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Courses_2018 Spring
 

 

 dec  lab


B2 Course Material
   Basic Molecular Biology II

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

 

Time: Tuesday 09:00-12:00

                                       

Chair: Dr. Chuan-Hsiung Chang and Dr. Sen-Lin Tang

 

Aim:

 

Outline: Big Data in Bioinformatics - From Data-Driven Analysis to Knowledge

 

Textbook: (Reference books, not required)

1.      Approaches in Integrative Bioinformatics: Towards the Virtual Cell [Springer; 2014 edition (January 18, 2014)] ISBN-13: 978-3642412806

2.      Big Data Analytics in Bioinformatics and Healthcare [IGI Global; 1 edition (October 31, 2014)] ISBN-13: 978-1466666115

3.      Biomedical Informatics: Discovering Knowledge in Big Data (2nd edition) 2015 (ISBN-13: 978-3319045276)

 

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

 

Email: N/A     Office hours: N/A

 

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

Week

Date

Topics/Brief Description

Lecturers

 

1

2018/02/27

Bio Big Data – Introduction & Overview

Dr. Chuan-Hsiung Chang

 

2

2018/03/06

NGS Analytics

Dr. I-Shen Tsai

 

3

2018/03/20

Microbiome @9:00-12:00

Dr. Sen-Lin Tang

 

4

2018/03/20

 

Metagenomics @14:00-17:00

Dr. Sen-Lin Tang

 

5

2018/03/27

Transcriptome Informatics

Dr. Ho-Ming Chen

 

6

2018/04/03

Proteomics Principle and applications

Dr. Victor Ng

 

7

2018/04/10

Comparative and Evolutionary Genomics

Dr. I-Sheng Tsai

 

8

2018/04/17

Review Week

 

9

2018/04/24

Midterm Exam

 

10

2018/05/01

Integration of Multidimensional Omics Data

Dr. Chuan-Hsiung Chang

 

11

2018/05/08

Medical Genomics

Dr. Ling-Hui Li

 

12

2018/05/15

Population Genomics

Dr. John Wang

 

13

2018/05/22

Biobank Genotyping

TBD

 

14

2018/05/29

Pharmacogenomics

Dr. Jung-Hsin Lin

 

15

2018/06/05

Translational Clinical Research

Dr. Ueng-Cheng Yang

 

16

2018/06/12

Precision medicine and clinical informatics

Dr. Ueng-Cheng Yang

 

17

2018/06/19

Review Week

 

18

2018/6/26

Final Exam

 

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C2 Course Material

Advanced Algorithms

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

 

Time: Friday 14:00-17:00

 

Chair: Dr. Ting-Yi Sung

 

Aim:

Outline: This course is basically about data mining, machine learning and statistical modeling from data, and some other algorithms and applications.

 

References: (reserved in the library of the Institute of Information Science)

1. First Course in Database Systems (3rd Edition, Ullman and Widom, 2007)

2. Learning from Data- A Short Course (Abu-Mostafa, Magdon-Ismail, Lin, 2012)

3. Learning Pattern Classification (Duda, Harg, and Stork, 2001)  

4. An Introduction to Support Vector Machines and Other Kernel-based Learning Methods   (Cristianini and Shawe-Taylor, 2000)    

 5. Convex optimization (Boyd and Vandenberghe, 2004; book and lecture slides available at http://www.stanford.edu/~boyd/cvxbook/ )

 

TA: Ming-Siang Huang (黃明祥) Email: elephant52381@iis.sinica.edu.tw

 

Office hours: TBD

 

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

Week

Date

Topics/Brief Description

Subtopics/Detail Descriptions/Examples

Lecturers

Slides

1

2018/02/23

Databases: An Overview

N/A

Dr. Chih-Ya Shen

 

2

2018/03/02

Introduction to Data Mining

N/A

Dr. Chih-Ya Shen

 

3

2018/03/09

Data Classification: Overview

N/A

Dr. Li Su

 

4

2018/03/16

Standard Optimization Algorithms

The outline of the optimization couse: basic idea of optimization, convex optimization, lagrangial method for optimization method, and gradient descent methods.

