Publications

Publications

After 2015

  1. Cao, F. et al., “Super-enhancers and broad H3K4me3 domains form complex gene regulatory circuits involving chromatin interactions”, Sci. Rep., 2017. Link to Pubmed.
  2. Ooi, W.F. et al., “Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity”, Nat. Commun., 2016. Collaboration with Patrick Tan’s lab. Link to Pubmed.
  3. Akincilar, S. et al., “Long-range chromatin interactions drive mutant Tert promoter activation”, Cancer Discovery, 2016. Collaboration with Vinay Tergaonkar’s lab. Link to Pubmed.
  4. Fang, Y. and Fullwood, M.J., “Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer”, Genomics Proteomics Bioinformatics, 2016. (Review) Link to PDF.
  5. Choy, J.Y.*, Boon, P.L.*, Bertin, N.*, and Fullwood, M.J., “A Resource of Ribosomal RNA-depleted RNA-Seq data from Different Normal Adult and Fetal Human Tissues”, Sci. Data, 2015. Link to PDF. *Co-first
  6. Babu, D. and Fullwood, M.J., “3D Genome Organization in Health and Disease: Emerging Opportunities in Cancer Translational Medicine”, Nucleus. 2015. (Review) Link to PDF.

Book Chapters and Other Publications

  1. Choy, J. and Fullwood, M.J., “Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET),” Methods Mol. Biol., scheduled for 2017 (book chapter). Link to Pubmed.

 

Before 2015

  1. Sandhu, K.S. et al., “Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks”, Cell Rep. 2012. Link to PDF.
  2. The ENCODE Project Consortium, “An Integrated Encyclopedia of DNA Elements in the Human Genome”, Nature. 2012. ENCODE Website.
  3. Djebali, S. et al., “Landscape of Transcription in Human Cells”, Nature. 2012. ENCODE Website.
  4. Li, G., et al., “Extensive Promoter-centered Interactions provide Higher-order Framework for Transcription Regulation in Human Cells”, Cell. 2012. PDF.
  5. Goh, Y., Fullwood, M.J., Poh, H.M., Peh, S.Q., Ong, C.T., Zhang, J.Y., , Ruan, X., Ruan, Y., “Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation”, J. Vis. Exp. 2012. Link.
  6. Fullwood, M.J., Lee, J., Lin, L., Li, G., Huss, M., Ng, P., Sung, W-K., and Shenolikar, S., “Next-generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations”, PLoS ONE. 2011. PDF.
  7. Fullwood, M.J., Han, Y.Y., Wei, C.L., Ruan, X., Ruan, Y. “Chromatin Interaction Analysis using Paired-End Tag Sequencing”, Current Protocols in Molecular Biology. 2010. PDF.
  8. Li, G., Fullwood, M.J., Han X., et al. “ChIA-PET Tool for Comprehensive Chromatin Interaction Analysis with Paired-End Tag Sequencing”, Genome Biology. 2010. PDF.
  9. Fullwood, M.J., et al. The Oestrogen Receptor α-mediated Human Chromatin Interactome, Nature. 2009. PDF. Supplement.
  10. Fullwood, M.J., Wei, C.L., Liu, E. T. and Ruan, Y. Ultra-High-Throughtput Sequencing of Paired-End Tags (PET) for Transcriptome and Genome Analyses, Genome Res. 2009. PDF.
  11. Fullwood, M.J. and Ruan, Y. ChIP-based Methods for the Identification of Long-Range Chromatin Interactions, Journal of Cellular Biochemistry. 2009. PDF.
  12. Fullwood, M.J.; Tan J. J.; et al. The Use of Multiple Displacement Amplification to Amplify Complex DNA Libraries, Nucleic Acids Res. 2008. PDF.
  13. Ng, P., Tan; J.J.; Ooi H.S.; Lee Y. L.; Chiu K. P.; Fullwood M.J., et al. Multiplex Sequencing of Paired End Ditags (MS-PET): A Strategy for the Ultra-High-Throughput Analysis of Transcriptomes and Genomes, Nucleic Acids Res. 2006. PDF.

Book Chapters and Other Publications

  1. Zhang et al., “ChIA-PET analysis of Transcriptional Chromatin Interactions”, Methods, 2012. PDF.
  2. Fullwood, M.J., Zhou W., and Shenolikar, S., “The role of the eIF2α serine 51 phosphorylation stress response pathway in human health and disease” in Shenolikar S. (editor), Progress in Molecular Biology and Translational Science, Vol. 106, Burlington: Academic Press, pp. 75-106. 2012.
  3. Fullwood, M.J. “Genome-Wide Chromatin Loops Regulate Transcription”, Science Online. 2010. Single-author winning essay for the GE and Science Regional Winner for “All Other Countries”. This essay was published on Science magazine’s website.
  4. Huang, Y.H.P, Han, Y.Y., Handoko, L., Velkov, S., Wong, E., Cheung, E., Ruan, X., Wei, C-L., Fullwood, M.J., and Ruan, Y., “Protocol: Sonication-based Circular Chromosome Conformation Capture with Next-Generation Sequencing Analysis for the Detection of Chromatin Interactions”, Nature Protocols (Protocol Exchange). 2010. Link.

Patents

  1. Chromatin Interaction Analysis (Inventors: Dr Yijun Ruan, Dr Chialin Wei, Dr Melissa Fullwood, and Ms Liu Jun. Granted in Singapore and the United States).
  2. Nucleic Acid Interaction Analysis (Inventors: Dr Yijun Ruan, Dr Chialin Wei, and Dr Melissa Fullwood. Granted in Singapore, World-wide, India and the United States; patent pending in other countries).
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  1. Pingback: Papers from 2015 | Fullwood Lab

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