Wisconsin Univ. Computer Sciences 838
Advanced Bioinformatics (Spring 2001)


 The biological sciences are undergoing a revolution in how they are practiced. In the last decade, a vast amount of data (DNA sequences, protein sequences, etc.) has become available, and computational methods are playing a fundamental role in transforming this data into scientific understanding.

Bioinformatics (computational molecular biology) is an exciting new area that involves developing computational methods for managing and analyzing information about the sequence, structure and function of biological molecules and systems.

The goals of this course are to provide an understanding of:

Introduction to Molecular Biology, Genomics and Bioinformatics

General Course Information

Introduction to Molecular Biology

Genomic Data and Bioinformatics

Pairwise Sequence Alignment

Pairwise Sequence Alignment, Part 1

Pairwise Sequence Alignment, Part 2

Heuristic Methods for Sequence Database Searching

Whole Genome Alignment

Sequence Assembly

C. Allex. Chapters 1 and 2: Computational Methods for Fast and Accurate DNA Fragment Assembly. Ph.D. thesis, University of Wisconsin

E. Myers et al. A Whole-Genome Assembly of Drosophila. Science 287:2196-2204, 2000

Dr. Carolyn Cassel (Allex). Methods for Fast and Accurate DNA Fragment Assembly

Probabilistic Sequence Models

Markov Chain Models

Finding Genes in Genomic DNA

Interpolated Markov Models

Learning Sequence Motifs Using Expectation Maximization

Hidden Markov Models

More on HMMs and Multiple Sequence Alignment

Gene Expression Analysis

Introduction to Microarrays

Classification of Gene Expression Profiles

Clustering Gene Expression Data, Part 1

Clustering Gene Expression Data, Part 2

Inferring Regulatory Networks from Gene Expression Data

Whole-Genome Operon Prediction

Modeling Cellular Systems

L. You and J. Yin, Simulating the Growth of Viruses. Pacific Symposium on Biocomputing, World Scientific Publishing, 532-543, 2000

Prof. John Yin

Protein Structure Prediction

B. Rost. Protein Structure Prediction in 1D, 2D and 3D. In P. von Rague-Schleyer et al., eds., The Encyclopedia of Computational Chemistry, 1998. John Wiley

R. Lathrop et al. Analysis and Algorithms for Protein Sequence-Structure Alignment. In S. Salzberg et al., eds., Computational Methods in Molecular Biology, 1998. Elsevier

Introduction to Protein Structure

Protein Structure Prediction

RNA Structure Modeling

Stochastic Context Free Grammars for RNA Modeling

Biomedical Text Analysis

S. Ray and M. Craven. Representing Sentence Structure in Hidden Markov Models for Information Extraction. Proceedings of the 17th International Joint Conference on Artificial Intelligence, 2001

H. Shatkay, S. Edwards, J. Wilbur and M. Boguski. Genes, Themes and Microarrays Using Information Retrieval for Large-Scale Gene Analysis. Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, 2000

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