Special Topics in Computer Science:

 

Bioinformatics

CIS 595 Spring 2005

 

syllabus

 

Week 1 (Jan 24, 2005):

Course Overview

Lecture 1: Inroduction to Molecular Biology

Reading assignment: Hunter, L., Molecular Biology for Computer Scientists. Artificial Intelligence for Molecular Biology, Ed. L. Hunter, pp. 1-46, AAAI Press, 1993. (download)

Homework 1 (due in class, Jan 31)

Week 2: (Jan 31, 2005):

Lecture 2: Inroduction to Molecular Biology (Part 2)

Reading assignment: Hunter, L., Molecular Biology for Computer Scientists. Artificial Intelligence for Molecular Biology, Ed. L. Hunter, pp. 1-46, AAAI Press, 1993. (download)

Lecture 2: Introduction to Bioinformatics

Reading assignment: NM Luscombe, D Greenbaum, M Gerstein, What is bioinformatics? A proposed definition and overview of the field, Methods Inf Med 40: 346-58. 2001 (download)

Week 3: (Feb 07, 2005):

Lecture 3: Basic algorithms for pairwise sequence alignment 

Course material: Lecture notes from Mark Craven's BMI/CS 576 Introduction to Bioinformatics course ("Pairwise Sequence Alignment", "Primer on Probability for Discrete Variables")

Reading assignment: Chapter 2 from Durbin textbook

Homework 2 (due Feb 14, in class; you can download the necessary files from here)

Week 4: (Feb 14, 2005):

Lecture 4: Alignment Statistics, Substitution Scores, Intro to Multiple Alignment

Course material: Lecture notes from Mark Craven's BMI/CS 576 Introduction to Bioinformatics course ("Alignment Statistics, Substitution Scores", "Multiple Alignments")

Reading assignment: Chapters 2, 6 from Durbin textbook

Week 5: (Feb 21, 2005):

Lecture 5: Multiple Sequence Alignment (ClustalW, Gibbs sampling)

Course material: Lecture notes from Mark Craven's BMI/CS 576 Introduction to Bioinformatics course ("Multiple Alignments", "Heuristic Algorithms for Sequence Database Searching")

Course material: Lecture notes from Russ Altman's Biomedical Informatics 214 Representations and Algorithms for Computational Molecular Biology course (Multiple Sequence Alignment lecture)

Homework 3 (due Feb 28, in class)

Week 6: (Feb 28, 2005):

Canceled due to snow storm

NOTE: HW3 is due in class on Mar 14.

Week 7: (Mar 14, 2005):

Lecture 7: Heuristic Algorithms for Sequence Database Searching (BLAST), 1D Motifs, Markov Chain Models

Course material: Lecture notes from Mark Craven's BMI/CS 576 Introduction to Bioinformatics course and Russ Altman's Biomedical Informatics 214 Representations and Algorithms for Computational Molecular Biology course

Week 8: (Mar 21, 2005):

Lecture 8: Markov Chain Models, Hidden Markov Models

Course material: Lecture notes from Mark Craven's BMI/CS 576 Introduction to Bioinformatics course ("Markov Chain Models", "Hidden Markov Models")

Homework 4 (due Mar 28, in class)

Week 9: (Mar 28, 2005):

Lecture 9: Hidden Markov Models Applications; Supervised and Unsupervised Learning for Bioinformatics

Course material: Lecture notes from Mark Craven's BMI/CS 576 Introduction to Bioinformatics course ("More on Hidden Markov Models")

Week 10: (Apr 04, 2005)

MIDTERM

Lecture 10: Supervised and Unsupervised Learning for Bioinformatics; Project Topics Discussion, Prediction of Protein Structure

Homework 5 (due Apr 11, in class)

Week 11: (Apr 11, 2005)

Lecture 11: Microarray Data Analysis

Week 12: (Apr 18, 2005)

Lecture 12: Interesting Topics: Structural Alignment, Genetic Networks, Comparative Genomics, Text Mining

Week 13: (Apr 25, 2005)

Presentations: 

Uros (Epitope Prediction) 

Prasanna (Human Genome Project) 

Benjamin (Quest algorithm for 2D Gels) 

Rajesh (CATH database) 

Week 14: (May 02, 2005)

Presentations:

Shamika (Prediction of Protein Contacts)

Weigen (Prediction of Protein Location)

Wei (Predicting Deleterious Amino Acid Substitutions)

Tek (Protein-Protein Interaction Prediction)