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Courses_2015 Fall
 

 

dec Special Lecture lab


B1 Course Material

Basic Molecular Biology I (B1)

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

Time: Tuesday 09:00-12:00

Chair: Dr. Chuan-Hsiung Chang

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

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. Molecular Biology of the Cell, 6th edition, 2014.

http://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06595&Rcg=53601

2. Molecular Biology : Principles of Genome Function, 2nd edition, 2014.

http://www.yihsient.com.tw/front/bin/ptdetail.phtml?Part=06594&Rcg=52559

3. 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.   

 

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, ie-rong Huang

TA: Yen-Hsieh Chen  Email: yhchen@iis.sinica.edu.tw

Office hours: Friday @ 10:00am-12:00pm

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

 

Week

Date

Topics/Brief Description

Lecturers

Slides/Video

1

2015/09/15

 

Molecules, Cells, and Evolution

moves to 10/14 (Wed)

2:00pm-5:00pm @Room107

 

Dr. Chuan-Hsiung Chang

Moodle 

2

2015/09/22

Chemical Foundations

 

Dr. Jie-Rong Huang

Moodle

3

2015/09/29

Protein Structure and Function

moves to 9/30 (Wed) 2:00pm-5:00pm@Room107

Dr. Jie-Rong Huang

Moodle

4

2015/10/06

Transcriptional Control of Gene Expression

Dr. Dar-Yi Wang

Moodle

5

2015/10/13

Basic Molecular Genetic Mechanisms

Dr. Ueng-Cheng Yang

Moodle

6

2015/10/20

Genes, Genomics, and Chromosomes

Dr. Chuan-Hsiung Chang

Moodle

7

2015/10/27

@RoomN101

Molecular Genetic Techniques

Dr. Ueng-Cheng Yang

Moodle

8

2015/11/03

Review Week

---

9

2015/11/10

@RoomO108

Midterm Exam

---

10

2015/11/17

Post-Transcriptional Gene Control

Dr. Ho-Ming Chen

Moodle

11

2015/12/12(Sat) @Room405B, IRBST

Biomembrane Structure and Transport

Dr. Jung-Hsin Lin

Moodle

12

2015/12/01

Cellular Energetics

Dr. Ueng-Cheng Yang

Moodle

13

2015/12/08

Signal Transduction and G Protein–Coupled Receptors

Dr. Wailap Victor Ng

Moodle

14

2015/12/15

Signaling Pathways That Control Gene Expression 

Dr. Wailap Victor Ng

Moodle

15

2015/12/22

The Eukaryotic Cell Cycle

Dr Sheau-Yann Shieh

Moodle

16

2015/12/29

Cancer

Dr. Yuh-Shan Jou

Moodle

17

2016/01/05

Review Week (no class)

---

18

2016/01/12

Final Exam

---

 
 
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C1 Course Material

Biological Computing  (C1)

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

Time: Friday 14:00-17:00

Chair: Dr. Huai-Kuang Tsai

Outline: Design and analysis of algorithms for biologists

Lecturers: Dr. Wen-Lian Hsu, Dr. Yu-Jung Chang, Dr. Huai-Kuang Tsai, Dr. Hsin-Nan Lin, Dr. Chun-Chieh Shih, Dr. Ting-Yi Sung, Dr. Ching-Tai Chen

Textbook:

Reference book:

TA: Chun-Yi Chen Email: chunyic@iis.sinica.edu.tw

Office hours: Thursday @ 12:00pm-2:00pm

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

 

Week

Date

Topics/Brief Description

Lecturers

Slides/Video

1

2015/09/18

Analysis of Algorithms

moves to 9/23 (Wed) 2:00pm-5:00pm

@ Room N107

Dr. Wen-Lian Hsu

Moodle

2

2015/09/25

Recurrence

Dr. Wen-Lian Hsu

Moodle

3

2015/10/02

Introduction to Data Structure (I)

Dr. Yu-Jung Chang

Moodle

4

2015/10/06(Tue)

Introduction to Data Structure (II)

 

Dr. Yu-Jung Chang

Moodle

5

2015/10/16

Algorithmic Techniques

Dr. Wen-Lian Hsu

Moodle

6

2015/10/23

Motif Finding

Dr. Ting-Yi Sung

Moodle

7

2015/10/30

@Room

O108

Graph Algorithms

Dr. Ting-Yi Sung

Moodle

8

2015/11/06

@Room N101

Review Week

 

