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AS-TIGP Research Progress Fellowship Program

B2 C2 S2 Seminar Student Presentation Lab Rotation
TIGP Bio 2020 Spring Syllabus Basic Molecular Biology II (B2)
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: introduce key concepts and methods to manage, integrate and analyze bio big data in the era of post-genomics life sciences
Outline:Big Data in Bioinformatics - From Data-Driven Analysis to Knowledge
Textbook: (Reference books, not required)
1. Scalable Big Data Analytics for Protein Bioinformatics [Publisher: Springer; 1st ed. 2018 edition (September 26, 2018)]
2. Computational Intelligence and Big Data Analytics: Applications in Bioinformatics [Publisher: Springer; 1st ed. 2019 edition (September 9, 2018)]
3. Big Data in Omics and Imaging [Publisher: Chapman and Hall/CRC; 1 edition (June 19, 2018)]
4. Big Data Analytics in Genomics [Publisher: Springer; Softcover reprint of the original 1st ed. 2016 edition (April 25, 2018)]

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

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

Week Date Topics/Brief Description Lecturers
1 2020/02/25 Genomics and Genome Analysis (I) Dr. Chuan-Hsiung Chang
2 2020/03/03 Microbiome Dr. Sen-Lin Tang
  2020/03/04
1420-1720
BioDiv B208		 NGS Analytics Dr. I-Sheng Tsai
3 2020/03/10 Metagenomics Dr. Sen-Lin Tang
4 2020/03/17
1400-1700		 Proteomics Informatics Dr. Victor Ng
5 2020/03/24 Moved to April 8 -----
7 2020/03/31 Transcriptome Informatics Dr. Ho-Ming Chen
8 2020/04/07 Review Week -----
  2020/04/08
1420-1720
BioDiv B208		 Comparative and Evolutionary Genomics Dr. I-Sheng Tsai
9 2020/04/14 Midterm Exam ---
10 2020/04/21 Genomics and Genome Analysis (II) Dr. Chuan-Hsiung Chang
11 2020/04/28 Population Genomics Dr. John Wang
12 2020/05/05 Medical Genomics Dr. Ling-Hui Li
13 2020/05/12 Biobank Genotyping Dr. Tzu-Pin Lu
14 2020/05/19 Structural Bioinformatics in Pharmacogenomics Dr. Jung-Hsin Lin
15 2020/05/26 Translational Clinical Research Dr. Ueng-Cheng Yang
16 2020/06/02 Precision medicine and clinical informatics Dr. Ueng-Cheng Yang
17 2020/06/09 Review Week ---
18 2020/06/16 Final Exam ---

Advanced Algorithms (C2)
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: Yu-Hsin Chen 陳瑜欣 Email: qqpigass@gmail.com
Office hours: TBD
Grades: Midterm exam 50%. Final exam 50%.
Week Date Topics/Brief Description
Subtopics/Detail Descriptions/Examples		 Lecturers
1 2020/02/21 Databases: An Overview Dr. Meng Chang Chen
2 2020/02/28
(Holiday)->
02/26 14-17		 Introduction to Data Mining Dr. Meng Chang Chen
3 2020/03/06 Data Classification: Overview Dr. Li Su
4 2020/03/13 Standard Optimization Algorithms
Basic idea of optimization, Convex optimization, Lagrangial method for optimization method, and Gradient descent methods.
 Dr. Wen-Liang Hwang
5 2020/03/20 Support Vector Machines and Large Margin and Kernel Methods
Hard and soft support vector machines (SVM) and kernel methods. SVM is a convex optimization method. So, I can use the results of week 1 in week 2.
 Dr. Wen-Liang Hwang
6 2020/03/27 Neural Networks and Deep Learning (I)
The shallow neural network, and universality theorem		 Dr. Wen-Liang Hwang
7 2020/04/03
(Holiday)->04/01		 Neural Networks and Deep Learning (II)
Mathematical formulation for deep neural network, learning techniques, architecture, and implications.		 Dr. Wen-Liang Hwang
8 2020/04/10 Review Week ---
9 2020/04/17 Midterm Exam ---
10 2020/04/24 Nonstandard Optimization Algorithms (GA, Random Forest, and others) Dr. Huai-Kuang Tsai
11 2020/05/01 Hidden Markov Models Dr. Yu Tsao
12 2020/05/08 Graphical Models (I) Dr. Hsing-Kuo Pao
13 2020/05/15 Graphical Models (II) Dr. Hsing-Kuo Pao
14 2020/05/22 Conditional Random Fields Dr. Richard Tzong-Han Tsai
15 2020/05/29 MapReduce in Cloud Computing Dr. Yu-Rong Chang
16 2020/06/05 Network Analysis Dr. Hsuan-Cheng Huang
17 2020/06/12 Review Week ---
18 2020/06/19 Final Exam ---

