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Courses_2017 Fall
 

 

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B1 Course Material

TIGP Bio 2017 Fall Syllabus

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

2017/09/12

Molecules, Cells, and Evolution

Dr. Chuan-Hsiung Chang

Moodle

2

2017/09/19

Chemical Foundations

Dr. Jie-Rong Huang

Moodle

3

2017/09/26

Protein Structure and Function

Dr. Jie-Rong Huang

Moodle

4

2017/10/03

Transcriptional Control of Gene Expression@N101

Dr. Jinn-Jy Lin

Moodle

5

2017/10/24

2pm-5pm

Cancelled

-->moves to 10/31 @ 9am-12pm

Basic Molecular Genetic Mechanisms @N107

Dr. Ueng-Cheng Yang

Moodle 

6

2017/10/17

Genes, Genomics, and Chromosomes

Dr. Chuan-Hsiung Chang

 

Moodle

7

2017/10/24

Cancelled

-->moves to 10/31 @ 2-5pm

Molecular Genetic Techniques

Dr. Ueng-Cheng Yang

Moodle 

8

2017/10/31

Review Week (Lecture 5 &7)

---

9

2017/11/07

Midterm Exam

---

10

2017/11/14

Post-Transcriptional Gene Control

Dr. Ho-Ming Chen

Moodle

11

2017/11/21

Biomembrane Structure and Transport@O108

Dr. Jung-Hsin Lin

Moodle

12

2017/11/28

 

Cellular Energetics

Dr. Ueng-Cheng Yang

 

13

2017/12/05

Signal Transduction and G Protein–Coupled Receptors

Dr. Wailap Victor Ng

 

14

2017/12/12

Signaling Pathways That Control Gene Expression

Dr. Wailap Victor Ng

 

15

2017/12/19

The Eukaryotic Cell Cycle

TBD

 

16

2017/12/26

Cancer

Dr. Yuh-Shan Jou

 

17

2018/01/02

Review Week

---

18

2018/01/09

Final Exam

---

 
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C1 Course Material

TIGP Bio 2017 Fall Syllabus

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 )

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. Jinn-Jy Lin, Dr. Ting-Yi Sung, Dr. Ching-Tai Chen

Textbook: N/A

Reference book: N/A

 TA: Neha Warikoo 倪荷 Email: nehawarikoo@iis.sinica.edu.tw

Office hours: Tuesday 2:00-4:00pm

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

 

Week

Date

Topics/Brief Description

Lecturers

 Slides

1

2017/09/15

Analysis of Algorithms

Dr. Wen-Lian Hsu

Moodle

2

2017/09/22

Recurrence

Dr. Wen-Lian Hsu

Moodle

3

2017/09/29

Introduction to Data Structure (I)

Dr. Yu-Jung Chang

Moodle

4

2017/10/06

Introduction to Data Structure (II)

Dr. Yu-Jung Chang

Moodle

5

2017/10/13 --> moves to 10/17

@13:30-16:30

Algorithmic Techniques

Dr. Wen-Lian Hsu

Moodle

6

2017/10/20

 

Motif Finding @N101

Dr. Ting-Yi Sung

Moodle

7

2017/10/27

Graph Algorithms  @N108

Dr. Ting-Yi Sung

Moodle

8

2017/11/03

Review Week

---

9

2017/11/10

Midterm Exam @N101

---

10

2017/11/17

Sequence Alignment (I)@Rm#B101, B1 of CITI

Dr. Huai-Kuang Tsai

Moodle

11

2017/11/24

Sequence Alignment (II) @O108

Dr. Huai-Kuang Tsai

Moodle

12

2017/12/01

Combinatorial Pattern Matching

Dr. Ching-Tai Chen

 

13

2017/12/08

Suffix Trees

Dr. Ching-Tai Chen

 

14

2017/12/15

The Analysis of Next Generation Sequencing Data(I)

Dr. Hsin-Nan Lin

 

15

2017/12/22

The Analysis of Next Generation Sequencing Data (II)

Dr. Hsin-Nan Lin

 

16

2017/12/29

Fundamentals of Molecular Evolution and Phylogenetic Tree Construction

Dr. Jinn-Jy Lin

 

17

2018/01/05

Review Week

---

18

2018/01/12

Final Exam

---

 

 
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S1 Course Material

 

TIGP Bio 2017 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:  Kshitij Tandon Email: kshitijtandon.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 2017/9/14

--> 9/13(Wed) 

