Publications

Publications

Manuscripts in preparation – posted on biorxiv (1)

  1. 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/10.1101/2020.04.18.047738v2 *Co-first authors ^Corresponding author. Benny Wang is a recently graduated PhD student from the lab. Lingshi Kong is a recently graduated PhD student from the lab. Deepak Babu is a previous post-doctoral fellow in the lab. Ruchi Choudhary is a current PhD students in the lab.  Melissa Fullwood is corresponding author and last author.

After 2015 (39 manuscripts published, 52 including manuscripts before 2015)

  1. Yeo SJ, Ying C, Fullwood MJ^, Tergaonkar V.^, “Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains”, Trends Genet, 2023 Jan 13;S0168-9525(22)00312-2. doi: 10.1016/j.tig.2022.12.003. ^Co-corresponding author.
  2. Tian SZ, Yin P, Jing K, Yang Y, Xu Y, Huang G, Ning D, Fullwood MJ, Zheng M.” MCI-frcnn: A deep learning method for topological micro-domain boundary detection.” Front Cell Dev Biol. 2022 Nov 30;10:1050769. doi: 10.3389/fcell.2022.1050769. eCollection 2022. Coauthor manuscript.
  3. Tian SZ, Li G, Ning D, Jing K, Xu Y, Yang Y, Fullwood MJ, Yin P, Huang G, Plewczynski D, Zhai J, Dai Z, Chen W, Zheng M. “MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification.” Brief Bioinform. 2022 Nov 19;23(6):bbac380. doi: 10.1093/bib/bbac380. Coauthor manuscript.
  4. Dao FY, Hao LV, Fullwood MJ^, Hao L^, “Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information”. Research (Wash D C). 2022 Oct 29 2022:9780293. doi: 10.34133/2022/9780293. eCollection 2022. ^Co-corresponding author. Fuying was a visiting PhD student in the lab. Melissa is co-corresponding author.
  5. Warrier T, El Farran C, Zeng Y, Ho BSQ, Bao Q, Zheng ZH, Bi X, Ng HH, Ong DST, Chu JJH, Sanyal A, Fullwood MJ, Collins JJ, Li H, Xu J, Loh YH. “SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates”, Nucleic Acids Res. 2022 Jul 1:gkac531. doi: 10.1093/nar/gkac531. Online ahead of print. PMID: 35776115. Coauthor manuscript.
  6. Tang SC*, Vijayakumar U*, Zhang Y*, Fullwood MJ^.,”Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer.” Cancers (Basel). 2022 Jun 10;14(12):2866. doi: 10.3390/cancers14122866. PMID: 35740532 *First author ^Corresponding author. Seng Chuan Tang and Zhang Ying are post-doctoral fellows in the lab. Udhaya Vijayakumar is a current PhD student in the lab. Melissa Fullwood is corresponding author and last author. This is a review paper.
  7. Akıncılar SC, Chua JYH, Ng QF, Chan CHT, Eslami-S Z, Chen K, Low JL, Arumugam S, Aswad L, Chua C, Tan IB, DasGupta R, Fullwood MJ, Tergaonkar V. “Identification of mechanism of cancer-cell-specific reactivation of hTERT offers therapeutic opportunities for blocking telomerase specifically in human colorectal cancer.” Nucleic Acids Res. 2022 Jun 14:gkac479. doi: 10.1093/nar/gkac479. Online ahead of print. PMID: 35697349
  8. Chan JJ, Zhang B, Chew XH, Salhi A, Kwok ZH, Lim CY, Desi N, Subramaniam N, Siemens A, Kinanti T, Ong S, Sanchez-Mejias A, Ly PT, An O, Sundar R, Fan X, Wang S, Siew BE, Lee KC, Chong CS, Lieske B, Cheong WK, Goh Y, Fam WN, Ooi MG, Koh BTH, Iyer SG, Ling WH, Chen J, Yoong BK, Chanwat R, Bonney GK, Goh BKP, Zhai W, Fullwood MJ, Wang W, Tan KK, Chng WJ, Dan YY, Pitt JJ, Roca X, Guccione E, Vardy LA, Chen L, Gao X, Chow PKH, Yang H, Tay Y. “Pan-cancer pervasive upregulation of 3′ UTR splicing drives tumourigenesis. “, Nat Cell Biol. 2022 Jun;24(6):928-939. doi: 10.1038/s41556-022-00913-z. Epub 2022 May 26. PMID: 35618746
  9. Nargund AM, Xu C, Mandoli A, Okabe A, Chen GB, Huang KK, Sheng T, Yao X, Teo JMN, Sundar R, Kok YJ, See YX, Xing M, Li Z, Yong CH, Anand A, A I ZF, Poon LF, Ng MSW, Koh JYP, Ooi WF, Tay ST, Ong X, Tan ALK, Grabsch HI, Fullwood MJ, Teh TB, Bi X, Kaneda A, Li S, Tan P.” Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer”, Cancer Res. 2022 May 18:canres.CAN-21-2072-E.2021. doi: 10.1158/0008-5472.CAN-21-2072. Online ahead of print. PMID: 35583999
  10. Zhang Y*, See YX*, Tergaonkar V, Fullwood MJ^., “Long-Distance Repression by Human Silencers: Chromatin Interactions and Phase Separation in Silencers. “, Cells. 2022 May 5;11(9):1560. doi: 10.3390/cells11091560. PMID: 35563864. *First author ^Corresponding author. Zhang Ying is a post-doctoral fellow in the lab. Yi Xiang See was a previous PhD student who has now graduated.  Melissa Fullwood is corresponding author and last author. This is a review paper.
  11. Teoh PJ, An O, Chung TH, Vaiyapuri T, Raju A, Hoppe MM, Toh SHM, Wang W, Chan MC, Fullwood MJ, Jeyasekharan AD, Tergaonkar V, Chen L, Yang H, Chng WJ., ”