Advanced Statistical Methods in Bioinformatics (S2)
Place: Room 107, New Building of the Institute of Information Science, Academia Sinica.
Time:Thursday, 09:00 am-12:00 pm
Chair:Dr. Grace S. Shieh
Outline:Introduction to 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-reductio nand 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/Detailed Description Lecturers
1 2020/02/20 No Class
2 2020/02/27
3 2020/03/02 Mon 1400-1700
Moved to 06/03 Wed 1400-1700		 Analysis of NGS data I N/A Dr. Hsuan-Yu Chen
Changed to Dr. Hao Ho
  2020/03/05 Maximum likelihood estimates and the EM algorithm I Maximum likelihood estimates Dr. Yen-Tsung Huang
4 2020/03/02 Mon 1400-1700
Moved to 06/10 Wed 1400-1700		 Analysis of NGS data II N/A Dr. Hsuan-Yu Chen
Changed to Dr. Hao Ho
  2020/03/12 Maximum likelihood estimates and the EM algorithm II The EM algorithm Dr. Yen-Tsung Huang
5 2020/03/19 Bayesian methods Bayesian methods Dr. Grace S. Shieh
6 2020/03/26 Monte Carlo Markov Chains Monte Carlo Markov Chains Dr. Shin-Sheng Yuan
7 2020/04/02
Moved to 03/30 Mon 1400-1700		 Resampling methods I Bootstrap Dr. Grace S. Shieh
8 2020/04/09 Review Week    
9 2020/04/16 Midterm Exam    
10 2020/04/23 Resampling methods II Permutation test, jacknife Dr. Grace S. Shieh
11 2020/04/30 Clustering, classification and data visualization (I) Clustering: K-Means, Hierarchical Clustering, Cluster Validation Dr. Han-Ming Wu
12 2020/05/07 Clustering, classification and data visualization (II) KNN, Decision Tree, Support Vector Machine, Data visualization in R Dr. Han-Ming Wu
13 2020/05/14 Statistics in Human Genetics I Concept of Statistical Genetics, International Genomic Projects, Linkage Analysis Dr. Hsin-Chou Yang
14 2020/05/21 Statistics in Human Genetics II Genetic Association, Gene-Gene interaction, Rare Variant Analysis Dr. Hsin-Chou Yang
15 2020/05/28 Advanced regression and dimension reduction I N/A Dr. Shinsheng Yuan
16 2020/06/04 Advanced regression and dimension reduction II N/A Dr. Shinsheng Yuan
17 2020/06/11 Review Week    
18 2020/06/18 Final Exam    


Student Presentation

Place:Room 101, New Building of the Institute of Information Science, Academia Sinica
Time:Thursday, 3:30 Pm-5:00 pm
Chair:Dr. Chuan-Hsiung Chang
*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 03/02/2020 (First Year Students: The paper will be assigned by your lab professor)
*The following schedule is confirmed and will not be changed. Please contact Dr. Chuan-Hsiung Chang 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.

*Seminar presentation guidelines for PhD program students_20200225
Week Date TIGP Bioinformatics
1 2020/03/05 N/A
2 2020/03/12 The Reaction of Dimerization by Itself Reduces the Noise Intensity of the Protein Monomer
3 2020/03/19 A Label-Free Mass Spectrometry Method to Predict Endogenous Protein Complex Composition
4 2020/03/26  Loss of Angiogenin Function Is Related To Earlier ALS Onset And A Paradoxical Increase In ALS Duration
5 2020/04/02 Holiday_No Class
6 2020/04/09 Comprehensive Molecular Characterization of Mitochondrial Genomes In Human Cancers
7 2020/04/16 Midterm Week_No Class
8 2020/04/23 Biomedical Named Entity Recognition Using Deep Neural Networks with Contextual Information
9 2020/04/30 Isoform-resolved Correlation Analysis Between mRNA Abundance Regulation and Protein Level Degradation
10 2020/05/07 PAGA: Graph Abstraction Reconciles Clustering with Trajectory Inference Through A Topology Preserving Map of Single Cells
11 2020/05/14 A Network Analysis to Identify Mediators of Germline-Driven Differences in Breast Cancer Prognosis
12 2020/05/21 Complete Deconvolution of Cellular Mixtures Based on Linearity of Transcriptional Signatures
13 2020/05/28 B Cells Are Associated with Survival and Immunotherapy Response in Sarcoma
14 2020/06/04 DeePromoter: Robust Promoter Predictor Using Deep Learning
15 2020/06/11 Review Week_No Class
16 2020/06/18 Final Exam Week_No Class

