Yijun Ruan

Summary

Country: Singapore

Publications

  1. ncbi RNA viral community in human feces: prevalence of plant pathogenic viruses
    Tao Zhang
    Genome Institute of Singapore, Singapore
    PLoS Biol 4:e3. 2006
  2. ncbi 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
  3. ncbi 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
  4. ncbi ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
    Guoliang Li
    Computational and Mathematical Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Republic of Singapore
    Genome Biol 11:R22. 2010
  5. ncbi Integrative model of genomic factors for determining binding site selection by estrogen receptor-α
    Roy Joseph
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
    Mol Syst Biol 6:456. 2010
  6. ncbi An oestrogen-receptor-alpha-bound human chromatin interactome
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
    Nature 462:58-64. 2009
  7. ncbi Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
    Axel M Hillmer
    Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 21:665-75. 2011
  8. ncbi 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. ncbi 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
  10. ncbi Evolution of the mammalian transcription factor binding repertoire via transposable elements
    Guillaume Bourque
    Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 18:1752-62. 2008

Research Grants

  1. Ditag technologies for complete transcriptome annotation
    Yijun Ruan; Fiscal Year: 2006
  2. Whole Genome Chromatin Interaction Analysis using Pair-End-diTagging (CIA-PET)
    Yijun Ruan; Fiscal Year: 2009
  3. Whole Genome Chromatin Interaction Analysis using Pair-End-diTagging (CIA-PET)
    Yijun Ruan; Fiscal Year: 2010

