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AS-TIGP Research Progress Fellowship Program

B1 C1 S1 P1 Seminar Student Presentation Lab Rotation



TIGP 2020 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
Outline:
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: Dr. Chuan-Hsiung Chang, Dr. Ueng-Cheng Yang, Dr. Ho-Ming Chen, Dr. Jung-Hsin Lin, Dr. Wailap Victor Ng, Dr. Yuh-Shan Jou, Dr. Jie-Rong Huang, Dr. An-Chi Wei

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

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

Week Date Topics/Brief Description Lecturers
1 2020/09/15
@N101		 Molecules, Cells, and Evolution Dr. Chuan-Hsiung Chang,
changed to Dr. Ueng-Cheng Yang
2 2020/09/22
Moved from 12/16		 Chemical Foundations,
changed to Cancer		 Dr. Yuh-Shan Jou
3 2020/09/29
@N101		 Protein Structure and Function Dr. Jie-Rong Huang
4 2020/10/06 Transcriptional Control of Gene Expression Dr. An-Chi Wei
5 2020/10/13
@N101		 Basic Molecular Genetic Mechanisms Dr. Ueng-Cheng Yang
6 2020/10/20 Post-Transcriptional Gene Control Dr. Ho-Ming Chen
7 2020/10/27 Molecular Genetic Techniques Dr. Ueng-Cheng Yang
8 2020/11/03 Review Week (no class) ---
9 2020/11/10 Midterm Exam ---
10 2020/11/17 Genes, Genomics, and Chromosomes Dr. Chuan-Hsiung Chang
11 2020/11/24 Biomembrane Structure and Transport Dr. Jung-Hsin Lin
12 2020/12/01 Cellular Energetics Dr. Ueng-Cheng Yang
13 2020/12/08 Signal Transduction and G Protein–Coupled Receptors Dr. Wailap Victor Ng
13 2020/12/09(Wed) Signaling Pathways That Control Gene Expression Dr. Wailap Victor Ng
14 2020/12/15 The Eukaryotic Cell Cycle Dr. An-Chi Wei
14 2020/12/16(Wed)
Moved to 09/22		 -- --
15 2020/12/22 Review Week (no class) ---
16 2020/12/29 Final Exam ---


TIGP Bio 2020 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. Yu Tsao (yu.tsao@citi.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. Meng-Chang Chen, Dr. Huai-Kuang Tsai, Dr. Jinn-Jy Lin, Dr. Ting-Yi Sung, Dr. Hsin-Nan Lin, Dr. Chen-Hsin Yu, Dr. Ching-Tai Chen, Dr. Jung-Hsin Lin
Textbook:
Reference book:
TA: Yu-Hsiang Chen 陳煜翔 Email: s871818@gmail.com
Office hours: Wednesday 10:00 am-12:00 pm
Office location: Room 103, Old Building of the Institute of Information Science, Academia Sinica
Grades: Midterm exam 50%. Final exam 50%.
Week Date Topics/Brief Description
Subtopics/Detail Descriptions/Examples		 Lecturers
1 2020/09/18  Analysis of Algorithms Dr. Wen-Lian Hsu
2 2020/09/25  Recurrence Dr. Wen-Lian Hsu
3 2020/10/02 (Holiday)
-> 09/30 (Wed)		  Introduction to Data Structure (I) Dr. Yu-Jung Chang
4 2020/10/09 (Holiday)
-> 10/07 (Wed)		  Introduction to Data Structure (II) Dr. Yu-Jung Chang
5 2020/10/16  Algorithmic Techniques Dr. Wen-Lian Hsu
6 2020/10/23  Databases : An Overview Dr. Meng-Chang Chen
7 2020/10/30  Introduction to Data Mining Dr. Meng-Chang Chen
8 2020/11/06  Review Week (no class)  
9 2020/11/13 Midterm Exam  
10 2020/11/18 (Wed)  Sequence alignment Dr. Huai-Kuang Tsai
10 2020/11/20 Fundamentals of Molecular Evolution and Phylogenetic Tree Construction Dr. Jinn-Jy Lin
11 2020/11/25 (Wed)  Motif finding Dr. Ting-Yi Sung
11 2020/11/27  The Analysis of Next Generation Sequencing Data Dr. Hsin-Nan Lin
12 2020/12/04  ChIP-seq Dr. Chen-Hsin Yu
13 2020/12/11 Computational Proteomics Dr. Ching-Tai Chen
14 2020/12/18 Fundamentals in Structural Bioinformatics Dr. Jung-Hsin Lin
15 2020/12/25  Review Week (no class)  
16 2020/01/04 (Mon)  Final Exam  


