My name:
Shih-Yen Ku
Address:
Office 408a, RRI hall, University of Sourthern California
e-mail address :
Telephone number :



Objective :

 
Motivated individual with strong academic training and research experience in Bioinformatics seeks for research position in bioinformatics or computational biology, special interest s in analysis and prediction of protein structures, functions, and sequences.

Education:
National Tsing-Hua University, 1999/07-2003/07
- Life Science (Major), Economics (Minor)
- Bachelor of Science, 2003/07
- Additional classes in Enterprise Resources Planning.
- Advisor : Ping-Chiang Lyu
National Chiao-Tung Unversity, 2003/08-2005/07
- Computer and Information Science
- Master of Engineering, 2005/07
- Additional classes in Digital Image Processing , Advanced Database System , Pattern Recognition
- Advisor: Yuh-Jyh Hu, Wei-Pang Yang



University of Southern California, 2008/08-now
- Computer and Information Science
- Ph.D of Computational Biology
- Advisor: Fengzhu Sun (Math), Frank Alber(Protein)


Skill:
Programming-related skills:
    Programming Language:
         - PERL, PHP, Python, C, C++, C#, JAVA, SQL Language, Verilog, Assembly, Mat Lab, R.
    Operating System:
         - Linux, Windows, Unix
    Database System:
        - MySQL, Postgre, MS SQL, Sybase.

Bioinformatics-related skills
    - Proteomics analysis
    - Clustering Algorithm Design
    - Data and Knowledge Base Design

Research interest:
Bioinformatics,Proteomics,Bioinfomatic Management Systems, Algorithms,Data mining,Biological Database/Knowledge Base,Database

Experience:

Institute of Statistical Science, Academia Sinica,                               Taipei , Taiwan
Research Assistant         2007/02 - Current                 
Principal Instructor: Ker-Chau Li
- Protein-Protein interaction and expression data analysis
- Identification of relationships among protein structures, functions, and sequences.
- Protein structural alphabet design and implementation of 1D structural alphabet alignment tools

Army, Military of ROC                                                                       Taichung , Taiwan
lieutenant        2005.10-2007.02
- Platoon leader
- Information officer

eBsuccess Solutions Inc.                                                                     Hsih-Chu , Taiwan
Part-time Engineer,         2005.08 - 2005.09
- Construction of front-end and back-end eB-portal web-based service.
- Integration of software packages.

National Chiao-Tung University                                                         Hsih-Chu , Taiwan
Teaching Assistant of Bioinformatics,         2005.02-2005.07
- Introduction to bioinformatics tools
- Running student discussion sessions

National Tsing-Hua University ,                                                         Hsih-Chu , Taiwan
Student of NSC research Project,         2002,06-2003,02
- Setting up Bioinformatics systems and platforms for molecular biologists
Extracurricular Activities :

Debate League         (1999)
member
- Debate team leader of freshman cup at NTHU
- Won the 2nd prize of freshman cup at NTHU

Chinese Medicine League         (1999-2001)
Instructor/member
- Teaching how to practice the Chinese traditional therapies
- Manage the materials and equipments of Chinese Medicine League

Life Science Camp of NTHU         (1999, 2000, 2001)
Instructor/member
- Introducing basic concepts of Bioinformatics to high school students

Statistical Cup         (2007)
athlete
- 4 th place of 5 km marathon

Membership

IEEE student member.
ASA student member.
ACM student member.

Awards & Honors :

Publication:  

• Thesis:

• Bachelor Thesis, Setup the Local Experimental Oriented Biological data Analysis Platform (LEOBAP),2003/07

• Master Thesis, Setup the proteomic database and knowledge base, 2005/07


• Journal Paper:

• 1. Shih-Yen Ku, Yuh -Jyh Hu: Protein structure searching and local structure characterization .BMC Bioinformatics 2008, 9:349
see also the website: SAFAST

• 2. Zhiyuan Zhai*, Shih-Yen Ku*, Yihui Luan, Gesine Reinert, Michael S. Waterman, Fengzhu Sun. The Power of Detecting Enriched Patterns: An HMM Approach. (Accepted by Journal of Computational Biology) Motif Power Calculator
* Equally Contribute

• 3. Shih-Yen Ku and Yuh-Jyh Hu. Discovery of Structural Motifs Using Protein Structural Alphabets and 1D Motif-finding Methods. (Accepted by Springer Publisher: Advances in Computational Biology)

• 4. Shih-Yen Ku and Yuh-Jyh Hu. Associative study on structural alphabet motifs reveals the relationships among function, sequence and structure (Submitted to Computers in Biology and Medicine)


• Conference Paper:

• 1. Shih-Yen Ku, Yuh-Jyh Hu: A Multi-strategy Approach to Protein Structural Alphabet Design. BIOCOMP 2006 : 285-291

• 2. Shih-Yen Ku, Yuh-Jyh Hu: Using Protein Structural Alphabet to Characterize Local Structure Features. Biocomp 2008 , p692-697.

• 3. Shih-Yen Ku,Chih-Ying Wei and Yuh-Jyh Hu: Discovery of Structural Motifs in Metalloproteins Using Protein Structural Alphabets and 1D Motif-finding Methods. Biocomp2009: 50-56

• 4. Shih-Yen Ku and Yuh-Jyh Hu: SA-Motifbase: A Database of Protein Structural Alphabet Motifs. Biocomp2010 ( Accepted )

• 5. Shih-Yen Ku, Chi-Ting Tseng, Hsueh-Jung Lu, Ker-Chau Li: An alignment approach to detect the position and type of tuna with encoding hydroacoustic signal to acoutics alphabet sequences. ( Submitted to AFAS 2010 )