toppic
news pstudents academic cstudents faculty about contact link
news green02
 
 
 
 
 
 
 
 
 
   
Courses_2014 Spring
 

 

dec Tutorial lab


B2 Course Material

Place: Room 108, Old 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.
 Biomedical Informatics: Discovering Knowledge in Big Data (2nd edition) 2014 (ISBN-13: 978-3319045276)2. Introduction to Bioinformatics (4th edition) 2014 (ISBN-13: 978019965166)
TA: Wan-Hsin Liu
Office hours: by appointment
Grades: Midterm exam 50%. Final exam 50%.
 

Week

Date

Topics/Brief Description

Lecturers

Video

1

2014/02/18

Bio Big Data Introduction & Overview

Dr. Chuan-Hsiung Chang

描述: http://tigpbp.iis.sinica.edu.tw/tigpbio/course1.gif

2

2014/02/25

NGS Analytics 

Dr. Chun-Chieh Shih

 

3

2014/03/04

Microbiome 

Dr.  Sen-Lin Tang

 

4

2014/03/11

Metagenomics

Dr.  Sen-Lin Tang

 

5

2014/03/18

Transcriptome and RNA-Seq Informatics 

Dr. Ho-Ming Chen

 

6

2014/03/25

Proteomics Informatics 

Dr. Ming-Jing Hwang

 

7

2014/04/01

Comparative and Evolutionary Genomics

Dr. Trees-Juen Chuang

 

8

2014/04/08

Review Week

 

 

9

2014/04/15

Midterm Exam

 

 

10

2014/04/22 Moves to 4/23

@2-5pm

Integration of Multidimensional Omics Data

Dr. Chuan-Hsiung Chang

 

11

2014/04/29

Medical Genomics

Dr. Ling-Hui Li

 

12

2014/05/06

Statistical and Population Genomics 

Dr. Hsin-Chou Yang

 

13

2014/05/13

Moves to 5/21@

 9am-12pm

 Biobank Genotyping

Dr. Chen-Yang Shen

 

14

2014/05/20

 Pharmacogenomics

Dr. Jung-Hsin Lin

 

15

2014/05/27

 Translational Clinical Research 

Dr. Ueng-Cheng Yang

 

16

2014/06/03

 Clinical Study Information System 

Dr. Ueng-Cheng Yang

 

17

2014/06/10

Review Week

 

 

18

2014/06/17

Final Exam

 

 

 

 
top
 
C2 Course Material

Biological Computing II (S1=C2)

Place: Room 108, Old 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, common 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 clustering, classification, survival analysis, 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 Yang, Hsin-Chou Yang, Shinsheng Yuan, Grace Shieh, Hsuan-Yu Chen, and Wei-Chung Liu
TA: Ignasius Joanito

Office hours: by appointment
Grades: Midterm exam 50%. Final exam 50%.
 

Week

Date

Topics/Brief Description

Lecturers

1

2014/02/20
Moved to 2014/2/17
14:00-17:00

Descriptive Statistics, Genomic Data Analysis

Dr. Yeang, Chen-Hsiang

2

2014/02/27

Probability

Dr. Yang, Hsin-Chou

3

2014/03/06

Discrete Distributions and Contingency Tables

Dr. Yang, Hsin-Chou

4

2014/03/13

Continuous Distributions, Expectations and Basic Statistics

Dr. Yang, Hsin-Chou

5

2014/03/20

Move half session to 3/27@15:30-17:30

Parameter Estimation and Confidence Interval

Dr. Yuan, Shinsheng

6

2014/03/27 moves to 2014/03/28@106

Hypothesis Testing, P-value, False Discovery Rate 

Dr. Shieh, Grace

7

2014/04/03

Comparative Study, Two Sample Test

Dr. Yuan, Shinsheng

8

2014/04/10

Review Week

 

9

2014/04/17

Midterm Exam

 

10

2014/04/24

Analysis of Categorical Data, Chisq and Multinomial

Dr. Chen, Hsuan-Yu

11

2014/05/01

Correlation, Regression Analysis and ANOVA

Dr. Shieh, Grace

12

2014/05/08

Clustering

Dr. Yeang, Chen-Hsiang

13

2014/05/15

Classification

Dr. Yeang, Chen-Hsiang

14

2014/05/22

Nonparametric Statistics (I)

Dr. Liu, Wei-Chung

15

2014/05/29 @room107

Survival Data Analysis

Dr. Chen, Hsuan-Yu

16

2014/06/05

Cancelled

(make up class:6/12)

Nonparametric Statistics (II)

Dr. Liu, Wei-Chung

17

2014/06/12

Review Week (make-up class :Nonparametric Statistics (II) )

 Dr. Liu, Wei-Chung

18

2014/06/19

Final Exam

 

 
top
 
C3 Course Material   Advanced Statistical Methods in Bioinformatics

Place: Room 108, Old 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: Khong-Loon Tiong
Office hours: by appointment
Grades: Midterm exam 50%. Final exam 50%.
 

