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Biological Computing I (C1)

 

Semester: Fall 2009, 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

2009/09/18

Analysis of Algorithms

Wen-Lian Hsu

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif  http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

2

2009/09/25

Programming Primer

Chia-Yu Su

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

3

2009/10/02

Recurrence

 

Wen-Lian Hsu

 

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif  http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif 

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  http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

4

2009/10/07(Wed.)2-5pm

Introduction to Data Structure I

@Rm.406

Chi-Jen Lu

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

5

2009/10/14(Wed.)2-5pm

Introduction to Data Structure II

@Rm.406

Chi-Jen Lu 

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

6

2009/10/21

 (Wed.)2-5pm

Algorithmic Techniques @Rm.406

Ting-Yi Sung

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http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

7

2009/10/30

Motif Finding

Ting-Yi Sung

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

8

  2009/11/06  

Review week

 

 

 

 

9

2009/11/13

Midterm Exam

 

 

 

 

10

2009/11/20

Pairwise Sequence Alignment

 Huai-Kuang Tsai 

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

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11

2009/11/27

Multiple Sequence Alignment

Huai-Kuang Tsai 

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gifhttp://tigpbp.iis.sinica.edu.tw/pic/icon_download.gifhttp://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

12

2009/12/04

Graph Algorithms (I)

Wen-Lian Hsu

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

13

2009/12/14

(Mon.)2-5pm

Graph Algorithms (II)

@Rm.722

Wen-Lian Hsu

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http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

14

2009/12/18

Combinatorial Pattern Matching 

Kun-Pin Wu 

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

 

15

2009/12/25

Suffix Trees

Kun-Pin Wu 

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

 

16

2009/12/29

(Tue.)2-5pm

Genome Evolution and Phylogenetic Trees @ISS R308

Chun-Chieh Shih 

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

http://tigpbp.iis.sinica.edu.tw/pic/icon_download.gif

 

17

2010/01/08

Programming Review

Chia-Yu Su

 

 

 

18

2010/01/15

Final Exam

 

 

 

 

 

 

Bioinformatics Program, TIGP , Academia Sinica , Taiwan c 2004 - 2005