CAP 6938: Data Mining in Bioinformatics (Fall 2010)


Lecture: MW 4:30PM - 5:45PM

Location: ENGR 0224

Instructor: Dr. Haiyan Nancy Hu


Office: HEC- 233

Phone Number: 407-882-0134

Office Hours: MW3:00PM - 4:30PM




This course will summarize computational techniques for bridging two fields: data mining and bioinformatics, for successful mining of biological data. Recent progress in biology, medical science, bioinformatics, and biotechnology has led to the accumulation of tremendous amounts of biodata that demands in-depth analysis. On the other hand, recent progress in data mining research has led to the development of numerous efficient and scalable methods for mining interesting patterns in large databases. In this class, we will provide an overview of the data mining methods that help biodata analysis. Also, we will outline some research problems that may motivate the further development of data mining tools for the analysis of various kinds of biological data.

Bioinformatics is an active and interdisciplinary research area. This course is open to all students with background such as computer science, biology, mathematics or statistics who are interested in bioinformatics research.




No formal prerequisite and open to all graduate students.



Book References:

Data Mining : Concepts and Techniques, by Jiawei Han and Micheline Kamber, Elsevier, 2000.ISBN 1558604898.550 pages.

Molecular Biology of the Cell, by Bruce Alberts et al., 4th edition, 2002.



Assignments (20%).

Paper presentation (20%). Each student will give a presentation of a course-related paper. Students are encouraged to discuss with the instructor to decide the topic he/she would like to present.

Final project (60%). We may have students from very diverse background such as biology and computer science. Final problem-solving projects can be either biology-oriented or programming-oriented depending on a student's own background. Students are required to discuss with the instructor to design the final projects during the early weeks of the class. A student is encouraged to discuss with the instructor on collaborating with another student with different background on the final project.


Preliminary Schedule:

Date Topic Notes and References*
W1: 08/23 Introduction/Administrivia Notes, Reference
08/25 Part I: Gene expression Notes
W2: 08/30 Identification of differential expressed genes Notes
09/01 Clustering of gene expression data Notes, Reference ; Reference
W3: 09/06 Labor day, no class  
09/08 Gene ontology and function annotation Notes
W4: 09/13 Gene expression pattern using PCA Notes, Reference;
09/15 Biclustering of gene expression data Notes, Reference;
W5: 09/20 Cancer classification using gene expression data Notes, Reference; Reference;(Final Project Proposal Due and HW1 assigned)
09/22 Part II: Biological network and pathway Notes
W6: 09/27 Protein and protein interaction network Notes, Reference
09/29 Pathway databases Notes;
W7: 10/04 Reconstruct biological pathway Notes, Reference; Reference
10/06 Infer disease relevant pathways Notes, Reference; Reference
W8: 10/11 Pathway simulation Notes, Reference; (Shawn) (HW1 Due, HW2 Assigned)
10/13 Mine disease-causal genes using Semantic web Notes, Reference (Ying and Lingfei)
W9: 10/18 biological literature mining I Notes, Reference
10/20 biological literature mining II Notes, Reference(John and Jun)
W10: 10/25 Part III: Genes and diseases Notes; Reference;
10/27 SNP databases Notes; Reference; (Michell and Anshu)
W11: 11/01 Linkage analysis Notes;
11/03 Mapping disease loci by linkage analysis Notes; (Everth and Ping)
W12: 11/08 Mapping disease gene by whole genome association study

Notes; Reference

11/10 Mapping determinants of human gene expression (EQTL) Notes, Reference; Reference; Reference ; Reference;
W13: 11/15 EQTL II Notes;
11/17 Frequent Pattern Mining Notes;
W14: 11/22 Integrative Genome-Phenome mapping Notes; Reference (HW2 Due) Final project presentation (Ping)
11/24 Final project presentation (Lingfei and Shawn)
W15: 11/29 Final project presentation (Ying and Jun)
12/01 Final project presentation (John and Anshu )
W16: 12/06 Final project presentation ,Class End (Everth and Michelle)
12/07~12/13 Final Exam Week