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Publications

For a full publications list, view Dr. Wang's Google Scholar publications list.

2025

Song B, Wang K, Na S, Yao J, Fattah FJ, Martin AL, von Itzstein MS, Yang DM, Liu J, Xue Y, Liang C, Guo Y, Raman I, Zhu C, Dowell JE, Homsi J, Rashdan S, Yang S, Gwin ME, Wu T, Hsiehchen D, Gloria-McCutchen Y, Lu CP, Raj P, Bai XC, Wang J, Conejo-Garcia J, Xie Y, Huang J, Gerber DE, Wang T. Profiling antigen-binding affinity of B cell repertoires in tumors by deep learning predicts immune-checkpoint inhibitor treatment outcomes. Nat Cancer. 2025 Sep;6(9):1570-1584. doi: 10.1038/s43018-025-01001-5. Epub 2025 Jun 27. PMID: 40579590.

2024

Zhu J, Wang Y, Chang WY, Malewska A, Napolitano F, Gahan JC, Unni N, Zhao M, Yuan R, Wu F, Yue L, Guo L, Zhao Z, Chen DZ, Hannan R, Zhang S, Xiao G, Mu P, Hanker AB, Strand D, Arteaga CL, Desai N, Wang X, Xie Y, Wang T. Mapping cellular interactions from spatially resolved transcriptomics data. Nat Methods. 2024 Oct;21(10):1830-1842. doi: 10.1038/s41592-024-02408-1. Epub 2024 Sep 3. PMID: 39227721.

Zhu M, Wang Y, Lu T, Guo J, Li L, Hsieh MH, Gopal P, Han Y, Fujiwara N, Wallace DP, Yu ASL, Fang X, Ransom C, Verschleisser S, Hsiehchen D, Hoshida Y, Singal AG, Yopp A, Wang T, Zhu H. PKD1 mutant clones within cirrhotic livers inhibit steatohepatitis without promoting cancer. Cell Metab. 2024 Aug 6;36(8):1711-1725.e8. doi: 10.1016/j.cmet.2024.05.015. Epub 2024 Jun 19. PMID: 38901424; PMCID: PMC12133308.

Xu Y, Yang Y, Wang Z, Sjöström M, Jiang Y, Tang Y, Cheng S, Deng S, Wang C, Gonzalez J, Johnson NA, Li X, Li X, Metang LA, Mukherji A, Xu Q, Tirado CR, Wainwright G, Yu X, Barnes S, Hofstad M, Chen Y, Zhu H, Hanker AB, Raj GV, Zhu G, He HH, Wang Z, Arteaga CL, Liang H, Feng FY, Wang Y, Wang T, Mu P. ZNF397 Deficiency Triggers TET2-Driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer. Cancer Discov. 2024 Aug 2;14(8):1496-1521. doi: 10.1158/2159-8290.CD-23-0539. PMID: 38591846; PMCID: PMC11285331.

Jiang F, Guo Y, Ma H, Na S, Zhong W, Han Y, Wang T, Huang J. GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity. Brief Bioinform. 2024 May 23;25(4):bbae343. doi: 10.1093/bib/bbae343. PMID: 39007599; PMCID: PMC11247411.

von Itzstein MS, Yang Y, Wang Y, Hsiehchen D, Sheffield TY, Fattah F, Popat V, Ahmed M, Homsi J, Dowell JE, Rashdan S, Lohrey J, Hammers HJ, Hughes RS, Wang T, Xie Y, Gerber DE. Highly variable timing renders immunotherapy efficacy and toxicity impractical biomarkers of one another in clinical practice. Front Immunol. 2024 Apr 16;15:1351739. doi: 10.3389/fimmu.2024.1351739. PMID: 38690281; PMCID: PMC11058939.

Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR. Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs. Nucleic Acids Res. 2024 Feb 28;52(4):1930-1952. doi: 10.1093/nar/gkad1155. PMID: 38109320; PMCID: PMC10899759.

