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Biological Computing I (C1)

 

Semester: Fall 2010, TIGP-BP
Place
: Institute of Information Science, Academia Sinica, New Building, Rm. 107
Time: Friday Afternoons,  2:00-5:00 PM
        
This course covers computer science topics that serve as building blocks of computational systems for bioinformatics. We will offer basic materials of data structures that are widely used in bioinformatics, including sequences, trees, and Graphs. Bioinformatics algorithms such as sequence alignment and pattern matching are then introduced. Students will also learn basic programming skills and analytic techniques to implement and analyze these data structures and bioinformatics algorithms.

Reference:

1. Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT Press, 2004

2. Dan Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, Cambridge Press, 1997

Week

Date

Topics

Lecturers

Slides

Online

asgmt.

1

2010/09/17

Analysis of Algorithms

Wen-Lian Hsu

 

2

2010/09/24

Programming Primer

Chia-Yu Su

 

3

2010/09/29

(Wed.)9-12am

Recurrence @Rm.107

 

Wen-Lian Hsu

 

 

 

4

2010/10/13

(Wed.)9-12am

Introduction to Data Structure I

Chia-Yu Su

 

5

2010/10/15

Introduction to Data Structure II

Chia-Yu Su 

 

6

2010/10/22

Algorithmic Techniques

Ting-Yi Sung

 

7

2010/10/29

Motif Finding

Ting-Yi Sung

 

8

  2010/11/05 

Review week

 

 

 

 

9

2010/11/12

Midterm Exam (10am~1pm)

 

 

 

 

10

 

2010/11/17

(Wed.)2-5pm

 

Pairwise Sequence Alignment

 Huai-Kuang Tsai 

 

 

11

2010/11/26

Multiple Sequence Alignment

Huai-Kuang Tsai 

 

 

12

2010/12/03

Graph Algorithms (I)

Wen-Lian Hsu

 

13

2010/12/10

Graph Algorithms (II)

Wen-Lian Hsu

 

14

2010/12/17

Combinatorial Pattern Matching 

Kun-Pin Wu 

 

 

15

2010/12/24

Suffix Trees

Kun-Pin Wu 

 

 

16

2010/12/31

Genome Evolution and Phylogenetic Trees

Chun-Chieh Shih 

 

17

2011/01/07

Programming Review

Chia-Yu Su

 

 

 

18

2011/01/14

Final Exam

 

 

 

 

 

 

Bioinformatics Program, TIGP , Academia Sinica , Taiwan c 2004 - 2010