9

2015/11/13

Midterm Exam

 

10

2015/11/20

Sequence Alignment (I)

Dr. Huai-Kuang Tsai

Moodle

11

2015/11/27

Sequence Alignment (II)

Dr. Huai-Kuang Tsai

Moodle

12

2015/12/04

Combinatorial Pattern Matching

Dr. Ching-Tai Chen

Moodle

13

2015/12/11

Suffix Trees

Dr. Ching-Tai Chen

Moodle

14

2015/12/18

@Room O108

The Analysis of Next Generation Sequencing Data (I)

 

Dr. Hsin-Nan Lin

Moodle

15

2015/12/25

The Analysis of Next Generation Sequencing Data (II)

 

Dr. Hsin-Nan Lin

Moodle

16

2015/12/29(Tue)@101

Fundamentals of Molecular Evolution and Phylogenetic Tree Construction

 

Dr. Chun-Chieh Shih

Moodle

17

2016/01/08

Review Week (no class)

---

18

2016/01/15

Final Exam

---

 

 
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S1 Course Material

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, random variables and 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 statistical meta analysis, survival analysis, clustering, classification, 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: Hsin-Chou Yang, Chen-Hsiang Yeang, Shinsheng Yuan, Grace Shieh, Hsuan-Yu Chen, and Wei-Chung Liu

TA: Hsiu-Man Chen Email: hsiuman@stat.sinica.edu.tw

Office hours: Wednesday , 2:00pm-4:00pm

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

Week

Date

Topics/Brief Description

Sub-topics/

Detailed Description

Lecturers/Slides

1

2015/09/17

Probability

moves to 9/23 (Wed) 9:00am-12:00pm

@ Room O101

 

(1)   Applications in statistical genetics

(2)   Combinatorial analysis

(3)   Axioms of probabilities

(4)   Conditional probability and independence

(5)   Random variable and distribution function

Dr. Hsin-Chou Yang

Moodle

 

2

2015/09/24

Discrete Distributions and Contingency Tables

(1)   An application in pharmacogenetic study

(2) Discrete / continuous / mixed distributions

(3)   Joint / marginal / conditional distributions

(4)   Special discrete distributions

(5)   Introduction to contingency table

Dr. Hsin-Chou Yang

Moodle

 

3

2015/10/01

Continuous Distributions, Expectations and Basic Statistics

(1)   Continuous random variable

(2)   Expectation

(3)   Basic statistics

(4)   Limit theorems (optional)

Dr. Hsin-Chou Yang

Moodle

 

4

2015/10/08

Descriptive Statistics, Genomic Data Analysis

(1)   Introduction to statistics

(2)   Descriptive statistics

(3)   Fundamental of molecular biology

(4)   Genomic data analysis

Dr. Chen-Hsiang Yeang

Moodle

5

2015/10/15

Parameter Estimation and Confidence Interval

(1)   Unbiasedness

(2)   Point estimation (substitution principles, least square estimate, maximum likelihood estimate)

(3)   Interval estimation

Dr. Shinsheng Yuan

Moodle

 

6

2015/10/22

Hypothesis Testing, P-value and False Discovery Rate

(1)   Hypothesis testing

(2)   Type I error and type II error

(3)   P-value

(4)   One-sample and two-sample z-tests

(5)   One-sample, two-sample, and paired t-tests

(6)   Bonferroni adjustment, false discovery rate, and q value

Dr. Grace Shieh

Moodle

7

2015/10/29

Analysis of Categorical Data, Chisq and Multinomial

(1)   Incidence proportion and odds ratio

(2)   Two-sample test for binomial proportions

(3)   Contingency-table approach

(4)   Fisher’s exact test

(5)   McNemar’s test

(6)   Kappa statistic

Dr. Hsuan-Yu Chen

Moodle

8

2015/11/05

Review Week

 

9

2015/11/12

Midterm Exam

 