Prakasam G, Mishra A, Christie A, Miyata J, Carrillo D, Tcheuyap VT, Ye H, Do QN, Wang Y, Reig Torras O, Butti R, Zhong H, Gagan J, Jones KB, Carroll TJ, Modrusan Z, Durinck S, Requena-Komuro MC, Williams NS, Pedrosa I, Wang T, Rakheja D, Kapur P, Brugarolas J. Comparative genomics incorporating translocation renal cell carcinoma mouse model reveals molecular mechanisms of tumorigenesis. J Clin Invest. 2024 Feb 22;134(7):e170559. doi: 10.1172/JCI170559. PMID: 38386415; PMCID: PMC10977987.

Rodriguez Tirado C, Wang C, Li X, Deng S, Gonzalez J, Johnson NA, Xu Y, Metang LA, Sundar Rajan M, Yang Y, Yin Y, Hofstad M, Raj GV, Zhang S, Lemoff A, He W, Fan J, Wang Y, Wang T, Mu P. UBE2J1 is the E2 ubiquitin-conjugating enzyme regulating androgen receptor degradation and antiandrogen resistance. Oncogene. 2024 Jan;43(4):265-280. doi: 10.1038/s41388-023-02890-5. Epub 2023 Nov 29. PMID: 38030789; PMCID: PMC10798893.

Zhu Z, Lou G, Teng XL, Wang H, Luo Y, Shi W, Yihunie K, Hao S, DeGolier K, Liao C, Huang H, Zhang Q, Fry T, Wang T, Yao C, Wu T. FOXP1 and KLF2 reciprocally regulate checkpoints of stem-like to effector transition in CAR T cells. Nat Immunol. 2024 Jan;25(1):117-128. doi: 10.1038/s41590-023-01685-w. Epub 2023 Nov 27. PMID: 38012417; PMCID: PMC10841689.

2023

Yang Y, Wang K, Lu Z, Wang T, Wang X. Cytomulate: accurate and efficient simulation of CyTOF data. Genome Biol. 2023 Nov 16;24(1):262. doi: 10.1186/s13059-023-03099-1. PMID: 37974276; PMCID: PMC10652542.

Johnson KC, Johnson ST, Liu J, Chu Y, Arana C, Han Y, Wang T, Corey DR. Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs. RNA. 2023 Aug;29(8):1166-1184. doi: 10.1261/rna.079647.123. Epub 2023 May 11. PMID: 37169394; PMCID: PMC10351893.

Zhang F, Mulvaney O, Salcedo E, Manna S, Zhu JZ, Wang T, Ahn C, Pop LM, Hannan R. Radiation-Induced Innate Neutrophil Response in Tumor Is Mediated by the CXCLs/CXCR2 Axis. Cancers (Basel). 2023 Dec 1;15(23):5686. doi: 10.3390/cancers15235686. PMID: 38067390; PMCID: PMC10705172.

Rong R, Wei Y, Li L, Wang T, Zhu H, Xiao G, Wang Y. Image-based quantification of histological features as a function of spatial location using the Tissue Positioning System. EBioMedicine. 2023 Aug;94:104698. doi: 10.1016/j.ebiom.2023.104698. Epub 2023 Jul 13. PMID: 37453365; PMCID: PMC10365985.

Lin YH, Wei Y, Zeng Q, Wang Y, Pagani CA, Li L, Zhu M, Wang Z, Hsieh MH, Corbitt N, Zhang Y, Sharma T, Wang T, Zhu H. IGFBP2 expressing midlobular hepatocytes preferentially contribute to liver homeostasis and regeneration. Cell Stem Cell. 2023 May 4;30(5):665-676.e4. doi: 10.1016/j.stem.2023.04.007. PMID: 37146585; PMCID: PMC10580294.

