Publications

Publications

Manuscripts in preparation – posted on biorxiv (3)

  1. Cao F., Zhang Y., Loh Y. P., Cai Y., Fullwood M.J., “Predicting chromatin interactions between open chromatin regions from DNA sequences”, https://www.biorxiv.org/content/10.1101/720748v1 . Cao Fan, the first author, was a PhD student, then postdoctoral fellow in the lab. Melissa Fullwood is corresponding author and last author.
  2. Cai Y*, Zhang Y*, Loh Y.P., Tng J.Q., Lim M.C., Cao Z., Anandhkumar R., Shang L., Lakshmanan M., Tergaonkar V.., Tucker-Kellogg G.^, Fullwood M.J.^, “H3K27me3-rich regions can function as silencers to repress gene expression via chromatin interactions”, https://www.biorxiv.org/content/10.1101/684712v4. Last author and co-corresponding manuscript. *Co-first authors ^Co-corresponding authors. Yichao was a co-supervised PhD student in the lab, and is now a post-doctoral fellow in the lab, and Zhang Ying is a current PhD student in the lab. Melissa Fullwood is co-corresponding author and last author.
  3. Wang, B.*, Kong, L.S.*, Babu, D.*, Choudhary, R., Fam, W., Tng, J.Q., Goh, Y., Liu, X., Song, F.F., Chia, P., Chan, M.C., An, O., Tham, C. Y., Benoukraf, T., Yang, H., Wang, W., Chng, W.J., Tenen, D.G., Fullwood, M.J.^ “Three-Dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia”, https://www.biorxiv.org/content/10.1101/2020.04.18.047738v1 *Co-first authors ^Corresponding author. Benny Wang, Lingshi Kong and Ruchi Choudhary are current PhD students in the lab. Deepak Babu is a current post-doctoral fellow in the lab. Melissa Fullwood is corresponding author and last author.

After 2015 (20 manuscripts published, 33 including manuscripts before 2015)