Dr. Wen-Liang Hwang

 

5

2018/03/23

 

Support Vector Machines and Large Margin

The outline of support vector machine: basic principles for maching learning, the support vector machine is a convex optimization method. So, I can use the results of week 1 in week 2.

Dr. Wen-Liang Hwang

 

6

2018/03/30

 

Kernel Methods

N/A

Dr. Wen-Liang Hwang

 

7

2018/04/06

Nonstandard Optimization Algorithms (GA, Random Forest, and others)

N/A

Dr. Huai-Kuang Tsai

 

8

2018/03/13

Review Week

9

2018/04/20

Midterm Exam

10

 

2018/04/27

Hidden Markov Models (I)

N/A

Dr. Yu Tsao

 

11

2018/05/04

Hidden Markov Models (II)

N/A

Dr. Yu Tsao

 

12

2018/05/11

Graphical Models  (I)

N/A

Dr. Hsing-Kuo Pao

 

13

2018/05/18

Graphical Models  (II)

N/A

Dr. Hsing-Kuo Pao

 

14

2018/05/25

Conditional Random Fields

N/A

Dr. Richard Tzong-Han Tsai

 

15

2018/06/01

MapReduce in Cloud Computing

N/A

Dr. Yu-Rong Chang

 

16

2018/06/08

Network Analysis

N/A

Dr. Huan-Cheng Hwang  

 

17

2018/06/15

Review Week

18

2018/06/22

Final Exam

 

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S2 Course Material
Advanced Statistical Methods in Bioinformatics (S2)

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

Time: Thursday 9:00-12:00

Chair: Dr. Grace Hsieh

Outline: Introduction to very useful and advanced statistical methods in computational biology. The topics include: Analysis of next generation sequencing (NGS) Data (e.g., RNA-Seq and ChIP-Seq), maximum likelihood estimation, the EM algorithm, Bayesian inference, Monte Carlo methods, Resampling (Bootstrap & permutation test), Human Genetics, clustering and classification, dimension-reduction and missing data.

Textbook: N/A

Reference book: papers will be given by instructors

Lecturers: Hsuan-Yu Chen, Yen-Tsung Huang, Grace S. Shieh, Han-Ming Wu, Hsin-Chou Yang, Shinsheng Yuan

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

sub-topics/Detail Descriptions

Lecturers

Slides

1

2018/02/22

Analysis of NGS data I

N/A

Dr. Hsuan-Yu Chen

 

2

2018/03/01

Analysis of NGS data II

N/A

Dr. Hsuan-Yu Chen

 

3

2018/03/8

Maximum likelihood estimates and the EM algorithm I

Maximum likelihood estimates

Dr. Yen-Tsung Huang

 

4

2018/03/15

Maximum likelihood estimates and the EM algorithm II

The EM algorithm

Dr. Yen-Tsung Huang

 

5

2018/03/22

Bayesian methods

Bayesian methods 

Dr. Grace S. Shieh

 

6

2018/03/29

Monte Carlo Markov Chains

Monte Carlo Markov Chains

Dr. Shin-Sheng Yuan

 

7

2018/04/05

Holiday

 N/A

N/A

 

8

2018/04/12

Resampling methods I

Permutation test, jacknife

Dr. Grace S. Shieh

 

9

2018/04/19

Midterm Exam

 

 

10

2018/04/26

Resampling methods II  

Bootstrap

Dr. Grace S. Shieh

 

11

2018/05/03

Statistics in Human Genetics I

Concept of Statistical Genetics, International Genomic Projects, Linkage Analysis

Dr. Hsin-Chou Yang

 

 

12

2018/05/10

Statistics in Human Genetics II

Genetic Association, Gene-Gene interaction, Rare Variant Analysis

Dr. Hsin-Chou Yang

 

 

13

2018/05/17

Advanced regression and dimension reduction I

N/A

Dr. Shinsheng Yuan

 

14

2018/05/24

Advanced regression and dimension reduction II

N/A

Dr. Shinsheng Yuan

 

15

2018/05/31

N/A

N/A

N/A

 

16

2018/06/07

Clustering, classification

and data visualization I

Clustering:

(a) K-Means Clustering, Fuzzy c-Means

(b) Self-Organizing Maps (SOM)

(c) Hierarchical Clustering

(d) Ward's Method

(e) Cluster Validation (Biologically)

 

Dr. Han-Ming Wu

 

17

2018/06/14

Clustering, classification

and data visualization II

Classification:

(a) Performance Measures

(b) K-Nearest Neighbors (KNN)

(c) Classification Tree (Decision Tree)

(d) Linear Discriminant Analysis (LDA)

(e) Support Vector Machine (SVM) (plus Kernel Methods)

Data visualization:

(a) Statistical Graphics

(b) Visualizing High-dimensional Data

(b1) Dimension Reduction Techniques

(b2) Dimension-free Visualization

(c) Visualizing Categorical Data

(d) Visualization of Clustering Results

Lab: exercise in R

 

Dr. Han-Ming Wu

 

18

2018/06/21

Final Exam

 

 

 

 
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 2/05/2018

*Your present 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

2018/02/22

 

 

 

N/A

 

2

2018/03/01

 

 

 

N/A

 

 

3

2018/03/08

 

 

                     

Ming-Siang Huang (2016) 

Topic:

 

 

4

2018/03/15

 

 Onkar Singh (2016)

 

Topic:

 

5

2018/03/22

 

 

Nam Nhut Phan潘日南 (2017)

 

Topic:

 

 

6

2018/03/29

 

 

Addisu Jember Zeleke 迪書 (2017)

 

Topic:

 

 

7

2018/04/05

 

 

N/A

 

 

8

2018/04/12

 

Review Week

 

9

2018/04/19

                    

 Midterm Exam

 

 

10

2018/04/26

 

 

N/A

 

 

11

2018/05/03

 

 

Topic:

 

 

 

12

2018/05/10

 

潘昭宇 (2017陽明YMU Student)

 

 

Topic:

 

 

 

13

2018/05/17

 

劉育丞(2017陽明YMU Student)

 

 

Topic:

 

14

2018/05/24

 

 

鄭中遠 (2017陽明YMU Student)

 

Topic:

 

 

 

 

15

2018/05/31

 

 

 

Topic:

 

 

16

2018/06/07

 

N/A

 

17

2018/06/14

 

Review Week (no class)

 

18

2018/06/21

 

Final Exam

 

 

 

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Seminar

TIGP Bio 2018 Spring Syllabus

            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), TBD (Biology), Dr. Wei-Chung Liu (Statistic);

Outline:

Remarks:1. Attend any 2 none-BP Seminars (either on campus or off campus ) and submit a report for each seminar to the 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

2018/02/22

 Refer to Remarks 1

 

2

2018/03/01

 

 

3

2018/03/08

TBD

Dr. Mei-Chu Huang

Institute of Statistical Sciences, Academia Sinica

 

Host:

4

2018/03/15

TBD

Dr. Krishna Swamy

Institute of Biomedical Science, Academia Sinica

 

Host:

5

2018/03/22

iTop-Q: an intelligent tool for top-down proteomics quantitation using DYAMOND algorithm

 

Dr. Chin-Tai Chen

Host: Dr. Ting-Yi Sung

6

2018/03/29

TBD

Dr. Amrita Sengupta

Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University

 

Host:

7

2018/04/05

Holiday

--

8

 

2018/04/12

Review Week

 

9

2018/04/19

Midterm Week  

 

10

 

2018/04/26

 

Dr.

Host:

11

2018/05/03

 

Dr.

Host:

12

2018/05/10

 

Dr.

Host:

13

 

 

2018/05/17

 

Dr.

Host:

14

 

2018/05/24

 

Dr.

Host:

15

 

2018/05/31

 

Dr.

Host:

16

 

 

2018/06/07

 Refer to Remarks 1

Dr.

Host:

17

2018/06/14

Review Week

 

18

2018/06/21

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 Spring Semester: 1/30/2018)

 

Student

Advisor

Student Name

Lab

Nam Nhut Phan潘日南 (2017)  
Addisu Jember Zeleke 艾迪書 (2017)  
 
 
 
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