Wang Z, Zhu S, Jia Y, Wang Y, Kubota N, Fujiwara N, Gordillo R, Lewis C, Zhu M, Sharma T, Li L, Zeng Q, Lin YH, Hsieh MH, Gopal P, Wang T, Hoare M, Campbell P, Hoshida Y, Zhu H. Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease. Cell. 2023 Apr 27;186(9):1968-1984.e20. doi: 10.1016/j.cell.2023.03.014. Epub 2023 Apr 10. PMID: 37040760; PMCID: PMC10321862.

Wang K, Yang Y, Wu F, Song B, Wang X, Wang T. Comparative analysis of dimension reduction methods for cytometry by time-of-flight data. Nat Commun. 2023 Apr 1;14(1):1836. doi: 10.1038/s41467-023-37478-w. Erratum in: Nat Commun. 2024 Apr 8;15(1):3006. doi: 10.1038/s41467-024-47234-3. PMID: 37005472; PMCID: PMC10067013.

Hannan R, McLaughlin MF, Pop LM, Pedrosa I, Kapur P, Garant A, Ahn C, Christie A, Zhu J, Wang T, Robles L, Durakoglugil D, Woldu S, Margulis V, Gahan J, Brugarolas J, Timmerman R, Cadeddu J. Phase 2 Trial of Stereotactic Ablative Radiotherapy for Patients with Primary Renal Cancer. Eur Urol. 2023 Sep;84(3):275-286. doi: 10.1016/j.eururo.2023.02.016. Epub 2023 Mar 8. PMID: 36898872; PMCID: PMC10440291.

Li X, Wang Y, Deng S, Zhu G, Wang C, Johnson NA, Zhang Z, Tirado CR, Xu Y, Metang LA, Gonzalez J, Mukherji A, Ye J, Yang Y, Peng W, Tang Y, Hofstad M, Xie Z, Yoon H, Chen L, Liu X, Chen S, Zhu H, Strand D, Liang H, Raj G, He HH, Mendell JT, Li B, Wang T, Mu P. Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer. Cancer Cell. 2023 Aug 14;41(8):1427-1449.e12. doi: 10.1016/j.ccell.2023.06.010. Epub 2023 Jul 20. PMID: 37478850; PMCID: PMC10530398.

Frank ML, Lu K, Erdogan C, Han Y, Hu J, Wang T, Heymach JV, Zhang J, Reuben A. T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy. Clin Cancer Res. 2023 Mar 14;29(6):994-1008. doi: 10.1158/1078-0432.CCR-22-2469. PMID: 36413126; PMCID: PMC10011887.

2022

Zhang Z, Chang WY, Wang K, Yang Y, Wang X, Yao C, Wu T, Wang L, Wang T. Interpreting the B-cell receptor repertoire with single-cell gene expression using Benisse. Nat Mach Intell. 2022 Jun;4(6):596-604. doi: 10.1038/s42256-022-00492-6.

Kim Y, Wang T, Xiong D, Wang X, Park S. Multiple instance neural networks based on sparse attention for cancer detection using T-cell receptor sequences. BMC Bioinformatics. 2022 Nov 8;23(1):469. doi: 10.1186/s12859-022-05012-2. PMID: 36348271; PMCID: PMC9644450.

Celen C, Chuang JC, Shen S, Li L, Maggiore G, Jia Y, Luo X, Moore A, Wang Y, Otto JE, Collings CK, Wang Z, Sun X, Nassour I, Park J, Ghaben A, Wang T, Wang SC, Scherer PE, Kadoch C, Zhu H. Arid1a loss potentiates pancreatic β-cell regeneration through activation of EGF signaling. Cell Rep. 2022 Nov 1;41(5):111581. doi: 10.1016/j.celrep.2022.111581. PMID: 36323264.

Lu T, Park S, Han Y, Wang Y, Hubert SM, Futreal PA, Wistuba I, Heymach JV, Reuben A, Zhang J, Wang T. Netie: inferring the evolution of neoantigen-T cell interactions in tumors. Nat Methods. 2022 Nov;19(11):1480-1489. doi: 10.1038/s41592-022-01644-7. Epub 2022 Oct 27. PMID: 36303017; PMCID: PMC10083098.

