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Courses_2015 Spring
 

 

dec Special Lecture  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:  Yen Chen (Chris) Lo 駱彥辰 Email: g30020006@gmail.com

Office hours: Thursdays 09:00-15:30 @ room 304, New building of IIS

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

 

Week

Date

Topics/Brief Description

Lecturers

   Video

1

2015/02/24

 Bio Big Data – Introduction & Overview

 

 

Dr. Chuan-Hsiung Chang

MOODLE

2

2015/03/03

NGS Analytics

 

Dr. Chun-Chieh Shih

MOODLE

3

2015/03/10

Microbiome

 

Dr. Sen-Lin Tang

MOODLE

4

2015/03/17

Metagenomics

Dr. Sen-Lin Tang

MOODLE

5

2015/03/24

Transcriptome Informatics

Dr. Ho-Ming Chen

MOODLE

6

2015/03/31

Proteomics Informatics

 

Dr. Ming-Jing Hwang

MOODLE

7

2015/04/07

Comparative and Evolutionary Genomics

 

 

Dr. Trees-Juen Chuang

MOODLE

8

2015/04/14

Review Week

 

9

2015/04/21

Midterm Exam

 

10

2015/04/28

Integration of Multidimensional Omics Data

 

 

Dr. Chuan-Hsiung Chang

MOODLE

11

2015/05/05

Medical Genomics

 

Dr. Ling-Hui Li

MOODLE

12

2015/05/12

Statistical Genomics

 

Dr. Hsin-Chou Yang

MOODLE

13

2015/05/19

Move to 5/25

@3-6pm

 

 

Biobank Genotyping

 

 

Dr. Chen-Yang Shen

MOODLE

14

2015/05/26

 

Pharmacogenomics

 

 

Dr. Jung-Hsin Lin

MOODLE

15

2015/06/02

Room#101

 

Translational Clinical Research

 

 

Dr. Ueng-Cheng Yang

MOODLE

16

2015/06/09

Clinical Study Information System

 

 

Dr. Ueng-Cheng Yang

MOODLE

17

2015/06/16

Review Week

 

18

2015/06/23

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

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@gmail.com

 

Office hours: Wednesday 14:00-16:00 @ room 304, New building of IIS

 

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

 

Week

Date

 Topics/Brief Description

Subtopics/ Detail Descriptions/Examples

Lecturers

Video

1

2015/02/24(Tue)

Databases: An Overview

 

Dr. Chih-Ya Shen

MOODLE 

2

2015/03/06

Introduction to Data Mining

 

Dr. Chih-Ya Shen

MOODLE 

3

2015/03/13

Data Classification: Overview

 

Dr. Yuh-Jye Lee

MOODLE

4

2015/03/20

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

2015/03/27

@Room 101(New Building)

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

2015/04/01(Wed)

 

Kernel Methods

 

Dr. Wen-Liang Hwang

MOODLE

7

2015/04/10

Lab – LibSVM and Weka

 

Dr. Jyh-Ying Peng

MOODLE

8

2015/04/17

Review Week

 

 

9

2015/04/24

Midterm Exam

 

 

10

 

2015/05/01

Genetic Algorithms and their Applications in Bioinformatics

 

Dr. Huai-Kuang Tsai

MOODLE

11

2015/05/08

Hidden Markov Models (I)

 

Dr. Yu Tsao

MOODLE

12

2015/05/15

Hidden Markov Models (II)

 

Dr. Yu Tsao

MOODLE 

13

2015/05/22

Graphical Models  (I)

 

Dr. Hsing-Kuo Pao

MOODLE 

14

2015/05/29

@1:30-4:30

Graphical Models  (II)

 

Dr. Hsing-Kuo Pao

MOODLE 

15

2015/06/05

Conditional Random Fields

 

Dr. Richard Tzong-Han Tsai

MOODLE 

16

2015/06/12

Comparative & Evolutionary Genomics

 

Dr. Trees-Juen Chuang

MOODLE 

17

2015/06/17 (Wed)

Review Week

 

 

18

2015/06/26

Final Exam

 

 

 
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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 some useful and advanced statistical methods in computational biology. The topics include:

next generation sequencing (NGS) Data, clustering and classification, dimension-reduction, maximum likelihood estimation, Bayesian inference, Monte Carlo (nonparametric and resampling) methods, missing data, analysis of RNA-Seq and ChIP-Seq  data, and Human Genetics

Textbook: N/A

Reference book: papers will be given by instructors

Lecturers: Grace S. Shieh, Hsuan-Yu Chen, Henry Horng-Shing Lu, Hsin-Chou Yang, Han-Ming Wu, 

