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- Huang B, Fong LWR, Chaudhari R, Zhang S*. Development and evaluation of a java-based deep neural network method for drug response predictions. Front Artif Intell. 2023 Mar 23;6:1069353. DOI: 10.3389/frai.2023.1069353.
- 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: 10.1101/2022.09.10.507145.
- Chang AT, Chen L, Song L, Zhang S*, Nikonowicz EP*. 2-Amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA). Biochemistry. 2020 Sep 8;59(35):3225-3234. DOI: 10.1021/acs.biochem.0c00369.
- 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.
2. Develop ubiquitination-based cancer therapies
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- 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. PMCID: PMC8847659.
- 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. PMCID: PMC6226490.
- Morrow JK, Lin HK, Sun SC, Zhang S*. Targeting ubiquitination for cancer therapies. Future Med Chem. 2015, 7(17):2333-50. PMCID: PMC4976843.
- 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, 154(3):556-68. PMCID: PMC3845452.
3. Target traditionally viewed "undruggable" pathways
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- 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. PMCID: PMC9091212.
- 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, et al. Syndecan1 is a critical mediator of macropinocytosis in pancreatic cancer. Nature. 2019. 568(7752):410-414. PMCID: PMC6661074.
- 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, et al. Tankyrase disrupts metabolic homeostasis and promotes tumorigenesis by inhibiting LKB1-AMPK signalling. Nat Commun. 2019, 10(1):4363. PMCID: PMC6761205.
- Chen L, Moses SA, Du-Cuny L, Mathew S, Dumas S, Song Z, Meuillet EJ, Zhang S*. Identification and evaluation of potent small molecule inhibitors targeting GAB1 pleckstrin homology domain. PLoS Comput. Biol. 2015 Jan 8;11(1):e1004021. PMCID: PMC4287437.
4. Conduct drug repurposing and predictive ADMET modeling
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- 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/HER2 exon 20-selective kinase inhibitor in non-small cell lung cancer. Nat Med. 2018. May;24(5):638-646. PMCID: PMC5964608.
- Alla SR, Tan Z, Zhang S*. Curation and Analysis of Multi-targeting Agents for Polypharmacological Modeling. J. Chem. Inf. Model. 2014, 54(9): 2536-43. PMCID: PMC4170814.
- Wu B, Dong D, Hu M, Zhang S*. Quantitative Prediction of Glucuronidation in Humans Using the In Vitro-In Vivo Extrapolation Approach. Curr Top Med Chem. 2013, 13(11):1343-52. DOI: 10.2174/15680266113139990038.
- Du-Cuny L, Chen L, Zhang S*. A Critical Assessment of Combined Ligand/Structure-based Approaches to hERG Channel Blocker Modeling. J Chem Inf Model. 2011, 51(11):2948-2960. PMCID: PMC3894065.
5. Develop novel technologies for non-coding RNA studies
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- 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.
- 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, et al. 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.
- 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, et al. A ROR1-HER3-LncRNA signaling axis modulates the Hippo-YAP pathway to regulate bone metastasis. Nat. Cell Biol. 2017,19(2):106-119. PMCID: PMC5336186.
- Chen L, Calin GA, Zhang S*. Novel insights of structure-based modeling for RNA-targeted drug discovery. J Chem Inf Model. 2012 Oct 22;52(10):2741-53. doi: 10.1021/ci300320t. Epub 2012 Sep 21. PMCID: PMC3869234.