Deng S, Wang C, Wang Y, Xu Y, Li X, Johnson NA, Mukherji A, Lo UG, Xu L, Gonzalez J, Metang LA, Ye J, Tirado CR, Rodarte K, Zhou Y, Xie Z, Arana C, Annamalai V, Liu X, Vander Griend DJ, Strand D, Hsieh JT, Li B, Raj G, Wang T, Mu P. Ectopic JAK-STAT activation enables the transition to a stem-like and multilineage state conferring AR-targeted therapy resistance. Nat Cancer. 2022 Sep;3(9):1071-1087. doi: 10.1038/s43018-022-00431-9. Epub 2022 Sep 5. Erratum in: Nat Cancer. 2022 Oct;3(10):1271. doi: 10.1038/s43018-022-00458-y. PMID: 36065066; PMCID: PMC9499870.

Wang Y, Song B, Wang S, Chen M, Xie Y, Xiao G, Wang L, Wang T. Sprod for de-noising spatially resolved transcriptomics data based on position and image information. Nat Methods. 2022 Aug;19(8):950-958. doi: 10.1038/s41592-022-01560-w. Epub 2022 Aug 4. PMID: 35927477; PMCID: PMC10229080.

Zhu J, Gouru A, Wu F, Berzofsky JA, Xie Y, Wang T. BepiTBR: T-B reciprocity enhances B cell epitope prediction. iScience. 2022 Jan 12;25(2):103764. doi: 10.1016/j.isci.2022.103764. PMID: 35128358; PMCID: PMC8803616.

2021

Hannan R, Mohamad O, Diaz de Leon A, Manna S, Pop LM, Zhang Z, Mannala S, Christie A, Christley S, Monson N, Ishihara D, Hsu EJ, Ahn C, Kapur P, Chen M, Arriaga Y, Courtney K, Cantarel B, Wakeland EK, Fu YX, Pedrosa I, Cowell L, Wang T, Margulis V, Choy H, Timmerman RD, Brugarolas J. Outcome and Immune Correlates of a Phase II Trial of High-Dose Interleukin-2 and Stereotactic Ablative Radiotherapy for Metastatic Renal Cell Carcinoma. Clin Cancer Res. 2021 Dec 15;27(24):6716-6725. doi: 10.1158/1078-0432.CCR-21-2083. Epub 2021 Sep 22. PMID: 34551906; PMCID: PMC9924935.

Foray AP, Candon S, Hildebrand S, Marquet C, Valette F, Pecquet C, Lemoine S, Langa-Vives F, Dumas M, Hu P, Santamaria P, You S, Lyon S, Scott L, Bu CH, Wang T, Xu D, Moresco EMY, Scazzocchio C, Bach JF, Beutler B, Chatenoud L. De novo germline mutation in the dual specificity phosphatase 10 gene accelerates autoimmune diabetes. Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2112032118. doi: 10.1073/pnas.2112032118. PMID: 34782469; PMCID: PMC8617500.

Kim K, Zhou Q, Christie A, Stevens C, Ma Y, Onabolu O, Chintalapati S, Mckenzie T, Tcheuyap VT, Woolford L, Zhang H, Singla N, Parida PK, Marquez-Palencia M, Pedrosa I, Margulis V, Sagalowsky A, Xie Z, Wang T, Durinck S, Modrusan Z, Seshagiri S, Kapur P, Brugarolas J, Malladi S. Determinants of renal cell carcinoma invasion and metastatic competence. Nat Commun. 2021 Oct 4;12(1):5760. doi: 10.1038/s41467-021-25918-4. PMID: 34608135; PMCID: PMC8490399.

