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Selected Publications

  1. Huang B, Fong LW, Chaudhari R, Zhang S*. Development and Evaluation of a Novel Java-based Deep Neural Network Method to Predict Drug Responses. Front. Artif. Intell. 2023 Mar 23; 6:1069353. doi: 10.3389/frai.2023.1069353.

  2. Huang B, Zhang E, Chaudhari R, Gimperlein H. Sequence-based Optimized Chaos Game Representation and Deep Learning for Peptide/Protein Classification. bioRxiv. 2022.09.10.507145; doi: https://doi.org/10.1101/2022.09.10.507145.

  3. Zhang L, Qu J, Qi Y, Duan Y, Huang YW, Zhou Z, Li P, Yao J, Huang B, Zhang S, Yu D. EZH2 engages TGFβ signaling to promote breast cancer bone metastasis via integrin β1-FAK activation. Nat Commun. 2022 May 10;13(1):2543. doi: 10.1038/s41467-022-30105-0.

  4. Fong LWR, Lee J, Lin HK, Ueno NT, Zhang S*. A gene signature consisting of ubiquitin ligases and deubiquitinating enzymes of SKP2 is associated with clinical outcome in breast cancer. Sci Rep. 2022 Feb 15;12(1):2478. doi: 10.1038/s41598-022-06451-w.

  5. Li Y, Tan Z, Zhang Y, Zhang Z, Hu Q, Liang K, Jun Y, Ye Y, Li YC, Li C, Liao L, Xu J, Xing Z, Pan Y, Chatterjee SS, Nguyen TK, Hsiao H, Egranov SD, Putluri N, Coarfa C, Hawke DH, Gunaratne PH, Tsai KL, Han L, Hung MC, Calin GA, Namour F, Guéant JL, Muntau AC, Blau N, Sutton VR, Schiff M, Feillet F*, Zhang S*, Lin C*, Yang L*. A noncoding RNA modulator potentiates phenylalanine metabolism in mice. Science. 2021 Aug 6;373(6555):662-673. doi: 10.1126/science.aba4991.

  6. Amero P, Lokesh GLR, Chaudhari RR, Cardenas-Zuniga R, Schubert T, Attia YM, Montalvo-Gonzalez E, Elsayed AM, Ivan C, Wang Z, Cristini V, Franciscis V, Zhang S, Volk DE, Mitra R, Rodriguez-Aguayo C, Sood AK, Lopez-Berestein G. Conversion of RNA Aptamer into Modified DNA Aptamers Provides for Prolonged Stability and Enhanced Antitumor Activity. J Am Chem Soc. 2021 May 26;143(20):7655-7670. doi: 10.1021/jacs.9b10460. Epub 2021 May 14.

  7. Seda V, Vojackova E, Ondrisova L, Kostalova L, Sharma S, Loja T, Pavlasova GM, Zicha D, Peskova MK, Krivanek J, Liskova K, Kren L, Benes V, Litzmanova KM, Borsky M, Oppelt J, Verner J, Pospisilova S, Brychtova Y, Panovska A, Tan Z, Zhang S, Doubek M, Cerna KA, Mayer J, Mraz M. FoxO1-GAB1 Axis Regulates Homing Capacity and Tonic AKT Activity in Chronic Lymphocytic Leukemia. Blood. 2021 Sep 2;138(9):758-772. doi: 10.1182/blood.2020008101.

  8. Chaudhari R, Fong LW, Tan Z, Huang B, Zhang S*. An Up-To-Date Overview of Computational Polypharmacology in Modern Drug Discovery. Expert Opin Drug Discov. 2020 May 26;1-20. doi: 10.1080/17460441.2020.1767063.

  9. Indarte M, Puentes R, Maruggi M, Ihle NT, Grandjean G, Scott M, Ahmed Z, Meuillet EJ, Zhang S, Lemos R Jr, Du-Cuny L, Layng FIAL, Correa RG, Bankston LA, Liddington RC, Kirkpatrick L, Powis G. An Inhibitor of the Pleckstrin Homology Domain of CNK1 Selectively Blocks the Growth of Mutant KRAS Cells and Tumors. Cancer Res. 2019 Oct 15;79(20):5457.