Descriptive Statistics, Genomic Data Analysis

Room# N101 

(1)  Introduction to statistics
(2)  Descriptive statistics
(3)  Fundamental of molecular biology
(4) Genomic data analysis
Dr. Chen-Hsiang Yeang Moodle 
2 2017/09/21 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 2017/9/28 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 2017/10/5 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 2017/10/12 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
6 2017/10/19 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
7 2017/10/26 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 2017/11/02 Review Week(no class)    
9 2017/11/09 Midterm Exam    
10 2017/11/16  -->11/14 @2-5PM Correlation, 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 2017/11/23 Logistic Regression and Statistical Meta Analysis @B101, B1 of CITI (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 2017/11/30 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 2017/12/07 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 2017/12/14 Classification@201 (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 2017/12/21 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 2017/12/28 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 2018/1/04 Review Week(no class)    
18 2018/1/11 Final Exam    
 
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P1 Course Material  

TIGP Bio 2017 Fall Syllabus

Programming (Python) (P1)

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

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

Chair: Dr. Wang, John (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. Krishna Swamy;
                  SHNCC- Dr. Wang, Chih-Yu;
Dr. Chang, Jia-Ming; Dr. Wang, Chuan-Ju ;

                                Dr. Huang, Jia Hsin

Textbook: Python for Biologists: A complete programming course for beginners

                  Advanced Python for Biologists

Reference book: Python for Everybody - Exploring Data In Python 3

                             Python Machine Learning by Sebastian Raschka

 TA: 陳志明(SNHCC)  Email: changecandy@gmail.com

       Maharasan Kathiresan (BP) Email: maharasan.k1991@iis.sinica.edu.tw

Office hours: Wednesdays 10:00am-12:00pm (Room #304 ) Maharasan Kathiresan

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

Week

Date

Topics/Brief Description

Lecturers

Slides

1

2017/09/15

Introduction to Python 

Dr. Wang, Chuan-Ju

Moodle

2

2017/09/22

Basic Elements of Python I

Dr. Wang, Chuan-Ju

Moodle

3

2017/09/29

Basic Elements of Python II

Dr. Wang, Chuan-Ju

Moodle

4

2017/10/06

Basic statements I: branching programs and inputs

 

Dr. Wang, John

Moodle

5

2017/10/13

Basic statements II: iterative programs Rm#N106

 

Dr. Wang, John

Moodle

6

2017/10/20

Functions: scope rules and passing arguments

 

Dr. Wang, John

Moodle

7

2017/10/27

Modules, Files, and Structured Types

 

Dr. Wang, Chih-Yu

Moodle

8

2017/11/03

Exception handling /

Sequence Aliment  Rm#N106

Dr. Wang, Chih-Yu /

Dr. Chang, Jia-Ming

Moodle

9

2017/11/10

Review week

10

2017/11/17

Midterm exam

11

2017/11/24

Introduction to Biopython

Dr. Krishna Swamy

Moodle

12

2017/12/01

Regular expressions

Dr. Krishna Swamy

 

13

2017/12/08

Object-oriented programming: classes

 

Dr. Krishna Swamy  

14

2017/12/15

Data analysis toolbox  : NumPy, Pandas, Matplotlib

Dr. Huang, Jia Hsin

 

15

2017/12/22

Machine learning I: scikit-learn

Dr. Huang, Jia Hsin

 

16

2017/12/29

Machine learning II: scikit-learn & keras

Dr. Huang, Jia Hsin

 

17

2018/01/05

Review week

18

2018/01/12

Final exam

 

 
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Student Presentation

2017 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 8/25/2017.

*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:  attendance is optional (except your scheduled  presentation date)

Week

Date

TIGP Bioinformatics

Host

1

2017/9/14  

 

 

 

N/A

 

2

2017/09/21

 

 

 

N/A

 

 

3

2017/9/28

 

                     

N/A

 

 

4

2017/10/5

 

 

N/A

 

5

2017/10/12

 

 Onkar Singh (2016)

 

Topic:

 

 

6

2017/10/19

 

 

 

Ming-Siang Huang (2016) 

Topic:

Simon Baker, Imran Ali, Ilona Silins, Sampo Pyysalo, Yufan Guo,Johan Hogberg, Ulla Stenius and Anna Korhonen, "Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer.", Bioinformatics. 14 July 2017, 1–9. doi: 10.1093/bioinformatics/btx454.

 

 

 

7

2017/10/26

 

 

N/A

 

 

8

2017/11/02

 

Review Week

 

9

2017/11/09

                    

 Midterm Exam

 

 

10

2017/11/16

 

N/A

 

 

11

2017/11/23

 

Nam Nhut Phan潘日南 (2017)

 

Topic:

Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani, Qianjin Feng, and Kun Huang, "Identification of Topological Features in Renal Tumor Microenvironment Associated with Patient Survival", Bioimage informatics

 

 

12

2017/11/30

 

Addisu Jember Zeleke 迪書 (2017)

 

Topic:

 

Yinglei Lai et.al ,Department of Statistics and Biostatistics Center, The George Washington University, 20052 Washington D.C., USA.
Title " A statistical m.ethod for the conservative adjustment of false discovery rate (q-value)" BMC Bioinformatics

 

 

13

2017/12/07

 

 

N/A

 

14

2017/12/14

 

潘昭宇 (2017陽明YMU Student)

 

Topic:

Angermueller C, Lee HJ, Reik W, Stegle O. "DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning." Genome Biology. 2017;18:67. doi:10.1186/s13059-017-1189-z.

