Associate Research Fellow

EDUCATION AND POSITIONS HELD:

• B.S., Biology, Fu-Jen University, 1984
• Ph.D., Microbiology, UC Davis, 1991
• Postdoctoral Associate, Harvard Medical School, 1993-1996
• R&D Scientist, Bio-Rad Laboratories, 1996-1998
• Principal Investigator, Development Center for Biotechnology, 1999-2000
• Research Scientist, Genome Institute of Singapore, 2002-2008
• Associate Professor, National Central University, 2007-present
• Associate Research Fellow, Genomics Research Center, Academia Sinica, 2008-present
• Associate Professor, National Taiwan University, 2011-present

PATENTS:

• Chiu, K. P. et al. Method of processing and/or genome mapping of ditag sequences. US patent application 20060281097, 2006
• Chiu, K. P. Multiplex barcoded paired-end ditag (mbPED) library construction for ultra high throughput sequencing. US patent application 20110015096, 2009
• Chiu, K. P.; Chou, Y.; Chen, S. C. Novel multiplex barcoded Paired-End Ditag (mbPED) sequencing approach and its application in fusion gene identification. US patent application provisional 61451613, 2011

RESEARCH INTERESTS:

Eukaryotic Gene Expression Regulation: Cancer biology

Cancer is a fascinating subject for studying gene expression and regulation in the eukaryotic system. The complexity of cancer, and many other diseases, requires a systematic and genome-wide approach, so to improve the reliability of results and to help identify the missing links in the cascade of gene expression regulation. We have setup a biotechnology-based sequencing platform at Genomics Research Center, which works closely with the TechComm sequencing facility at the National Taiwan University campus. These sequencing platforms are linked to multiple bioinformatics pipelines for various types of sequence data analysis. Besides cancer biology, we are also working on biotechnology development, anti-cancer mechanism of A. cinnamomea, developmental reprogramming, and a number of collaborative projects, including studies of cancer stem cell (CSC) transcriptomes, early onset breast cancer (EOBC), T-cell tolerance, and micro-RNAs. 

Research collaborations are not limited within Academia Sinica. The idea is to facilitate Genomics researches by taking practical actions and by realistic sharing of sequencing experiences and software applications. Through broad connections and collaborations, we would like to help facilitate the study of Genomics and basic sciences and to strengthen the education system. Hopefully more people will focus on science instead of politics, and more people will spend time on scientific thinking instead of political arguing.

SELECTED PUBLICATIONS:

