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Courses_2016 Fall
 

 

dec lab


B1 Course Material

Basic Molecular Biology I (B1)

Place: Room 107, New Building of the Institute of Information Science, Academia Sinica.

Time: Tuesday 09:00-12:00

Chair: Dr. Chuan-Hsiung Chang (cchang@ym.edu.tw)

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. Molecular Biology of the Cell, 6th edition, 2014.

http://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06595&Rcg=53601

2. Molecular Biology : Principles of Genome Function, 2nd edition, 2014.

http://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06594&Rcg=52559

3. 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.   

Lecturers: Chuan-Hsiung Chang, Ueng-Cheng Yang, Dar-Yi Wang , Ho-Ming Chen, Jung-Hsin Lin , Wailap Victor Ng, Sheau-Yann Shieh, Yuh-Shan Jou, ie-rong Huang 

TA: N/A (Please refers to the lectures respectively shall you have any questions of each class

Grades: Midterm exam 50%. Final exam 50%.

 

Week

Date

Topics/Brief Description

Lecturers

Slides

1

2016/09/13

Chemical Foundations

Dr. Jie-Rong Huang

Moodle

2

2016/09/20

Protein Structure and Function

Dr. Jie-Rong Huang

Moodle

3

2016/09/27 -->moves to 10/11 @2:00-5:00pm

Molecules, Cells, and Evolution

Dr. Chuan-Hsiung Chang

Moodle

4

2016/10/04

Transcriptional Control of Gene Expression

Dr. Dar-Yi Wang

Moodle

5

2016/10/11

Basic Molecular Genetic Mechanisms

Dr. Ueng-Cheng Yang

 

6

2016/10/18

Genes, Genomics, and Chromosomes

Dr. Chuan-Hsiung Chang

 

Moodle

7

2016/10/25

Molecular Genetic Techniques

Dr. Ueng-Cheng Yang

Moodle

8

2016/11/01

Review Week

---

9

2016/11/08

Midterm Exam

---

10

2016/11/15

Post-Transcriptional Gene Control

Dr. Ho-Ming Chen

Moodle

11

2016/11/22

Biomembrane Structure and Transport

Dr. Jung-Hsin Lin

Moodle

12

2016/11/29

@Room 101

Cellular Energetics

Dr. Ueng-Cheng Yang

Moodle

13

2016/12/06

Signal Transduction and G Protein–Coupled Receptors

Dr. Wailap Victor Ng

Moodle

14

2016/12/13

Signaling Pathways That Control Gene Expression

Dr. Wailap Victor Ng

Moodle

15

2016/12/20

The Eukaryotic Cell Cycle

Dr Sheau-Yann Shieh

Moodle

16

2016/12/27

Cancer

Dr. Yuh-Shan Jou

 

17

2017/01/03

Review Week

---

18

2017/01/10

Final Exam

---

 
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C1 Course Material

Biological Computing  (C1)

Place: Room 107, New Building of the Institute of Information Science, Academia Sinica.

Time: Friday 14:00-17:00

Chair: Dr. Huai-Kuang Tsai (hktsai@iis.sinica.edu.tw )

Outline: Design and analysis of algorithms for biologists

Lecturers: Dr. Wen-Lian Hsu, Dr. Yu-Jung Chang, Dr. Huai-Kuang Tsai, Dr. Hsin-Nan Lin, Dr. Chun-Chieh Shih, Dr. Ting-Yi Sung, Dr. Ching-Tai Chen

Textbook:

Reference book:

 

TA: Chi-Chun Chen 陳奇君 Email: chichunchen@iis.sinica.edu.tw

Office hours: by appointment

Grades: Midterm exam 50%. Final exam 50%.