  1. Wang, H.F., Warrier, T., Farran, C.A., Zheng, Z.H., Xing, Q.R., Fullwood, M.J., Zhang, L.F., Li, H., Xu, J., Lim, T.M., and Loh, Y.H., “Defining Essential Enhancers for Pluripotent Stem Cells using a Features-Oriented CRISPR-Cas9 Screen”, Cell Rep.2020 Oct 27;33(4):108309. doi: 10.1016/j.celrep.2020.108309.
  2. Jiang, Y.*, Jiang, Y.*, Li, C.*, Zhang, Y.*, Dakle, P.*, Kaur, H., Deng, J., Lin, Y., Han, L., Xie, J., Mayakonda, A., Hazawa, M., Xu, L., Li, Y., Aswad, L., Jeitany, M., Kanojia, D., Guan, X., Fullwood, M.J.^, Lin, D.^ and Koeffler, H.P.^ “TP63, SOX2 and KLF5 Establish Core Regulatory Circuitry and Construct Cancer Specific Epigenome in Esophageal Squamous Cell Carcinoma”, 2020 Oct;159(4):1311-1327.e19. doi: 10.1053/j.gastro.2020.06.050. *Co-first authors ^Co-corresponding authors. Zhang Ying is a current PhD student in the lab. Melissa Fullwood is co-corresponding author.
  3. Zhang Y., Jia, C., Fullwood, M.J., Kwoh C.K., “DeepCPP: A Deep Neural Network Based on Nucleotide Bias Information and Minimum Distribution Similarity Feature Selection for RNA Coding Potential Prediction”, Briefings in Bioinformatics, 2020
    Mar 30;bbaa039. doi: 10.1093/bib/bbaa039.
  4. Tham C.Y., Tirado-Magallanes R., Goh Y., Fullwood M.J., Koh B.T.H., Wang W., Ng C.H., Chng W.J., Thiery A., Tenen D.G., Benoukraf T. “NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing”, Genome Biology, 2020 Mar 3;21(1):56. doi: 10.1186/s13059-020-01968-7.
  5. Jadhav S., Kumari N., Ng L., Tan P.F., Yeo-Teh N.S.L, Goh Y., Fam W.N., Tng J.Q., Tian J.S., Koh B.T.H., Chun C.M., Wang W., Chng W.J., Fullwood MJ, Guccione E., Karnani N., Tenen D.G., Jha S., “circASXL1-1 regulates BAP1 deubiquitinase activity in leukemia”, Haematologica, 2019 Nov 28. pii: haematol.2019.225961. doi: 10.3324/haematol.2019.225961. [Epub ahead of print]. PMID:31780633. Link to free article.
  6. Nama S., Muhuri M., Di Pascale F., Quah S., Aswad L., Fullwood M., Sampath P. “MicroRNA-138 is a Prognostic Biomarker for Triple-Negative Breast Cancer and Promotes Tumorigenesis via TUSC2 repression.,” Sci. Rep., 2019 Sep 3;9(1):12718. doi: 10.1038/s41598-019-49155-4. PMID:31481748. Link to free article.
  7. Cao F. and Fullwood, M.J., “Inflated performance measures in enhancer-promoter interaction-prediction methods”, Nature Genetics, 2019 Aug;51(8):1196-1198. doi: 10.1038/s41588-019-0434-7. PMID:31332378. Link to Pubmed.  This is a correspondence article. Featured on Science Daily. Cao Fan, a PhD student in the lab (now graduated) is first author and Melissa Fullwood is the corresponding author.
  8. Tan S.H., Leong W.Z., Ngoc P.C.T., Tan T.K., Bertulfo F.C., Lim M.C., An O., Li Z., Yeoh A.E.J., Fullwood M.J., Tenen D.G., Sanda T., “The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia”, Blood, 2019 Jul 18;134(3):239-251. doi: 10.1182/blood.2018874503. Epub 2019 May 10. PMID: 31076442. Link to Pubmed.
  9. Shyamsunder P., Shanmugasundaram M., Mayakonda A., Dakle P., Teoh W.W., Han L., Kanojia D., Lim M.C., Fullwood M., An O., Yang H., Shi J., Hossain M.Z., Madan V., Koeffler H.P. “Identification of a novel enhancer of CEBPE essential for granulocytic differentiation”, Blood, 2019 Jun 6;133(23):2507-2517. doi: 10.1182/blood.2018886077. Epub 2019 Apr 5. PMID: 30952671. Link to Pubmed.
  10. Lee D.P., Tan W.L.W., Anene-Nzelu C.G., Lee C.J.M., Li P.Y., Luu T.D.A., Chan C.X., Tiang Z., Ng S.L., Huang X., Efthymios M., Autio M.I., Jiang J., Fullwood M.J., Prabhakar S., Lieberman Aiden E., Foo R.S., “A Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response”, Circulation., 2019 Apr 16;139(16):1937-1956. doi: 10.1161/CIRCULATIONAHA.118.036726. PMID:30717603. Link to Pubmed.
  11. See, Y.*, Wang, B.*, and Fullwood, M.J., “Chromatin Interactions and Regulatory Elements in Cancer: From Bench to Bedside,” Trends in Genetics, 2019 Feb;35(2):145-158. doi: 10.1016/j.tig.2018.11.007. Epub 2018 Dec 18. Review. PMID:30577989. Link to Pubmed. This is a review paper. *Co-first authors. Yi Xiang See and Benny Wang are PhD students in the lab, and Melissa Fullwood is corresponding author.
