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Courses_2018 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

Aim: understanding the key concepts in molecular and cell biology and their experimental underpinnings

Outline:

Textbook: (Required)

1. Molecular Cell Biology, 8th edition, by Harvey Lodish(Author), Arnold Berk (Author)
    Publisher: W. H. Freeman. 8th Edition (1 Apr, 2016). ISBN-13: 9781464187445.

Local book store: http://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06585

Reference: (Recommended but not required)

1. Molecular Cell Biology, 7th edition, by Harvey Lodish et al. Publisher: W. H. Freeman. International    Edition (13 Aug, 2012). ISBN-13: 9781464109812.

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

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

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

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

4. 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, Ho-Ming Chen, Jung-Hsin Lin , Wailap Victor Ng, Yuh-Shan Jou, ie-rong Huang

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

E-mail:N/A

Office hours: N/A

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

Week

Date

Topics/Brief Description

Lecturers

1

2018/09/11

Molecules, Cells, and Evolution

Dr. Chuan-Hsiung Chang

2

2018/09/18

Chemical Foundations

Dr. Jie-Rong Huang

3

2018/09/25

Protein Structure and Function

Dr. Jie-Rong Huang

4

2018/10/02

Transcriptional Control of Gene Expression

Dr. Sen-Lin Tang

5

2018/10/09

Basic Molecular Genetic Mechanisms

Dr. Ueng-Cheng Yang

6

2018/10/16

Genes, Genomics, and Chromosomes

Dr. Chuan-Hsiung Chang

7

2018/10/23

Molecular Genetic Techniques

Dr. Ueng-Cheng Yang

8

2018/10/30

Review Week

---

9

2018/11/06

Midterm Exam

---

10

2018/11/13

Post-Transcriptional Gene Control

Dr. Ho-Ming Chen

11

2018/11/20

Biomembrane Structure and Transport

Dr. Jung-Hsin Lin

12

2018/11/27

Cellular Energetics

Dr. Ueng-Cheng Yang

13

2018/12/04

Signal Transduction and G Protein–Coupled Receptors

Dr. Wailap Victor Ng

14

2018/12/11

Signaling Pathways That Control Gene Expression

Dr. Wailap Victor Ng

15

2018/12/18

The Eukaryotic Cell Cycle

Dr. An-Chi Wei

16

2018/12/25

Cancer

Dr. Yuh-Shan Jou

17

2019/01/02

(Wed)

Review Week

---

18

2019/01/08

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

Aim: The aim of the course is to link issues in computer science to biology and thus capture the interest of students in both areas. It is expected that students will acquire and retain important knowledge about computational biology

Outline: The course provides an introduction to the basic computational concepts and methods used in molecular biology and genetics. It covers classic algorithmic techniques (for examples: divide and conquer algorithm, dynamic programming …), data structures (e.g. queue, tree…), and common computational problems in biology (such as motif finding, sequence alignment …).  In addition, Bioinformatics approaches for next generation sequencing and the most up-to-date technology will be addressed as well.

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: N/A

Reference book:N/A

TA: Nam Nhut Phan潘日南 Email: namphanpro@iis.sinica.edu.tw

Office hours: Tuesday 10-12. Room 304

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

Week

Date

Topics/Brief Description

Lecturers

1

2018/09/14

Analysis of Algorithms

Dr. Wen-Lian Hsu

2

2018/09/21

Recurrence

Dr. Wen-Lian Hsu

3

2018/09/28

Introduction to Data Structure (I)

Dr. Yu-Jung Chang

4

2018/10/05

Introduction to Data Structure (II)

Dr. Yu-Jung Chang

5

2018/10/12

Algorithmic Techniques

Dr. Wen-Lian Hsu

6

2018/10/19

Motif Finding

Dr. Ting-Yi Sung

7

2018/10/26

Graph Algorithms

Dr. Ting-Yi Sung

8

2018/11/02

 

Review Week

---

9

2018/11/09

Midterm Exam

 

---

10

2018/11/16

Sequence Alignment (I)

Dr. Huai-Kuang Tsai

11

2018/11/23

Sequence Alignment (II)

Dr. Huai-Kuang Tsai

12

2018/11/30

Combinatorial Pattern Matching

Dr. Ching-Tai Chen

13

2018/12/07

Suffix Trees

Dr. Ching-Tai Chen

14

2018/12/14

The Analysis of Next Generation Sequencing Data (I)

Dr. Hsin-Nan Lin

15

2018/12/21

The Analysis of Next Generation Sequencing Data (II)

Dr. Hsin-Nan Lin

16

2018/12/28

Fundamentals of Molecular Evolution and Phylogenetic Tree Construction

Dr. Jynn-Jy Lin

17

2018/01/04

Review Week

---

18

2018/01/11

Final Exam

---

 
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S1 Course Material
   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.