 

Week

Date

Topics/Brief Description

Lecturers

 Slides

1

2016/09/13(Tue)

2:00-5:00

Analysis of Algorithms

Dr. Wen-Lian Hsu

Moodle

2

2016/09/27 --> 10/3 @2:00-5:00

Recurrence

Dr. Wen-Lian Hsu

Video       (I) , (II) , (III)

3

2016/09/30

Introduction to Data Structure (I)

Dr. Yu-Jung Chang

Moodle

4

2016/10/07

Introduction to Data Structure (II)

Dr. Yu-Jung Chang

Moodle

5

2016/10/14

Algorithmic Techniques

Dr. Wen-Lian Hsu

Moodle

6

2016/10/21

Motif Finding

Dr. Ting-Yi Sung

Moodle

7

2016/10/28

Graph Algorithms @O108

Dr. Ting-Yi Sung

Moodle

8

2016/11/04

Review Week

---

9

2016/11/11

Midterm Exam @N101

---

10

2016/11/18

Combinatorial Pattern Matching

Dr. Ching-Tai Chen

Moodle

11

2016/11/25

Suffix Trees

Dr. Ching-Tai Chen

Moodle

12

2016/12/02

Sequence Alignment (I)

Dr. Huai-Kuang Tsai

Moodle

13

2016/12/09

Sequence Alignment (II)

Dr. Huai-Kuang Tsai

Moodle

14

2016/12/16

The Analysis of Next Generation Sequencing Data(I)

Dr. Hsin-Nan Lin

 

15

2016/12/23

The Analysis of Next Generation Sequencing Data (II)

Dr. Hsin-Nan Lin

 

16

2016/12/28(Wed)

9:00-12:00

Fundamentals of Molecular Evolution and Phylogenetic Tree Construction

Dr. Chun-Chieh Shih

 

17

2017/01/06

Review Week

---

18

2017/01/13

Final Exam

---

 

 
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S1 Course Material

 

TIGP Bio 2016 Fall Syllabus
Fundamental Statistical Methods in Bioinformatics (S1)
Place: Room 107, New Building of the Institute of Information Science, Academia Sinica.
Time: Thursday 9:00-12:00
Chair:  Dr. Hsin-Chou Yang
Outline:This course covers the fundamentals of statistics and basic tools for bioinformatics analysis. In the first part students will learn basic statistical concepts and methods, including probability, random variables and distributions, parameter estimation, hypothesis testing, regression analysis, and categorical data analysis. In the second part several commonly used methods in bioinformatics will be introduced, including statistical meta analysis, survival analysis, clustering, classification, and nonparametric statistics.
Lecturers: Chen-Hsiang Yeang, Hsin-Chou Yang, Shinsheng Yuan, Grace S. Shieh, Hsuan-Yu Chen, and Wei-Chung Liu
Textbook: Fundamentals of Biostatistics (author: Bernard Rosner), Cengage Learning
Reference book:
 
TA: Lovely Raghav (羅芙琳) Email: lovely@iis.sinica.edu.tw
Office hours: Wednesday 2:00 to 4:00 PM
Grades: Midterm exam 50%. Final exam 50%.
Week Date Topics/Brief Description   Lecturers  Slides
1 2016/9/14  (Wed) Descriptive Statistics, Genomic Data Analysis  (1)  Introduction to statistics
(2)  Descriptive statistics
(3)  Fundamental of molecular biology
(4) Genomic data analysis
Dr. Chen-Hsiang Yeang Moodle
2 2016/9/22 Probability (1) Applications in statistical genetics
(2)  Combinatorial analysis
(3)  Axioms of probabilities
(4)  Conditional probability and independence
(5) Random variable and distribution function
 
Dr. Hsin-Chou Yang Moodle
3 2016/9/29 Discrete Distributions and Contingency Tables (1)  An application in pharmacogenetic study
(2) Discrete/continuous/mixed distributions
(3) Joint/marginal/conditional distributions
(4) Special discrete distributions
(5) Introduction to contingency table
 
Dr. Hsin-Chou Yang Moodle
4 2016/10/6 Continuous Distributions, Expectations and Basic Statistics (1) Continuous random variable
(2) Expectation
(3) Basic statistics
(4) Limit theorems (optional)
 
Dr. Hsin-Chou Yang Moodle
5 2016/10/13 Hypothesis Testing, P-value and False Discovery Rate  (1)  Hypothesis testing
(2)  Type I error and type II error
(3)  P-value
(4)  One-sample and two-sample z-tests
(5)  One-sample, two-sample, and paired t-tests
(6)  Bonferroni adjustment, false discovery rate, and q value
 
Dr. Grace S. Shieh Moodle
6 2016/10/20 Parameter Estimation and Confidence Interval  (1)  Unbiasedness
(2)  Point estimation (substitution principles, least square estimate, maximum likelihood estimate)
(3)  Interval estimation
 
