Kuo Ping Chiu

Summary

Country: Singapore

Publications

  1. pmc PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
    Kuo Ping Chiu
    Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome 02 01, 138672, Singapore
    BMC Bioinformatics 7:390. 2006
  2. pmc Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes
    Kuo Ping Chiu
    Genome Institute of Singapore, Genome 02 01, Singapore
    BMC Cancer 7:109. 2007
  3. pmc De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis
    Mohamed Sabry Hamza
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
    PLoS ONE 4:e4907. 2009
  4. ncbi request reprint Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
    Patrick Ng
    Genome Institute of Singapore, 60 Biopolis Street, Genome 02 01, Singapore 138672
    Nat Methods 2:105-11. 2005
  5. pmc The use of multiple displacement amplification to amplify complex DNA libraries
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research A STAR, 60 Biopolis Street, Genome 02 01, Singapore
    Nucleic Acids Res 36:e32. 2008
  6. pmc Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes
    Patrick Ng
    Genome Institute of Singapore, 60 Biopolis Street, 02 01, Genome, Singapore 138672, Singapore
    Nucleic Acids Res 34:e84. 2006
  7. pmc Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
    Yijun Ruan
    Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 17:828-38. 2007
  8. doi request reprint Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells
    Xiao Dong Zhao
    Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore
    Cell Stem Cell 1:286-98. 2007
  9. pmc Whole-genome cartography of estrogen receptor alpha binding sites
    Chin Yo Lin
    Genome Institute of Singapore, Singapore, Republic of Singapore
    PLoS Genet 3:e87. 2007
  10. pmc 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation
    Chia Lin Wei
    Genome Institute of Singapore, 60 Biopolis Street, Genome 02 01, Singapore 138672
    Proc Natl Acad Sci U S A 101:11701-6. 2004

Detail Information

Publications15

  1. pmc PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
    Kuo Ping Chiu
    Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome 02 01, 138672, Singapore
    BMC Bioinformatics 7:390. 2006
    ..To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable...
  2. pmc Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes
    Kuo Ping Chiu
    Genome Institute of Singapore, Genome 02 01, Singapore
    BMC Cancer 7:109. 2007
    ..Here we applied the robust Gene Identification Signature Paired End diTag (GIS-PET) approach to investigate the melanoma transcriptome and characterize the global pathway aberrations...
  3. pmc De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis
    Mohamed Sabry Hamza
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
    PLoS ONE 4:e4907. 2009
    ..In order to obtain a genome-wide view of PPARgamma binding sites, we applied the pair end-tagging technology (ChIP-PET) to map PPARgamma binding sites in 3T3-L1 preadipocyte cells...
  4. ncbi request reprint Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
    Patrick Ng
    Genome Institute of Singapore, 60 Biopolis Street, Genome 02 01, Singapore 138672
    Nat Methods 2:105-11. 2005
    ..The concept of paired-end ditagging described here for transcriptome analysis can also be applied to whole-genome analysis of cis-regulatory and other DNA elements and represents an important technological advance for genome annotation...
  5. pmc The use of multiple displacement amplification to amplify complex DNA libraries
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research A STAR, 60 Biopolis Street, Genome 02 01, Singapore
    Nucleic Acids Res 36:e32. 2008
    ....
  6. pmc Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes
    Patrick Ng
    Genome Institute of Singapore, 60 Biopolis Street, 02 01, Genome, Singapore 138672, Singapore
    Nucleic Acids Res 34:e84. 2006
    ....
  7. pmc Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
    Yijun Ruan
    Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 17:828-38. 2007
    ..The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes...
  8. doi request reprint Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells
    Xiao Dong Zhao
    Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore
    Cell Stem Cell 1:286-98. 2007
    ..These global histone methylation maps provide an epigenetic framework that enables the discovery of novel transcriptional networks and delineation of different genetic compartments of the pluripotent cell genome...
  9. pmc Whole-genome cartography of estrogen receptor alpha binding sites
    Chin Yo Lin
    Genome Institute of Singapore, Singapore, Republic of Singapore
    PLoS Genet 3:e87. 2007
    ..Taken together, this genome-scale analysis suggests complex but definable rules governing ERalpha binding and gene regulation...
  10. pmc 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation
    Chia Lin Wei
    Genome Institute of Singapore, 60 Biopolis Street, Genome 02 01, Singapore 138672
    Proc Natl Acad Sci U S A 101:11701-6. 2004
    ..The apparent precision and deep coverage makes 5'LS and 3'LS an advanced approach for genome annotation through whole-transcriptome characterization...
  11. ncbi request reprint Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection
    Yi Jun Ruan
    Genome Institute of Singapore, Singapore
    Lancet 361:1779-85. 2003
    ..Whole genome sequence analysis of various isolates might provide an indication of potential strain differences of this new virus. Moreover, mutation analysis will help to develop effective vaccines...
  12. ncbi request reprint A global map of p53 transcription-factor binding sites in the human genome
    Chia Lin Wei
    Genome Institute of Singapore, Singapore 138672
    Cell 124:207-19. 2006
    ....
  13. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  14. pmc Global mapping of c-Myc binding sites and target gene networks in human B cells
    Karen I Zeller
    Department of Medicine and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 103:17834-9. 2006
    ....
  15. ncbi request reprint Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation
    Ching Aeng Lim
    Laboratory of Immunology and Virology, Genome Institute of Singapore, 138672 Singapore
    Mol Cell 27:622-35. 2007
    ..Global gene expression profiling subsequently revealed a spectrum of NF-kappaB target genes that are positively regulated by E2F1, further demonstrating the critical role of E2F1 in the Toll-like receptor 4 pathway...