Textbook: Fundamentals of Biostatistics (author: Bernard Rosner), Cengage Learning.

Reference book: Pattern Recognition (author: Richard O. Duda, Peter E. Hart, and David G. Stork), Wiley.

Lecturers: Chen-Hsiang Yeang, Hsin-Chou Yang, Shinsheng Yuan, Grace Shieh, Hsuan-Yu Chen, and Wei-Chung Liu

TA: Addisu Zember Zeleke 艾迪書 Email: addisu@iis.sinica.edu.tw

Office hours: TBD

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

Week

Date

Topics/Brief Description

Sub-topics/

Detailed Description

Lecturers

1

2018/09/13

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

2

2018/09/20

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

3

2018/09/27

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

4

2018/10/04

Continuous Distributions, Expectations and Basic Statistics

(1)   Continuous random variable

(2)   Expectation

(3)   Basic statistics

(4)   Limit theorems (optional)

Dr. Hsin-Chou Yang

5

2018/10/11

Parameter Estimation and Confidence Interval

(1)   Unbiasedness

(2)   Point estimation (substitution principles, least square estimate, maximum likelihood estimate)

(3)   Interval estimation

Dr. Shinsheng Yuan

6

2018/10/18

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)  False Discovery Rate, and q value

Dr. Grace Shieh

7

2018/10/25

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

8

2018/11/01

Review Week

 

9

2018/11/08

Midterm Exam

 

11

2018/11/15

Correlation, Regression Analysis and ANOVA

(1)   Linear regression with one independent variable

(2)  Simultaneous inferences and other topics

(3)  Diagnostic and remedial measures

(4)  Multiple linear regression

(5)  Building the regression model

(6)  Qualitative predictor variables

Dr. Grace Shieh

10

2018/11/22

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. Shinsheng Yuan

12

2018/11/29

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

2018/12/06

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

14

2018/12/13

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

2018/12/20

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

2018/12/27

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

2019/01/03

Review Week

 

18

2019/01/10

Final Exam

 

 

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P1 Course Material
Programming (Python) (P1)

Place: Room 106, New Building of the Institute of Information Science, Academia Sinica.

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

Chair: Dr. Wang, John (BP) / Wang, Chih-Yu (SNHCC)

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. Krishna Swamy, Dr. Huang, Jia Hsin
        
         SHNCC-Dr. Wang, Chih-Yu; Dr. Li, Su

Textbook: Python for Biologists: A complete programming course for beginners
Advanced Python for Biologists
(Reference) Python for Everybody - Exploring Data In Python 3

TA: DJ 邰迪杰  Email: mikeychoudhary68@gmail.com

      Sarwar Khan Email: say2sarwar@gmail.com

      Chih-Ming Chen Email: changecandy@gmail.com

Office hours: TBD

Grades: Midterm exam 25%. Final exam 30%. Homework 35%. Class performance (10%)

 

Week

Date

Topics/Brief Description

Lecturers

1

2018/09/14

Introduction to Python

Dr. Su, Li

2

2018/09/21

Basic Elements of Python I

Dr. Huang, Yu-Fen

3

2018/09/28

Basic Elements of Python II

Dr. Huang, Yu-Fen

4

2018/10/05

Basic statements I: branching programs and inputs

Dr. Wang, John

5

2018/10/12

Basic statements II: iterative programs

Dr. Wang, John

6

2018/10/19

Functions: scope rules and passing arguments

Dr. Wang, John

7

2018/10/26

Modules, Files, and Structured Types

Dr. Wang, Chih-Yu

8

2018/11/02

Exception handling

Dr. Wang, Chih-Yu

9

2018/11/09

Review week

10

2018/11/16

Midterm exam

11

2018/11/23

Introduction to Biopython

Dr. Krishna Swamy

12

2018/11/30

Regular expressions

Dr. Krishna Swamy

13

2018/12/07

Object-oriented programming: classes

Dr. Krishna Swamy

14

2018/12/14

Data analysis toolbox  : NumPy, Pandas, Matplotlib 

Dr. Huang, Jia Hsin

15

2018/12/21

Machine learning I: scikit-learn

Dr. Huang, Jia Hsin

16

2018/12/28

Machine learning II: scikit-learn & keras

Dr. Huang, Jia Hsin

17

2018/01/04

Review week

18

2018/01/11

Final exam

 

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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 by 08/20/2018 (First Year Students: The paper will be assigned by your lab professor)

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

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

Week

Date

TIGP Bioinformatics

Host

1

2018/09/13

 

 

 

N/A

 

2

2018/09/20

 

 

 

N/A

 

 

3

2018/09/27

 

                     

Addisu Jember Zeleke 迪書 (2017)

 

Topic: Predictive Big Data Analytics: A Study of Parkinson’s Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations

