Optimization Models in Computational Biology

http://www.math.wsu.edu/math/faculty/bkrishna/Math574_S08.html

First submitted by Classroom Resources Team on 30 Jul 2008

Updated by Classroom Resources Team on 19 Jun 2009

Graduate course on computational problems in bioinformatics and their applications

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Date	Contributor	Description	Rating
19 Jun 2009	Classroom Resources Team	This course will introduce a series of optimization models that find applications to various problems in bioinformatics and computational biology. The basics of the following topics will be covered: dynamic programming; graph algorithms (paths and flows); clustering and trees; linear, non-linear, and integer programming (including convex polytopes); certain probabilistic models; and very limited algebraic statistics. The applications of these optimization models to bioinformatics and computational biology will be illustrated by studying problems such as sequence motif search, DNA sequence alignment (including parametric sequence alignment), recombinations and other related phylogenetic problems, protein sequencing, and protein structure prediction (including side-chain positioning, scoring functions for threading, molecular dynamics etc.). Course material created by Professor Bala Krishnamoorthy. Target audience: Graduate Institution: Washington State University Materials available: Problem sets or projects, Course outline or syllabus, Textbook recommendations Products: MATLAB

19 Jun 2009

Classroom Resources Team

This course will introduce a series of optimization models that find applications to various problems in bioinformatics and computational biology. The basics of the following topics will be covered: dynamic programming; graph algorithms (paths and flows); clustering and trees; linear, non-linear, and integer programming (including convex polytopes); certain probabilistic models; and very limited algebraic statistics. The applications of these optimization models to bioinformatics and computational biology will be illustrated by studying problems such as sequence motif search, DNA sequence alignment (including parametric sequence alignment), recombinations and other related phylogenetic problems, protein sequencing, and protein structure prediction (including side-chain positioning, scoring functions for threading, molecular dynamics etc.).
Course material created by Professor Bala Krishnamoorthy.

Target audience: Graduate

Institution: Washington State University

Materials available: Problem sets or projects, Course outline or syllabus, Textbook recommendations

Products: MATLAB

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Tag Activity

Tag	Applied By	Date/Time
resource	Classroom Resources Team	24 Nov 2009 at 11:11am
academic	Classroom Resources Team	24 Nov 2009 at 11:11am
course materials	Classroom Resources Team	24 Nov 2009 at 11:11am
downloadable code	Classroom Resources Team	24 Nov 2009 at 11:11am
computer science	Classroom Resources Team	24 Nov 2009 at 11:11am
biological and health sciences	Classroom Resources Team	24 Nov 2009 at 11:11am
programming and computer science	Classroom Resources Team	24 Nov 2009 at 11:11am
computational biology	Classroom Resources Team	24 Nov 2009 at 11:11am

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