toppic
news pstudents academic cstudents faculty about contact link
news green02
 
 
 
 
 
 
 
 
 
 
Courses_2017 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

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

Slides

1

2017/02/14

Bio Big Data – Introduction & Overview

Dr. Chuan-Hsiung Chang

Moodle

2

2017/02/21

NGS Analytics

 

Dr. I-Shen Tsai

Moodle

3

2017/03/01

(Wed)

 

Microbiome

-->Cancelled (moves to 3/7)

 

Dr. Sen-Lin Tang

Moodle

4

2017/03/07

 

 

Microbiome (9:00-12:00)

Metagenomics(13:30-16:30)

 

Dr. Sen-Lin Tang

Moodle

5

2017/03/14

Transcriptome Informatics

 

Dr. Ho-Ming Chen

Moodle

6

2017/03/21

Proteomics Informatics

 

Dr. Victor Ng

Moodle

7

2017/03/28

--> moves to 3/14 @ 14:00-17:00 N108

Comparative and Evolutionary Genomics

Dr. I-Sheng Tsai

Moodle

8

2017/04/05

(Wed)

Review Week (No Class)

 

9

2017/04/11

Midterm Exam

 

10

2017/04/18

Cancelled (Moves to 5/9)

 

 

11

2017/04/25

Medical Genomics

Dr. Ling-Hui Li

Moodle

12

2017/05/02

Population Genomics

Dr. John Wang

Moodle

13

2017/05/09

Integration of Multidimensional Omics Data

Dr. Chuan-Hsiung Chang

Moodle

14

2017/05/16

Translational Clinical Research

Dr. Ueng-Cheng Yang

Moodle

15

2017/05/23

Precision medicine and clinical informatics

 

Dr. Ueng-Cheng Yang

Moodle

16

2017/05/31

(Wed)

Structural bioinformatics in pharmacogenomics

Dr. Jung-Hsin Lin

 

17

2017/06/06

Biobank Genotyping

 Dr. Chuan-Hsiung Chang

18

2017/06/13

Final Exam

 






 
top
 
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

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: Cheng-Kai Shiau (蕭丞凱) Email: shiauck@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

2017/02/17

Databases: An Overview

N/A

Dr. Chih-Ya Shen

Moodle

2

2017/02/24

Introduction to Data Mining

N/A

Dr. Chih-Ya Shen

Moodle

3

2017/03/03

Data Classification: Overview

N/A

Dr. Yi-Ren Yeh

Moodle

4

2017/03/10

 9:30am-12:30pm

Room#O108

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

Moodle 

5

2017/03/17

 

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

Moodle 

6

2017/03/24

Kernel Methods

N/A

Dr. Wen-Liang Hwang

Moodle

7

2017/03/31

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

N/A

Dr. Huai-Kuang Tsai

Moodle

8

2017/04/07

Review Week (No Class)

 

 

9

2017/04/14

Midterm Exam

 

 

10

2017/04/21

Hidden Markov Models (I)

N/A

Dr. Yu Tsao

Moodle

11

2017/04/28

9:00am-12:00pm

@N108

Hidden Markov Models (II)

N/A

Dr. Yu Tsao

Moodle

12

2017/05/05

Graphical Models (I)

N/A

Dr. Hsing-Kuo Pao

Moodle

13

2017/05/12

Graphical Models (II)

N/A

Dr. Hsing-Kuo Pao

Moodle

14

2017/05/19

Conditional Random Fields

N/A

Dr. Richard Tzong-Han Tsai

Moodle 

15

2017/05/26

MapReduce in Cloud Computing

 

N/A

Dr. Yu-Rong Chang

Moodle 

16

2017/06/02

Network Analysis

 

N/A

Dr. Hsuan-Cheng Hwang  

Moodle 

17

2017/06/09

Review Week (No Class)

 

 

18

2017/6/16

Final Exam

 

 

 

 

top
 

S2 Course Material

    Advanced Statistical Methods in Bioinformatics

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)

Office hours: N/A

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

Week

Date

Topics/Brief Description

sub-topics/Detail Descriptions

Lecturers

Slides

1

2017/02/16

Analysis of NGS data I

N/A

Dr. Hsuan-Yu Chen

Moodle

2

2017/02/23

-->moves to 3/3(Fri)