                  Ker-Chau Li, Shinsheng Yuan

TA: N/A

Office hours: N/A

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

Week

Date

Topics/Brief Description

sub-topics/Detail Descriptions

Lecturers

Video

1

2015/02/26

Analysis of NGS data I

       N/A

Dr. Hsuan-Yu Chen

MOODLE

2

2015/03/05

Analysis of NGS data II

       N/A

Dr. Hsuan-Yu Chen

MOODLE

3

2015/03/11

(Wed)

@ Rm#108

(Old building)

2:00pm-

5:00pm

Maximum likelihood estimates and the EM algorithm I 

 

Motivated examples

Dr. Henry Horng-Shing Lu

MOODLE 

4

2015/03/18

(Wed)

2:00pm-

5:00pm

 

Maximum likelihood estimates and the EM algorithm II

 

Maximum likelihood estimates

Dr. Henry Horng-Shing Lu

MOODLE

5

2015/03/25

(Wed)

2:00pm-

5:00pm

Maximum likelihood estimates and the EM algorithm III

 

The EM algorithm

Dr. Henry Horng-Shing Lu

MOODLE

6

2015/03/31

(Tue)

@ Rm#108

(Old building)

1:30pm-

4:30pm

Bayesian methods with Monte Carlo Markov Chains I Bayesian methods     Dr. Henry   Horng-Shing Lu

MOODLE
 

 

7

2015/04/07

(Tue)@ Rm#108

1:30pm-

4:30pm

Bayesian methods with Monte Carlo Markov Chains II

 

Monte Carlo Markov Chains

Dr. Henry Horng-Shing Lu

MOODLE

8

2015/04/16

Non-parametric methods by permutation and bootstrap methods I      N/A

Dr. Grace S. Shieh

MOODLE

9

2015/04/23

Midterm Exam

 

10

2015/04/30

Non-parametric methods by permutation and bootstrap methods II

  N/A

Dr. Grace S. Shieh

MOODLE

11

2015/05/07

Statistics in Human Genetics I

Concept of Statistical Genetics, International Genomic Projects, Linkage Analysis

Dr. Hsin-Chou Yang

 

MOODLE

12

2015/05/14

Statistics in Human Genetics II

Genetic Association, Gene-Gene interaction, Rare Variant Analysis

Dr. Hsin-Chou Yang

 

MOODLE 

13

2015/05/21

Clustering, classification and data visualization I

 

(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

2015/05/28

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

2015/06/04

Advanced regression and dimension reduction I

 N/A

Dr. Shinsheng Yuan

MOODLE  

16

2015/06/11

move to 6/10(Wed)@14:00-17:00

Advanced regression and dimension reduction II

  N/A

Dr. Shinsheng Yuan

MOODLE  

17

2015/06/18

Review Week

 

18

2015/06/25

Final Exam

 

 

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P1 Course Material  
    Programming (Python)

 

Place: Room 108, New Building of the Institute of Information Science, Academia Sinica.

 

Time: Friday, 10:00am-12:00pm

 

Chair: Dr. Wu, Kun-Pin (BP)  & Dr. Wang, Chih-Yu (SNHCC)

 

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:  BP-Dr. Wu, Kun-Pin; Dr. Wang, John; Dr. Tsai, Huai-Kuang/ Dr. Lin, Chan-Hsien (Eric).

                    SHNCC-Dr. Wang, Chih-Yu; Dr. Chen, Kung;

Textbook: Introduction to Computation and Programming Using Python (revised and expanded edition) by John V. Guttag, 2013, The MIT Press (滄海圖書代理)

TA: Jerome Penaflor Panibe (杰羅姆)  Email: jerome.panibe@gmail.com

Office hours: Wednesday 10:00am-12:00pm

Grades: Midterm exam 25%. Final exam 30%. Homework 35%. Class performance (10%)

 

Week

Date

Topics/Brief Description

Lecturers

Video

1

2015/02/24

(Tue)

Introduction to Python

12:00-14:00

Dr. Wu, Kun-Pin

MOODLE

2

2015/03/06

Basic Elements of Python I

Dr. Wu, Kun-Pin

MOODLE

3

2015/03/13

Basic Elements of Python II

Dr. Wu, Kun-Pin

MOODLE

4

2015/03/20

Basic statements I: branching programs and inputs

Dr. Wang, John

MOODLE

5

2015/03/27

Basic statements II: iterative programs

Dr. Wang, John

MOODLE

6

2015/04/01

(Wed)