Week

Date

Topics/Brief Description

Lecturers

1

2014/02/21

Databases: An Overview

Dr. Chih-Ya Shen

2

2014/02/28
Moved to
2014/02/26 (Wed.) @106

Introduction to Data Mining

Dr. Chih-Ya Shen

3

2014/03/07

Data Classification: Overview

Dr. Yuh-Jye Lee

4

2014/03/14

Optimization Algorithms

Dr. Wen-Liang Hwang

5

2014/03/21

Support Vector Machines and Large Margin

Dr. Wen-Liang Hwang

6

2014/03/28
Moved to
2014/03/26(Wed.)

Kernel Methods

Dr. Hsuan-Tien Lin

7

2014/04/04
Moved to 2014/04/02 (Wed.)

Lab LibSVM and Weka

Dr. Jyh-Ying Peng

8

2014/04/11

Review Week

 

9

2014/04/18

Midterm Exam

 

10

 2014/04/25

Genetic Algorithms and their Applications in Bioinformatics

Dr. Huai-Kuang Tsai

11

2014/05/02

Hidden Markov Models (I)

Dr. Yu Tsao

12

2014/05/09
Moved to 2014/05/14 (Wed.)@9:00-12:00

Hidden Markov Models (II)

Dr. Yu Tsao

13

2014/05/16

Graphical Models  (I)

Dr. Hsing-Kuo Pao

14

2014/05/23

Graphical Models  (II)

Dr. Hsing-Kuo Pao

15

2014/05/30

Conditional Random Fields

Dr. Richard Tzong-Han Tsai

16

2014/06/06

Comparative & Evolutionary Genomics

Dr. Trees-Juen Chuang

17

2014/06/13

Review Week

 

18

2014/06/20

Final Exam

 

 

 
top

 

Dynamics in systems (Elective Course)

For the latest information, please visit Dr.Chao-Ping Hsu's webpage at http://idv.sinica.edu.tw/berrylab/courses/dynbio102/general.htm

Place: Room 108, Old Building of the Institute of Information Science, Academia Sinica.
Time: Tuesday 14:20-17:10
Chair: Chao-Ping Hsu
Outline: Link
Textbook:
"Nonlinear dynamics and chaos" by S. H. Strogatz, Published by Perseus Book, Cambridge, USA in 1994.
(optional)
"An introduction to systems biology" by U. Alon, Published by Chapman & Hall/CRC, London, UK in 2006.
"Advanced Engineering Mathematics" by Peter V. O'Neil, Published by Thomson Brooks/Cole.
Grading: 30% Midterm + 40% Homeworks  + 30%  final report
 

Week

Date

Topics/Brief Description

Lecturers

1

2014/02/18

Class setup.
Introductory information.
Central dogma in molecular biology.
Survey on mathematical backgrounds.
Michaelis-Menten kinetics
Appendices A and B (Alon) (I)

Dr. Chao-Ping Hsu

2

2014/02/25@106

Michaelis-Menten kinetics
Appendices A and B (Alon) (II)
Basic functions, differential and integration.
Taylor expansion.
Review of Differential equations and Linear Algebra. 

Dr. Chao-Ping Hsu

3

2014/03/04
moved to
2014/03/07 (Fri.)9:40-12:20

 

Bifurcation analysis I (Chapters 2-3 Strogatz)

Dr. Chao-Ping Hsu

4

2014/03/11

Bifurcation analysis II (Chapters 3-4 Strogatz)

Dr. Chao-Ping Hsu

5

2014/03/18

Two-dimensional flows (Chapter 5 Strogatz)
 

Dr. Chao-Ping Hsu

6

2014/03/25 class canceled, moves to 2014/04/11(Fri)9:40-12:30

Two-dimensional flows (Chapter 6 Strogatz) 

Dr. Chao-Ping Hsu

7

2014/04/01

Limit Cycles (Chapter 7, Strogatz)  

Dr. Chao-Ping Hsu

8

2014/04/08

Review Week

 

9

2014/04/15

Midterm Exam

 

10

2014/04/22

 Limit Cycles (Chapter 7, Strogatz)

Dr. Chao-Ping Hsu

11

2014/04/29

Hopf bifurcation (Chapter 8)

Dr. Chao-Ping Hsu

12

2014/05/06

Oscillations in Biology

Dr. Chao-Ping Hsu

13

2014/05/13

Noises in biology-introduction
Where are noise from?
How noisy is it?
Noises: theory
Binomial random variable
Poisson random variable
Gaussian probability distribution.
 