11

2015/11/19

Correlation, Regression Analysis and ANOVA

(1)   Linear regression with one independent variable

(2)   Inference in regression analysis

(3)   Diagnostic and remedial measures

(4)   Simultaneous inferences and other topics

(5)   Matrix approach to simple linear regression

(6)   Multiple linear regression

(7)   Building the regression model

(8)   Qualitative predictor variables

(9)   Analysis of variance

Dr. Grace Shieh

Moodle

10

2015/11/26

Logistic Regression and Statistical Meta Analysis

(1)   Logistic regression

(2)   Meta analysis (effect size, precision, study weights, summary effect, heterogeneity, fixed-effect model, random-effect model, software)

Dr. Shinsheng YuanMoodle

12

2015/12/03

Survival Data Analysis

(1)   Mantel-Haenszel test

(2)   Survival and hazard functions

(3)   Kaplan Meier estimate

(4)   Log-rank test

(5)   Proportional-hazards model

(6)   Lung cancer study

Dr. Hsuan-Yu ChenMoodle

13

2015/12/10

Clustering

(1)   Clustering by geometry (K-means, EM algorithm, hierarchical clustering, self- organizing map, principal component analysis, independent component analysis)

(2)   Clustering on graphs (Basic concepts, max flow – min cut, normal cuts, spectral clustering, and community detection)

(3)   Advanced topics (Chinese restaurant process and affinity propagation)

Dr. Chen-Hsiang Yeang

Moodle

14

2015/12/17

Classification

(1)   Binary classifications (Bayesian detection theory, naïve Bayes and other generative models, non-parametric methods, Fisher linear discriminant, support vector machines and kernel techniques, artificial neural networks, and boosting)

(2)   Advanced topics in supervised learning (multi-class classification, feature selection, semi-supervised learning, active learning)

Dr. Chen-Hsiang Yeang

Moodle

15

2015/12/24

Nonparametric Statistics (I)

(1)   Bootstrap

(2)   One-sample sign test

(3)   One-sample Wilcoxon signed-rank test

(4)   Wilcoxon rank-sum test (Mann-Whitney U test)

(5)   Sign test for paired data

(6)   Wilcoxon signed-rank test for paired data

Dr. Wei-Chung LiuMoodle

16

2015/12/31

Nonparametric Statistics (II)

(1)   Kruskal-Wallis test

(2)   Randomization/permutation test for two-way ANOVA

(3)   The product-moment correlation coefficient

(4)   Spearman rank correlation

(5)   Kendall’s coefficient of rank correlation

Dr. Wei-Chung LiuMoodle

17

2016/01/07

Review Week (no class)

 

18

2016/01/14

Final Exam

 

         

 

 
 
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P1 Course Material  

Programming (Python) (P1)

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)

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. Wang, John; Dr. Lin, Chen-Ching.  SHNCC-Dr. Wang, Chih-Yu; Dr. Shen, Chih-Ya

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: Chia-Hung Lin(林佳鴻) Email: redlin@iis.sinica.edu.tw

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

Slides/Video

1

2015/09/18

Introduction to Python moves to 9/25 (Fri) 10:00am-12:00pm @Room108

 

   Dr. Su, Li  

Moodle

2

2015/09/25

Basic Elements of Python I

moves to 10/7 (Wed)

2:00pm-4:00pm

@Room108

   Dr. Su, Li

Moodle

 

3

2015/10/02

Basic Elements of Python II

 

    Dr. Su, Li

Moodle

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

4

2015/10/07(Wed)

Basic statements I:

branching programs and inputs

 

Dr. Wang, John

 Moodle

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

Video

 

5

2015/10/16

 

Basic statements II:

iterative programs

Dr. Wang, John

Moodle

6

2015/10/23

 

Functions:

scope rules and passing arguments

Dr. Wang, John

Moodle

7

2015/10/30

 

Modules, Files, and Structured Types

Dr. Wang, Chih-Yu

Moodle

8

2015/11/06

Exception handling

 

Dr. Wang, Chih-Yu

Moodle

9

2015/11/13

Review Week

 

10

2015/11/20

Midterm Exam

 

11

2015/11/27

 

Introduction to Biopython

 

Dr. Lin, Chen-Ching

Moodle

12

2015/12/04

Regular expressions

 

Dr. Lin, Chen-Ching

Moodle

13

2015/12/11

 

Object-oriented programming:

classes

 

Dr. Lin, Chen-Ching

Moodle

14

2015/12/18

 

Data analysis toolbox  

 

Dr. Shen, Chih-Ya

Moodle

15

2015/12/25

 

Data analysis toolbox               

Web programming

 

Dr. Shen, Chih-Ya

Moodle

 

16

2016/12/30(Wed)

Web programming

 

Dr. Shen, Chih-Ya

Moodle

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

17

2016/01/08

Review Week (no class)

 

18

2016/01/15

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 8/25/2015.

