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Courses_2015 Spring

 

dec Tutorial lab


B1 Course Material

Place: Room 108, Old Building of the Institute of Information Science, Academia Sinica.
Time: Tuesday 09:00-12:00
Chair: Dr. Chuan-Hsiung Chang and Dr. Wen-Chang Lin
Aim: understanding the key concepts in molecular and cell biology and their experimental underpinnings

Textbook: (Required)
1. Molecular Cell Biology, 7th edition, by Harvey Lodish et al. Publisher: W. H. Freeman. International Edition (13 Aug, 2012). ISBN-13: 9781464109812.
Local book store: http://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06585
Reference: (Recommended but not required)
1. Biochemistry: A Short Course, 2nd edition, by Lubert Stryer et al. Publisher: W. H. Freeman (December 23, 2011). ISBN-10: 1429283602, ISBN-13: 978-1429283601.   
2. Molecular Biology, 5th edition, by Robert Weaver. Publisher: McGraw-Hill (February 11, 2011). ISBN-10: 0073525324, ISBN-13: 978-0073525327.

TA: Tung-Shing Lih (tsmlih@iis.sinica.edu.tw)
Office hours: by appointment
Grades: Midterm exam 50%. Final exam 50%.

Week

Date

Topics/Brief Description

Lecturers

1

2013/09/17

Molecules, Cells, and Evolution

Chuan-Hsiung Chang

2

2013/09/24

Chemical Foundations

Ming-Jing Hwang

3

2013/10/01

Protein Structure and Function

Ming-Jing Hwang

4

2013/10/08

Basic Molecular Genetic Mechanisms

Ueng-Cheng Yang

5

2013/10/15

Molecular Genetic Techniques

Ueng-Cheng Yang

6

2013/10/22

Genes, Genomics, and Chromosomes

Chuan-Hsiung Chang

7

2013/10/29

Transcriptional Control of Gene Expression

Wen-Chang Lin

8

2013/11/05

Review Week

 

9

2013/11/12

Post-Transcriptional Gene Control

Ho-Ming Chen

10

2013/11/19

Midterm Exam

 

11

2013/11/26

Biomembrane Structure and Transport

Jung-Hsin Lin

12

2013/12/03

Cellular Energetics

Ueng-Cheng Yang

13

2013/12/10

Signal Transduction and G Protein–Coupled Receptors

Wailap Victor Ng

14

2013/12/17

Signaling Pathways That Control Gene Expression

Wailap Victor Ng

15

2013/12/24

The Eukaryotic Cell Cycle

Sheau-Yann Shieh

16

2013/12/31

Cance

Yuh-Shan Jou

17

2014/01/07

Review Week

 

18

2013/01/14
moved to 2014/01/17

Final Exam 9:00-12:00 @108 IIS

 







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C1 Course Material

Place: Room 108, Old Building of the Institute of Information Science, Academia Sinica.
Time: Friday 14:00-17:00
Chair: Dr Kun-Pin Wu
Outline: Design and analysis of algorithms for biologists

 

TA: Meng-Ting Liu (littlemong7205@iis.sinica.edu.tw)
Office hours: by appointment
Grades: Midterm exam 50%. Final exam 50%.

Week

Date

Topics/Brief Description

Lecturers

1

2013/09/20
→2013/9/18
9:00-12:00@108

Analysis of Algorithms

Wen-Lian Hsu

2

2013/09/27

Recurrence

Wen-Lian Hsu

3

2013/10/04
→2013/10/2
9:00-12:00@108

Introduction to Data Structure (I)

Chia-Yu Su

4

2013/10/11
→2013/10/9
9:00-12:00@108

Introduction to Data Structure (II)

Chia-Yu Su

5

2013/10/18
→2013/10/16
9:00-12:00@108

Algorithmic Techniques

Chia-Yu Su

6

2013/10/25
→2013/10/23
9:00-12:00@108

Motif Finding

Chia-Yu Su

7

2013/11/01

Graph Algorithms

Wen-Lian Hsu

8

2013/11/08

Review Week

 

9

2013/11/15

Pairwise Sequence Alignment

Jyh-Ying Peng

10

2013/11/22

Midterm Exam

 

11

2013/11/29

Multiple Sequence Alignment

Jyh-Ying Peng

12

2013/12/06

The Analysis of Next Generation Sequencing Data (I)

Hsin-Nan Lin

13

2013/12/13

The Analysis of Next Generation Sequencing Data (II)

Hsin-Nan Lin

14

2013/12/20

Combinatorial Pattern Matching

Kun-Pin Wu

15

2013/12/27

Suffix Trees

Kun-Pin Wu

16

2014/01/03

Fundamentals of Molecular Evolution and Phylogenetic Tree Construction

Chun-Chieh Shih

17

2014/01/10

Review Week

 

18

2014/01/17

Final Exam

 







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P1 Course Material

Place: Room 108, Old Building of the Institute of Information Science, Academia Sinica.
Time: Tuesday 14:00-16:00
Chair: Dr. Emily Chia-Yu Su
Outline:
This course introduces basic aspects of programming language and its application in bioinformatics. First, fundamental programming techniques in Python are introduced. After that, this course focuses on the practical implementation of programs to analyze various biological data. The use of existing available resources from the Internet is also incorporated. Finally, the students implement bioinformatics projects (i.e., motif finding, pattern matching, sequence alignment, biomedical database analysis, etc.)

