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Courses_2014 Fall
 

 

    B1  C1  S1  Special Lecture  Seminar  Lab Rotation

Moodle System :  http://db1x.sinica.edu.tw/tdCourse/

B1 Course Material 

Place: Room 107, New Building of the Institute of Information Science, Academia Sinica.

 

Time: Tuesday 09:00am-12:00pm

 

Chair: Dr. Chuan-Hsiung Chang

Aim: understanding the key concepts in molecular and cell biology and their experimental underpinning

 

Textbook: (Required)

1. Molecular Cell Biology, 7th edition, by Harvey Lodish et al. Publisher: W. H. Freeman. International Edition (13 Aug, 2012). ISBN-13: 9781464109812.

Local book store: http://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06585

Reference: (Recommended but not required)

1. Biochemistry: A Short Course, 2nd edition, by Lubert Stryer et al. Publisher: W. H. Freeman (December 23, 2011). ISBN-10: 1429283602, ISBN-13: 978-1429283601.   

2. Molecular Biology, 5th edition, by Robert Weaver. Publisher: McGraw-Hill (February 11, 2011). ISBN-10: 0073525324, ISBN-13: 978-0073525327.

 

Lecturers: Chuan-Hsiung Chang, Ueng-Cheng Yang, Dar-Yi Wang , Ho-Ming Chen, Jung-Hsin Lin , Wailap Victor Ng, Sheau-Yann Shieh, Yuh-Shan Jou, Jie-rong Huang

 

TA: Nikhil Pathak (E-mail: nikhilpathak@iis.sinica.edu.tw)

Office hours: Thursday,06:00pm-09:00pm @Rm #304, old building of IIS

Grades: Midterm exam 50%. Final exam 50%.                                        *MOODLE: slides available  on

                                                                                                                                     MOODLE System

 

Week

Date

Topics/Brief Description

Lecturers

Video

1

2014/09/16

Molecules, Cells, and Evolution

Dr. Chuan-Hsiung Chang

MOODLE

2

2014/09/23

Chemical Foundations

Dr. Jie-rong Huang

MOODLE

3

2014/09/30

Protein Structure and Function

Dr. Jie-rong Huang

MOODLE

4

2014/10/07

Basic Molecular Genetic Mechanisms

Dr. Ueng-Cheng Yang

MOODLE

5

2014/10/14

Molecular Genetic Techniques

Dr. Ueng-Cheng Yang

http://tigpbp.iis.sinica.edu.tw/icon_download.gif   http://tigpbp.iis.sinica.edu.tw/icon_download.gif

6

2014/10/21

Genes, Genomics, and Chromosomes

Dr. Chuan-Hsiung Chang

MOODLE

7

2014/10/28

Transcriptional Control of Gene Expression

Dr. Dar-Yi Wang

MOODLE

8

2014/11/04

Review Week

 

---

9

2014/11/11

Midterm Exam

 

---

10

2014/11/18

Post-Transcriptional Gene Control

 

Dr. Ho-Ming Chen

MOODLE

11

2014/11/25

Biomembrane Structure and Transport

 

Dr. Jung-Hsin Lin

MOODLE 

12

2014/12/02

9:00am-1:00pm

Cellular Energetics

Dr. Ueng-Cheng Yang

      http://tigpbp.iis.sinica.edu.tw/icon_download.gif

 

13

2014/12/09

Signal Transduction and G Protein–Coupled Receptors

 

Dr. Wailap Victor Ng

MOODLE  

14

2014/12/16

Signaling Pathways That Control Gene Expression

 

Dr. Wailap Victor Ng

MOODLE  

15

2014/12/23

The Eukaryotic Cell Cycle

 

Dr Sheau-Yann Shieh

MOODLE  

16

2014/12/30

Cancer

Dr. Yuh-Shan Jou

MOODLE  

17

2015/01/06

Review Week

 

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18

2015/01/13

Final Exam

 

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C1 Course Material

Place: Room 107, New Building of the Institute of Information Science, Academia Sinica.