9:00-12:00

Analysis of NGS data II @room 0108 of IIS

N/A

Dr. Hsuan-Yu Chen

Moodle 

3

2017/03/02

Maximum likelihood estimates and the EM algorithm I

Maximum likelihood estimates

Dr. Yen-Tsung Huang

Moodle  

4

2017/03/09

Maximum likelihood estimates and the EM algorithm II

The EM algorithm

Dr. Yen-Tsung Huang

 Moodle

5

2017/03/16

Cancelled

-->moves to 5/17@9:00-12:00

Bayesian methods

Bayesian methods 

Dr. Grace S. Shieh

  Moodle

6

2017/03/23--->moves to 3/29 @2-5pm

Monte Carlo Markov Chains

Monte Carlo Markov Chains

Dr. Shin-Sheng Yuan

 Moodle

7

2017/03/30

Resampling methods I

Permutation test, jacknife

Dr. Grace S. Shieh

  Moodle

8

2017/04/06

Review week

 

 

9

2017/04/13

Midterm Exam

 

10

2017/04/20

Resampling methods II  

Bootstrap

Dr. Grace S. Shieh

  Moodle

11

2017/04/27

Statistics in Human Genetics I

Concept of Statistical Genetics, International Genomic Projects, Linkage Analysis

Dr. Hsin-Chou Yang

 

 

Moodle

 

12

2017/05/04

Statistics in Human Genetics II

Genetic Association, Gene-Gene interaction, Rare Variant Analysis

Dr. Hsin-Chou Yang

 

 

Moodle

 

13

2017/05/11

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

Moodle 

14

2017/05/18

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

 Moodle

15

2017/05/25

Advanced regression and dimension reduction I

N/A

Dr. Shin-Sheng Yuan

 

16

2017/06/01

Advanced regression and dimension reduction II

N/A

Dr. Shin-Sheng Yuan

 

17

2017/06/08

Review Week

 

18

2017/06/15

Final Exam

 

 

top
 
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 2/05/2017

*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

2017/2/16

N/A

 

2

2017/2/23

N/A

 

3

2017/03/02

Neha Warikoo (2015)

Topic:

DOI: 10.18653/v1/W16-2906
Conference: Proceedings of the 15th Workshop on Biomedical Natural Language Proces

 

 

 

4

2017/03/09

Kshitj Tandon (2015)

Topic: Yan He and Hong-wei Zhou et. al " Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity" He et al. Microbiome (2015) 3:20 DOI 10.1186/s40168-015-0081-x

 

 

5

2017/03/16

 N/A 

 

6

2017/03/23

 

Maharasan Kathiresan (2016)

Topic:

C. Wang and Y. Zhang.  "

Improving Scoring-Docking-Screening Powers of Protein–Ligand Scoring Functions using Random Forest" J. Comput. Chem. 2017, DOI: 10.1002/jcc.24667.

  

 

7

2017/03/30

 

 Ming-Siang Huang (2016)

Topic:

(Topic will be assigned by Lab Professor )

 

 

8

2017/04/06

 

Onkar Singh (2016)

Topic:

(Topic will be assigned by Lab Professor )

 

 

9

2017/04/13

 

Midterm Week 

 

 

10

2017/04/20

N/A

 

 

11

2017/04/27

 

N/A

 

 

12

2017/05/04

鄭中遠 (2016 陽明YMU Student)

Topic:

GeorgeGkotsis, AnikaOellrich, SumithraVelupillai, Maria Liakata, Tim J. P. Hubbard, Richard J. B. Dobson& Rina Dutta, "Characterisation of mental health conditions in social media using Informed Deep Learning ", Scientific Reports | 7:45141 | DOI: 10.1038/srep45141 

 

13

2017/05/11

 

N/A

 

 

14

2017/05/18

 

N/A

 

15

2017/05/25

 

N/A

 

 

16

2017/06/01

Chun-Liang Lu 呂俊良

(2016 陽明YMU Student)

