..::Special Topics Course::..

Spring 2022

Algorithms for Computational Molecular Biology

CS499/599  BB499/599

Time: TR 2:00-3:20 pm                                    Professor: David Hendrix

Location: Covell Hall 221                                Office: ALS2077A, Phone: 737-6224

Email: david.hendrix@oregonstate.edu

Description: Algorithms for Computational Molecular Biology will provide an introduction to numerous algorithms for studying biological sequences.

Topics will include:

Dynamic Programming: Edit distance, longest common substring, Smith Waterman, Needleman Wunsch, Viterbi Algorithm, Motif Finding Algorithms: Expectation Maximization, Gibb’s Sampling, RNA Secondary Structure Prediction: Nussinov and Zucker Algorithm, Pattern Matching, Suffix Trees, Hidden Markov Models, K-means clustering, Phylogenetic Trees, Assembly problems

Prerequisite: Computational/Algorithmic experience, CS325 recommended

David Hendrix is an Assistant Professor in BB and EECS who has worked on analysis of RNA structure, genomics, DNA motif finding, microRNA discovery and long noncoding RNAs. Questions? Contact David Hendrix at david.hendrix@oregonstate.edu