Publications

1. Xianyu Z, Correia C, Ung CY, Zhu S, Billadeau DD, Li H. The Rise of Hypothesis-Driven Artificial Intelligence in Oncology. Cancers 2024, 16(4), 822.
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2. Ung CY, Correia C, Li H, Adams CM, Westendorf JJ, Zhu S. The Multi-Organ Locked-State Model of Chronic Diseases and Systems Pharmacology Opportunities. Drug Discov Today. 2023 Nov 13;29(1):103825.
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3. Meng-Lin K, Ung CY, Zhang C, Weiskittel TM, Wisniewski P, Zhang Z, Tan SH, Yeo KS, Zhu S, Correia C, Li H. SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes. Biomolecules. 2023 May 27;13(6):895.
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4. Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state. J Clin Invest. 2023 May 15; 133 (10).
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5. Weiskittel TM, Cao A, Meng-lin K, Lehmann ZJ, Feng B, Correia C, Zhang C, Wisniewski P, Zhu S, Ung CY, Li H. Network biology inspired machine learning features predict cancer gene targets and reveals target coordinating mechanisms. Pharmaceuticals (Basel). 2023 May 16;16(5):752.
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6. Ung CY, Correia C, Billadeau DD, Zhu S, Li H. Manifold Epigenetics: A conceptual model that guides engineering strategies to improve whole-body regenerative health. 2023 Feb 14;11:1122422.
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7. Ung CY, Levee TM, Zhang C, Correia C, Yeo KS, Li H, Zhu S. Gene utility recapitulates chromosomal aberrancies in advanced stage neuroblastoma. Comput Struct Biotechnol J. 2022 Jun 20;20:3291-3303.
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8. Zhang C, Correia C, Weiskittel T, Tan SH, Meng-Lin K, Yu GT, Yao J, Yeo KS, Zhu S, Ung CY, Li H. A knowledge-based discovery approach couples' artificial neural networks with weight engineering to uncover immune-related processes underpinning clinical traits of breast cancer. Front Immunol. 2022 Jul 14;13:920669.
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9. Dong Z, Yeo KS, Lopez G, Zhang C, Dankert Eggum E, Rokita JL, Ung CY, Levee T, Her ZP, Howe C, Hou X, van Ree J, Li S, He S, Tao T, Fritchie K, Torres-Mora J, Lehman J, Meves A, Razidlo G, Rathi K, Weroha SJ, Look AT, van Deursen J, Li H, Westendorf J, Maris J, Zhu S. GAS7 Deficiency Promotes Metastasis of MYCN-driven Neuroblastoma. Cancer Research. 2021 Jun 1; 81 (11):2995-3007 Epub 2021 Feb 18.
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10. Anderson NM, Qin X, Finan JM, Lam A, Athoe J, Missiaen R, Skuli N, Kennedy A, Saini AS, Tao T, Zhu S, Nissim I, Look AT, Qing G, Simon MC, Feng H. Metabolic Enzyme DLST Promotes Tumor Aggression and Reveals a Vulnerability to OXPHOS Inhibition in High-Risk Neuroblastoma. Cancer Research. 2021 Sep 1; 81 (17):4417-4430.
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11. Li S, Yeo KS, Levee TM, Howe CJ, Her ZP, Zhu S. Zebrafish as a Neuroblastoma Model: Progress Made, Promise for the Future. Cells. 2021 Mar; 10(3): 580.
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12. Cheung BB, Kleynhans A, Mittra R, Kim PY, Holien JK, Nagy Z, Ciampa OC, Seneviratne JA, Mayoh C, Raipuria M, Gadde S, Massudi H, Wong IPL, Tan O, Gong A, Suryano A, Diakiw SM, Liu B, Arndt GM, Liu T, Kumar N, Sangfelt O, Zhu S, Norris MD, Haber M, Carter DR, Parker MW, Marshall GM. A novel combination therapy targeting ubiquitin-specific protease 5 in MYCN-driven neuroblastoma. Oncogene. 2021 Apr;40(13):2367-2381.
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13. Her ZP, Yeo KS, Howe C, Levee T, Zhu S. Zebrafish Model of Neuroblastoma Metastasis. J. Vis. Exp. 2021 Mar 14;(169).
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14. Koach J, Holien JK, Massudi H, Carter DR, Ciampa OC, Herath M, Lim T, Seneviratne JA, Milazzo G, Murray JE, McCarroll JA, Liu B, Mayoh C, Keenan B, Stevenson BW, Gorman MA, Bell JL, Doughty L, Huttelmaier S, Oberthuer A, Fischer M, Gifford AJ, Liu T, Zhang X, Zhu S, Gustafson WC, Haber M, Norris MD, Fletcher JI, Perini G, Parker MW, Cheung BB, Marshall GM. Drugging MYCN oncogenic signalling through the MYCN-PA2G4 binding interface. Cancer Research. 2019 Nov 1;79(21):5652-5667.
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15. Zimmerman MW, Liu Y, He S, Durbin AD, Abraham BJ, Easton J, Shao Y, Xu B, Zhu S, Zhang X, Li Z, Weichert-Leahey N, Young RA, Zhang J, Look AT. c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification. Cancer Discovery. 2018 Mar; 8 (3):320-335.
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16. Dankert E, Look AT, Zhu S. Unraveling Neuroblastoma Pathogenesis with the Zebrafish. Cell Cycle. 2018 Jan 2; 1-2.