Time: Friday 14:00-17:00

Chair: Dr Kun-Pin Wu

Outline: Design and analysis of algorithms for biologists

Lecturers: Wen-Lian Hsu, Jyh-Ying Peng, Huai-Kuang Tsai, Hsin-Nan Lin, Kun-Pin Wu, Chun-Chieh Shih,  Ting-Yi Sung, Chia-Yu Su

Textbook:

Reference book:

TA: Chi Chun Chen (E-mail: chichunchen@iis.sinica.edu.tw)

Office hours: Friday @ 10:00am-12:00pm @Rm #304, old building of IIS

Grades: Midterm exam 50%. Final exam 50%.                                  *MOODLE: slides available   on 

                                                                                                                               MOODLE System

 

Week

Date

Topics/Brief Description

Lecturers

Video

1

2014/09/19

Analysis of Algorithms

Dr. Wen-Lian Hsu

http://tigpbp.iis.sinica.edu.tw/icon_download.gifhttp://tigpbp.iis.sinica.edu.tw/icon_download.gif

2

2014/09/26

Recurrence

Dr. Wen-Lian Hsu

http://tigpbp.iis.sinica.edu.tw/icon_download.gif

3

2014/10/03

Introduction to Data Structure (I)

Dr. Jyh-Ying Peng

    N/A

4

2014/10/8 @6:00-9:00pm

Introduction to Data Structure (II)

Dr. Jyh-Ying Peng

    N/A

5

2014/10/17

Algorithmic Techniques

Dr. Kun-Pin Wu (Dr. Wen-Lian Hsu will sub. the class)

    http://tigpbp.iis.sinica.edu.tw/icon_download.gif http://tigpbp.iis.sinica.edu.tw/icon_download.gif

6

2014/10/24

Motif Finding

Dr. Ting-Yi Sung

    http://tigpbp.iis.sinica.edu.tw/icon_download.gif

7

2014/10/31

Graph Algorithms@Rm108

Dr. Jyh-Ying Peng

     N/A

8

2014/11/07

Review Week @Rm 108

---

9

2014/11/14

Midterm Exam

---

10

2014/11/21

Pairwise Sequence Alignment

Dr. Huai-Kuang Tsai

MOODLE

11

2014/11/28

Multiple Sequence Alignment

Dr. Huai-Kuang Tsai

MOODLE

12

2014/1205

The Analysis of Next Generation Sequencing Data (I)

Dr. Hsin-Nan Lin

MOODLE 

13

2014/12/12

The Analysis of Next Generation Sequencing Data (II)

Dr. Hsin-Nan Lin

MOODLE 

14

2014/12/19

Combinatorial Pattern Matching @Rm108

Dr. Kun-Pin Wu

MOODLE 

15

2014/12/26

Suffix Trees

Dr. Kun-Pin Wu

MOODLE 

16

2015/12/24(Wed)9:00am-12:00pm

Fundamentals of Molecular Evolution and Phylogenetic Tree Construction @ Rm 107

Dr. Chun-Chieh Shih

MOODLE 

17

2015/01/09

Review Week

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18

2015/01/16

Final Exam

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S1 Course Material

TIGP Bio 2014 Fall Syllabus

Fundamental Statistical Methods in Bioinformatics (S1)

Place: Room 107, New 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: Ker-Chau Li, Hsin-Chou Yang, Shinsheng Yuan, Grace Shieh, Horng-Shing Lu, Hsuan-Yu Chen, and Wei-Chung Liu

TA: Kidane Gebreyesus (Email: kidu@iis.sinica.edu.tw)

Office hours: Wednesdays, 2:00pm-5:00pm @Rm #304, old building of IIS

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

 

Week

Date

Topics/Brief Description

Lecturers

    Video

1

2014/09/18

Descriptive Statistics, Genomic Data Analysis

Dr. Li, Ker-Chau

MOODLE

2

2014/09/25

Probability

Dr. Yang, Hsin-Chou

http://tigpbp.iis.sinica.edu.tw/icon_download.gif

3

2014/10/02

Discrete Distributions and Contingency Tables

Dr. Yang, Hsin-Chou

http://tigpbp.iis.sinica.edu.tw/icon_download.gif

4

2014/10/09

Continuous Distributions, Expectations and Basic Statistics

Dr. Yang, Hsin-Chou

      http://tigpbp.iis.sinica.edu.tw/icon_download.gif

5

2014/10/16

Parameter Estimation and Confidence Interval

Dr. Yuan, Shin-sheng

MOODLE

6

2014/10/23

Hypothesis Testing, P-value and False Discovery Rate

Dr. Shieh, Grace

MOODLE

7

2014/10/30

Comparative Study, Two Sample Test

Dr. Yuan, Shin-sheng

MOODLE

8

2014/11/06

Review Week

 

9

2014/11/13

Midterm Exam

 