Dr. Shin-Sheng Yuan Moodle
7 2016/10/27 Analysis of Categorical Data, Chisq and Multinomial (1)  Incidence proportion and odds ratio
(2)  Two-sample test for binomial proportions
(3)  Contingency-table approach
(4)  Fisher’s exact test
(5)  McNemar’s test
(6)   Kappa statistic
 
Dr. Hsuan-Yu Chen Moodle
8 2016/11/3 Review Week(no class)    
9 2016/11/10 Midterm Exam    
10 2016/11/17 Regression Analysis and ANOVA (1)  Linear regression with one independent variable
(2)  Inference in regression analysis
(3)  Diagnostic and remedial measures
(4)  Simultaneous inferences and other topics
(5)  Multiple linear regression
(6)  Building the regression model
(7)  Qualitative predictor variables
(8)  Analysis of variance
 
Dr. Grace S. Shieh Moodle
11 2016/11/24 @Rm#101 Logistic Regression and Statistical Meta Analysis (1)  Logistic regression
(2)  Meta analysis (effect size, precision, study weights, summary effect, heterogeneity, fixed-effect model, random-effect model, software)
 
Dr. Shin-Sheng Yuan Moodle
12 2016/12/1

moves to 11/28

@

2-5pm

Survival Data Analysis (1)  Mantel-Haenszel test
(2)   Survival and hazard functions
(3)  Kaplan Meier estimate
(4)  Log-rank test
(5)  Proportional-hazards model
(6)  Lung cancer study
 
Dr. Hsuan-Yu Chen  
13 2016/12/8 Clustering (1)  Clustering by geometry (K-means, EM algorithm, hierarchical clustering, self- organizing map, principal component analysis, independent component analysis)
(2)  Clustering on graphs (Basic concepts, max flow – min cut, normal cuts, spectral clustering, and community detection)
(3)  Advanced topics (Chinese restaurant process and affinity propagation)
 
Dr. Chen-Hsiang Yeang Moodle
14 2016/12/15 Classification (1)  Binary classifications (Bayesian detection theory, naïve Bayes and other generative models, non-parametric methods, Fisher linear discriminant, support vector machines and kernel techniques, artificial neural networks, and boosting)
(2)  Advanced topics in supervised learning (multi-class classification, feature selection, semi-supervised learning, active learning)
 
Dr. Chen-Hsiang Yeang  
15 2016/12/22 Nonparametric Statistics (I) (1)  Bootstrap
(2)  One-sample sign test
(3)  One-sample Wilcoxon signed-rank test
(4)  Wilcoxon rank-sum test (Mann-Whitney U test)
(5)  Sign test for paired data
(6)  Wilcoxon signed-rank test for paired data
 
Dr. Wei-Chung Liu  
16 2016/12/29 Nonparametric Statistics (II) (1) Kruskal-Wallis test
(2)     Randomization/permutation test for two-way ANOVA
(3)  The product-moment correlation coefficient
(4)  Spearman rank correlation
(5)  Kendall’s coefficient of rank correlation
 
Dr. Wei-Chung Liu  
17 2017/1/5 Review Week(no class)    
18 2017/1/12 Final Exam    
 
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P1 Course Material  

2016 Programming (Python) (P1)

Place: Room 108, New Building of the Institute of Information Science, Academia Sinica.

Time: Friday, 10:00am-12:00pm

Chair: Dr. Wu, Kun-Pin (BP), Dr. Chih-Yu Wang (SNHCC) (cywang@citi.sinica.edu.tw)

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.)

Lecturers: BP- Dr. Wang, John; Dr. Chang, Hui-Yin; Dr. Mamie Lih
         SHNCC-Dr. Wang, Chih-Yu; Dr. Wang, Chuan-Ju ; Dr. Shen, Chih-Ya

Textbook: Introduction to Computation and Programming Using Python (revised and expanded edition) by John V. Guttag, 2013, The MIT Press (滄海圖書代理)

 TA: Chia-Hung Lin(林佳鴻)  Email: redlin@stat.sinica.edu.tw

Office hours: Tue, 14:00-16:00

Grades: Midterm exam (25%). Final exam (30%). Homework (25%). Projects (10%). Class performance (10%).

