
HMM notes (Only Baum-Welch/Viterbi algorithms were covered)
An EST primer
10/17 Project Outline
Ab initio Gene Finding
L8,9 questions
10/19 DNA signals
DNA sequencing
DNA sequencing
Lander Waterman Stats
10/24 No class
10/26 Midterm 1
10/31 Lander Waterman statistics
Shotgun genome assembly
L10 Questions
DNA sequencing
Lander Waterman Stats
Arachne (A WGS assembler)
11/2 Basics of Mass Spectrometry
Isotope Distribution
L11 Aebersold-Mann Overview
11/7 Mass Spectrometry
de novo sequencing
L12 de novo sequencing algorithm
11/9 Mass Spectrometry
11/14 MS quantitation
MS applications
Microarray data analysis
L14 Map comparison
11/16 Microarray data analysis (classification) L15
11/17 Microarray data analysis
(dimensionality reduction
L16 preview
11/21 Population Genetics Basics L17 preview
11/23 Thanksgiving Holiday
11/28 Population Genetics Basics (possible) L18 preview
11/30 Final Project Presentation

We are always looking for motivated students. If you are interested in exploring undergraduate research opportunities in Computational Biology, please email me.