CS 91.350.204/580.204 Topics in Computer Science: Bioinformatics

Instructor: Office: 229 OS
Office Hours: M 3-5 pm; W 9-11 am;
978-934-3617
kim@cs.uml.edu CLICK HERE TO EMAIL

TA: Baochen Sun
bsun@cs.uml.edu

Textbook:

Jonathan Pevsner, Bioinformatics and Functional Genomics, 2nd ed., Wiley-Blackwell, 2009

Objectives:

Designed for both Computer Science and Biology students, this course strives to cover the following topics:

Sequence Alignment: Given a DNA sequence, search public databases for similar sequences
Clustering: Data points from multiple attributes need to be grouped in terms of their similarities.
Sequencing Algorithms: From short fragments of DNA sequences, assemble them into a genomic sequence.
Phylogeny: Modeling of gene evolutions can lead to phylogenetic trees.
Protein Structures: 3-D protein structures determine their interactions.
Inference and prediction models: Hidden Markov Model (HMM) and Data Mining models.

Schedule
Class Date	Contents	Note
02/27	Alternative Splicing	Lab Lab Sheet
03/05	Sequence Assembly
03/12	Spring Break
03/19	Phylogeny
03/26	Data Analysis
04/02	OLC sequencing Gene to Protein	Prog. 3 (Due 4/18)
04/09	Replication Protein Structure
04/16	Holiday
04/23	Machine Learning
04/30	Genomes	Final (Due 5/9)
05/07	No class