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Courses_2016 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: N/A (Please refer to the lectures respectively shall you have any questions for each class)

Office hours: N/A

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

* First lecture is on 2/16 !

 

Week

Date

Topics/Brief Description

Lecturers

   Slides /  Video

1

2016/03/08

 Bio Big Data – Introduction & Overview

 

Dr. Chuan-Hsiung Chang

Moodle

2

    2016/02/23

NGS Analytics

 

Dr. Chun-Chieh Shih

Moodle 

3

    2016/02/16

 

Microbiome

 

Dr. Sen-Lin Tang

Moodle 

4

    2016/03/01

-->3/9 9:00-12:00

Metagenomics

Dr. Sen-Lin Tang

Moodle 

5

    2016/03/15

Transcriptome Informatics

Dr. Ho-Ming Chen

Moodle

6

    2016/03/22

Proteomics Informatics

 

Dr. Victor Ng

Moodle

7

    2016/03/29

(Wed)-->

5/3 @2:00-5:00pm

Comparative and Evolutionary Genomics

 

 

Dr. I-sheng Tsai

Moodle

8

    2016/04/06

Review Week

No class

 

9

    2016/04/12

Midterm Exam

 

10

    2016/04/19

Integration of Multidimensional Omics Data

 

 

Dr. Chuan-Hsiung Chang

Moodle

11

    2016/04/26

Medical Genomics

 

Dr. Ling-Hui Li

Moodle

12

    2016/05/03

Population Genomics

 

Dr. John Wang

Moodle

13

    2016/05/10

 

Biobank Genotyping

 

 

Dr. Chin-Yang Shen

Moodle

14

    2016/05/17

-->5/25(W)Rm#108

 

Pharmacogenomics

 

 

Dr. Jung-Hsin Lin

Moodle

15

    2016/05/24

 

Translational bioinformatics

 

 

Dr. Ueng-Cheng Yang

Moodle

16

    2016/05/31

Precision medicine and clinical informatics

 

 

Dr. Ueng-Cheng Yang

Moodle

17

    2016/06/07

Review Week

 No Class

18

    2016/06/14

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: Wayne Cheng (鄭成偉) Email: Chengwei@iis.sinica.edu.tw

 

Office hours:  Friday 10:00am-12:00pm@ room 304, New building of IIS

 

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

 

Week

Date

 Topics/Brief Description

Subtopics/ Detail Descriptions/Examples

Lecturers

Video/

Slides

1

2016/02/19

Databases: An Overview

 

Dr. Chih-Ya Shen

Moodle 

2

2016/02/26

Introduction to Data Mining

 

Dr. Chih-Ya Shen

Moodle 

3

2016/03/04

Data Classification: Overview

 

Dr. Yuh-Jye Lee

Moodle 

4

2016/03/11

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

2016/03/18

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

2016/03/25

Kernel Methods

 

Dr. Wen-Liang Hwang

Moodle

7

2016/03/30(Wed)@Room O108

Nonstandard Optimization Algorithms

 GA, Random Forest, and others

Dr. Huai-Kuang Tsai

Moodle

8

2016/04/08

Review Week

 

  No Class

9

2016/04/15

Midterm Exam

 

 

10

2016/04/22    -->moves to 4/27 @9am-12pm (Rm#101)

Hidden Markov Models (I)

 

Dr. Yu Tsao

Moodle

11

2016/04/29    -->moves to 5/11 @10am-12pm (Rm#O101) 

Hidden Markov Models (II)

 

Dr. Yu Tsao

Moodle

12

2016/05/06

Graphical Models  (I)

 

Dr. Hsing-Kuo Pao

Moodle

13

2016/05/13    -->5/10 @2-5pm

Graphical Models  (II)

 

Dr. Hsing-Kuo Pao

Moodle

14

2016/05/20

Conditional Random Fields

 

Dr. Richard Tzong-Han Tsai

Moodle

15

2016/05/27

MapReduce in Cloud Computing

 

Dr. Yu-Rong Chang

Moodle

16

2016/06/03

Network Analysis

 

Dr. Hsuan-Cheng Huang

Moodle

17

2016/06/10

Review Week

 

 No Class

18

2016/06/17

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/ Slides

1

2016/02/18--> moves to 4/19 (Wed)@2-5pm Analysis of NGS data I

       N/A

Dr. Hsuan-Yu Chen

Moodle

2

2016/02/25--> moves to 4/26 (Tue)2-5pm Analysis of NGS data II

       N/A

Dr. Hsuan-Yu Chen

Moodle

3

2016/03/01(Tue) --> 3/08 (Tue)@14:00-17:00 Maximum likelihood estimates and the EM algorithm I 

 

Motivated examples

Dr. Henry Horng-Shing Lu

Moodle 

4

2016/03/10 @Room#126, CITI Maximum likelihood estimates and the EM algorithm II

 