Topic: Junhua Zhang and Shihua Zhang, "Discovery of cancer common and specific driver gene sets ", Nucleic Acids Research, DOI: https://doi.org/10.1093/nar/gkx089, Published: 07 February 2017

 

17

2017/06/08

 

 

Review Week

 

 

18

2017/06/15

Final Exam Week

  

 

 

top
 
Seminar

TIGP Bio 2017 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), Dr. Ho-Min Chen (Biology), Dr. Wei-Chung Liu (Statistic);

Outline:

Remarks:

A. Attendance for IMB Education Series--the talk on Feb. 13th and 17th are required. (In replace of two sessions of BP Seminar). Online Reiteration is required before attendance. (*Session I is rescheduled to 2/13 @ 15:00-17:00 )

B. Please choose one of the options below to replace 2 sessions of seminar :

1. Submit at least 1 article to Life Science Library blog (Adivsor/lab professor’s approval is required before submission). Acceptance from the blog is recommended but not required. Credits will be earned upon proves of advisor/lab professor’s approval & submission mail)

2. 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

2017/02/16

 

 (Replaced by IMB Education Series Session I- 2/13 @15:00-17:00, 1F Auditorium , IMB, AS)

 

N/A

2

2017/02/23

@Room#106

 Decoding Big Data with Business Intelligence Solutions in Health Care

Dr. Xuefeng Bruce Ling

Assistant Professor,

Translational Medicine Program, Stanford Univeristy, USA

 

Host: Chung-Yen Lin

3

2017/03/02

 Influence of alignment uncertainty on homology and phylogenetic modeling

Dr. Jia-Ming Chang Assistant Professor, Dep. Of Computer Science, National Chengchi University

Host: Wei-Chun Liu

4

2017/03/9

 

Dr.

Host:

5

2017/03/16

 

Dr.

Host:

6

2017/03/23

 

Dr.

Host:

7

2017/03/30

My experience in de novo transcriptome assembly

Dr. Jen-Chih Chen Associate Professor, Institute of Biotechnology, National Taiwan University          

 

Host: Dr. Ho-Ming Chen

8

 

 

2017/04/06

 

Data repurposing reveals hallmarks of slow translation initiation in mitochondrially localizing mRNA sequences

Dr. Paul Horton

National Institute of Advanced Industrial Science and Technology, Tokyo, Japan

 

Host: Chung-Yen Lin

9

2017/04/13

Midterm Week  

 

10

 

2017/04/17 (Mon)

 

Genomics Discovery from Medical Diagnosis to Agricultural Research

Dr. Phoebe Chen Department of Computer Science and Information Technology
La Trobe University, Australia                     

Host: Dr. Emily Su

11

2017/04/27

Mining plant genomes - from reads to comparative genomics

 

Dr. Yao-Cheng Lin

Bioinformatics and Computational Genomics

Agricultural Biotechnology Research Center

Biotechnology Center in Southern Taiwan
Academia Sinica

 

Host: Dr. Ho-Ming Chen

12

2017/05/04

 

Dr.

Host:

13

 

 

2017/05/11

 

Dr.

Host:

14

 

2017/05/18

 

Dr.

Host:

 

15

 

2017/05/25

Genomic approaches to identifying genes contributing to cancer development

Dr. Lin-Hui Li

Host: Dr. Chung-Yen Lin

16

 

 

2017/06/01

(Replaced by IMB Education Series Session II -2/17 @10:30-12:00, 1F Auditorium , IMB, AS)

 

 

17

2017/06/08

Computational Drug Discovery--Chances and Challenges

 

Dr. Zhng-Ru Xie

Assistant Professor

College of Engineering, University of Georgia, USA

 

Host: Wei-Chung Liu

18

2017/06/15

Final Exam

 

              

 

top
Lab Rotation

 

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

(Deadline for 2017 Spring Semester: 1/30/2017)

 

Student

Advisor

Ming-Siang Huang 黃明祥 Dr. Ting-Yi Sung
Onkar Singh 歐克爾 Dr. Haui-Kuan Tsai
Abdul Waheed Khan 阿布杜

N/A

Maharasan Kathiresan 馬和拉

Dr. Jung-Hsin Lin

 
 
 
top

















   
TIGP Sinica IIS