TIGP Bio 2020 Fall Syllabus Fundamental Statistical Methods in Bioinformatics (S1)
Place: Room 107, New Building of the Institute of Information Science, Academia Sinica.
Time: Thursday 09:00-12:00
Chair: Dr. Shinsheng Yuan (shinshengyuan@gmail.com)
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: Erickson Erigio Fajiculary 艾瑞克  Email: efajiculay@yahoo.com
Office hours: Tuesday 16:00 pm-18:00 pm
Office location: Room 304, Old Building of the Institute of Information Science, Academia Sinica
Grades: Midterm exam 50%. Final exam 50%.
Week Date Topics/Brief Description Sub-topics/Detailed Description Lecturers
1 2020/09/16 (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
1 2020/09/17
@N106		 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
2 2020/09/24 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 2020/10/01 (Holiday)
-> 10/08		 Continuous Distributions, Expectations and Basic Statistics (1) Continuous random variable
(2) Expectation
(3) Basic statistics
(4) Limit theorems (optional)		 Dr. Hsin-Chou Yang
5 2020/10/15 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 2020/10/22 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 Shieh
7 2020/10/29
@O108		 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 2020/11/05 Review Week (no class)  
9 2020/11/12 Midterm Exam  
10 2020/11/19 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) Matrix approach to simple linear regression
(6) Multiple linear regression
(7) Building the regression model
(8) Qualitative predictor variables
(9) Analysis of variance		 Dr. Grace Shieh
11 2020/11/25 (Wed) 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
11 2020/11/26 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
12 2020/12/02 (Wed) 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
12 2020/12/03 Classification 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
13 2020/12/10 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
14 2020/12/17 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
15 2020/12/24 Review Week (no class)  
16 2020/12/31 Final Exam  

TIGP Bio 2020 Fall Syllabus Programming (Python) (P1)
Place: Room 108, Old Building of the Institute of Information Science, Academia Sinica.
Time: Friday, 10:00am-12:00pm
Chair: Dr. John Wang (johnwang@gate.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: Dr. John Wang, Dr. Li Su, Dr. Te-Chuan Chiu, Dr. Ching-Fen Chang, Dr. An-Chi Wei, Dr. Guan-Shuo Mai, Dr. Yu-Lun Hsieh
Textbook: Python for Biologists: A complete programming course for beginners
                    Advanced Python for Biologists
                    (Reference) Python for Everybody - Exploring Data In Python 3

TA: Chayanika Goswami 祁雅卡  Email: chayabinf@gmail.com
Office hours: Wednesday, 14:00pm-16:00pm
Office location: Room 304, Old Building of the Institute of Information Science, Academia Sinica

TA: Cheng-Kuo Lai 賴政國  Email: lihowfun@gmail.com
Office hours: Wednesday, 14:00pm-16:00pm
Office location: B303, Interdisciplinary Research Building, Academia Sinica

Grades: Midterm exam 25%. Final exam 30%. Homework 35%. Class performance (10%)
Week Date Topics/Brief Description
Subtopics/Detail Descriptions/Examples		 Lecturers
1 2020/09/18 Introduction to Python Dr. John Wang
2 2020/09/23 (Wed) Basic Elements of Python I Dr. Li Su
2 2020/09/25 Basic Elements of Python II Dr. Li Su
3 2020/10/02(Holiday)
-> 09/30 (Wed)		 Basic statements I: branching programs and inputs Dr. John Wang
4 2020/10/09(Holiday)
-> 10/07 (Wed)		 Basic statements II: iterative programs Dr. John Wang
5 2020/10/16 Functions: scope rules and passing arguments Dr. John Wang
6 2020/10/23 Modules, Files, and Structured Types Dr. Te-Chuan Chiu
7 2020/10/30 Exception handling Dr. Te-Chuan Chiu
8 2020/11/06 Review week (No Class)
9 2020/11/13 Midterm exam
10 2020/11/18 (Wed) Introduction to Biopython Dr. Ching-Fen Chang
10 2020/11/20 Regular expressions Dr. Ching-Fen Chang
11 2020/11/27 Object-oriented programming: classes Dr. Li Su
12 2020/12/04 Data analysis toolbox: NumPy, Pandas, Matplotlib Dr. An-Chi Wei
13 2020/12/11 Machine learning I: scikit-learn Mr. Guan-Shuo Mai
14 2020/12/18 Machine learning II: scikit-learn & keras Dr. Yu-Lun Hsieh
15 2020/12/25 Review week (No Class)
16 2020/12/30(Wed) Final exam


Student Presentation

Place: Room 101, New Building of the Institute of Information Science, Academia Sinica
Time: Thursday, 3:30 Pm-5:00 pm
Chair: Dr. Chuan-Hsiung Chang, Dr. Chen-Ching Lin
*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 Sep 3, 2020 (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 Chang 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.