Lu T, Zhang Z, Zhu J, Wang Y, Jiang P, Xiao X, Bernatchez C, Heymach JV, Gibbons DL, Wang J, Xu L, Reuben A, Wang T. Deep learning-based prediction of the T cell receptor-antigen binding specificity. Nat Mach Intell. 2021 Oct;3(10):864-875. doi: 10.1038/s42256-021-00383-2. Epub 2021 Sep 23. PMID: 36003885; PMCID: PMC9396750.

Zhang C, Wang X, Chen M, Wang T. A comparison of hypothesis tests for homogeneity in meta-analysis with focus on rare binary events. Res Synth Methods. 2021 Jul;12(4):408-428. doi: 10.1002/jrsm.1484. Epub 2021 Mar 14. PMID: 34231330.

Udayakumar D, Zhang Z, Xi Y, Dwivedi DK, Fulkerson M, Haldeman S, McKenzie T, Yousuf Q, Joyce A, Hajibeigi A, Notgrass H, de Leon AD, Yuan Q, Lewis MA, Madhuranthakam AJ, Sibley RC, Elias R, Guo J, Christie A, McKay RM, Cadeddu JA, Bagrodia A, Margulis V, Brugarolas J, Wang T, Kapur P, Pedrosa I. Deciphering Intratumoral Molecular Heterogeneity in Clear Cell Renal Cell Carcinoma with a Radiogenomics Platform. Clin Cancer Res. 2021 Sep 1;27(17):4794-4806. doi: 10.1158/1078-0432.CCR-21-0706. Epub 2021 Jul 1. PMID: 34210685; PMCID: PMC8493519.

Lu Q, Liu J, Zhao S, Gomez Castro MF, Laurent-Rolle M, Dong J, Ran X, Damani-Yokota P, Tang H, Karakousi T, Son J, Kaczmarek ME, Zhang Z, Yeung ST, McCune BT, Chen RE, Tang F, Ren X, Chen X, Hsu JCC, Teplova M, Huang B, Deng H, Long Z, Mudianto T, Jin S, Lin P, Du J, Zang R, Su TT, Herrera A, Zhou M, Yan R, Cui J, Zhu J, Zhou Q, Wang T, Ma J, Koralov SB, Zhang Z, Aifantis I, Segal LN, Diamond MS, Khanna KM, Stapleford KA, Cresswell P, Liu Y, Ding S, Xie Q, Wang J. SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through C-type lectin receptors and Tweety family member 2. Immunity. 2021 Jun 8;54(6):1304-1319.e9. doi: 10.1016/j.immuni.2021.05.006. Epub 2021 May 9. PMID: 34048708; PMCID: PMC8106883.

Zhang M, Sheffield T, Zhan X, Li Q, Yang DM, Wang Y, Wang S, Xie Y, Wang T, Xiao G. Spatial molecular profiling: platforms, applications and analysis tools. Brief Bioinform. 2021 May 20;22(3):bbaa145. doi: 10.1093/bib/bbaa145. PMID: 32770205; PMCID: PMC8138878.

Xiong D, Zhang Z, Wang T, Wang X. A comparative study of multiple instance learning methods for cancer detection using T-cell receptor sequences. Comput Struct Biotechnol J. 2021 May 24;19:3255-3268. doi: 10.1016/j.csbj.2021.05.038. PMID: 34141144; PMCID: PMC8192570.

SoRelle JA, Chen Z, Wang J, Yue T, Choi JH, Wang KW, Zhong X, Hildebrand S, Russell J, Scott L, Xu D, Zhan X, Bu CH, Wang T, Choi M, Tang M, Ludwig S, Zhan X, Li X, Moresco EMY, Beutler B. Dominant atopy risk mutations identified by mouse forward genetic analysis. Allergy. 2021 Apr;76(4):1095-1108. doi: 10.1111/all.14564. Epub 2020 Sep 20. PMID: 32810290; PMCID: PMC7889751.