Detail Information

Publications49

  1. ncbi RNA viral community in human feces: prevalence of plant pathogenic viruses
    Tao Zhang
    Genome Institute of Singapore, Singapore
    PLoS Biol 4:e3. 2006
    ..Intriguingly, the fecal PMMV was infectious to host plants, suggesting that humans might act as a vehicle for the dissemination of certain plant viruses...
  2. ncbi 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...
  3. ncbi 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
    ....
  4. ncbi ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
    Guoliang Li
    Computational and Mathematical Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Republic of Singapore
    Genome Biol 11:R22. 2010
    ..ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source (available at http://chiapet.gis.a-star.edu.sg)...
  5. ncbi Integrative model of genomic factors for determining binding site selection by estrogen receptor-α
    Roy Joseph
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
    Mol Syst Biol 6:456. 2010
    ..These results suggest a definable interplay between sequence motifs and local chromatin in selecting TF binding...
  6. ncbi An oestrogen-receptor-alpha-bound human chromatin interactome
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
    Nature 462:58-64. 2009
    ..We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes...
  7. ncbi Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
    Axel M Hillmer
    Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 21:665-75. 2011
    ....
  8. ncbi 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. ncbi 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...
  10. ncbi Evolution of the mammalian transcription factor binding repertoire via transposable elements
    Guillaume Bourque
    Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 18:1752-62. 2008
    ..Our results demonstrate that transcriptional regulatory networks are highly dynamic in eukaryotic genomes and that transposable elements play an important role in expanding the repertoire of binding sites...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    Xi Chen
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Cell 133:1106-17. 2008
    ..Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity...
  14. ncbi 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...
  15. ncbi Paired-end diTagging for transcriptome and genome analysis
    Patrick Ng
    Genome Institute of Singapore, Singapore
    Curr Protoc Mol Biol . 2007
    ..A recent innovation (Multiplex Sequencing of Paired-End ditags; MS-PET) enables PETs to be sequenced using high-throughput 454 sequencing, greatly increasing the amount of data that can be collected in each run...
  16. ncbi 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
    ....
  17. ncbi 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
    ....
  18. ncbi ChIA-PET analysis of transcriptional chromatin interactions
    Jingyao Zhang
    Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
    Methods 58:289-99. 2012
    ..Here, we describe the detailed procedures of the ChIA-PET methodology, unraveling transcription-associated chromatin contacts in a model human cell line...
  19. ncbi Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons
    Fei Yao
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
    PLoS ONE 7:e46152. 2012
    ..This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer...
  20. ncbi Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
    Genome Res 19:521-32. 2009
    ..With its versatile and powerful nature for DNA analysis, the PET sequencing strategy has a bright future ahead...
  21. ncbi 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...
  22. ncbi SARS transmission pattern in Singapore reassessed by viral sequence variation analysis
    Jianjun Liu
    Genome Institute of Singapore, Singapore
    PLoS Med 2:e43. 2005
    ....
  23. ncbi Tackling the epigenome in the pluripotent stem cells
    Xiaodong Zhao
    Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore
    J Genet Genomics 35:403-12. 2008
    ....
  24. ncbi Chromatin interaction analysis using paired-end tag sequencing
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
    Curr Protoc Mol Biol . 2010
    ..This unit describes ChIA-PET for genome-wide analysis of chromatin interactions in mammalian cells, with the application of Roche/454 and Illumina sequencing technologies...
  25. ncbi CTCF-mediated functional chromatin interactome in pluripotent cells
    Lusy Handoko
    Genome Institute of Singapore, Singapore
    Nat Genet 43:630-8. 2011
    ..This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function...
  26. ncbi Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    Guoliang Li
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Cell 148:84-98. 2012
    ..Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells...
  27. ncbi Transcriptional consequences of genomic structural aberrations in breast cancer
    Koichiro Inaki
    Cancer Biology and Pharmacology, Genome Institute of Singapore, Genome, Singapore 138672, Singapore
    Genome Res 21:676-87. 2011
    ..This gene fusion is caused by tandem duplication on 17q23 and appears to be an indicator of local genomic instability altering the expression of oncogenic components such as MIR21 and RPS6KB1...
  28. ncbi The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    Yuin Han Loh
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Nat Genet 38:431-40. 2006
    ..The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination...
  29. ncbi Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003
    Vinsensius B Vega
    Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
    BMC Infect Dis 4:32. 2004
    ..The recent emergence of this new pathogen, the careful tracing of its transmission patterns, and the ability to propagate in culture allows the exploration of the mutational dynamics of the SARS-CoV in human populations...
  30. ncbi Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments
    Vladimir A Kuznetsov
    Genome Institute of Singapore, Biopolis Street, 60, 138672 Singapore
    Genome Inform 19:83-94. 2007
    ....
  31. ncbi Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness
    Axel M Hillmer
    Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
    Hum Genet 126:255-64. 2009
    ..It is therefore probable that the AGA risk haplotype rose to high frequency in combination with this EDA2R variant, possibly by hitchhiking on a positively selected 57K haplotype...
  32. ncbi 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...
  33. ncbi Multiplex parallel pair-end-ditag sequencing approaches in system biology
    Yijun Ruan
    Genome Technology and Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Singapore
    Wiley Interdiscip Rev Syst Biol Med 2:224-34. 2010
    ....
  34. ncbi Chromatin interaction networks and higher order architectures of eukaryotic genomes
    Kuljeet Singh Sandhu
    Genome Institute of Singapore, Singapore
    J Cell Biochem 112:2218-21. 2011
    ....
  35. ncbi ChIP-based methods for the identification of long-range chromatin interactions
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
    J Cell Biochem 107:30-9. 2009
    ....
  36. ncbi Interrogating the transcriptome
    Yijun Ruan
    Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore, Republic of Singapore
    Trends Biotechnol 22:23-30. 2004
  37. ncbi Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET)
    Xiaoan Ruan
    Genome Institute of Singapore, Singapore, Singapore
    Methods Mol Biol 809:535-62. 2012
    ..Therefore, RNA-PET has been regarded as the best PET for genome annotation (1). Here in this chapter, we describe the details of the RNA-PET protocol and discuss the critical issues...
  38. ncbi A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence
    Tannistha Nandi
    Genome Institute of Singapore, Singapore, Republic of Singapore
    PLoS Pathog 6:e1000845. 2010
    ..These findings improve our understanding of the pathogenesis of melioidosis, and establish Bp as a model system for studying the genetics of accidental virulence...
  39. ncbi 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...
  40. ncbi The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)
    Daniela S Gerhard
    Genome Res 14:2121-7. 2004
    ..Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline...
  41. ncbi 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
    ....
  42. ncbi Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:839-51. 2007
    ..These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues...
  43. ncbi Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  44. ncbi Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies
    Ghia M Euskirchen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    Genome Res 17:898-909. 2007
    ..Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies...
  45. ncbi 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...
  46. ncbi Biodiversity and biogeography of phages in modern stromatolites and thrombolites
    Christelle Desnues
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:340-3. 2008
    ..Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community...
  47. ncbi The airborne metagenome in an indoor urban environment
    Susannah G Tringe
    Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 3:e1862. 2008
    ..This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens...
  48. ncbi Laboratory-acquired severe acute respiratory syndrome
    Poh Lian Lim
    Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
    N Engl J Med 350:1740-5. 2004
  49. ncbi A genomics approach to understanding host response during dengue infection
    Martin L Hibberd
    Genome Institute of Singapore, Biopolis, Singapore 138670
    Novartis Found Symp 277:206-14; discussion 214-7, 251-3. 2006
    ..This data will be further refined through interlinking with similar data obtained from a large study of dengue patients, initiated in Singapore, that is able to look at the early host response to infection...

Research Grants7

  1. Ditag technologies for complete transcriptome annotation
    Yijun Ruan; Fiscal Year: 2006
    ..We seek to identify all genes that are responsive to p53, and to ascertain through GIS-ChIP cloning and through our novel GIS analysis strategy all possible cis-regulatory fragments. ..
  2. Whole Genome Chromatin Interaction Analysis using Pair-End-diTagging (CIA-PET)
    Yijun Ruan; Fiscal Year: 2009
    ..This project will provide unprecedented insight into the mechanisms of transcription regulations allowing us to better understand how cancer cells develop and how stem cells retain pluripotency. ..
  3. Whole Genome Chromatin Interaction Analysis using Pair-End-diTagging (CIA-PET)
    Yijun Ruan; Fiscal Year: 2010
    ..This project will provide unprecedented insight into the mechanisms of transcription regulations allowing us to better understand how cancer cells develop and how stem cells retain pluripotency. ..