Time & Place:
TBD
Instructor:
Jun Ni, Ph.D., Associate Professor
Department of Radiology, Carver College of Medicine,
Biomedical Engineering
Mechanical Engineering
University of Iowa, Iowa City, IA, USA
Tel: (319) 335-9490
E-mail: jun-ni@uiowa.edu
Office Hours and Place:
TBD
Textbook:
 Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition
Edited by Andreas D. Baxevanis, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
Edited by B. F. Francis Ouellette, Bioinformatics Core Facility at the Centre for Molecular Medicine and Therapeutics, University of British Columbia
ISBN: 0-471-47878-4
©2005
Class Lecture Notes:
Additional notes or handouts may be available in classroom.
Course Description: this course is designed for students who wish to develop
considerable competence in bioinformatics. It emphasizes basis and methodology
of bioinformatics, among details of computational approaches to biological
science. It addresses basic concepts of bioinformatics. It reviews and summarizes
the computational skills needed to solve problems in biology. It discusses
how to obtain, establish, and maintain research information in biology. It
presents many solutions to bioinformatics, including software packages available,
usages, and development. It provides great learning opportunity for students
who are computer/computational science or engineering major to understand
the needs in computational biology. It also provides potentials for students
who are majors of biological science to learn knowledge of computer science
and technology and computational skills, which can be used to their research.
Pre-requisites:
TBD
Course Contents:
PART ONE: BIOLOGICAL DATABASES.
1. Sequence Databases (Rolf Apweiler).
2. Mapping Databases (Peter S. White and Tara C. Matise).
3. Information Retrieval from Biological Databases (Andreas D. Baxevanis).
4. Genomic Databases (Tyra G. Wolfsberg).
PART TWO: ANALYSIS AT THE NUCLEOTIDE LEVEL.
5. Predictive Methods Using DNA Sequences (Enrique Blanco and Roderic Guigó).
6. Predictive Methods Using RNA Sequences (David Mathews and Michael Zuker).
7. Sequence Polymorphisms (James C. Mullikin and Stephen T. Sherry).
PART THREE: ANALYSIS AT THE PROTEIN LEVEL.
8. Predictive Methods Using Protein Sequences (Yanay Ofran and Burkhard Rost).
9. Protein Structure Prediction and Analysis (David Wishart).
10. Intermolecular Interactions and Biological Pathways (Gary D. Bader and Anton J. Enright).
PART FOUR: INFERRING RELATIONSHIPS.
11. Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis).
12. Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton).
13. Sequence Assembly and Finishing Methods (Nancy F. Hansen, Pamela Jacques Thomas and Gerard G. Bouffard).
14. Phylogenetic Analysis (Fiona S. L. Brinkman).
15. Computational Approaches in Comparative Genomics (Andreas D. Baxevanis).
16. Using DNA Microarrays to Assay Gene Expression (John Quackenbush).
17. Proteomics and Protein Identification (Mark R. Holmes, Kevin R. Ramkissoon and Morgan C. Giddings).
PART FIVE: DEVELOPING TOOLS.
18. Using Perl to Facilitate Biological Analysis (Lincoln D. Stein).
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