*Your present schedule is confirmed and will not be changed. Please contact Dr. Chuan-Hsiung Change if you do have a schedule conflict on the assigned date.

*The presenter shall introduce the host and attended professors in the beginning of each seminar.

*1st year students: attendance for every session is required

  2nd and 3rd year students: attendance is optional (except your scheduled  presentation date)

Week

Date

TIGP Bioinformatics

Host

1

2015/9/17

 

Nikhil Pathak(2013)

Topic: 

"Panorama of ancient metazoan macromolecular complexes", Nature, 2015.DOI:10.1038/nature14877

 

 

2

2015/9/24

 

Chiahung Lin(2013)

 

Topic:

Eric R Gamazon et al, "A gene-based association method for mapping traits using reference transcriptome data", Nature Genetics (2015 Aug 10), doi:10.1038/ng.3367

 

 

3

2015/10/01

 

                     

Jerome Penaflor Panibe(2013)

 

Topic:

    Takagi et al. "MutMap accelerates breeding of a salt-tolerant rice cultivar" Nature Biotechnology (2015) doi:10.1038/nbt.3188

 

 

4

2015/10/08

 

Divya Sahu(2013)

 

Topic:

W Zhao et al, Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications”, Scientific Fic Reports | 4: 6591 | DOI: 10.1038/srep06591

 

 

5

2015/10/15

 

Kidane Gebereyesus(2013)

 

Topic:

Merler S, et al. ''Spatiotemporal spread of the 2014 outbreak of Ebola virus disease in Liberia and the eff ectiveness of non-pharmaceutical interventions: a computational modelling analysis."  Lancet Infect Dis 2015

 

 

6

2015/10/22

 

(2015陽明YMU Students)

 

呂俊良

 

Topic:

Özgün Babur1*, Mithat Gönen2, Bülent Arman Aksoy13, Nikolaus Schultz1, Giovanni Ciriello1, Chris Sander1 and Emek Demir1 "Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations" , Genome Biology, 26 Feb 2015, doi:10.1186/s13059-015-0612-6

 

 

 

 

7

2015/10/29

 

Hsiu-man Chen(2013)

 

Topic:

 

Dopico et al, "Widespread seasonal gene expression reveals annual differences in human immunity and physiology", Nature Communications, 12 May 2015, doi:10.1038/ncomms8000

 

 

8

2015/11/05

 

Yen Hsieh Chen(2013)

Topic:

Hansen L. et al. "A glycogene mutation map for discovery of diseases of glycosylation."Glycobiology. 2015 Feb;25(2):211-24. doi: 10.1093/glycob/cwu104.
 

 

9

2015/11/12

                     Midterm Exam

 

 

Chi-Chun Chen(2013)

 

Topic:

 

Han J, Shi X, Zhang Y, Xu Y, Jiang Y, Zhang C, Feng L, Yang H, Shang D, Sun Z, Su F, Li C, Li X., "ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis."Scientific Reports  12;5:13044. doi: 10.1038/srep13044.

 

 

10

2015/11/19

Chun-Yi Chen (2014)

 

Topic:

Yang et. al., "Parent–progeny sequencing indicates higher mutation rates in heterozygotes", Nature 523, 463–467 (July 2015)

 

 

11

2015/11/26

 

Lovely Raghav(2014)

 

Topic:

Jing Hang, Ruixue Wang, Chuangye Yan, Yigong Shi"Structural basis of pre-mRNA splicing", 11 September 2015, DOI: 10.1126/science.aac8159

 

 

12

2015/12/03

Cheng-Wei Cheng(2014)

 

Topic:

Yinan Shi et al., "Position-specific prediction of methylation sites from sequence conservation based on information theory " Scientific Reports, 2015.