10

2014/11/20

Correlation, Regression Analysis and ANOVA

Dr. Shieh, Grace

MOODLE

11

2014/11/27

Analysis of Categorical Data, Chisq and Multinomial

Dr. Chen, Hsuan-Yu

MOODLE

12

2014/11/26

(Wed)

Clustering @Rm106

(14:00-17:00)

Dr. Lu, Horng-Shing

MOODLE

13

2014/12/10

(Wed)

Classification @Rm106

(14:00-17:00)

Dr. Lu, Horng-Shing

MOODLE

14

2014/12/18

Survival Data Analysis @Rm101

Dr. Chen, Hsuan-Yu

MOODLE

15

2014/12/25

Nonparametric Statistics (I) @Rm101

Dr. Liu, Wei-Chung

MOODLE 

16

2015/12/31(Wed)

Nonparametric Statistics (II)

Dr. Liu, Wei-Chung

MOODLE

17

2015/01/08

Review Week

 

18

2015/01/15

Final Exam

 


*Bonus class for S1:

    Topic:An Introduction to R Language

    Date: 10/15 (Wed)

    Time:14:00~15:00

    Location: Rm204, New Building of IIS

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Special Lecture
Place: Room 101, New Building of the Institute of Information Science, Academia Sinica.
Time: Thursdays 14:00-15:10
Chair: Dr. Ting-Yi Sung, Dr. Ho-Ming Chen, and Dr. Wei-Chung Liu
Outline:

Grades: Attendance

Week Date Topics/Brief Description Lecturers
1

2014/09/18

Hsp90 regulates non-genetic variation in response to environmental stress Dr. Jun-Yi Leu
Re: Bio
2

2014/09/25

Ant genetics and genomics Dr. John Wang
Re: Bio
3

2014/10/02

Metagenomic approaches to understand microbial interaction. Dr. Dar-Yi Wang
Re: Bio
4

2014/10/09

Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs) Dr. Lee Wei Yang    Re: NTHU
5

2014/10/16

Identifying Synthetic lethal interactions and prognosis markers for cancers Dr. Grace Shieh           Re: Statistics
6

2014/10/23

Human Proteome Project and Current Progress on Human Proteome Mr. Reta Birhanu Kitata   (MST)         Host: Dr. Ting Yi Sung
7

2014/10/30

Bioinformatic study of cancer genomes Dr. Wen-Hsiung Li
8

2014/11/06

Review Week  
9

2014/11/13

Midterm Exam  
10

2014/11/20

Profiling Genome Wide DNA Methylation in Zoo Dr. Pao-Yang Chen
Re: Bio
11

2014/11/27

Small RNA and Exome Sequencing Reveals Novel Roles and Clinical Implications of MicroRNAs Dr. Hsei-Wei Wang
Re: Bio
12

2014/12/04

Rigorous determination and systematic detection of missing proteins in human proteome Dr. Ting Yi Sung          Re: Computing
13

2014/12/11

Contribution of sequence motif, chromatin state, and DNA structure features to predictive models of transcription factor binding Dr. Huai-Kuang Tsai Re: Computing
14

2014/12/18

The role of noise and dynamics in the migration regulation of Dorsal tip cell of C. elegans Dr. Cherri Hsu            Re: Bio
15

2014/12/25

Homozygosity disequilibrium and its importance in medical genomics and population genomics Dr. Hsin-Chou Yang Re: Statistics
16

2015/12/31(Wed)

TBD Dr. Wei-Chung Liu
Re: Statistics
17

2015/01/08

Review Week  
18

2015/01/15

Final Exam  







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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 9/13/2014.

*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.

 

Date TIGP Bioinformatics Host
 

Professor

Dr. Chuan-Hsiung Chang 

2014/09/18  Ignasius Joanito(2012)

Topic:

M.S. Avendano, C Leidy and J. M. Pedraza, "Tuning the range and stability of multiple phenotypic states with coupled positive–negative feedback loops", NATURE COMUNICATION 4:2605 DOI: 10.1038/ncomms3605
 
  Thejkiran Pitti(2012)

Topic:

"Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the generalform of Chou’s PseAAC" Protein Engineering, Design & Selection vol. 26 no. 11 pp. 735–742, 2013
Published online September 18, 2013 doi:10.1093/protein/gzt042

http://peds.oxfordjournals.org/content/early/2013/09/17/protein.gzt042.abstract 

 

 
2014/09/25

 

 
     
2014/10/02  Jerome Penaflor Panibe(2013)

Topic:

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome"
Genetics. 2014 Mar;196(3):875-90. doi: 10.1534/genetics.113.159715.

