Home » Publications



  1. Kuo Ping Chiu, 2016, Next-Generation Sequencing and Sequence Data Analysis, 150 pages, Sharjah, United Arab Emirates: Bentham Science Publishers.


  1. Yu-Shin Nai, Yu-Feng Huang, Tzu-Han Chen, Kuo-Ping Chiu and Chung-Hsiung Wang. , 2017, “Determination of Nucleopolyhedrovirus’ Taxonomic Position”, editor(s): Shields VDC, Biological Control of Pest and Vector Insects, pp. 169-200, Rijeka, Croatia: InTech.
  2. Kuo Ping Chiu, 2016, “Applications of Single Cell Sequencing in Cancer”, editor(s): Fan-Gang Tseng and Tuhin Subhra Santra, Essentials of Single Cell Analysis, pp. 347-361, Heidelberg, Germany: Springer-Verlag GmbH.


  1. Mohit K. Midha, Mengchu Wu, Kuo‑Ping Chiu, 2019, “Long‑read sequencing in deciphering human genetics to a greater depth.”, Human Genetics. (SCI)
  2. Kuo-Ping Chiu and Alice L. Yu, 2019, “Application of cell-free DNA sequencingin characterization of bloodborne microbes and the study of microbe-disease interactions.”, PeerJ 7:e7426. (SCI)
  3. Yu-Feng Huang, Tzu-Han Chen, Zih-Ting Chang, Tai-Chuan Wang, Se Jin Lee, Jong Cheol Kim, Jae Su Kim, Kuo-Ping Chiu, Yu-Shin Nai, 2019, “Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features”. BMC Genomics. (SCI)
  4. Huang YF, Chen YJ, Fan TC, Chang NC, Chen YJ, Midha MK, Chen TH, Yang HH, Wang YT, Yu AL, Chiu KP, 2018, “Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females.”, BMC medical genomics, 11(Suppl 1), 16. (SCI)
  5. Chiang YS, Huang YF, Midha MK, Chen TH, Shiau HC, Chiu KP, 2018, “Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions.”, PloS one, 13(6), e0199471. (SCI)
  6. Nai YS, Chen TH, Huang YF, Midha MK, Shiau HC, Shen CY, Chen CJ, Yu AL, Chiu KP, 2017, “T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids.”, Scientific reports, 7, 40767. (SCI)
  7. Yu-Feng Huang, Tzu-Han Chen, Yu-Tai Wong, David Glenn Smith, Kurtis Jai-Chyi Pei, and Kuo Ping Chiu., 2015, “Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy”, PLoS One, 10(6), e0130673. (SCI)
  8. Chen, H.-S., S.-C. Hou, J.-W. Jian, K.-S. Goh, S.-T. Shen, Y.-C. Lee, J.-J. You, H.-P. Peng, W.-C. Kuo, S.-T. Chen, M.-C. Peng, H.-J. Wang, C.-M. Yu, I.-C. Chen, C.-P. Tung, T.-H. Chen, K. P. Chiu, C. Ma, C. Y. Wu, S.-W. Lin and A.-S. Yang, 2015, “Predominant structural configuration in natural antibody repertoires enables potent antibody responses against protein antigens”, Scientific Reports, 5, 12411. (SCI)
  9. Hsu, H.-J., K. H. Lee, J.-W. Jian, H.-J. Chang, C.-M. Yu, Y.-C. Lee, I.-C. Chen, H.-P. Peng, C. Y. Wu, Y.-F. Huang, C.-Y. Shao, K.P. Chiu and A.-S. Yang, 2014, “Antibody variable domain interface and framework sequence requirements for stability and function by high throughput experiments”, Structure, 22(1), 22-34. (SCI)
  10. Chang, H.-J., J.-W. Jian, H.-J. Hsu, Y.-C. Lee, H.-S. Chen, J.-J. You, S.-C. Hou, C.-Y. Shao, Y.-J. Chen, K.P. Chiu, H.-P. Peng, K. H. Lee and A.-S. Yang., 2014, “Loop sequence features and stability determinants in antibody variable domains by high throughput experiments”, Structure, 22(1), 9-21. (SCI)
  11. Yen-Ju Chen, Mike W.C. Thang, Yu-Tzu Chan, Yu-Feng Huang, Nianhan Ma, Alice L. Yu, Chung-Yi Wu, Miao-Lin Hu, and Kuo-Ping Chiu, 2013, “Global assessment of Antrodia cinnamomea-induced microRNA alterations in hepatocarcinoma cells”, PLoS One, 8(12), e82751. (SCI)
  12. 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)
  13. 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)
  14. Yih-Shien Chiang, Lock Ying Seng, You-Yu Lin, Shih-Hao Chen, Yu-Chang Su, Tzu-Han Chen, Hong-Chih Kuo, Chung-Hsuan Chen, Kuo Ping Chiu, 2010, “Single cell transcriptome analysis upon MCF-7 breast cancer”, 2 pages, paper presented at Beyond the Genome: The true gene count, human evolution and disease genomics, Boston, MA, USA: Genome Biology, 2010-10-11 ~ 2010-10-13.
  15. 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)
  16. Kuo Ping Chiu, 2008, “Review: Novel Applications of the Paired-End diTag (PET) Technology in Pharmacogenomics”, Current Pharmacogenomics and Personalized Medicine, 6, 23-32.
  17. 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)
  18. 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)
  19. 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)
  20. 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)
  21. 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)
  22. 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)
  23. 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)
  24. 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)
  25. 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)
  26. 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)
  27. 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)
  28. 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)
  29. The FANTOM3 Consortium, 2005, “The transcriptional landscape of the mammalian genome”, Science, 309, 1559-1563. (SCI)
  30. 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)
  31. 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)
  32. Chiu KP, Sullivan T, Bursztajn S, 1996, “Improved in situ hybridization: color intensity enhancement procedure for the alkaline phosphatase/Fast Red system.”, BioTechniques, 20(6), 964-6, 968. (SCI)
  33. 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)