Functions: scope rules and passing arguments

Dr. Wang, John

MOODLE

7

2015/04/10

Modules, Files, and Structured Types

Dr. Wang, Chih-Yu

MOODLE

8

2015/04/17

Exception handling

Dr. Wang, Chih-Yu

MOODLE

9

2015/04/24

Review week

 

10

2015/05/01

Midterm exam

 

11

2015/05/08

Introduction to Biopython

Dr. Lin, Chan-Hsien (Eric)

MOODLE

12

2015/05/15

Regular expressions

Dr. Lin, Chan-Hsien (Eric)

MOODLE

13

2015/05/22

Object-oriented programming: classes

Dr. Lin, Chan-Hsien (Eric)

MOODLE

14

2015/05/29

Data analysis toolbox  

Dr. Chen, Kung

MOODLE 

15

2015/06/05

Data analysis toolbox,

Web programming

Dr. Chen, Kung

MOODLE 

16

2015/06/12

Web programming

Dr. Chen, Kung

MOODLE 

17

2015/06/17

(Wed)

Review week

 

18

2015/06/26

Final exam

 


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Seminar

Seminar

*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 2/05/2015.

*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

2015/2/26

 

 

2

2015/3/5

 

Tsai-Yang Sun孫在陽(2013陽明)

Topic:

Alberto Risueño, Beatriz Roson-Burgo, Anna Dolnik, Jesus M Hernandez-Rivas, Lars Bullinger and Javier De Las Rivas, “A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples”, BMC Genomics 2014, 15:879, doi:10.1186/1471-2164-15-879

                        Article URL

 

 

3

2015/3/12

 

Ignasius Joanito(2012)

                                 Topic:

Seaton et al, 'Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature.',  2015 Jan 19;11:776. doi: 10.15252/msb.20145766.                        Article URL

                        

 

4

2015/3/19

 

Divya Sahu(2013)

Topic:

Tian Xia*, Qi Liao, Xiaoming Jiang, Yongfu Shao, Bingxiu Xiao, Yang Xi & Junming Guo, "Long noncoding RNA associated-competing endogenous

RNAs in gastric cancer",Sci Rep. 2014 Aug 15;4:6088. doi: 10.1038/srep06088.

 

 

5

2015/3/26

 

Kidane Gebereyesus(2013)

Topic:

'Clinical Presentation of Patients with Ebola Virus Disease in Conakry, Guinea ( Nov. 5, 2014, NEJM.org)

                       Article URL


 

Nikhil Pathak(2013)

Topic:

Recognition determinants of broadly neutralizing human antibodies against dengue viruses", Nature(2015)doi:10.1038/nature14130.

                       Article URL

 

 

6

2015/4/1(Wed)

N/A (schedule conflict-C2)

 

7

2015/4/9

 

Hsiu-man Chen(2013)

Topic:

J. P. Dumanski et al, "Smoking is associated with mosaic loss of chromosome Y", Science Vol. 347 no. 6217 pp. 81-83, DOI: 10.1126/science.1262092.

                       Article URL

 

 

8

2015/4/16

 

Yen Hsieh Chen(2013)

Topic:

Moncunill V et al., "Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads",  Nat Biotechnol. 2014 Nov;32(11):1106-12. doi: 10.1038/nbt.3027

                       Article URL

 

 

9

2015/4/23

                     Midterm Exam

Thejkiran Pitti(2012)

Topic:

"Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features" SCIENTIFIC REPORTS | 4 : 5765 | July 2014, DOI: 10.1038/srep05765

                    Article URL

 

 

10

2015/4/30

Chiahung Lin(2013)

Topic:

Matthew K Iyer et al. "The landscape of long noncoding RNAs in the human transcriptome" 

Nature Genetics 47, 199–208 (2015) doi:10.1038/ng.3192

                       Article URL

 

 

 

11

2015/5/7

Chi-Chun Chen(2013)

Topic:

"Uncovering disease-disease relationships through the incomplete interactome."Science 20 February 2015: Vol. 347 no.6224 DOI:10.1126/SCIENCE.1257601

                     Article URL

 

 

12

2015/5/14

Cheng-Kai Shiau(2013)

Topic:

Internal models direct dragonfly interception steering, Nature 517, 333–338. DOI: 10.1038/nature14045

 

 

13

2015/5/21

 

Yenchen Lo(2013)

Topic:

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure

Journal: nature scientific reports 8 April 2014 IF: 5.078

                         Article URL 

 

 

14

2015/5/28

Jerome Penaflor Panibe(2013)

Topic:

Fuguang Li, et. al. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.
Nature Biotechnology (2015) doi:10.1038/nbt.3208
                      Article URL

 

 

