This course provides a comprehensive overview of bioinformatics where living matters are modeled and analyzed as information systems. The fundamental notions and methods in genome sequence analysis, protein structural bioinformatics, and system biology are introduced with illustrative examples of recent research.
This course is aiming to show students live instances of computing technology application in our society, especially via the combination of various mathematical methods in order to extract meanings from vast and vague real-world data.
By the end of this course, students will be able to:
1) Explain fundamental knowledge on bioinformatics.
2) Explain novel mathematical methods to extract meanings from various data
3) Explain instances of computing technology application in society
Genome sequence analysis, protein structural bioinformatics, system biology, computational biology
|Intercultural skills||Communication skills||✔ Specialist skills||✔ Critical thinking skills||Practical and/or problem-solving skills|
Each class starts with the explanation of a new topic. In the class occasionally, students are given exercise problems to solve. Students are asked to submit final reports.
|Course schedule||Required learning|
|Class 1||Sequence bioinformatics overview||Genome sequence, sequence analysis, global/local alignment|
|Class 2||Multiple alignments and sequence motifs||Approximation methods for multiple alignments, regular expression/profile matrix/HMM representation|
|Class 3||Homology search from databases||E-value, FASTA, BLAST, PSI-BLAST, BLAT|
|Class 4||Phylogenetic tree estimation||Distance matrix methods, character state methods, bootstrapping|
|Class 5||Coding region prediction||Gene coding region prediction by Markov model, etc.|
|Class 6||Structure bioinformatics overview||Protein structure, structure-function relationship, structure comparison, structure classification|
|Class 7||Protein secondary structure prediction||Protein structure prediction based on machine learning methods|
|Class 8||Protein tertiary structure prediction||Comparative modeling, de novo prediction|
|Class 9||Protein docking||Protein-protein docking, protein-ligand docking, virtual screening|
|Class 10||Molecular simulation||Molecular dynamics, Molecular orbital method|
|Class 11||System biology overview||Biological system, complex network, network biology|
|Class 12||Gene expression regulation network analysis||Gene expression, transcription factor, Boolean network, Bayesian network|
|Class 13||Metabolic pathway network analysis||Metabolites, metabolic pathway, flux analysis|
|Class 14||Pharmacokinetic modeling and analysis||Drugs, pharmacokinetics, compartment model, PBPK model|
Original class slides are provided.
Mount, David. Bioinformatics: Sequence and Genome Analysis (2nd edition). Cold Spring Harbor Laboratory Press; ISBN-13: 978-087969712-9
Students' knowledge and their ability to apply them to solving problems will be assessed with final report.