Dr. Chao-Ping Hsu

14

2014/05/20

Noises: theory -continued
Poisson random variable
Stochastic processes - what do we mean? what assumption have we made?
Chemical master equation.
Gillespie's algorithm

Dr. Chao-Ping Hsu

15

2014/05/27

Noises: Theory
Gillespie algorithm (continued)
Chemical Lengevin equation
Noises in biology
Simulation tools and usage

Dr. Chao-Ping Hsu

16

2014/06/03

Noises: Literature examples

Dr. Chao-Ping Hsu

17

2014/06/10

Term paper discussion

 

18

2014/06/17

Final Exam

 

 

top

 
Seminar

Place: Room 106, New Building of the Institute of Information Science, Academia Sinica.
Time: Thursday 14:00-15:10
Chair: Dr. Ting-Yi Sung, Dr. Wen-Chang Lin, Dr. Wei-chung Liu
Outline:
Grades: attendance 100%.
 

Week

Date

Topics/Brief Description

Lecturers / Host

1

2014/02/20

De novo assembly of large genomes by short read sequences

Dr. Arthur Chun-ChiehShih

2

2014/02/27

Making sense of next generation sequencing data: a biologists perspective

Dr. Ho-Ming Chen

3

2014/03/06
@101,new building of IIS

Response network of ectopic ATP synthase blockade

Dr. Hsueh-Fen Juan

4

2014/03/13

Exploring free energy landscapes of intrinsically disordered proteins and highly dynamic multi-domain proteins at atomic resolution

Dr. Jie-rong Huang

5

2014/03/20

Computational approaches for the identification of structural variations in human populations

Dr. Yao-Ting Huang

6

2014/03/27

Homopolymeric Guanine Repeats Cause a Localized Mutator Effect

Dr. Jun-Yi Leu

7

2014/04/03

Bioinformatic exploration to the genetic and epigenetic mechanisms associated with duplicate gene evolution

Dr. Ben-Yang Liao

8

2014/04/10

Review Week

 

9

2014/04/17

Midterm Exam

 

10

2014/04/24

Discovery of Plant Defense Peptide Hormone and Its Application on Immune Regulation

Dr. Yet-Ran Chen

11

2014/05/01

  Signaling Mediated Epigenetic Silencing of TGF-beta Targets in

   Ovarian Cancer

Dr.  Michael Chan

12

2014/05/08 @room101

 Pharmacogenetics studies in Taiwan Han Chinese

Dr. Chien-Hsiun Chen

(Host: Dr. Wei-chung Liu)

13

2014/05/15

The new schemes for characterization and identification of protein post-translational modifications.

Dr. Tzong-Yi Lee

(Host: Dr.Ting-Yi Sung)

14

2014/05/22

 The effects of miRNAs in the signaling pathway and the disease

Dr. NianHan Ma

(Host: Dr. Wen-chang Lin)

15

2014/05/29

  A Hybrid parameter estimation algorithm for S-system model of gene regulatory networks.

Dr. Wesson Wu

(Host: Dr.Ting-Yi Sung)

16

2014/06/05

@room101

  Long non-coding RNA and disease

Dr. Jan-Gowth Chang

(Host:Dr. Wei-chung Liu/ Dr. Grace Shieh)

17

2014/06/12

Review Week

 

18

2014/06/19

Final Exam

 

 
top
 
Tutorial Reading

Date

TIGP Bioinformatics

Host

 

Dr. Chuan-Hsiung Chang
Dr. Michael Jyh-Ying Peng
Dr. Ho-Ming Chen
Dr. Shin-sheng Yuan
Dr. Lee-Wei Yang
Dr. An-Suei Yang

 

March 6

x

 

 

x

 

March 13

張慧如

(Title : Additive effect of the AZGP1, PIP, S100A8 and UBE2C molecular biomarkers improves outcome prediction in breast carcinoma)

Dr. Chuan-Hsiung Chang
Dr. Ho-Ming Chen

 