Maximum likelihood estimates

Dr. Henry Horng-Shing Lu

Moodle 

5

2016/03/15(Tue) @14:00-17:00 Maximum likelihood estimates and the EM algorithm III

 

The EM algorithm

Dr. Henry Horng-Shing Lu

Moodle 

6

2016/03/22(Tue) @14:00-17:00 Bayesian methods with Monte Carlo Markov Chains I Bayesian methods     Dr. Henry   Horng-Shing Lu Moodle   

7

2016/03/29(Tue) @14:00-17:00 Bayesian methods with Monte Carlo Markov Chains II

 

Monte Carlo Markov Chains

Dr. Henry Horng-Shing Lu

Moodle 

8

2016/04/07 Non-parametric methods by permutation and bootstrap methods I      N/A

Dr. Grace S. Shieh

Moodle

9

2016/04/14

Midterm Exam

 

10

2016/04/21 Non-parametric methods by permutation and bootstrap methods II

  N/A

Dr. Grace S. Shieh

Moodle

11

2016/04/28 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

12

2016/05/05 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

13

2016/05/12 Statistics in Human Genetics I

 

Concept of Statistical Genetics, International Genomic Projects, Linkage Analysis

 

Dr. Hsin-Chou Yang

 

Moodle

14

2016/05/19 Statistics in Human Genetics II

Genetic Association, Gene-Gene interaction, Rare Variant Analysis

Dr. Hsin-Chou Yang

Moodle

15

2016/05/26 Advanced regression and dimension reduction I

 N/A

Dr. Shinsheng Yuan

Moodle

16

2016/06/02 Advanced regression and dimension reduction II

  N/A

Dr. Shinsheng Yuan

Moodle

17

2016/06/04

(Sat)

 

Review Week

 No Class

18

2016/06/16

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 2/05/2016.

*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

2016/2/18

Yenchen Lo(2013) 

Topic:

Perez, Alberto, Justin L. MacCallum, and Ken A. Dill. "Accelerating molecular simulations of proteins using Bayesian inference on weak information." Proceedings of the National Academy of Sciences 112.38 (2015): 11846-11851. 

 

 

2

2016/2/25

 Hsiu-man Chen(2013) 

Topic:

Zhang et al, "Germline Mutations in Predisposition Genes in Pediatric Cancer",  N Engl J Med 2015; 373:2336-2346, December 10, 2015, DOI: 10.1056/NEJMoa1508054

 

 

3

2016/03/03

Divya Sahu(2013) 

Topic:

Guo Q et al., “Comprehensive analysis of lncRNA-mRNA co-expression pattern identifies immune associated lncRNA biomarkers in ovarian cancer malignant progression”, Sci Rep. 2015 Dec 3; 5:17683. doi: 10.1038/srep17683

 

4

2016/03/10

 Kidane Gebereyesus(2013) 

Topic: "lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection.'' Bioinformatics Advance Access (January 22, 2016)

 

 

5

2016/03/17

 Yen Hsieh Chen(2013) 

Topic: "Identification of GALNT14 as a novel neuroblastoma predisposition gene" Oncotarget

 

 

6

2016/03/24

Jerome Penaflor Panibe(2013) 

Topic:

  Zhang, X., et. al (2015). "A genome-wide survey reveals abundant rice blast R genes in resistant cultivars". The Plant Journal (2015) 84, 20–28, doi: 10.1111/tpj.12955
 

 

7

2016/03/31

 Chiahung Lin(2013)

 Topic:

Ayuko Hoshino et al., "Tumour exosome integrins determine organotropic metastasis"

Nature 527, 329335, doi:10.1038/nature15756

 

 

8

2016/04/07

 N/A

 

9

2016/04/14

Chi-Chun Chen(2013) 

Topic:Zhang W, Chang JW, Lin L, Minn K, Wu B, Chien J, Yong J, Zheng H, Kuang R., "Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis", PLoS Comput Biol. 2015 Dec 23;11(12):e1004465. doi: 10.1371/journal.pcbi.1004465. eCollection 2015 Dec.

 

Nikhil Pathak(2013)

Topic:


 

 

10

2016/04/21

Midterm Week

 Cheng-Kai Shiau(2013) 

Topic: Bruno Hudry, Sanjay Khadayate & Irene Miguel-Aliaga, "The sexual identity of adult intestinal stem cells controls organ size and plasticity", Nature 530, 344–348 (18 February 2016) doi:10.1038/nature16953

 

 

11

2016/04/28

 Lovely Raghav(2014)

Topic:

"Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma", Bonilla X. et al, Nature Genetics 2016

 

 

12

2016/05/05

Chun-Yi Chen (2014)  

Topic:

Kleinstiver BP and Pattanayak V, et.al., "High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects", Nature. 2016 Jan 28;529(7587):490-5. doi: 10.1038/nature16526

 

 

13

2016/05/12

Cheng-Wei Cheng(2014)

Topic:

VM Bui et al., "MDD–SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs", Bioinformatics (2016) 32 (2): 165-172.