 

TA: Thejkiran Pitti
Office hours: by appointment
Grades: Midterm exam 25%. Final exam 30%. Homework 35%. Class performance (10%)

Week

Date

Topics/Brief Description

Lecturers

1

2013/09/17

Introduction to Python

Emily Chia-Yu Su

2

2013/09/24

Object types and operations I: basic and container object types

Emily Chia-Yu Su

3

2013/10/01

Object types and operations II: tuples and file handling

Emily Chia-Yu Su

4

2013/10/08

Basic statements I: assignments, expressions, and if tests

Emily Chia-Yu Su

5

2013/10/15

Basic statements II: while and for loops

Emily Chia-Yu Su

6

2013/10/22

Functions: scope rules and passing arguments

Emily Chia-Yu Su

7

2013/10/29

Modules: coding basics and packages

Emily Chia-Yu Su

8

2013/11/05

Exception handling

Emily Chia-Yu Su

9

2013/11/12

Review week

 

10

2013/11/19

Introduction to Biopython

Emily Chia-Yu Su

11

2013/11/26 moved to→ 2013/11/25

Midterm exam @ Media Conference 3F of Building 24 HSSB

 

12

2013/12/03

Regular expressions

Emily Chia-Yu Su

13

2013/12/10

Object-oriented programming: classes and operator overloading

Emily Chia-Yu Su

14

2013/12/17

Graphical user interfaces

Emily Chia-Yu Su

15

2013/12/24

Structured text

Emily Chia-Yu Su

16

2013/12/31

Web programming

Emily Chia-Yu Su

17

2014/01/07

Review week

 

18

2014/01/14

Final exam @ Media Conference 3F of Building 24 HSSB

 







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Seminar
Place: Room 106, Old Building of the Institute of Information Science, Academia Sinica.
Time: Thursday 14:00-15:10
Chair: Dr. Ting-Yi Sung, Dr. Wen-Chang Lin, and Dr. Wei-Chung Liu
Outline:

 

Grades: Attendance
Week Date Topics/Brief Description Lecturers
1 2013/09/19 中秋節

 

 

 
2 2013/09/26  

Dynamic network modeling: effects of noise

 

Chao-Ping Hsu
3 2013/10/03  

Boolean Networks

 

Henry Horng-Shing Lu
4 2013/10/10 國慶日

 

 

 
5 2013/10/17  

TBD

 

Wen-Hsiung Li

 

6 2013/10/24  

Uncovering Synthetic lethal interactions for Cancer Therapeutics

 

 

Grace S. Shieh
7 2013/10/31  

Development of robust scoring functions for protein-ligand interactions

 

Jung-Hsin Lin
8 2013/11/07 Review Week  
9 2013/11/14 Midterm Exam  
10 2013/11/21  

SecretePipe: a screening pipeline for secreted proteins with competence to identify potential membrane-bound shed markers.

 

Kun-Pin Wu
11 2013/11/28  

Computational structural biology in antibody design and engineering

 

An-Suei Yang
12 2013/12/05  

Computational data analysis for mass spectrometry-based proteomics

 

Ting-Yi Sung
13 2013/12/12  

Reverse engineering of genome organization for genome design

 

Chuan-Hsiung Chang
14 2013/12/19  

TBD

 

Trees-Juen Chuang
15 2013/12/26  

Recurrent structural motifs reflect characteristics of distinct networks

 

Chen-Hsiang Yeang
16 2014/01/02  

Molecular responses to ligand perturbations can be described by linear response theories

 

Lee-Wei Yang
17 2014/01/09 Review Week  
18 2014/01/16 Final Exam  







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Tutorial Reading
Date TIGP Bioinformatics Host
Professor Dr. Chuan-Hsiung Chang  
Oct 17    
     
Oct 24 孫在揚  
  Jerome Penaflor Panibe  
  x  
Oct 31 Chi-Chun Chen  
  張慧如  
Nov 7

x

 
  x  
x x  
Nov 28 Alcides Bernardo Tello  
  Cheng-Kai Shiau  
Dec 5 Yenchen Lo  
  Chiahung Lin  
Dec 12 Yen Hsieh Chen  
  Hsiu-man Chen  
Dec 19 Nikhil Pathak   
  Kidane Gebereyesus Dr. Grace S. Shieh
Dec 26 Divya Sahu  







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Lab Rotation

Students need to inform the BIO office the laboratory they are rotating with within two weeks 

Student

Advisor

 Nikhil Pathak 倪齊歐 

Dr. Yang, An-Suei

 Jerome Penaflor Panibe杰羅姆 

Dr. Li, Wen-Hsiung

 Chi-Chun Chen 陳奇君

Dr. Huang, Hsuan-Cheng

 Divya Sahu笛芙亞 

Dr. Chang, Chuan-Hsiung

 Kidane Gebereyesus祈丹 

Dr. Shieh Shwu-Rong Grace

 Alcides Bernardo Tello愛希德

Dr. Hsu, Chao-Ping

 Cheng-Kai Shiau蕭丞凱 

Dr. Chen, Pao-Yang

 Yenchen Lo駱彥辰 

Dr. Chang, Chuan-Hsiung

 Chiahung Lin林佳鴻 

Dr. Li, Ker-Chau

 Yen Hsieh Chen陳彥劦 

Dr. Jou, Yuh-Shan

 Hsiu-man Chen陳秀曼 

Dr. Yeang, Chen-Hsiang

 
 
 
 
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TIGP Sinica IIS