 

 

 

15

2017/12/21

 

 

劉育丞(2017陽明YMU Student)

 

Topic:

 

Kelly Mulholland and Chun WuKelly Mulholland and Chun Wu J. Chem. Inf. Model., 2016, 56 (10), pp 2093–2102. "Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent" DOI: 10.1021/acs.jcim.6b00473
Publication Date (Web): September 15, 2016

 

16

2017/12/28

 

鄭中遠 (2017陽明YMU Student)

Topic:

Mowery D, Smith H, Cheney T, Stoddard G, Coppersmith G, Bryan C, Conway M, "
Understanding Depressive Symptoms and Psychosocial Stressors on Twitter: A Corpus-Based Study."
, J Med Internet Res. 2017 Feb 28;19(2):e48. doi: 10.2196/jmir.6895.
 

 

17

2018/1/04

 

Review Week (no class)

 

18

2018/1/11

 

Final Exam

 

 


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Seminar

TIGP Bio 2017 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. Wei-Chung Liu (Statistic)

Grades: attendance 100%.

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

          2. Student who attends TIGP-Distinguished Lecture on 10/13 could be waived for 1 none-BP Seminar as stated in Remarks 1 and does not need to write a report.

Week

Date

Topics/Brief Description

Speaker / Host

1

2017/9/14   N/A (Refer to Remarks 1)

Dr.

Host:

2

2017/09/21 Life is too dynamic to be captured on bench - understanding life in silico driven by data science and first principles

Dr. Lee-Wei Yang

Institute of Bioinformatics and Structural Biology, NTHU

3

2017/9/28 Alternative trans-splicing and cis-backsplicing in human cells

Dr. Trees-Juen Chuang   Genomics Research Center,
Academia Sinica

4

2017/10/5 Epigenome-wide association studies for human diseases

Dr. Pei-Chien Tsai

Dep. of Biomedical Sciences, Chang Gung University

 Host: Dr. Pao-Yang Chen

5

2017/10/13

(15:30-17:30@ 3F of  HSS)

TIGP- Distinguished Lecture

My Journey

Register Here

(1. Signature is required as attendance credit. 2. could replace 1 none-BP Seminar. 3. No report is required)

   Dr. Morris Chang

Founding Chairman, Taiwan Semiconductor Manufacturing Company

Host:

6

2017/10/19 Advance the understanding of regulatory genomics by data integration

Dr. Zing Tsung-Yeh Tsai

University of Michigan Department of Computational Medicine and Bioinformatics

Host: Dr. Huai-Kuang Tsai

7

2017/10/26

N/A

 

8

 

2017/11/02

Review Week (no class)

 

9

2017/11/09

Midterm Exam

 

10

  

2017/11/16

@N107

Computational modelling to understand the dynamics and noise propagation in biological systems Dr. Surendhar Reddy
Institute of Chemistry, Academia Sinica
Host: Cherri Hsu
 

11

2017/11/23 Replaced by 2017 TIGP Ethic Course

9/23(Sat) 9:00am-15:30pm  Location: 1st Conference Rm, 2F Activity Center, Academia Sinica

Dr. Tien-Hsien Chang, Deputy Director, Genomics Research Center

Host: Genomics Research Center

12

2017/11/30

N/A

 

13

  

2017/12/07 Genomic analyses of Mycobacterium tuberculosis isolates and identification of drug resistant mutations

Dr. Wen-Hsiung Li

Biodiversity Center, Academia Sinica

Host: Dr. Wen-Lian Hsu

14

2017/12/14 Replaced by 2017 TIGP Ethic Course

9/23(Sat) 9:00am-15:30pm  Location: 1st Conference Rm, 2F Activity Center, Academia Sinica

Dr. Tien-Hsien Chang, Deputy Director, Genomics Research Center

Host: Genomics Research Center 

15

 

2017/12/21 A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data

Dr. En-Yu Lai

Host: Yen-Tsung Huang

16

  

2017/12/28 Translating knowledge gained from alternative splicing into precision medicine tools

Dr. Younghee Lee

    Department of       Biomedical Informatics, University of Utah, Asia Campus

Host: TBD/Nikhil Pathak

 17

2018/1/04

Review Week (no class)

 

18

2018/1/11

Final Exam

 

 

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Lab Rotation

 

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

(Deadline for 2017 Fall Semester: 9/23/2017)

 

Student Name

Lab

Nam Nhut Phan潘日南 (2017) Dr. Eric Y. Chuang
Addisu Jember Zeleke 艾迪書 (2017) ------
 
 
 
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