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B1 C1 S1 P1 Seminar Student Presentation Lab Rotation
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 et al. Publisher: W. H. Freeman. International Edition (1 April, 2016). ISBN-13: 978-1464183393.
Local book store: https://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06906
Reference: (Recommended but not required)
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: 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. Seng-Ling Tang, 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 2019/09/10 Molecules, Cells, and Evolution Dr. Chuan-Hsiung Chang
2 2019/09/17 Chemical Foundations Dr. Cherri Hsu
3 2019/09/24 Protein Structure and Function file Dr. Jie-Rong Huang
4 2019/10/15 2-5pm Transcriptional Control of Gene Expression Dr. An-Chi Wei
5 2019/10/08 Basic Molecular Genetic Mechanisms Dr. Ueng-Cheng Yang
6 2019/10/15 Genes, Genomics, and Chromosomes Dr. Chuan-Hsiung Chang
7 2019/10/22 Molecular Genetic Techniques Dr. Ueng-Cheng Yang
8 2019/10/29 Review Week ---
9 2019/11/05 Midterm Exam ---
10 2019/11/12 Post-Transcriptional Gene Control Dr. Ho-Ming Chen
11 2019/11/19 Biomembrane Structure and Transport Dr. Jung-Hsin Lin
12 2019/11/26 Cellular Energetics Dr. Ueng-Cheng Yang
13 2019/12/03 Signal Transduction and G Protein–Coupled Receptors Dr. Wailap Victor Ng
14 2019/12/10 Signaling Pathways That Control Gene Expression Dr. Wailap Victor Ng
15 2019/12/17 The Eukaryotic Cell Cycle Dr. An-Chi Wei
16 2019/12/24 Cancer Dr. Yuh-Shan Jou
17 2019/12/31 Review Week ---
18 2020/01/07 Final Exam ---

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
TA: Onkar Singh Email: onkarsinghgmt@gmail.com
Office hours: TBD
Grades: Midterm exam 50%. Final exam 50%.
Week Date Topics/Brief Description Lecturers
1 2019/09/13
(Holiday)
-09/16 14:00-17:00		 Analysis of Algorithms file Dr. Wen-Lian Hsu
2 2019/09/20 Recurrence file Dr. Wen-Lian Hsu
3 2019/09/27 Introduction to Data Structure (I) Dr. Yu-Jung Chang
4 2019/10/04 Introduction to Data Structure (II) Dr. Yu-Jung Chang
5 2019/10/11
(Holiday)
-10/21(Mon.) 2-5pm		 Algorithmic Techniques Dr. Wen-Lian Hsu
6 2019/10/18 Motif Finding file Dr. Ting-Yi Sung
7 2019/10/25 Graph Algorithms file Dr. Ting-Yi Sung
8 2019/11/01 Review Week ---
9 2019/11/08 Midterm Exam ---
10 2019/11/15 Sequence Alignment (I) Dr. Huai-Kuang Tsai
11 2019/11/22 Sequence Alignment (II) Dr. Huai-Kuang Tsai
12 2019/11/29 Combinatorial Pattern Matching Dr. Ching-Tai Chen
13 2019/12/06 Suffix Trees Dr. Ching-Tai Chen
14 2019/12/13 The Analysis of Next Generation Sequencing Data (I) Dr. Hsin-Nan Lin
15 2019/12/20 The Analysis of Next Generation Sequencing Data (II) Dr. Hsin-Nan Lin
16 2019/12/27 Fundamentals of Molecular Evolution and Phylogenetic Tree Construction Dr. Jynn-Jy Lin
17 2020/01/03 Review Week ---
18 2020/01/10 Final Exam ---

S1 course Material
Fundamental Statistical Methods in Bioinformatics (S1)
Place:Room 108, Old Building of the Institute of Information Science, Academia Sinica
Time:Thursday, 09:00 am-12:00 pm
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: Jen-Hung Wang 王人弘 Email: why2kill@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 2019/09/12 Descriptive Statistics, Genomic Data Analysis file (1) Introduction to statistics
(2) Descriptive statistics
(3) Fundamental of molecular biology
(4) Genomic data analysis		 Dr. Chen-Hsiang Yeang
2 2019/09/19 Probability file (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 2019/09/26 Discrete Distributions and Contingency Tables file (1) An application inpharmacogenetic 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 2019/10/03 Continuous Distributions, Expectations and Basic Statistics file (1) Continuous random variable
(2) Expectation
(3) Basic statistics
(4) Limit theorems (optional)		 Dr. Hsin-Chou Yang
5 2019/10/10
(Holiday)
-10/16 14:00-17:00 		Parameter Estimation and Confidence Interval (1) Unbiasedness
(2) Point estimation (substitution principles, least square estimate, maximum likelihood estimate)
(3) Interval estimation		 Dr. Grace Shieh
6 2019/10/17 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. Shinsheng Yuan
7 2019/11/06 9:00-12:00 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 2019/10/31 Review Week
9 2019/11/07 Midterm Exam
10 2019/11/14 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 2019/11/21 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 2019/11/28 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

2019/12/02(Mon.)