 
  Chi-Chun Chen(2013)

Topic:

Activation pathway of Src kinase reveals intermediate states as targets for drug design

 

 
2014/10/09 Cheng-Kai Shiau(2013)

Topic:

"Timed regulation of P-Element-induced wimpy testis-interacting RNA expression during rat liver regeneration." Hepatology, Vol. 60(3), p.798-806, 2014.

http://onlinelibrary.wiley.com/doi/10.1002/hep.27267/abstract

 

 
 

 

孫在陽(2013陽明)

Topic:

D.P. Cariveau, J.E. Powell, H.Koch, R. Winfree and N.A. Moran, "Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)", The ISME Journal (2014), 1–11, 1751-7362/14 http://www.nature.com/ismej/journal/vaop/ncurrent/pdf/ismej201468a.pdf

 
 
2014/10/16 Yenchen Lo(2013)

Topic:  

PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes Journal: Nucleic Acids Research, Vol. 12 , May 2014.

http://www.ncbi.nlm.nih.gov/pubmed/24829450

 
  Chiahung Lin(2013)

Topic:

Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs Scot J. Matkovich, John R. Edwards, Tiffani C. Grossenheider, Cristina de Guzman Strong, Gerald W. Dorn II PNAS.

2014 Aug 19;111(33):12264-9.

http://www.pnas.org/content/111/33/12264.full?sid=805f5f18-794f-46f5-a690-3b04752ea08e

 
2014/10/23 Yen Hsieh Chen(2013)

Topic:

"Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer." 2014 Jun 15;74(12):3238-47. doi: 10.1158/0008-5472.CAN-14-0013. Epub 2014 Apr22.

Cancer Res.

 
 

 

 
2014/10/30 Hsiu-man Chen(2013)

Topic:

N.A. Christakis, and J.H. Fowler, "Friendship and natural selection", PNAS:pROCEEDINGS OF THE nATIONAL aCADEMY OF sCIENCES 111:10796-10801, DOI: 10.1073/PNAS.1400825111
http://www.pnas.org/content/111/Supplement_3/10796

 
     
2014/11/20 Nikhil Pathak(2013)

Topic:

Spectinamides: a new class of semisynthetic antituberculosis agents that overcome native drug efflux,

Nature Medicine,20 p.152–158, 2014

http://www.nature.com/nm/journal/v20/n2/full/nm.3458.html

 

 
     
2014/11/27 Kidane Gebereyesus(2013)

Topic:

"Estimating the Reproduction Number of Ebola Virus (EBOV) During the 2014 Outbreak in West Africa"

http://currents.plos.org/outbreaks/article/estimating-the-reproduction-number-of-zaire-ebolavirus-ebov-during-the-2014-outbreak-in-west-africa/

 
  Divya Sahu(2013)

Topic:

in-Kyung Seok, Sun Hee Lee, Min Jung Kim and You- Mie Lee, " MicroRNA-382 induced by HIF-1 α is an angiogenic miR targeting the tumor suppressor phosphatase and tensin homolog", Nucleic Acids Res. 2014;42(12):8062-72. doi: 10.1093/nar/gku515. Epub 2014 Jun 9.

http://nar.oxfordjournals.org/content/42/12/8062/suppl/DC1

 
2014/12/04

Chun-Yi Chen(2014)

Topic:

Clonal evolution in breast cancer revealed by single nucleus genome sequencing
Yong Wang et al. Nature 512, 155–160 (2014)
http://www.nature.com/nature/journal/v512/n7513/full/nature13600.html 

 
     
2014/12/11

Cheng-Wei Cheng(2014)

Topic:

"Combinatorial Approach for Large-scale Identification of Linked Peptides from Tandem Mass Spectrometry Spectra"

http://www.mcponline.org/content/13/4/1128.short

 
     
2014/12/18 Lovely Raghav(2014)

Topic: 

 "Extensive transduction of nonrepetitive DNA mediated by L retrotransposition in cancer genomes."

http://www.sciencemag.org/content/345/6196/1251343.full

Dr. Chen, Ho-Ming
     
2014/12/25    
     
2014/12/31(Wed)

 

 







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Lab Rotation

 

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

(Deadline for 2014 Fall Semester: 9/26/2014)

 

Student

Advisor

Chun-Yi Chen Dr. Wen-Hsiung Li
Cheng-Wei Cheng Dr. Wen-Lian Hsu
Lovely Raghav Dr. Huai-Kuang Tsai
 
 
 
 
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