  12. Teoh P.J., An O., Chung T.H., Chooi J.Y., Toh S.H.M., Fan S., Wang W., Koh B.T.H., Fullwood M.J., Ooi M.G., de Mel S., Soekojo C.Y., Chen L., Ng S.B., Yang H., Chng W.J., “Aberrant hyperediting of myeloma transcriptome by ADAR1 confers oncogenicity and is a marker of poor prognosis”, Blood, 2018 Sep 20;132(12):1304-1317. doi: 10.1182/blood-2018-02-832576. Epub 2018 Jul 30. PMID:30061158 Link to Pubmed.
  13. Xie J.J., Jiang Y.Y., Jiang Y., Li C.Q., Lim M.C., An O., Mayakonda A., Ding L.W., Long L., Sun C., Lin L.H., Chen L., Wu J.Y., Wu Z.Y., Cao Q., Fang W.K., Yang W., Soukiasian H., Meltzer S.J., Yang H., Fullwood M., Xu L.Y., Li E.M., Lin D.C., Koeffler H.P., “Super-Enhancer-Driven Long Non-Coding RNA LINC01503, Regulated by TP63, Is Over-Expressed and Oncogenic in Squamous Cell Carcinoma”, Gastroenterology., 2018 Jun;154(8):2137-2151.e1. doi: 10.1053/j.gastro.2018.02.018. Epub 2018 Feb 15. PMID: 29454790. Link to Pubmed.
  14. Yan T., Ooi W.F., Qamra A., Cheung A., Ma D., Sundaram G.M., Xu C., Xing M., Poon L., Wang J., Loh Y.P., Ho J.H.J., Ng J.J.Q., Ramlee M.K., Aswad L., Rozen S.G., Ghosh S., Bard F.A., Sampath P., Tergaonkar V., Davies J.O.J., Hughes J.R., Goh E., Bi X., Fullwood M.J., Tan P., Li S., “HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis”, Nat Commun., 2018 Jan 8;9(1):100. doi: 10.1038/s41467-017-02601-1. PMID: 29311615. Link to Pubmed.
  15. Cao F.*, Fang Y.*, Tan H.K., Goh Y., Choy J.Y.H., Koh B.T.H., Hao Tan J., Bertin N., Ramadass A., Hunter E., Green J., Salter M., Akoulitchev A., Wang W., Chng WJ., Tenen D.G., Fullwood M.J., “Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions”, Sci. Rep., 2017. Link to free PMC article. *Co-first authors. Cao Fan was a PhD student in the lab, and Yiwen Fang was a post-doctoral fellow in the lab. Melissa Fullwood is corresponding author and last author.
  16. Akıncılar S.C., Khattar E., Boon P.L., Unal B., Fullwood M.J., Tergaonkar V., “Long-range chromatin interactions drive mutant Tert promoter activation”, Cancer Discovery, 2016 Nov;6(11):1276-1291. Epub 2016 Sep 20. PMID:27650951.  Link to Pubmed. 
  17. Ooi W.F., Xing M., Xu C., Yao X., Ramlee M.K., Lim M.C., Cao F., Lim K., Babu D., Poon L.F., Lin S.J., Qamra A., Irwanto A., Qu Z.J., Nandi T., Lee-Lim A.P., Chan Y.S., Tay S.T., Lee M.H., Davies J.O., Wong W.K., Soo K.C., Chan W.H., Ong H.S., Chow P., Wong C.Y., Rha S.Y., Liu J., Hillmer A.M., Hughes J.R., Rozen S., Teh B.T., Fullwood M.J., Li S., Tan P., “Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity”, Nat. Commun., 2016 Sep 28;7:12983. doi: 10.1038/ncomms12983. PMID:27677335. Link to Pubmed.
  18. Fang, Y. and Fullwood, M.J., “Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer”, Genomics Proteomics Bioinformatics, 2016 Feb;14(1):42-54. doi: 10.1016/j.gpb.2015.09.006. Epub 2016 Feb 12. Review. PMID:26883671 Link to PDF.  This is a review paper. Yiwen Fang is the first author and she was a postdoctoral fellow in the lab. Melissa Fullwood is the last author and corresponding author. Listed as a “Highly Cited Paper” by Web of Science Core Collection (159 citations).
  19. 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 Nov 10;2:150063. doi: 10.1038/sdata.2015.63. eCollection 2015. PMID:26594381. Link to PDF. *Co-first authors. Jocelyn Choy was a senior lab executive in the lab, Priscilla Boon was a research assistant in the lab and Nicolas Bertin was a senior research scientist in the lab. Melissa Fullwood is last author and corresponding author.
  20. Babu, D. and Fullwood, M.J., “3D Genome Organization in Health and Disease: Emerging Opportunities in Cancer Translational Medicine”, Nucleus. 2015;6(5):382-93. doi: 10.1080/19491034.2015.1106676. PMID: 26553406. Link to PDF. This is a review paper. Deepak Babu is a post-doctoral fellow in the lab. Melissa Fullwood is last author and corresponding author.