15

2015/6/4

Lovely Raghav(2014)

Topic:

Karen AgaronyanYaroslav I. MorozovMichael AnikinDmitry Temiakov Science. 2015 Jan 30;347(6221):548-51. doi: 10.1126/science.aaa0986 "Replication-transcription switch in human mitochondria

Article URL

 

 

16

2015/6/11

 

Cheng-Wei Cheng(2014)

Topic:

Fuyi Li et al., “GlycoMine--a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome”, Bioinformatics, 2015, DOI: 10.1093/bioinformatics/btu852

                        Article URL

 

 

17

2015/6/18

 

Chun-Yi Chen(2014)

Topic:

Cahova H. et al., "NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs", Nature (2014 Dec) doi:10.1038/nature14020

                       Article URL

 

 

18

2015/6/25

Final Exam

 


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Special Lecture

TIGP Bio 2015 Spring Syllabus

 Special Lecture

Place: Room 101, Old Building of the Institute of Information Science, Academia Sinica.

Time: Thursday 14:00-15:10

Chair: Dr. Ting-Yi Sung (Informatics), Dr. Ho-Min Chen (Biology), Dr. Wei-Chung Liu (Statistic)

Outline:

Grades: attendance 100%.

Week

Date

Topics/Brief Description

Speaker / Host

1

2015/02/26

Mass spectrometry-based metabolite quantitation and identification

Dr. Ke-Shiuan Lynn(Assitant Professor, Department of Math, Fu-Jen University)

Host: Dr. Ting-Yi Sung

2

2015/03/05

 Of pathogens and men

Dr. Isheng Jason Tsai(BRC, AS)

 

Host: Dr.Chung-Yen Lin

3

2015/03/12

Genome Evolution in Host-associated Bacteria

Dr. Chih-Horng Kuo (IPMB,AS)

 

Host: Ho-Ming Chen

4

2015/03/19

 NO CLASS

N/A

5

2015/03/26

A dictionary based approach for protein localization site prediction 

Dr. Hsin-Nan Lin (IIS, AS)

 

Host:Dr. Chung-Yen Lin

6

2015/04/02

Algorithms for next generation sequencing

Dr. Jui-Hung Hung (Institute Biotechnology, NCTU)

 

Host: Dr. Pao-Yang Chen

7

2015/04/09

Room#108

Application of high throughput platforms for bio-medical study

Dr. Tsai, Mong-Hsun

(Institute of Biotechnology, NTU)

 

Host:Dr. Chung-Yen Lin

  2015/04/15(Wed) Make-up Class   Understanding the dynamic behaviors of biological networks by mathematical modeling and simulation      Dr. Chiang, Wan-Tien

(Institute of Biomedical Science, AS)

 Host: Dr. Liu, Wei-Chung

8

2015/04/16

Review Week

 

9

2015/04/23

Midterm Exam

 

10

2015/04/30

Whole transcriptome study and miRNA identification in non-model organism

 

Dr. Shih-Shun Lin (Institute

Biotechnology, NTU)

 

Host: Ho-Ming Chen

11

2015/05/07

Genome-wide analysis for stress-responsive alternative splicing in plants

 

Dr. Shih-Long Tu (IPMB, AS)

 

Host: Ho-Ming Chen

12

2015/05/14

Beyond cleaved small RNA targets: new insights into RNA degradome

Dr. Ho-Ming Chen (ABRC,AS)

Re: Biology

13

2015/05/21

Using MapReduce Framework to Analyze Big Data in Bioinformatics

Dr. Yu-Jung Chang (IIS, AS)

 

Host: Chung-Yen Lin

14

2015/05/28

Genomic approaches to identifying genes involved in malignant transformation of benign tumors

Dr. Lin-Hui Li (IBMS, AS)

 

Host: Dr. Chung-Yen Lin

15

2015/06/04

Association of genetic and metabolomic profile with cognitive impairment in the elderly 

Dr. Karen Chen

 

Host: Chung-Yen Lin

16

2015/06/11

Next generation sequencing in Taiwan Bio-industry

Dr. 詹佳翰

CEO,Yourgene Bioscience

 

Host:Pao-Yang Chen

17

2015/06/18

Review Week

 

18

2015/06/25

Final Exam

 

 

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Lab Rotation

 

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

(Deadline for 2015 Spring Semester: 1/30/2015)

 

Student

Advisor

Chun-Yi Chen Dr. Huai-Kuang Tsai
Cheng-Wei Cheng Dr. Hsin-Chou Yang
Lovely Raghav Dr. Huan-Yu Chen
 
 
 
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TIGP Sinica IIS