Special Topics in Computer Science:

 

Bioinformatics

CIS 595 – Spring 2003

 

syllabus

 

links

 

Course material:

 

Week 1:

Intro to Molecular Biology

Week 2:

Pairwise Sequence Alignment  

Week 3:

Substitution Matrices and Alignment Statistics

Week 4:

Heuristic Methods for Sequence Database Searching

Week 5:

Multiple Sequence Alignment

Week 6:

Markov Models and Hidden Markov Models

Week 7:

Introduction to Machine Learning in Bioinformatics (no slides available)

Week 8:

Matlab Tutorial

Protein Structure Prediction

Clustering of Gene Expression Data

Week 9:

MIDTERM (check for pages to read)

Topics for Class Projects

Week 10:

Class Presentations:

Despina Kontos: Classification of Microarray Gene Expression Data Using Support Vector Machines

Kang Peng: Automatic Information Retrieval from Bioinformatics Website (Visual Basic examples)

Hongbo Xie - Mike: Building a Local SwissProt Database and its Interface with Matlab

Biomedical Text Analysis

Week 11:

Class Presentations:

Roland Miezianko: Transformational Grammars and PROSITE Patterns

Bo Han: Seeking Abbreviations From MEDLINE

Tim O'Connor: Evolution of Amino Acid Frequencies in Proteins

Genetic Networks

Week 12:

Class Presentations:

Yijian Yang: Distributed Computing in Life Science Research

Qifang Xu: Gene Expression Data

Hao Sun: Proteomics and Functional Genomics

Xiaoyong Wu: Including Biological Literature Improves Homology Search

Week 13:

Class Presentations:

Swetha Nandyala: Prediction of Secondary Structure of RNA

Pallavi Vedam: Genome Sequencing and Objectives

Rajvi Shah: XML and Bioinformatics

Kanishka Pathak: Lemur Application toolkit

Sudeshna Banerji: DB2 Net Search Extender

 

 

class presentation instructions

 

class project information

 

 

homework:

Homework 1

 

Homework 2

 

Homework 3

S.F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, "Basic local alignment search tool," Journal of Molecular Biology, vol. 215, pp. 403-410, 1990.

 

Homework 4

Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-80.

Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.

 

Homework 5

 

Homework 6

Jones DT., (1999) Protein secondary structure prediction based on position-specific scoring matrices, J Mol Biol., 17;292(2):195-202.

Rost B., (2001) Review: protein secondary structure prediction continues to rise, J Struct Biol., 134(2-3):204-18.