  10. Yao W, Rose JL, Wang W, Seth S, Jiang H, Taguchi A, Liu J, Yan L, Kapoor A, Hou P, Chen Z, Wang Q, Nezi L, Xu Z, Yao J, Hu B, Pettazzoni PF, Ho IL, Feng N, Ramamoorthy V, Jiang S, Deng P, Ma GJ, Den P, Tan Z, Zhang S, Wang H, Wang YA, Deem AK, Fleming JB, Carugo A, Heffernan TP, Maitra A, Viale A, Ying H, Hanash S, DePinho RA, Draetta GF. Syndecan 1 is a critical mediator of macropinocytosis in pancreatic cancer. Nature. 2019 Apr;568(7752):410-414.

  11. Li N, Wang Y, Neri S, Zhen Y, Fong LWR, Qiao Y, Li X, Chen Z, Stephan C, Deng W, Ye R, Jiang W, Zhang S, Yu Y, Hung MC, Chen J, Lin SH. Tankyrase disrupts metabolic homeostasis and promotes tumorigenesis by inhibiting LKB1-AMPK signalling. Nat Commun. 2019 Sep 25;10(1):4363.

  12. Huang B, Tan Z, Bohinc K, Zhang S*. Interaction between nanoparticles and charged phospholipid membranes. Phys Chem Chem Phys. 2018 Nov 28;20(46):29249-29263.

  13. Han F, Li CF, Cai Z, Zhang X, Jin G, Zhang WN, Xu C, Wang CY, Morrow J, Zhang S, Xu D, Wang G, Lin HK. The critical role of AMPK in driving Akt activation under stress, tumorigenesis and drug resistance. Nat Commun. 2018 Nov 9;9(1):4728.

  14. Robichaux JP, Elamin YY, Tan Z, Carter BW, Zhang S, Liu S, Li S, Chen T, Poteete A, Estrada-Bernal A, Le AT, Truini A, Nilsson MB, Sun H, Roarty E, Goldberg SB, Brahmer JR, Altan M, Lu C, Papadimitrakopoulou V, Politi K, Doebele RC, Wong KK, Heymach JV. Mechanisms and clinical activity of an EGFR and HER2 exon 20-selective kinase inhibitor in non-small cell lung cancer. Nat Med. 2018 May;24(5):638-646.

  15. Vannini I, Wise PM, Challagundla KB, Plousiou M, Raffini M, Bandini E, Fanini F, Paliaga G, Crawford M, Ferracin M, Ivan C, Fabris L, Davuluri RV, Guo Z, Cortez MA, Zhang X, Chen L, Zhang S, Fernandez-Cymering C, Han L, Carloni S, Salvi S, Ling H, Murtadha M, Neviani P, Gitlitz BJ, Laird-Offringa IA, Nana-Sinkam P, Negrini M, Liang H, Amadori D, Cimmino A, Calin GA, Fabbri M. Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs. Nat Commun. 2017 Nov 27;8(1):1801.

  16. Li C, Wang S, Xing Z, Lin A, Liang K, Song J, Hu Q, Yao J, Chen Z, Park PK, Hawke DH, Zhou J, Zhou Y, Zhang S, Liang H, Hung MC, Gallick GE, Han L, Lin C, Yang L. A ROR1-HER3-lncRNA signalling axis modulates the Hippo-YAP pathway to regulate bone metastasis. Nat Cell Biol. 2017 Feb;19(2):106-119.

  17. Tan Z, Chen L, Zhang S*. Comprehensive Modeling and Discovery of Mebendazole as a Novel TRAF2- and NCK-interacting Kinase Inhibitor. Sci Rep. 2016 Sep 21;6:33534. PMCID:27650168.

  18. Tan Z, Zhang S*. Editorial: The Elephant in the Room: Targeting Ras for Therapeutic Development. Mini Rev Med Chem. 2016;16(5):343-4. PMCID:26873479.

  19. Morrow JK, Lin HK, Sun SC, Zhang S*. Targeting ubiquitination for cancer therapies. Future Med Chem. 2015;7(17):2333-50. PMCID:26630263.

  20. Chan CH, Morrow JK, Li CF, Gao Y, Jin G, Moten A, Stagg LJ, Ladbury JE, Cai Z, Xu D, Logothetis CJ, Hung MC, Zhang S*, Lin HK*. Pharmacological inactivation of Skp2 SCF ubiquitin ligase restricts cancer stem cell traits and cancer progression. Cell. 2013 Aug 1;154(3):556-68.

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