Yao-Ting Huang (黃耀廷)

Assistant Professor
Department of Computer Science and Information Engineering
National Chung Cheng University

Email:

ythuang at cs.ccu.edu.tw

Phone:

+886-5-2720411

Fax:

+886-5-2720859


Education:

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Ph.D., Computer science and Information Engineering, National Taiwan University. 2003-2006 (Advisor: Kun-Mao Chao).

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M.S., Computer science and Information Engineering, National Taiwan University, 2001-2003.

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B.S., Computer science and Information Engineering, National Chiao Tung University, 1997-2001.

Research Interests:

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Bioinformatics (SNP analysis, evolutionary analysis, comparative genomics)

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Approximation Algorithms

Lab Information (R405)

Teaching Courses:

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Introduction to Algorithms (計算方法概論): 2007 Fall; 2008 Fall

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Algorithms in Bioinformatics: 2007 Fall; 2008 Fall
bullet Algorithms (計算方法): 2008 Spring
bullet Introduction to Computational Biology: 2008 Spring.

Journal Papers:

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Huang Y.-T., Chen, F.-C., Chen, C.-J., Chen, H.-L., and Chuang, T.-J. Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons, Genome Research, 2008 (in press).
bullet Huang Y.-T. and Chao, K.-M. A new framework for the selection of tag SNPs using multimarker haplotypes. Journal of Biomedical Informatics, 2008 (in press).

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Chen, F.-C., Wang, S.-S., Chaw, S.-M., Huang Y.-T., and Chuang, T.-J. PGAA: a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species EST conservation from seven plant species. Plant Physiology, 143(3):1086-1095, 2007.

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Chang, C.J., Huang, Y.-T., and Chao, K.-M. A greedier approach for finding tag SNPs. Bioinformatics, 22: 685-691, 2006.

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Huang, Y.-T., Chao, K.-M., and Chen, T. An approximation algorithm for haplotype inference by maximum parsimony, Journal of Computational Biology, 12: 1261-1274, 2005.

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Huang, Y.-T., Zhang, K., Chen, T., and Chao, K.-M. Selecting additional tag SNPs for tolerating missing data in genotyping. BMC Bioinformatics, 6:263, 2005.

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Lai, Y.-C., Lin, Phone and Huang, Y.-T., Design and implementation of a wireless Internet remote access platform, Wireless Communications and Mobile Computing, 6: 413-429, 2004.

Conference Papers:

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Huang, Y.-T. and Chao, K.-M, Approximation algorithms for the optimization problems of SNPs and haplotypes, IEEE Emerging Information Technology Conference (EITC), 2005.

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Huang, Y.-T., Chao, K.-M, and Chen, T. An approximation algorithm for haplotype inference by maximum parsimony. The 20th Annual ACM Symposium on Applied Computing (SAC), 146-150, USA, 2005.

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Huang, Y.-T., Zhang, K., Chen, T. and Chao, K.-M. Approximation algorithms for the selection of robust tag SNPs. The 4th Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science / Lecture Notes in Bioinformatics, 278-289, Norway, 2004.

 

Huang, Y.-T. and Chao, K.-M. On the selection of robust tag SNPs. The 21th Workshop on Combinatorics Math and Computation Theory, Taiwan, 241-248, 2004.

 

Book chapters:

 

 

Huang, Y.-T., Zhang, K., Chen, T., and Chao, K. -M. “Approximation Algorithms for the Selection of Robust Tag SNPs,” Chapter 77 of the book “Handbook of Approximation Algorithms and Metaheuristics,” edited by Teofilo F. Gonzalez (University of California, Santa Barbara), Chapman & Hall/CRC Press, USA, 2007.

Award and Honors

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1999, 國立交通大學資訊工程系專題競賽優勝 (First Prize of Project Contest, Department of Computer Science and Information Engineering, National Chiao Tung University)

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2000, 國立交通大學十屆思源科技研發競賽第一名 (First Prize of Undergraduate Research and Development Contest, National Chiao Tung University)

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2001, 行政院國科會國家高速電腦中心全國軟體設計競賽第三名 (Third Prize of Software Contest by National Center for High-performance Computing; 72 teams, 243 contestants; Title: Remote Access Platform for Wireless Internet)

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2002, MobileHero經濟部工業局無線通訊軟體研發競賽第一名 (First Prize of Mobile Hero Contest by Industrial Development Bureau of Ministry of Economic Affairs; 99 teams, 384 contestants, awarded USD 30,000; Title: A Session Management Mechanism for Heterogeneous Wireless Network)

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 2002, 中國科技管理學會學生創新育成競賽第二名

Professional Experience

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Postdoctoral fellow, Computational Genomics Laboratory, Genomics Research Center, Academia Sinica, 2006/8 -- 2007/7.

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Exchange student, National Science Council Project-based Personnel Exchange Program, University of Leipzig, Germany, Project Name: Algorithms for structured sequences and trees in phylogeny, 2006/6 -- 2006/7.

 

Reviewer of Journals and Conference

 

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Journals: Bioinformatics, BMC Bioinformatics, Journal of Bioinformatics and Computational Biology, Phamagenomics, Computer Methods and Programs in Biomedicine.

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Conference: RECOMB 2008, NCS 2007.

 

Invited Talks

 

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“The challenges of computational SNP studies - tag SNP selection and haplotype inference,” 國家衛生研究院, 2007.

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“A study on some optimization problems related to single nucleotide polymorphisms,” Department of Computer Science and Information Engineering, National Taipei University, National Chung Cheng University, and National Chia Yi University, 2007.

Professional Activities

全國大專軟體競賽命題評審委員, 2007.

Research Description

       DNA序列蘊含各種生命現象運作之密碼。近年來各種生物的DNA序列逐漸被鑑定出來(人類、老鼠、稻米、黑猩猩等)，隱藏在DNA序列中的遺傳資訊，帶來了治療各種疾病的契機 (例如，癌症、糖尿病、器官移植抗排斥)，以及探究各種生物演化之歷史。然而大量的DNA序列 (人類中約有30億個核柑酸)，必需仰賴電腦的高速運算來解碼與分析。生物資訊是一種電腦科學領域與生命科學領域的結合，希望能藉由電腦的計算，軟體的盼讀，解答普遍存在人類之疾病、個體的差異、演化的歷史、生命的機制、或協助開發新藥物等。我們實驗室目前的研究主軸方向，主要探討人類之間或跨物種間的基因序列差異，序列差異與疾病之關連性，演化之分析，以及設計各種生物資訊軟體。歡迎有興趣的同學加入我們的團隊。

Other Information

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This site was last updated 07/02/08