Week

Date

Topics/Brief Description

Lecturers

Slides

1

2016/09/23

Introduction to Python 

Dr. Wang, Chuan-Ju

 Moodle

2

2016/09/28 (Wed)--cancelled 

Basic Elements of Python I

Dr. Wang, Chuan-Ju

 Moodle

3

2016/09/30

9:00-12:30

Basic Elements of Python II

Dr. Wang, Chuan-Ju

 Moodle

4

2016/10/07

Basic statements I: branching programs and inputs

 

Dr. Wang, John

Moodle

5

2016/10/14

Basic statements II: iterative programs

 

Dr. Wang, John

Moodle

6

2016/10/21

Functions: scope rules and passing arguments

 

Dr. Wang, John

Moodle

7

2016/10/28

Modules, Files, and Structured Types

 

Dr. Wang, Chih-Yu

Moodle

8

2016/11/04

Exception handling

Dr. Wang, Chih-Yu

Moodle

9

2016/11/11

Review week

10

2016/11/18

Midterm exam

11

2016/11/25

Introduction to Biopython

Dr. Chang, Hui-Yin

Moodle

12

2016/12/02

Regular expressions

Dr. Mamie Lih

Moodle

13

2016/12/09

Object-oriented programming: classes

 

Dr. Mamie Lih

    Moodle

14

2016/12/16

Cancelled

 

Data analysis toolbox  

Dr. Shen, Chih-Ya

 

15

2016/12/23

9:00-12:00

Data analysis toolbox / Web programming

 

Dr. Shen, Chih-Ya

 

16

2016/12/30

9:00-12:00

 

Web programming

Dr. Shen, Chih-Ya

 

17

2017/01/06

Review week

18

2017/01/13

Final exam

 

 
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Student Presentation

2016 Fall Student Presentation

*Effective from 2014 Fall semester, all TIGP-BP students are required to present once a semester in seminar.

*Students are required to submit the topics of the papers by 8/25/2016.

*Your present schedule is confirmed and will not be changed. Please contact Dr. Chuan-Hsiung Change if you do have a schedule conflict on the assigned date.

*The presenter shall introduce the host and attended professors in the beginning of each seminar.

*1st year students: 1. attendance for every session is required.  2. Presentation paper will be assigned by lab professor.

 *2nd and 3rd year students: 1. attendance is optional (except your scheduled  presentation date)

Week

Date

TIGP Bioinformatics

Host

1

2016/09/14

(Wed)

 

 

 

 

N/A

 

2

2016/09/22

 

 

 

N/A

 

3

2016/09/29

 

                     

N/A

 

4

2016/10/06

 

 

Lovely Raghav(2014)

 

Topic:

Goldmann J. et al., "Parent-of-origin-specific sigatures of de novo mutations", Nature Genetics, (2016) | doi:10.1038/ng.3597

 

 

5

2016/10/13

 

Kshitij Tandon (2015)

 

Topic:

 

 

6

2016/10/20

 

Neha Warikoo (2015)

 

 

Topic:

 

"Science Question Answering using Instructional Materials"Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics, pages 467–473, Berlin, Germany, August 7-12, 2016. 

 

 

7

2016/10/27

 

N/A

 

8

2016/11/03

 

Review Week

 

9

2016/11/10

                    

 Midterm Exam

 

 

10

2016/11/17

 

潘昭宇(2016陽明YMU Student)

 

Topic:

"Drug discovery using clinical outcome-based Connectivity Mapping"BMC Genomics, doi10.1186/s12864-016-3149-5, Oct 19, 2016. 

 

11

2016/11/24

 

Ming-Siang Huang (2016)

 

Topic:

"DrugQuest - a text mining workflow for drug association discovery"
Papanikolaou et al. BMC Bioinformatics 2016, 17(Suppl 5):182|DOI       10.1186/s12859-016-1041-6

 

12

2016/12/01

 

 

Onkar Singh (2016)

 

Topic:

 

 

13

2016/12/08

 

 

Abdul Waheed Khan (2016)

 

Cancelled

 

 

14

2016/12/15

 

Cancelled

 

15

 

 

2016/12/22

 

 

 

 

N/A

 

16

2016/12/29

 

鄭中遠(2015陽明YMU Student)

Topic:

 

 Ioannidis K, Chamberlain SR, Treder MS, Kiraly F, Leppink EW, Redden SA, Stein DJ, Lochner C, Grant JE.  , "

Problematic internet use (PIU): Associations with the impulsive-compulsive spectrum. An application of machine learning in psychiatry.