Jerome Penaflor Panibe

(Title : An environmental bacterial taxon with a large and distinct metabolic repertoire)

March 20

Chi-Chun Chen

(Title : Multiple e-Pharmacophore Modeling, 3D-QSAR, and High-Throughput Virtual Screening of Hepatitis C Virus NS5B Polymerase Inhibitors)

Dr. Chuan-Hsiung Chang

 

 

March 27

x

 

 

x

 

April 3

x

 

 

x

 

April 10

x

 

 

 

April 17

x

 

 

x

 

April 24

孫在陽

(Title : Count-based differential expression analysis of RNA sequencing data using R and Bioconductor)

Dr. Chuan-Hsiung Chang,
Dr. Ho-Ming Chen

 

Cheng-Kai Shiau

(Title:Poly(A)-tail profiling reveals an embryonic switch in translational control", published on Nature, Vol. 508, pp. 66-74, April 3, 2014)

May 1

x

 

 

x

 

May 8

Chiahung Lin

(Title: Maximizing the Power of Principal Components Analysis of Correlated Phenotypes in Genome-wide Association Studies)
http://www.sciencedirect.com/science/article/pii/S0002929714001189
 

 

Dr. Chuan-Hsiung Chang
Dr. Ho-Ming Chen
Dr. Shin-sheng Yuan

May 15

Yen Hsieh Chen 

(Title: Clonal evolution and clinical correlates of somatic mutations in myeloproliferative neoplasms', which is published on Blood, Volume 123, page 2220-8.)

Dr. Chuan-Hsiung Chang
Dr. Shin-sheng Yuan

 

Hsiu-man Chen

 (Title: Laayouni et al, 2014, Convergent evolution in European and Rroma populations reveals pressure exerted by plague on Toll-like receptors,PNAS.1317723111)

May 22

Nikhil Pathak

(Title: Reprogramming Microbes to Be Pathoge-Seeking Killers

      Reprogramming Microbes to Be Pathogen-Seeking Killers.         ACS Synth. Biol., 2014, 3 (4), pp 228237.)(http://pubs.acs.org/doi/abs/10.1021/sb400077j)

 

Kidane Gebereyesus

(Title: Scale Selection Properties of Generalized Scale-space Interest Point Detectors, published in June 2013)http://link.springer.com/article/10.1007%2Fs10851-012-0378-3 

 

Dr. Chuan-Hsiung Chang     Dr. An-Suei Yang

Dr. Lee-Wei Yang

May 29

Emmanuel O Salawu

(Title: Molecular Dynamics Simulations Reveal Atomic Details of Structural and Thermal Stability of Biomolecules)

                        Yenchen Lo                           

 (Title: Inferring homologous protein-protein interactions through pair position specific scoring matrix. )

     Journal: BMC Bioinformatics. 2013; 14(Suppl 2):S11             http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549806/

 

Dr. Chuan-Hsiung Chang

Dr. An-Suei Yang

Dr. Lee-Wei Yang

Jun 5 

Divya Sahu

(Title: Adenosine Stimulates the Migration of Human Endothelial Progenitor Cells. Role of CXCR4 and MircroRNA-150)

Dr. Chuan-Hsiung Chang

 

 

top
 
Lab Rotation

Students need to inform the BIO office the laboratory they are rotating with within two weeks 

Student

Advisor

Nikhil Pathak 倪齊歐

 Dr. Chuan-Hsiung Chang張傳雄

Jerome Penaflor Panibe杰羅姆

 Dr. Huai-Kuang Tsai 蔡懷寬

Chi-Chun Chen 陳奇君 

 Dr. Henry Lu, Horng-Shing 盧鴻興

Divya Sahu笛芙亞

 Dr. Hsei - Wei Wang 王學偉 (陽明)

Kidane Gebereyesus祈丹 

 Dr. Peng, Jyh-Ying 彭智楹 (陽明)

Alcides Bernardo Tello愛希德 

 -------------------------------

Cheng-Kai Shiau蕭丞凱 

Dr. Li, Wen-Hsiung 李文雄

Yenchen Lo駱彥辰 

Dr. Yang, Lee-Wei 楊立威

Chiahung Lin林佳鴻 

Dr. Yuan, Shin-Seng 袁新盛

Yen Hsieh Chen陳彥劦 

Dr. Jou, Yuh-Shan 周玉山

Hsiu-man Chen陳秀曼 

Dr. Yuan, Shin-Sheng  袁新盛

 
top
   
TIGP Sinica IIS