Link to the most updated list on Pubmed.

Before 2015 (13)

  1. Sandhu K.S., Li G., Poh H.M., Quek Y.L., Sia Y.Y., Peh S.Q., Mulawadi F.H., Lim J., Sikic M., Menghi F., Thalamuthu A., Sung W.K., Ruan X., Fullwood M.J., Liu E., Csermely P., Ruan Y., “Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks”, Cell Rep. 2012 Nov 29;2(5):1207-19. doi: 10.1016/j.celrep.2012.09.022. Epub 2012 Oct 25. PMID:23103170. Link to PDF.
  2. Djebali S., Davis C.A., Merkel A., Dobin A., Lassmann T., Mortazavi A., Tanzer A., Lagarde J., Lin W., Schlesinger F., Xue C., Marinov G.K., Khatun J., Williams B.A., Zaleski C., Rozowsky J., Röder M., Kokocinski F., Abdelhamid R.F., Alioto T., Antoshechkin I., Baer M.T., Bar N.S., Batut P., Bell K., Bell I., Chakrabortty S., Chen X., Chrast J., Curado J., Derrien T., Drenkow J., Dumais E., Dumais J., Duttagupta R., Falconnet E., Fastuca M., Fejes-Toth K., Ferreira P., Foissac S., Fullwood M.J., Gao H., Gonzalez D., Gordon A., Gunawardena H., Howald C., Jha S., Johnson R., Kapranov P., King B., Kingswood C., Luo O.J., Park E., Persaud K., Preall J.B., Ribeca P., Risk B., Robyr D., Sammeth M., Schaffer L., See L.H., Shahab A., Skancke J., Suzuki A.M., Takahashi H., Tilgner H., Trout D., Walters N., Wang H., Wrobel J., Yu Y., Ruan X., Hayashizaki Y., Harrow J., Gerstein M., Hubbard T., Reymond A., Antonarakis S.E., Hannon G., Giddings M.C., Ruan Y., Wold B., Carninci P., Guigó R., Gingeras T.R., “Landscape of Transcription in Human Cells”, Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. PMID:22955620. ENCODE Website. Listed as a “Highly Cited Paper” by Web of Science Core Collection (2,318 citations).
  3. The ENCODE Project Consortium (594 authors) Dunham I., …. Fullwood M.J., …. Birney E., “An Integrated Encyclopedia of DNA Elements in the Human Genome”, Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PMID:22955616. ENCODE Website. Listed as a “Highly Cited Paper” by Web of Science Core Collection (7,470 citations).
  4. 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 Apr 30;(62). pii: 3770. doi: 10.3791/3770. PMID:22564980. Link. *Co-first authors.
  5. Li G., Ruan X., Auerbach R.K., Sandhu K.S., Zheng M., Wang P., Poh H.M., Goh Y., Lim J., Zhang J., Sim H.S., Peh S.Q., Mulawadi F.H., Ong C.T., Orlov Y.L., Hong S., Zhang Z., Landt S., Raha D., Euskirchen G., Wei C.L., Ge W., Wang H., Davis C., Fisher-Aylor K.I., Mortazavi A., Gerstein M., Gingeras T., Wold B., Sun Y., Fullwood M.J., Cheung E., Liu E., Sung W.K., Snyder M., Ruan Y., “Extensive Promoter-centered Interactions provide Higher-order Framework for Transcription Regulation in Human Cells”, Cell. 2012 Jan 20;148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014. PMID:22265404. PDF. Listed as a “Highly Cited Paper” by Web of Science Core Collection (644 citations).
  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;6(11):e26054. doi: 10.1371/journal.pone.0026054. Epub 2011 Nov 8. PMID:22087219. PDF. Melissa Fullwood was a first author on this manuscript.
  7. 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;11(2):R22. doi: 10.1186/gb-2010-11-2-r22. Epub 2010 Feb 25. PMID:20181287. PDF *Co-first authors. Melissa Fullwood was a co-first author on this manuscript.
  8. 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 Jan;Chapter 21:Unit 21.15.1-25. doi: 10.1002/0471142727.mb2115s89. PMID:20069536. PDF. Peer-reviewed protocol manuscript. Melissa Fullwood was the first author.
  9. Fullwood M.J., Liu M.H., Pan Y.F., Liu J., Xu H., Mohamed Y.B., Orlov Y.L., Velkov S., Ho A., Mei P.H., Chew E.G., Huang P.Y., Welboren W.J., Han Y., Ooi H.S., Ariyaratne P.N., Vega V.B., Luo Y., Tan P.Y., Choy P.Y., Wansa K.D., Zhao B., Lim K.S., Leow S.C., Yow J.S., Joseph R., Li H., Desai K.V., Thomsen J.S., Lee Y.K., Karuturi R.K., Herve T., Bourque G., Stunnenberg H.G., Ruan X., Cacheux-Rataboul V., Sung W.K., Liu E.T., Wei C.L., Cheung E., Ruan Y. “The Oestrogen Receptor α-mediated Human Chromatin Interactome”, Nature. 2009 Nov 5;462(7269):58-64. doi: 10.1038/nature08497. PMID:19890323. PDF. Supplement. This was a research article in Nature. Melissa Fullwood was the first author. Listed as a “Highly Cited Paper” by Web of Science Core Collection (877 citations).
  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 Apr;19(4):521-32. doi: 10.1101/gr.074906.107. Review. PMID:19339662. PDF. This is a review paper. Melissa Fullwood was the first author.
  11. Fullwood, M.J. and Ruan, Y. “ChIP-based Methods for the Identification of Long-Range Chromatin Interactions”, Journal of Cellular Biochemistry. 2009 May 1;107(1):30-9. doi: 10.1002/jcb.22116. Review. PMID:19247990. PDF. This is a review paper. Melissa Fullwood was the first author.
  12. Fullwood M.J.*, Tan J.J.*, Ng P.W., Chiu K.P., Liu J., Wei C.L., Ruan Y. “The Use of Multiple Displacement Amplification to Amplify Complex DNA Libraries”, Nucleic Acids Res. 2008 Mar;36(5):e32. doi: 10.1093/nar/gkn074. Epub 2008 Feb 19. PDF. Melissa Fullwood was a co-first author.
  13. Ng, P., Tan; J.J.; Ooi H.S.; Lee Y. L.; Chiu K. P.; Fullwood M.J., Srinivasan K.G., Perbost C., Du L., Sung W.K., Wei C.L., Ruan Y., “Multiplex Sequencing of Paired End Ditags (MS-PET): A Strategy for the Ultra-High-Throughput Analysis of Transcriptomes and Genomes”, Nucleic Acids Res. 2006 Jul 13;34(12):e84. PMID:16840528. PDF.