", J Psychiatr Res. 2016 Aug 15;83:94-102. doi: 10.1016/j.jpsychires.

 

 

 

17

2017/01/05

 

Maharasan Kathiresan (2016)

 

Topic:

Rodrigues T, Reker D, Welin M, Caldera M, Brunner C, Gabernet G, Schneider P. Walse B, Schneider G. PubMed. "De Novo Fragment Design for Drug Discovery and Chemical Biology." 2015 Dec 7;54(50):15079-83. doi: 10.1002/anie.201508055. Epub 2015 Oct 21.

 

 

 

18

2017/01/12

Final Exam

 


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Seminar

TIGP Bio 2016 Fall Seminar

Place: AS-Room 101, New Building of the Institute of Information Science, Academia Sinica.

Time: Thursday 14:00-15:20

Chair: Dr. Chung-Yen Lin (Informatics), Dr. Ho-Min Chen (Biology), Dr. Wei-Chung Liu (Statistic), Dr. Lin, Chen-Ching (YMU)

Grades: attendance 100%.

Remarks:

          Please choose any two 45-minute sessions to attend for the 30th Anniversary & Symposium. in replace of the first two weeks of Seminar.  Credits will be given only if you sign up at the registration table by then.

Week

Date

Topics/Brief Description

Speaker / Host

1

2016/9/14  (Wed)

 Replaced by 30th Anniversary & Symposium

Dr.

Host:

2

2016/9/22

 Replaced by 30th Anniversary & Symposium

 

Host:

3

2016/9/29

YMU (Topic: Identification of lncRNA-modulated MYCN regulatory networks in neuroblastoma)

Dr. Chia-Lang Hsu      Department of Life Science, National Taiwan University

Host: Dr. Lin, Chen-Ching (YMU)

4

2016/10/6

 Integration of bio- and clinical information in the absence of personally identifiable information

Dr. Ueng-Cheng Yang

5

2016/10/13

YMU (Topic: Integrated Approaches for Feature Selection and Fuzzy Rule Extraction for Classification)

Dr. I-Fang Chung

Host: Dr. Chen-Ching Lin

6

2016/10/20

 YMU (Topic: Exploring Ecological Networks)

Dr. Wei-Chung Liu

Host: Dr. Chen-Ching Lin

7

2016/10/27

YMU (Topic: Identification of Regulatory Bridges in Pan-cancer)

Dr. Chen-Ching Lin

Host: Dr. Chen-Ching Lin

8

 

2016/11/3

Review Week

 

9

2016/11/10

Midterm Week

 

 

10

  

2016/11/17

    N/A

Dr.

Host:

11

2016/11/24

    N/A

 

Dr.

12

2016/12/1

YMU (Topic: How transcription factors read the genome)

Dr. Chuan-Hsiung Chang

Host: Dr. Chen-Ching Lin

13

  

2016/12/8

YMU (Topic: Biological modeling and its applications in computational biology)

Dr. Yu-Chao Wang

Host: Dr. Chen-Ching Lin

14

2016/12/15

Epigenetic variability from individuals to single cells

Dr. Christine Cheng

Host: Huai-Kung Tsai

15

 

2016/12/22

Decoding post-transcriptional gene control with next generation sequencing

Dr. Ho-Ming Chen

16

  

2016/12/29

Atypical translational mechanism jointly revealed by structural biology, single molecule and resolution exchanged simulation techniques 

Dr. Lee-Wei Yang

 17

2017/1/5

Review Week (no class)

Dr.

Host:

18

2017/1/12

Final Exam

 

 

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Lab Rotation

 

All 1st year students: Please inform BP office for the laboratory you are rotating

(Deadline for 2016 Fall Semester: 9/23/2016)

 

Student Name

Lab

Ming-Siang Huang 黃明祥 Dr. Wen-Lian Hsu
Onkar Singh 歐克爾 Dr. Wen-Lian Hsu
Abdul Waheed Khan 阿布杜

Dr. Chen, Ho-Ming

Maharasan Kathiresan 馬和拉

Dr. Shin-Sheng Yuan

 
 
 
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