Vinsensius B Vega

Summary

Country: Singapore

Publications

  1. pmc Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites
    Vinsensius B Vega
    Estrogen Receptor Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672
    Genome Biol 7:R82. 2006
  2. pmc Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells
    Chin Yo Lin
    Genome Institute of Singapore, Singapore 117528
    Genome Biol 5:R66. 2004
  3. pmc 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
  4. pmc 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
  5. pmc BEARR: Batch Extraction and Analysis of cis-Regulatory Regions
    Vinsensius B Vega
    Genome Institute of Singapore, 60 Biopolis Street, 02 01, Singapore 138672
    Nucleic Acids Res 32:W257-60. 2004
  6. pmc 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
  7. pmc A human in vitro model system for investigating genome-wide host responses to SARS coronavirus infection
    Lisa F P Ng
    Genome Institute of Singapore, 60 Biopolis Street, Genome, 02 01, Singapore 138672
    BMC Infect Dis 4:34. 2004
  8. pmc 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
  9. pmc Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer
    Chin Yo Lin
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Breast Cancer Res 9:R25. 2007
  10. pmc Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays
    Christopher W Wong
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Genome Res 14:398-405. 2004

Collaborators

Detail Information

Publications26

  1. pmc Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites
    Vinsensius B Vega
    Estrogen Receptor Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672
    Genome Biol 7:R82. 2006
    ..We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model...
  2. pmc Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells
    Chin Yo Lin
    Genome Institute of Singapore, Singapore 117528
    Genome Biol 5:R66. 2004
    ..In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target genes...
  3. pmc 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)...
  4. pmc 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...
  5. pmc BEARR: Batch Extraction and Analysis of cis-Regulatory Regions
    Vinsensius B Vega
    Genome Institute of Singapore, 60 Biopolis Street, 02 01, Singapore 138672
    Nucleic Acids Res 32:W257-60. 2004
    ..The software is publicly available at http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/...
  6. pmc 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...
  7. pmc A human in vitro model system for investigating genome-wide host responses to SARS coronavirus infection
    Lisa F P Ng
    Genome Institute of Singapore, 60 Biopolis Street, Genome, 02 01, Singapore 138672
    BMC Infect Dis 4:34. 2004
    ..In this study, we therefore examine the immune response of SARS-CoV in human peripheral blood mononuclear cells (PBMCs) over the first 24 hours...
  8. pmc 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...
  9. pmc Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer
    Chin Yo Lin
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Breast Cancer Res 9:R25. 2007
    ..The goal of this study was to examine transcriptomic alterations in cancer cells co-expressing both receptors and the association of gene expression signatures with disease outcome...
  10. pmc Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays
    Christopher W Wong
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Genome Res 14:398-405. 2004
    ....
  11. 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
    ....
  12. doi request reprint 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...
  13. doi request reprint Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb
    Bo Feng
    Gene Regulation Laboratory, Genome Institute of Singapore, 60 Biopolis Street, 02 01, Genome Building, Singapore 138672
    Nat Cell Biol 11:197-203. 2009
    ..Our findings also indicate that it is possible to reprogram MEFs without exogenous Klf transcription factors and link a nuclear receptor to somatic cell reprogramming...
  14. pmc An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
    Lance D Miller
    Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
    Proc Natl Acad Sci U S A 102:13550-5. 2005
    ..Our results show the primary importance of p53 functional status in predicting clinical breast cancer behavior...
  15. ncbi request reprint 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...
  16. 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...
  17. ncbi request reprint Comment on " 'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature"
    Nicolas O Fortunel
    Science 302:393; author reply 393. 2003
  18. 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...
  19. ncbi request reprint 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
  20. ncbi request reprint Identification of discriminators of hepatoma by gene expression profiling using a minimal dataset approach
    Soek Ying Neo
    Genome Institute of Singapore, Singapore
    Hepatology 39:944-53. 2004
    ....
  21. pmc Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology
    Siew Hong Lam
    Department of Biological Sciences, National University of Singapore, Singapore
    PLoS Genet 4:e1000121. 2008
    ..These findings place zebrafish in a strategic position to bridge the wide gap between cell-based and rodent models in chemogenomics research and applications, especially in preclinical drug discovery and toxicology...
  22. ncbi request reprint Genome-wide expression profiling; a panel of mouse tissues discloses novel biological functions of liver X receptors in adrenals
    Knut R Steffensen
    Department of Biosciences, Karolinska Institutet at NOVUM, Huddinge, Sweden
    J Mol Endocrinol 33:609-22. 2004
    ..These results indicate novel biological roles of the LXR including regulation of energy metabolism, glycolysis and steroidogenesis in the adrenals via alteration of expression profiles of putative target genes...
  23. 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...
  24. 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...
  25. ncbi request reprint Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression
    Siew Hong Lam
    Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543
    Nat Biotechnol 24:73-5. 2006
    ..This approach provides a useful strategy for identifying an expression signature that is strongly associated with a disease phenotype...
  26. ncbi request reprint Gene expression preferentially regulated by tamoxifen in breast cancer cells and correlations with clinical outcome
    Jonna Frasor
    Department of Molecular and Integrative Physiology and Cell and Developmental Biology, University of Illinois and College of Medicine, Urbana, Illinois 61801 3704, USA
    Cancer Res 66:7334-40. 2006
    ..This may have a potential effect on the choice of tamoxifen versus aromatase inhibitors as adjuvant endocrine therapy...