 

 

14

2016/05/19

Kshitij Tandon (2015)

(Topic will be assigned by Lab Professor )

 

 

15

2016/05/26

 Neha Warikoo (2015)

(Topic will be assigned by Lab Professor )

 

 

16

2016/06/02

(2015 YMU Students陽明)

呂俊良

 Topic:

C Mark DM Leiserson, Hsin-Ta Wu, Fabio Vandin and Benjamin J. Raphael, "CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer", Genome Biology 2015, DOI: 10.1186/s13059-015-0700-7

 

 

17

2016/06/08

(Wed)

鄭中遠

Topic:

 Duda MMa RHaber NWall DP., "

Use of machine learning for behavioral distinction of autism and ADHD

", Transl Psychiatry (2016) 6, e732; doi:10.1038/tp.2015.221

 

 

18

2016/06/16

Final Exam Week

  

 

 

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Special Lecture

TIGP Bio 2016 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

2016/02/18 Translational bioinformatics: from gene regulatory network to biologic therapeutics discovery Dr.  Yang, Hsih-Te          Assistant Professor, Institute of Medical Informatics, National Cheng Kung University Resources                                     Host: Dr. Wei-Chung Liu

 

2

2016/02/25 Parasitism in ecological networks Dr. Chen, Hsuan-Wien
National Chia Yi University, Department of Bioloigcal Resources                                     Host: Dr. Wei-Chung Liu

3

2016/03/03 Application of bioinformatics in Plant Virology Dr. Hsin-Hung, Yeh         Agricultural Biotechnology Research Center, Academia Sinica                                      Host: Dr. Chen, Ho-MIng

4

2016/03/10 ----

-----

5

2016/03/17 Pathway Extraction with Text Mining Dr. Richard Tzong-Han Tsai
Host: Ting-Yi Sung

6

2016/03/24 Interrogating translating mRNAs with next-generation sequencing Dr. Shu-Hsing Wu                Institute of Plan and Microbial Biology, Academia Sinica
Host: Dr. Chen, Ho-Ming
 

7

2016/03/31 ---- ----

8

2016/04/07 Review Week (No Class) ----

9

2016/04/14 Midterm Week

(4/13 ) @106, IIS

3:00pm-4:30pm

Dr. Mariko Okada
Laboratory for Integrated Cellular Systems
RIKEN Center for Integrative Medical Sciences (IMS)
Host: Dr. Huai-Kuang Tsai
 

10

2016/04/21 Genome Annotation and Comparative Genomic Analysis of Orchids and Other Popular Model Plants Dr. Ya-Ting Chao                   Agricultural Biotechnology Research Center, Academia Sinica
Host: Dr. Chen, Ho-Ming

11

2016/04/28 Genomics -- promise for  small crops: oat as an example Dr. Yung-Fen Huang                     Dep. of Agronomy, NTU
Host: Dr. Chen, Ho-Ming
 

12

2016/05/05 Dietary Patterns and Cognitive Change in Taiwanese Elderly Dr. Yen-Ching Chen (Karen)  National Taiwan  University      Host: Dr. Chung-Yen Lin

13

2016/05/12 The roles of ecology and behavior in the evolution of a forest bird community Dr. Chih-Ming Hung    Biodiversity Research Center, Academia Sinica                         Host: Dr. Wei-Chung Liu

 

14

2016/05/19

@N106

Identification of B-cell epitopes based on immunoinformatics approaches   Dr. Emily Chia-Yu Su            Taipei Medical University          Host: Dr. Ting-Yi Sung

 

15

2016/05/26 Micro Big Data Dr. Chi-Ming Chu                  School of Public Health, National Defense Medical Center                                           Host: Dr. Wei-Chung Liu

16

2016/06/02 Identification and analysis of non-co-linear RNAs: trans-splicing, circular RNA, and gene fusion events Dr. Chuang, Trees-Juen
Genomics Research Center, Academia Sinica
Host: Dr. Ting-Yi Sung

17

2016/06/08

(Wed)

 

 Mining biomarker candidates by personalized membrane proteomics and multiple reaction monitoring mass spectrometry analysis Dr. Chia-Li Han                            Taipei Medical University            Host: Dr. Sung, Ting-Yi

18

2016/06/16

Final Exam

No Class

 

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Lab Rotation

 

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

(Deadline for 2016 Spring Semester: 1/30/2016)

 

Student

Advisor

Neha Warikoo   倪荷 Dr. Ting-Yi Sung
Kshitij Tandon   斯提吉 Dr. Sen-Lin Tang
   
 
 
 
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