Research Topics
Species | Kuo Ping ChiuSummaryCountry: Singapore Publications
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Publications
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence dataKuo 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...- Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomesKuo 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... - De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesisMohamed 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... 
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotationPatrick 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...- Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomesPatrick Ng
Genome Institute of Singapore, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore
Nucleic Acids Res 34:e84. 2006.... - 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... - Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cellsXiao 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... - Whole-genome cartography of estrogen receptor alpha binding sitesChin 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... - The use of multiple displacement amplification to amplify complex DNA librariesMelissa 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.... - 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotationChia-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... - Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infectionYi Jun Ruan
Genome Institute of Singapore, Singapore
Lancet 361:1779-85. 2003.... - A global map of p53 transcription-factor binding sites in the human genomeChia-Lin Wei
Genome Institute of Singapore, Singapore 138672
Cell 124:207-19. 2006.... - Global mapping of c-Myc binding sites and target gene networks in human B cellsKaren 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.... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activationChing 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...