 

 

4

2018/10/04

 

 

 

Nam Nhut Phan 潘日南 (2017)

 

Topic:

 

 

5

2018/10/11

 

 

倪崇恩(YMU)

 

Topic:

 

 

6

2018/10/18

 

 

 劉育丞(YMU)

  

Topic:

 

 

7

2018/10/25

 

段惟芳(YMU)

Topic:

 

 

8

2018/11/01

 

Review Week

 

9

2018/11/08

                    

 Midterm Exam

 

 

10

2018/11/15

 

呂俊良 (YMU)

 

Topic: Phuong Dao,  Yoo-Ah Kim, Damian

Wojtowicz, Sanna Madan, Roded Sharan and Teresa M. Przytycka, "BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions", PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1005695, Published: October 12, 2017.

 

 

11

2018/11/22

 

 

Erickson Erigio Fajiculary 艾瑞克 (2018)

 

Topic:

 

 

 

12

2018/11/29

 

 

Yu-Hsin Chen 陳瑜欣 (2018)

 

Topic:

 

 

 

13

2018/12/6

 

 

Chayanika Goswami 祁雅卡 (2018)

 

Topic:

 

14

2018/12/13

 

 

Adeshina Oyedele Bello 艾迪納 (2018)

 

Topic:

 

 

 

 

15

2018/12/20

 

Jen-Hung Wang 王人弘 (2018)

 

Topic:

 

 

16

2018/12/27

 

Yu-Hsiang Chen 陳煜翔 (2018)

 

Topic:

 

17

2019/1/3

 

Review Week (no class)

 

18

2019/1/10

 

Final Exam

 

 

 

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Seminar

TIGP Bio 2018 Fall Syllabus

   

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

Time: Thursday 14:00-15:20

Chair: Academia Sinica: Dr. Chun-Yen Lin (Informatics), Dr. Chien-Ling Lin (Biology), Dr. Wei-Chung Liu (Statistic);

    

Remarks:

 

1. Attend any 2 none-BP Seminars (either on campus or off campus is fine) and submit a report for each seminar to advisor/lab professor (Format: 1 page A4, 12pts font, single space). Please download the report form from BP web-page

 

Grades: attendance 100%.

Week

Date

Topics/Brief Description

Speaker / Host

1

2018/09/13

Refers to Remarks 1

Dr.

Host:  

2

2018/09/20

Refers to Remarks 1

Dr.

Host:

3

2018/09/27

Using single-cell RNA-seq technology to reveal the role of tissue resident memory (TRM) T-cells in Breast Cancer

Dr. Agus Salim from La Trobe University Australia

Host: Hsin-Chou Yang

4

2018/10/04

p53 Dynamics in Single Cells Unveil Regulatory Principles for Cancer Combination Therapy

Dr. Sheng-Hong Chen

Host:

5

2018/10/11

Ultrasound, nanoparticles, and bioeffects

Dr. Nelson Chen

Assistant Professor, Electrical and Computer Engineering, National Chiao-Tung Univeristy

Host: Dr. Huai-Kaung Tsai

6

2018/10/18

Mining MYCN Regulated Long Noncoding RNAs in Neuroblastoma

Dr. Dyvia Sahu

Host: N/A

7

2018/10/25

-->10/3 (Wed)

Find and drug allosteric sites using first-principle-based simulations and data driven approaches

Dr. D. Sundar

DuPont Young Professor, Dep. of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi

Host: Dr. Lee-Wei Yang

8

2018/11/01

Review Week

 

9

2018/11/08

Midterm Week  

 

10

2018/11/15

Replaced by TIGP-Ethic Course (9/22)

Dr.

Host:

11

2018/11/22

 TBD

Dr. Grace Shieh

Host: N/A

12

2018/11/29

 TBD

Dr. Chu Hsueh-Ping

Assistant Professor

Institute of Molecular and Cellular Biology, National Taiwan University

Host: Chien-Ling Lin

13

 

 

2018/12/06

 

Dr.

Host:

14

 

2018/12/13

 

Dr.

Host:

15

 

2018/12/20

 

Dr.

Host:

16

 

 

2018/12/27

 Replaced by TIGP-Ethic Course (9/22)

Dr.

Host:

17

2019/01/03

Review Week

 

 

18

2019/01/10

Final Exam

 

 

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Lab Rotation

 

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

(Deadline for 2018 Fall Semester: 9/30/2018)

 

Student

Advisor

Student Name

Lab

Yu-Hsiang Chen陳煜翔  
Ren-Hung Wang王人弘  

Erickson Erigio Fajiculay   艾瑞克

 
Yu-Hsin Chen 陳瑜欣  
Adeshina Oyedele Bello 艾迪納  

Chayanika Goswami 祁雅卡

 

















   
TIGP Sinica IIS