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), Chien-Ling Lin (Biology), Dr. Wei-Chung Liu (Statistic);
Remarks:
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 2020/02/20 @ N106 A Machine Learning Method for Large-Scale Predictions of Transcription Factor Binding Sites Dr. Wen-Hsiung Li
Host: John Wang
2 2020/02/27 Computational Proteomics and Its Application to Cancer Tissue Data Analysis Dr. Ching-Tai Chen
Host: Dr. Ting-Yi Sung
3 2020/03/05 N/A N/A
4 2020/03/12 Translational Bioinformatics for Breast Cancer Research Dr. Ueng-Cheng Yang
Host: Dr. Hsin-Chou Yang
5 2020/03/19 Precision Medicine in Taichung VGH Dr. Tzu-Hung Hsiao
Host: Jen-Hung Wang
6 2020/03/26
(Moved to 05/11)		 N/A Dr. Yen-Fu Cheng
Host: Yueh-Hua Tu
7 2020/04/02 Holiday ----
8 2020/04/09 Review Week ----
9 2020/04/16 Midterm Week ----
10 2020/04/23 Population Genomics Reveals Genome Plasticity in Paramecium Bursaria Dr. Jun-Yi Leu
Host: Nam Nhut Phan
11 2020/04/30 Emotional First Aid: Heal Your Daily Emotional Hurt Immediately Ms. Mei Wen Fong
Host: Yu-Hsin Chen
12 2020/05/07 Integrated Microfluidic Platforms for Biosensing Applications Dr. Nien-Tsu Huang
Host: Yu-Hsiang Chen
13 2020/05/11
(Moved from 03/26)		 A New Era of Clinical Otology- Gene, App, AI and Beyond Dr. Yen-Fu Cheng
Host: Dr. Yu Tsao
13 2020/05/14 Combining Movement Data and Mathematical Models to Understand the Potential Spread of COVID-19 in Taiwan Dr. Hsiao-Han Chang
Host: Yueh-Hua Tu
14 2020/05/21 Applications of SNP Arrays: Beyond GWAS Dr. Ling-Hui Li
Host: Erickson Erigio Fajiculary
15 2020/05/28 Single-Cell Transcriptomics of Giant Virus Infection Dr. Chuan Ku
Host: Samarth Gupta
16 2020/06/04 Mycena Genomes Resolve the Evolution of Fungal Bioluminescence Dr. Isheng Jason Tsai
Host: Chayanika Goswami
17 2020/06/11 Review Week  
18 2020/06/18 Final Exam  

Lab Rotation

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

(Deadline for 2020 Spring Semester: 02/27/2020)
Student Advisor
Yueh-Hua Tu 杜岳華(2019) Dr. Chen-Ching Lin
Samarth Gupta 山瑪斯(2019) Dr. Eric Y. Chuang

https://tigpbp.iis.sinica.edu.tw/tigpbio/old/publications.html

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2019 TIGP-BP Orientation Agenda

Date: 2019/10/07 (Mon.) ????? ?
Venue: Room 201, IIS old building, AS????
Host: Dr. Hsin-Chou Yang (Program Coordinator)


Time

Activity

Details

12:00-12:05

Opening

By Dr. Hsin-Chou Yang (Program Coordinator)

12:05-12:25

Program Session-BP slides

Dr. Wei-Chung Liu ( Student Affair Chair )

12:25-12:30

New Student Session

Self ?ntroduction ( 2 new students)

12:30-13:00

Open Discussion

Lunch box for all attendees

13:00-13:15

Senior Students Session

Student Representatives/ Senior Students

13:15-13:20

Closing

Dr. Hsin-Chou Yang (Program Coordinator)

13:20-13:30

Group Picture

Entrance of IIS


Bioinformatics Program, TIGP , Academia Sinica , Taiwan穢2019