    p53-NEIL1 co-abnormalities induce genomic instability and promote synthetic lethality with Chk1 inhibition in multiple myeloma having concomitant 17p13(del) and 1q21(gain)”, Oncogene. 2022 Apr;41(14):2106-2121. doi: 10.1038/s41388-022-02227-8. Epub 2022 Feb 21. PMID: 35190641
  12. See, Y.X.*, Chen K.J., and Fullwood, M.J.^ “MYC overexpression leads to increased chromatin interactions at superenhancers and c-MYC binding sites”, Genome Research, 2022 Apr;32(4):629-642. doi: 10.1101/gr.276313.121. Epub 2022 Feb 3.. Link to main text *First author ^Corresponding author. Yi Xiang See and Chen Kaijing are current PhD students in the lab. Melissa Fullwood is corresponding author and last author
  13. Jia Y, Zhou J, Tan TK, Chung TH, Chen Y, Chooi JY, Sanda T, Fullwood MJ, Xiong S, Toh SHM, Balan K, Wong RWJ, Lim JSL, Zhang E, Cai Z, Shen P, Chng WJ., “Super Enhancer-Mediated Upregulation of HJURP Promotes Growth and Survival of t(4;14)-Positive Multiple Myeloma”, Cancer Res. 2022 Feb 1;82(3):406-418. doi: 10.1158/0008-5472.CAN-21-0921. Epub 2021 Dec 10. PMID: 34893510.
  14. Animesh S.*, Choudhary R.*, Wong J. H. B., Koh C.T.J., Ng X. Y., Tay J.K.X., Chong W.Q., Jian H., Chen L., Goh B.C., Fullwood, M.J.^, “Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach”, Frontiers in Genetics, 2021 Sep 3;12:673530. doi: 10.3389/fgene.2021.673530. eCollection 2021. PMID: 34539729 . Link to main text *Co-first authors ^Corresponding author. Sambhavi Animesh is a current post-doctoral fellow in the lab. Ruchi Choudhary is a current PhD student in the lab. Melissa Fullwood is corresponding author and last author.
  15. Cao F.*, Zhang Y*., Cai Y.*, Animesh S., Zhang Y., Akincilar S., Loh Y. P., Chng W.J., Tergaonkar V., Kwoh C.K., Fullwood M.J.^, “Chromatin interaction Neural Network (ChINN): A machine learning-based method for predicting chromatin interactions from DNA sequences”, Genome Biology, 2021. Link to free main text. (An earlier version is also available on biorxiv at https://www.biorxiv.org/content/10.1101/2020.12.30.424817v2). *Co-first authors ^Corresponding author. Cao Fan was a PhD student, then postdoctoral fellow in the lab, Zhang Yu is a PhD student from a collaborating lab, the lab of Prof Kwoh C.K., and Cai Yichao is a post-doctoral fellow in the lab. Melissa Fullwood is corresponding author and last author.
  16. Zhang, Y.*, Cai, Y.*, Roca, X., Kwoh C.K.^, Fullwood M.J.^, “Chromatin loop anchors predict transcript and exon usage”, Briefings in Bioinformatics, 2021, Jul 14; bbab254, https://doi.org/10.1093/bib/bbab254. Last author and co-corresponding manuscript. *Co-first authors ^Co-corresponding authors. Cai Yichao was a co-supervised PhD student in the lab, and is now a post-doctoral fellow in the lab. Melissa Fullwood is co-corresponding author and last author. Link
  17. Li LY, Yang Q, Jiang YY, Yang W, Jiang Y, Li X, Hazawa M, Zhou B, Huang GW, Xu XE, Gery S, Zhang Y, Ding LW, Ho AS, Zumsteg ZS, Wang MR, Fullwood MJ, Freedland SJ, Meltzer SJ, Xu LY, Li EM, Koeffler HP, Lin DC., “Interplay and cooperation between SREBF1 and master transcription factors regulate lipid metabolism and tumor-promoting pathways in squamous cancer”, Nat Commun, 2021, Jul 16;12(1):4362. doi: 10.1038/s41467-021-24656-x. PMID: 34272396.
  18. 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”, Nat Commun, 2021, Jan 29;12(1):719. doi: 10.1038/s41467-021-20940-y. PMID: 33514712. Last author and co-corresponding manuscript. *Co-first authors ^Co-corresponding authors. Cai 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. Link: https://www.nature.com/articles/s41467-021-20940-y
  19. Zhou, Q., Yu, M., Tirado-Magallanes, R., Li, B., Kong, L., Guo, M., Tan, Z.H., Lee, S., Chai, L., Numata, A., Benoukraf, T., Fullwood, M.J., Osato, M., Ren, B., Tenen, D.G., “ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine haematopoietic stem and progenitor cell function”, Nat Commun., 2021, Jan 4;12(1):43. doi: 10.1038/s41467-020-20282-1. PMID: 33397967
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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. 
  36. 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.
  37. 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).
  38. 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.
  39. 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: 20, Sum of times cited: 15,775.

Web of Knowledge Citation Report 6 Sept 2021

Information last updated on 8 Jan 2021.

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