Bioinformatics & Computational Biology
This course will provide an overview of bioinformatics, covering a broad selection of the most important techniques used to analyze biological sequence and expression data. Students will acquire a working knowledge of bioinformatics applications through hands-on use of software to ask and answer biological questions. In addition, the course will provide students with an introduction to the theory behind some of the most important algorithms used to analyze sequence data (for example, alignment algorithms and the use of hidden Markov models). Topics covered will include protein and DNA sequence alignments, evolutionary analysis and phylogenetic trees, obtaining protein secondary structure from sequence, and analysis of gene expression including clustering methods. Students may not receive credit for both BCB 4001 and BCB 501. (Prerequisite: knowledge of genetics, molecular biology, and statistics at the undergraduate level.)
This course will use interactive visualization to model and analyze biological information, structures, and processes. Topics will include the fundamental principles, concepts, and techniques of visualization (both scientific and information visualization) and how visualization can be used to study bioinformatics data at the genomic, cellular, molecular, organism, and population levels. Students will be expected to write small to moderate programs to experiment with different visual mappings and data types. (Prerequisite: strong programming skills, an undergraduate or graduate course in algorithms, and one or more undergraduate biology courses.) Students may not receive credit for both CS 582 and CS 4802.
This course will investigate computational techniques for discovering patterns in and across complex biological and biomedical sources including genomic and proteomic databases, clinical databases, digital libraries of scientific articles, and ontologies. Techniques covered will be drawn from several areas including sequence mining, statistical natural language processing and text mining, and data mining. (Prerequisite: strong programming skills, an undergraduate or graduate course in algorithms, an undergraduate course in statistics, and one or more undergraduate biology courses.) Students may not receive credit for both CS 583 and CS 4803.
This course provides students with knowledge and understanding of the applications of statistics in modern genetics and bioinformatics. The course generally covers population genetics, genetic epidemiology, and statistical models in bioinformatics. Specific topics include meiosis modeling, stochastic models for recombination, linkage and association studies (parametric vs. nonparametric models, family-based vs. population-based models) for mapping genes of qualitative and quantitative traits, gene expression data analysis, DNA and protein sequence analysis, and molecular evolution. Statistical approaches include log-likelihood ratio tests, score tests, generalized linear models, EM algorithm, Markov chain Monte Carlo, hidden Markov model, and classification and regression trees. Students may not receive credit for both MA 584 and MA 4603. (Prerequisite: knowledge of probability and statistics at the undergraduate level.)