Other Publications (6)

  1. Babu, D. and Fullwood, M.J., “Expanding the effects of ERG on chromatin landscapes and dysregulated transcription in prostate cancer”, Nature Genetics, 2017 Aug 30;49(9):1294-1295. doi: 10.1038/ng.3944. PMID:28854182.  Link to Pubmed. Commentary on another article.
  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 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009. Epub 2012 Aug 25. PMID: 22926262. Link to Pubmed. Methods paper.
  3. Zhang J., Poh H.M., Peh S.Q., Sia Y.Y., Li G., Mulawadi F.H., Goh Y., Fullwood M.J., Sung W.K., Ruan X., Ruan Y., “ChIA-PET analysis of Transcriptional Chromatin Interactions”, Methods, 2012 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009. Epub 2012 Aug 25. PMID: 22926262. PDF. Methods paper.
  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. Book chapter.
  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. ^Co-corresponding. Protocol paper.

Patents and Invention Disclosures (4)

  1. Invention Disclosure, 2018, A method for predicting 3D genome organization (chromatin interactions) through machine learning of DNA sequence features (Inventors: Dr Cao Fan and Dr Melissa Fullwood)
  2. Patent, Length Controlled Tag Concatenation and Multiplex Sequencing of Paired End diTags (LCT and MSPET) (Inventors: Dr Yijun Ruan, Dr Patrick Ng, Dr Melissa Fullwood, Ms Lee Yen Ling)
  3. Patent, Nucleic acid interaction analysis (a variant of the ChIA-PET method) (Inventors: Dr Yijun Ruan, Dr Chialin Wei, Dr Melissa Fullwood, and Ms Liu Jun).
  4. Patent, Chromatin interaction analysis (Inventors: Dr Yijun Ruan, Dr Chialin Wei, and Dr Melissa Fullwood).

Detailed patent and invention disclosure listing as of Feb 2020.

Citation Analyses

H-index: 16, Citing articles: 10,900 (excluding self-citations)

Web of Science Citation Report Feb 12 2020.

Information last updated on 12 February 2020.

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