BMI 730 - Biomedical Informatics
This course provides basic knowledge in bioinformatics, computational and systems biology to a broad constituency of trainees with specialization in the biomedical, basic, natural, computational, and engineering sciences with general interest in the biomedical informatics domain. The course introduces students to basic topics of bioinformatics including, but not limited to, sequence analyses, proteomics, microarrays, regulatory networks, sequence and protein databases, etc.
The course will provide combination of the lectures by the BMI faculty and homework, presentations and research projects performed by the students. Such combination is ultimately intended to enable participants to comprehend basic concepts and current state-of-the art, critically evaluate and understand current research, development, and best-practice findings in the area, and apply them to their respective areas of scholarly activity.
Prerequisite:
Open to undergraduate, graduate, and professional students who have completed CS&E 230. Not open to students with credit for IBGP 730.
Course Credits: 3 credit hours
Class Schedule: Autumn Quarter, Mondays and Wednesdays, 3:00-4:30 pm
Course Director: Kun Huang, PhD
Textbooks and Readings
Required Textbooks:
- Essential Bioinformatics, by Jin Xiong.
Other Suggested Texts:
- An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), by N.C. Jones and P.A. Pevsner
- Bioinformatics: Sequence and Genome Analysis, by D.W. Mount.
Readings:
- Original journal articles representing up-to-date state-of-the-art on respective syllabus topics.
Course Schedule
Class |
Topic |
1 a 1 b |
Introduction to biomedical informatics Sequence alignment: dynamical programming and BLAST algorithm |
2 a 2 b |
Sequence alignment: Scoring matrix and multiple sequence alignment Protein databases and structural alignment |
3 a 3 b |
Protein structure classification and prediction Proteomics |
4 a 4 b |
Protein structure / proteomics (Students’ presentation) Microarray: introduction, database, data format, normalization |
5 a 5 b |
Microarray: normalization and analysis (Presentation) Microarray: clustering and network inference |
6 a 6 b |
Other array-based techniques (ChIP-Chip, MicroRNA, Sequencing) Polymorphisms and SNP |
7 a 7 b |
Cis-regulatory network Cis-regulatory network (Presentation) |
8 a 8 b |
System biology: databases and scale free networks System biology: Motifs |
9 a 9 b |
System biology: kinetic and dynamic modeling (Presentations) Literature mining and ontology. Imaging informatics |
10 a 10 b |
Project presentations Project presentations |