Publications

Publications

Link to the most updated list on Pubmed.

Manuscripts on biorxiv

  1. Cao F. et al., “Predicting chromatin interactions between open chromatin regions from DNA sequences”, https://www.biorxiv.org/content/10.1101/720748v1
  2. Cai, Zhang et al., “H3K27me3-rich regions can function as silencers to repress gene expression via chromatin interactions”, https://www.biorxiv.org/content/10.1101/684712v2

After 2015

  1. Cao F. and Fullwood, M.J., “Inflated performance measures in enhancer-promoter interaction-prediction methods”, Nature Genetics, 2019. Link to full text.
  2. Tan, S.H. et al., “The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia”, Blood, 2019. Link to Pubmed.
  3. Lee, D.P. et al., “A Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response”, Circulation., 2019. Link to Pubmed.
  4. See, Y., Wang, B., and Fullwood, M.J., “Chromatin Interactions and Regulatory Elements in Cancer: From Bench to Bedside,” Trends in Genetics, 2019. Link to Pubmed.
  5. Teoh, P.J. et al., “Aberrant hyperediting of myeloma transcriptome by ADAR1 confers oncogenicity and is a marker of poor prognosis”, Blood, 2018. Link to Pubmed.
  6. Xie, J.J. et al., “Super-Enhancer-Driven Long Non-Coding RNA LINC01503, Regulated by TP63, Is Over-Expressed and Oncogenic in Squamous Cell Carcinoma”, Gastroenterology., 2018. Link to Pubmed.
  7. Yan, T. et al., “HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis”, Nat Commun., 2018. Link to Pubmed.
  8. Cao, F. et al., “Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions”, Sci. Rep., 2017. Link to free PMC article.
  9. 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.
  10. 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.
  11. 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.
  12. 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
  13. 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.

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.

Other Publications

  1. Babu, D. and Fullwood, M.J., “Expanding the effects of ERG on chromatin landscapes and dysregulated transcription in prostate cancer”, Nature Genetics, 2017.  Link to Pubmed.
  2. 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., 2017. Link to Pubmed
  3. Zhang et al., “ChIA-PET analysis of Transcriptional Chromatin Interactions”, Methods, 2012. PDF.
  4. 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.
  5. 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.
  6. 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 thought on “Publications

  1. Pingback: Papers from 2015 | Fullwood Lab

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