2-5pm

 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 2019/12/12 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
15 2019/12/19 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
16 2019/12/26 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 2020/01/02 Review Week
18 2020/01/09 Final Exam

P1 Course Material
Programming (Python) (P1)
Place:Room 108, Old Building of the Institute of Information Science, Academia Sinica
Time:Friday, 10:00am-12:00pm
Chair:Dr. Wang, John
Outline:This course introduces basic aspects f 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. 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: Erickson Erigio Fajiculary 艾瑞克 Email: efajiculay@yahoo.com
Office hours: TBD
Grades: Midterm exam 25%. Final exam 30%. Homework 35%. Class performance (10%).
Week Date Topics/Brief Description Lecturers
1 2019/09/13
(Holiday)
09/18 09:00-11:00		 Introduction to Python Dr. Li Su
2 2019/09/20 Basic Elements of Python I Dr. Su Li
3 2019/09/27 Basic Elements of Python II Dr. Su Li
4 2019/10/04 Basic statements I: branching programs and inputs Dr. John Wang
5 2019/10/11
(Holiday) -
10/5 10:00-12:00		 Basic statements II: iterative programs Dr. John Wang
6 2019/10/18 Functions: scope rules and passing arguments Dr. John Wang
7 2019/10/25 Modules, Files, and Structured Types Dr. Te-Chuan Chiu
8 2019/11/01 Exception handling Dr. Te-Chuan Chiu
9 2019/11/08 Review week
10 2019/11/15 Midterm exam
11 2019/11/22 Introduction to Biopython Dr. Ching-Fen Chang
12 2019/11/29 Regular expressions Dr. Ching-Fen Chang
13 2019/12/06 Object-oriented programming: classes Dr. John Wang (Chih-Ming Chen)
14 2019/12/13 Data analysis toolbox : NumPy, Pandas, Matplotlib Dr. Jia Hsin Huang
15 2019/12/20 Machine learning I: scikit-learn Dr. Jia Hsin Huang
16 2019/12/27 Machine learning II: scikit-learn & keras Dr. Jia Hsin Huang
17 2019/01/03 Review week
18 2019/01/10 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
*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 09/12/2019 (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.

*Seminar presentation guidelines for PhD program students_20190909
Week Date TIGP Bioinformatics
1 2019/09/12 N/A
2 2019/09/19 N/A
3 2019/09/26 倪崇恩 (YMU)Topic: DeepInsight: A methodology to transform a non-image data to an image for convolution neural network architecture
4 2019/10/03 N/A
5 2019/10/10(Holiday) N/A
6 2019/10/17 段惟芳(YMU)Topic:
7 2019/10/24 Erickson Erigio Fajiculary
艾瑞克
(2018)Topic:
8 2019/10/31 Review Week
9 2019/11/07 Midterm Exam
10 2019/11/14 葉奕成(YMU)
(2018)Topic: Clinical-grade computational pathology using weakly supervised deep learning on whole slide images
11 2019/11/21 Yu-Hsin Chen
陳瑜欣
(2018)Topic:
12 2019/11/28 Chayanika Goswami
祁雅卡
(2018)Topic:
13 2019/12/05 Adeshina Oyedele Bello
艾迪納
(2018)Topic:
14 2019/12/12 Jen-Hung Wang
王人弘
(2018)Topic:
15 2019/12/19 Yu-Hsiang Chen
陳煜翔
(2018)Topic::
16 2019/12/26 Yueh-Hua Tu
杜岳華
(2019)Topic:
17 2020/01/02 Samarth Gupta
山瑪斯
(2019)Topic
18 2020/01/09 Final Exam

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), Dr. 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 2019/09/12 N/A
Refers to Remarks 1
2 2019/09/19 N/A
Refers to Remarks 1
3 2019/09/26 Novel insights on green sulfur bacteria in coral skeletons Dr. Shan-Hua Yang
Institute of fisheries science,National Taiwan UniversityHost: Yu-Hsiang Chen
4 2019/10/03-2019/10/02
14:00-16:00		 AI Democratization in Taiwan Dr. Sheng-Wei (Kuan-Ta) Chen
5 2019/10/10
(Holiday)		 N/A
6 2019/10/17

A-to-I RNA editing: a possible explanation for the persistence of predicted damaging mutations in healthy individuals

Dr. Trees-Juen Chuang
Host: Dr. Chien-Ling Lin
7 2019/10/24 TBD Prof. Cho-Yi Chen
8 2019/10/29 Weighing the Options: Non-academic Career Paths that New Ph.D. Holders Should Consider Dr. Emmanuel Salawu
9 2019/11/07 Midterm Week
10 2019/11/14 TBD Prof. Chen-Ching Lin
11 2019/11/21 TBD Dr. Hsueh-Fen Juan
12 2019/11/28 TBD Dr. Chao-Yuan Yeh
13 2019/12/05 TBD Dr. Ming-Jing Hwang
14 2019/12/12 TBD Prof. Chun-Yu lin
15 2019/12/19 TBD Dr. Ching-Tai Chen
16 2019/12/26 TBD Dr. Hsin-Nan Lin
17 2019/01/02 Review Week
18 2019/01/09 Final Exam

Lab Rotation

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

(Deadline for 2019 Fall Semester: 09/30/2019)
Student Advisor
Student Name Lab
Yueh-Hua Tu 杜岳華 (2019)
Samarth Gupta 山瑪斯 (2019)

2019 TIGP-BP Orientation Agenda

Date: 2019/10/07 (Mon.)        
Venue: Room 201, IIS old building, AS    
Host: Dr. Hsin-Chou Yang (Program Coordinator)


Time

Activity

Details

12:00-12:05

Opening

By Dr. Hsin-Chou Yang (Program Coordinator)

12:05-12:25

Program Session-BP slides

Dr. Wei-Chung Liu ( Student Affair Chair )

12:25-12:30

New Student Session

Self –introduction ( 2 new students)

12:30-13:00

Open Discussion

Lunch box for all attendees

13:00-13:15

Senior Students Session

Student Representatives/ Senior Students

13:15-13:20

Closing

Dr. Hsin-Chou Yang (Program Coordinator)

13:20-13:30

Group Picture

Entrance of IIS


Bioinformatics Program, TIGP , Academia Sinica , Taiwan©2019