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17. Zhu S, Zhang X, Weichert-Leahey N, Dong Z, Zhang C, Lopez G, Tao T, He S, Wood AC, Oldridge D, Ung CY, van Ree JH, Khan A, Salazar BM, Lummertz da Rocha E, Zimmerman MW, Guo F, Cao H, Hou X, Weroha SJ, Perez-Atayde AR, Neuberg DS, Meves A, McNiven MA, van Deursen JM, Li H, Maris JM, Look AT. LMO1 Synergizes with MYCN to Promote Neuroblastoma Initiation and Metastasis. Cancer Cell. 2017 Sep 11;32(3):310-323.e5. Epub 2017 Aug 31.
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18. Zhang X, Dong Z, Zhang C, Ung CY, He S, Tao T, Oliveira AM, Meves A, Ji B, Look AT, Li H, Neel BG, Zhu S. Critical Role for GAB2 in Neuroblastoma Pathogenesis through the Promotion of SHP2/MYCN Cooperation. Cell Reports. 2017 Mar 21;18(12):2932-2942.
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19. Ghanat Bari M, Ung CY, Zhang C, Zhu S, Li H. Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks. Sci Rep. 2017 Aug 1;7(1):6993.
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20. Tao T, Sondalle SB, Shi H, Zhu S, Perez-Atayde AR, Peng J, Baserga SJ, Look AT. The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma. Oncogene. 2017 Jul 6;36(27):3852-3867.
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21. Salazar BM, Balczewski EA, Ung CY, Zhu S. Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. International Journal of Molecular Sciences. 2016 Dec 27; 18 (1).
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22. He S, Mansour MR, Zimmerman MW, Ki DH, Layden HM, Akahane K, Gjini E, de Groh ED, Perez-Atayde AR, Zhu S, Epstein JA, Look AT. Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain. Elife. 2016 Apr 27; 5.
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23. Zhu S, Look AT. Neuroblastoma and Its Zebrafish Model. Advances in Experimental Medicine and Biology. 2016; 916:451-78
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24. Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, Anders L, Tian L, Zhang S, Wei JS, Khan J, Bramlett K, Rahman N, Capasso M, Iolascon A, Gerhard DS, Guidry Auvil JM, Young RA, Hakonarson H, Diskin SJ, Look AT, Maris JM. Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Nature. 2015 Dec 17; 528 (7582):418-21 Epub 2015 Nov 11.
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25. Ung CY, Guo F, Zhang X, Zhu Z, Zhu S. Mosaic zebrafish transgenesis for functional genomic analysis of candidate cooperative genes in tumor pathogenesis. J Vis Exp. 2015 Mar 31; (97).
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26. Zhu S, Lee JS, Guo F, Shin J, Perez-Atayde AR, Kutok JL, Rodig SJ, Neuberg DS, Helman D, Feng H, Stewart RA, Wang W, George RE, Kanki JP, Look AT. Activated ALK collaborates with MYCN in neuroblastoma pathogenesis. Cancer Cell. 2012 Mar 20; 21(3):362-73.
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27. Zhu S, Low BC. Using zebrafish for studying Rho GTPases signaling in vivo. Methods Mol Biol. 2012; 827:321-37.
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28. Gutierrez A, Grebliunaite R, Feng H, Kozakewich E, Zhu S, Guo F, Payne E, Mansour M, Dahlberg SE, Neuberg DS, den Hertog J, Prochownik EV, Testa JR, Harris M, Kanki JP, Look AT. Pten mediates Myc oncogene dependence in a conditional zebrafish model of T cell acute lymphoblastic leukemia. J Exp Med. 2011 Aug 1; 208(8):1595-603. Epub 2011 Jul 4.
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29. Lee JS, Padmanabhan A, Shin J, Zhu S, Guo F, Kanki JP, Epstein JA, Look AT. Oligodendrocyte progenitor cell numbers and migration are regulated by the zebrafish orthologs of the NF1 tumor suppressor gene. Hum Mol Genet. 2010 Dec 1; 19(23):4643-53. Epub 2010 Sep 21.
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30. Stewart RA, Sanda T, Widlund HR, Zhu S, Swanson KD, Hurley AD, Bentires-Alj M, Fisher DE, Kontaridis MI, Look AT, Neel BG. Phosphatase-dependent and -independent functions of Shp2 in neural crest cells underlie LEOPARD syndrome pathogenesis. Developmental Cell 2010 May 18; 18(5):750-62.
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31. Zhu S, Korzh V, Gong Z, Low BC. RhoA prevents apoptosis during zebrafish embryogenesis through activation of Mek/Erk pathway. Oncogene. 2008 Mar 6; 27(11):1580-9. Epub 2007 Sep 17.
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32. Liu L, Zhu S, Gong Z, Low BC. K-ras/PI3K-Akt signaling is essential for zebrafish hematopoiesis and angiogenesis. PLoS One 2008; 3(8):e2850. Epub 2008 Aug 06.
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33. Zhu S, Liu L, Korzh V, Gong Z, Low BC. RhoA acts downstream of Wnt5 and Wnt11 to regulate convergence and extension movements by involving effectors Rho kinase and Diaphanous: use of zebrafish as an in vivo model for GTPase signaling. Cell Signal. 2006 Mar; 18(3):359-72. Epub 2005 Jul 14.
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34. Kong X, Li Z, Gou X, Zhu S, Zhang H, Wang X, Zhang J. A monomeric L-aspartase obtained by in vitro selection. J Biol Chem. 2002 Jul 5; 277(27):24289-93. Epub 2002 Apr 30.
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35. Kong XD, Zhu S, Gou XJ, Wang XP, Zhang HY, Zhang J. A circular RNA-DNA enzyme obtained by in vitro selection. Biochem Biophys Res Commun. 2002 Apr 12;292(4):1111-5.
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36. Kong X, Liu Y, Gou X, Zhu S, Zhang H, Wang X, Zhang J. Directed evolution of alpha-aspartyl dipeptidase from Salmonella typhimurium. Biochem Biophys Res Commun. 2001 Nov 23; 289(1):137-42.
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