*Seminar presentation guidelines for PhD program students_2020
Week Date Topic Student
1 2020/09/17 TBA Yueh-Hua Tu 杜岳華
2 2020/09/24 TBA Samarth Gupta 山瑪斯
3 2020/10/01 Mid-Autumn Festival (No class) ----
4 2020/10/08 TBA Yu-Ching Hsu 徐于晴
5 2020/10/15 TBA Po-Yuan Chen 陳柏元
6 2020/10/22 TBA Chung-En Ni 倪崇恩
7 2020/10/29 TBA David Nicola Streuli 施大衛
8 2020/11/05 Review Week (No class) ----
9 2020/11/12 Midterm Week (No class) ----
10 2020/11/19 TBA Jia-Ying Su 蘇家瑩
11 2020/11/26 TBA Yu-Chun Huang 黃郁珺
12 2020/12/03 TBA Hsin-Han Lee 李昕翰
13 2020/12/10 TBA Yi-Chen Yeh 葉奕成
14 2020/12/17 TBA Shu-Chuan Chen 陳淑娟
15 2020/12/24 Review Week (No class) ----
16 2020/12/31 Final Exam (No class) ----

Seminar
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), Chien-Ling Lin (Biology), Dr. Wei-Chung Liu (Statistic)

Remarks: 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 2020/09/17 Billiard Ball Therapy - Toward a Rational Repurposing of FDA Drugs that Target Multiple Sites in a Disease-Relevant Protein Dr. Lee-Wei Yang
Host: Chayanika Goswami
2 2020/09/24 The Roles of Endogenous Ligand for Aryl Hydrocarbon Receptor in Neural Development and Tumorigenesis of Neuroblastoma Dr. Hsin-Yu Lee
Host: Yueh-Hua Tu
3 2020/10/01 Mid-Autumn Festival (No class) ----
4 2020/10/08 A Simple Approach for Quantifying Node Importance in Signed And Directed Networks Dr. Wei-Chung Liu
Host: Yu-Hsin Chen
5 2020/10/15 TBA Dr. Chao-Ping Hsu
Host: Yu-Hsiang Chen
6 2020/10/22 TBA Dr. Y. Jane Tseng
Host: Yu-Ching Hsu
7 2020/10/29 TBA Dr. Nikhil Pathak
Host: Jen-Hung Wang
8 2020/11/05 Review Week (No class) ----
9 2020/11/12 Midterm Week (No class) ----
10 2020/11/19 TBA Dr. Ching-Te Kuo
Host: Hsin-Han Lee
11 2020/11/26 TBA Dr. Ting-Yi Sung
Host: Jia-Ying Su
12 2020/12/03 TBA Dr. Ben Yang Liao
Host: Samarth Gupta
13 2020/12/10 TBA Dr. Sen-Lin Tang
Host: Erickson Erigio Fajiculary
14 2020/12/17 TBA Dr. Wen-Hsiung Li
Host: Yu-Chun Huang
15 2020/12/24 Review Week (No class) ----
16 2020/12/31 Final Exam (No class) ----

Lab Rotation

All 1st year students:
Please inform BP office for the laboratory you are rotating (Deadline for 2020 Fall Semester is on 09/30/2020)
Student Advisor
Yu-Ching Hsu 徐于晴 (2020)  
Hsin-Han Lee 李昕翰 (2020)  
Jia-Ying Su 蘇家瑩 (2020)  
Hsin-Ju Hung 洪欣如 (2020)  
Yu-Chun Huang 黃郁珺 (2020)  
Po-Yuan Chen 陳柏元 (2020)  
David Nicola Streuli 施大衛 (2020)  
Aishwarya Tiwari 艾希雅 (2020)  

https://tigpbp.iis.sinica.edu.tw/tigpbio/old/publications.html

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Bioinformatics Program, TIGP , Academia Sinica , Taiwan 2019