 

 

13

2015/12/10

@4:30-6:00pm

Cheng-Kai Shiau(2013)

 

Topic:

Nadia D. Singh, Dallas R. Criscoe, Shelly Skolfield, Kathryn P. Kohl, Erin S. Keebaugh, Todd A. Schlenke. "Fruit flies diversify their offspring in response to parasite infection", Science 14 August 2015: Vol. 349 no. 6249 pp. 747-750. DOI: 10.1126/science.aab1768

 

 

14

2015/12/17

 

鄭中遠

 

Topic:

S Sandin, D Schendel, P Magnusson, C Hultman, P Surén, E Susser, T Grønborg, M Gissler, N Gunnes, R Gross, M Henning, M Bresnahan, A Sourander, M Hornig, K Carter, R Francis, E Parner, H Leonard, M Rosanoff, C Stoltenberg and A Reichenberg, "Autism risk associated with parental age and with increasing difference in age between the parents

"Molecular Psychiatry advance online publication 9 June 2015; doi: 10.1038/mp.2015.70

 

 

15

2015/12/24

Neha Warikoo (2015)

 

Topic:Cheng D1, Knox C, Young N, Stothard P, Damaraju S, Wishart DS. "PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites." Nucleic Acides Res. 2008 Jul 1; doi:10.1093/nar/gkn296.

 

16

2015/12/31

Kshitij Tandon (2015)

 

Topic:

 

 

17

2016/01/04

 

 

N/A

 

 

18

2016/01/11

Final Exam

 


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Special Lecture

TIGP Bio 2015 Fall Special Lecture

replaced by ISEGB(11/6-7)="width: 34.4pt; height: 22.95pt; border-left: 1.0pt solid windowtext; border-right: 1.0pt solid windowtext; border-top: medium none; border-bottom: 1.0pt solid windowtext; padding-left: 5.4pt; padding-right: 5.4pt; padding-top: 0cm; padding-bottom: 0cm; background: #BFBFBF">     17

Place: Room 101, New 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%.

Note: Students are required to attend at least 2 Keynote speeches + 2 concurrent or lecture sessions for ISEGB (attendance sheet will provided)

 

Week

Date

Topics/Brief Description

 

Lecturers

1

2015/09/17

replaced by ISEGB(11/6-7)  

2

2015/09/24

The role of noise and dynamics in biology Dr. Shieh, Grace

3

2015/10/01

MAGIC: an automated N-linked glycoprotein identification tool using a Y1-ion pattern matching algorithm and in silico MS² approach Dr. Sung, Ting-Yi

4

2015/10/08

The role of noise and dynamics in biology Dr. Hsu, Chao-Ping

5

2015/10/15 

TBD Dr. Liu, Wei-Chung

6

2015/10/22 

Translational bioinformatics:

from information integration to in silico discovery

Dr. Yang, Ueng-Cheng

7

2015/10/29 

replaced by ISEGB(11/6-7)  

8

     2015/11/05    

9

2015/11/12 (Wed)

 

   

10

 2015/11/19

 

2:30pm-3:25pm

Data Analysis of Mass Spectrometry-Based Proteomics

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

Dr. Yet-Ran Chen     

 (ABRC, AS)              

Host: Dr.Yang, Lee-Wei (NTHU)

 

11

2011/11/26

An introduction to NGS normalization in the quantitative analysis Dr. Chia-Chen(Mirrian)  Ho

Host: Dr. H.K.Tsai

12

2015/12/03

 

The aboriginal crops – Omics studies on the treasures Dr. Hsing, Yue-ie        

 Host: Dr. Chen, Ho-Ming

13

2015/12/10

 

Diversity of Parasitism Dr. Tsai, IShen Jason

14

 2015/12/17 

replaced by ISEGB(11/6-7)  

15

2015/12/24 

 

Metagenomic insights into biodiversity and function of aquatic microbial communities Dr. Sen-Lin Tang

16

    2015/12/30 

   (Wed)

replaced by ISEGB(11/6-7)

 

2016/01/08

Review Week

 

18

2016/01/15

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 Fall Semester: 9/25/2015)

 

Student

Lab

Neha Warikoo   倪荷 Dr. Wen-Lian Hsu
Kshitij Tandon   卡斯提 Dr. Pao-Yang Chen
 
 
 
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TIGP Sinica IIS