• Chan YT, Lin YC, Lin RJ, Kuo HH, Thang WC, Chiu KP, Yu AL, 2013, “Concordant and Discordant Regulation of Target Genes by miR-31 and Its Isoforms.”, PloS one, 8(3), e58169. (SCI)
• Yu-Feng Huang†, Sheng-Chung Chen†, Yih-Shien Chiang, Tzu-Han Chen and Kuo-Ping Chiu, 2012, “Palindromic sequence impedes sequencing-by-ligation mechanism”, BMC Systems Biology, 6(Suppl 2):S10. (SCI)
• Mohamed Sabry Hamza, Sebastian Pott, Vinsensius B. Vega, Jane S. Thomsen, Gopalan Srinivasan Kandhadayar, Patrick Ng, Kuo Ping Chiu, Sven Pettersson, Chia Lin Wei, Yijun Ruan, and Edison T. Liu., 2009, “De-Novo identification of PPAR /RXR binding sites and direct targets during adipogenesis”, PLoS ONE, 4(3): e4907. (SCI)
• Kuo Ping Chiu, 2008, “Review: Novel Applications of the Paired-End diTag (PET) Technology in Pharmacogenomics”, Current Pharmacogenomics and Personalized Medicine, 6, 23-32.
• Melissa Fullwood, Jack Tan, Patrick Ng, Kuo Ping Chiu, Jun Liu, Chia Lin Wei, and Yijun Ruan, 2008, “The Use of Multiple Displacement Amplification to Amplify Complex DNA libraries”, Nucleic Acid Research, 36(5), e32. (SCI)
• Ching-Aeng Lim, Fei Yao, Joyce Jing-Yi Wong, Joshy George, Han Xu, Kuo Ping Chiu, Wing-Kin Sung, Leonard Lipovich, Vinsensius B. Vega, Joanne Chen, Atif Shahab, Xiao Dong Zhao, Martin Hibberd, Chia-Lin Wei, Bing Lim, Huck-Hui Ng, Yijun Ruan, and Keh-Chuang Chin, 2007, “Genome-wide Mapping of RELA(p65) Binding Identifies E2F1 as a Transcriptional Activator Recruited by NF-kB upon TLR4 Activation”, Molecular Cell, 27(4), 622-635. (SCI)
• The ENCODE Project Consortium, 2007, “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project”, Nature, 447, 799-816. (SCI)
• Kuo Ping Chiu, Pramila Ariyaratne, Han Xu, Adrian Tan, Patrick Ng, Edison Tak-Bun Liu, Yijun Ruan, Chia-Lin Wei, and Wing-Kin Ken Sung , 2007, “Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes”, BMC Cancer, 7, 109. (SCI)
• Xiao Dong Zhao, Xu Han, Joon Lin Chew, Jun Liu, Kuo Ping Chiu, Andre Choo, Yuriy L. Orlov, Wing-Kin Sung, Atif Shahab, Vladimir A. Kuznetsov, Guillaume Bourque, Steve Oh, Yijun Ruan, Huck-Hui Ng, and Chia-Lin Wei, 2007, “Whole genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells”, Cell Stem Cell, 1(3), 286-298. (SCI)
• Chin-Yo Lin, Vinsensius B Vega, Jane S Thomsen, Tao Zhang, Say Li Kong, Min Xie, Kuo Ping Chiu, Leonard Lipovich, Daniel H Barnett, Fabio Stossi, Ailing Yeo, Joshy George, Vladimir A Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D Miller, Edwin Cheung, Benita S Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia-Lin Wei, and Edison T Liu. , 2007, “Whole-Genome Cartography of Estrogen Receptor alpha Binding Sites”, PLoS Genet, 3(6), e87. (SCI)
• Chia Lin Wei, Qiang Wu, Vinsensius B. Vega, Kuo Ping Chiu, Patrick Ng, Tao Zhang, Atif Shahab, Azmi Ridwan, YuTao Fu, Zhiping Weng, Jian Jun Liu, Vladimir A. Kuznetsov, Ken Sung, Bing Lim, Edison Liu, Qiang Yu, Huck Hui Ng, and Yijun Ruan , 2006, “A global mapping of p53 transcription factor binding sites in the human genome”, Cell, 124, 207-219. (SCI)
• Karen I. Zeller, XiaoDong Zhao, Charlie W. H. Lee, Kuo Ping Chiu, Hong Sain Ooi, Fei Yao, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, Vladimir A. Kuznetsov, Wing-Kin Sung, Yijun Ruan, Chi V. Dang, and Chia-Lin Wei , 2006, “Global mapping of c-Myc binding sites and target gene networks in human B cells”, Proceedings of the National Academy of Sciences of the United States of America, 103, 17834-17839. (SCI)
• Patrick Ng, Jack J.S. Tan, Hong Sain Ooi, Yen Ling Lee, Kuo Ping Chiu, Melissa J. Fullwood, Clotilde Perbost, Lei Du, Wing-Kin Sung, Chia-Lin Wei, and Yijun Ruan , 2006, “Multiplex sequencing of Paired-End Ditag (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptome and genomes”, Nucleic Acid Research, 34(12), e84. (SCI)
• Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Sain Ooi, Chia-Lin Wei, Wing-Kin Ken Sung, and Yijun Ruan , 2006, “PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data”, BMC Bioinformatics, 7, 390. (SCI)
• Yuin-Han Loh, Qiang Wu, Joon-Lin Chew, Vinsensius B. Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Ken W. Sung, Charlie W.H. Lee, Xiao-Dong Zhao, Kuo-Ping Chiu, Leonard Lipovich, Vladimir A. Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia-Lin Wei, Yijun Ruan, Bing Lim, and Huck-Hui Ng. , 2006, “The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. ”, Nature Genetics, 38, 431-440. (SCI)
• Patrick Ng, Chia Lin Wei, Wing-Kin Ken Sung, Kuo Ping Chiu, Leonard Lipovich, Chin Chin Ang, Sanjay Gupta, Atif Shahab, Chee Hong Wong, Azmi Ridwan, Edison T. Liu, and Yijun Ruan , 2005, “Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation ”, Nature Methods, 2, 105-111. (SCI)
• The FANTOM3 Consortium, 2005, “The transcriptional landscape of the mammalian genome”, Science, 309, 1559-1563. (SCI)
• Chia Lin Wei, Patrick Ng, Kuo Ping Chiu, Chee Hong Wong, Chin Chin Ang, Leonard Lipovich, Edison T. Liu, and Yijun Ruan , 2004, “5’ long serial analysis of gene expression (LongSAGE) and 3’ LongSAGE for transcriptome characterization and genome annotation”, Proceedings of the National Academy of Sciences of the United States of America, 101, 11701-11706. (SCI)
• Kuo Ping Chiu, Karen Duca, Steve A. Berman, Thomas Sullivan, and Sherry Bursztajn, 1996, “A novel in situ double labeling method for simultaneous detection of mRNA and expressed protein or two different mRNAs”, Journal of Neuroscience Methods, 66, 69-79. (SCI)
• Kuo Ping Chiu, Steve H. Cohen, David W. Morris, and George W. Jordan, 1992, “Intracellular amplification of proviral DNA in tissue sections using the polymerase chain reaction”, Journal of Histochemistry & Cytochemistry, 40, 333-341. (SCI)