Cai L, Liu H, Huang F, Fujimoto J, Girard L, Chen J, Li Y, Zhang YA, Deb D, Stastny V, Pozo K, Kuo CS, Jia G, Yang C, Zou W, Alomar A, Huffman K, Papari-Zareei M, Yang L, Drapkin B, Akbay EA, Shames DS, Wistuba II, Wang T, Johnson JE, Xiao G, DeBerardinis RJ, Minna JD, Xie Y, Gazdar AF. Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. Commun Biol. 2021 Mar 9;4(1):314. doi: 10.1038/s42003-021-01842-7. PMID: 33750914; PMCID: PMC7943563.

Wei Y, Wang YG, Jia Y, Li L, Yoon J, Zhang S, Wang Z, Zhang Y, Zhu M, Sharma T, Lin YH, Hsieh MH, Albrecht JH, Le PT, Rosen CJ, Wang T, Zhu H. Liver homeostasis is maintained by midlobular zone 2 hepatocytes. Science. 2021 Feb 26;371(6532):eabb1625. doi: 10.1126/science.abb1625. Erratum in: Science. 2021 Sep 3;373(6559):eabl8195. doi: 10.1126/science.abl8195. PMID: 33632817; PMCID: PMC8496420.

Lu C, Guan J, Lu S, Jin Q, Rousseau B, Lu T, Stephens D, Zhang H, Zhu J, Yang M, Ren Z, Liang Y, Liu Z, Han C, Liu L, Cao X, Zhang A, Qiao J, Batten K, Chen M, Castrillon DH, Wang T, Li B, Diaz LA Jr, Li GM, Fu YX. DNA Sensing in Mismatch Repair-Deficient Tumor Cells Is Essential for Anti-tumor Immunity. Cancer Cell. 2021 Jan 11;39(1):96-108.e6. doi: 10.1016/j.ccell.2020.11.006. Epub 2020 Dec 17. PMID: 33338425; PMCID: PMC9477183.

Lu T, Park S, Zhu J, Wang Y, Zhan X, Wang X, Wang L, Zhu H, Wang T. Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data. Cell Rep. 2021 Jan 5;34(1):108589. doi: 10.1016/j.celrep.2020.108589. PMID: 33406427.

Zhang Z, Xiong D, Wang X, Liu H, Wang T. Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics. Nat Methods. 2021 Jan;18(1):92-99. doi: 10.1038/s41592-020-01020-3. Epub 2021 Jan 6. PMID: 33408405; PMCID: PMC7799492.

2020

Reese B, Silwal A, Daugherity E, Daugherity M, Arabi M, Daly P, Paterson Y, Woolford L, Christie A, Elias R, Brugarolas J, Wang T, Karbowniczek M, Markiewski MM. Complement as Prognostic Biomarker and Potential Therapeutic Target in Renal Cell Carcinoma. J Immunol. 2020 Dec 1;205(11):3218-3229. doi: 10.4049/jimmunol.2000511. Epub 2020 Nov 6. PMID: 33158953; PMCID: PMC7703597.

Chung AS, Mettlen M, Ganguly D, Lu T, Wang T, Brekken RA, Hsiehchen D, Zhu H. Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma. Cancer Prev Res (Phila). 2020 Nov;13(11):911-922. doi: 10.1158/1940-6207.CAPR-20-0200. Epub 2020 Aug 24. PMID: 32839204; PMCID: PMC8284815.

Park S, Wang X, Lim J, Xiao G, Lu T, Wang T. Bayesian multiple instance regression for modeling immunogenic neoantigens. Stat Methods Med Res. 2020 Oct;29(10):3032-3047. doi: 10.1177/0962280220914321. Epub 2020 May 13. PMID: 32401701; PMCID: PMC8009201.

Wang Z, Chen K, Jia Y, Chuang JC, Sun X, Lin YH, Celen C, Li L, Huang F, Liu X, Castrillon DH, Wang T, Zhu H. Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes. Nat Cancer. 2020 Sep;1(9):909-922. doi: 10.1038/s43018-020-00109-0. Epub 2020 Sep 7. PMID: 34386776; PMCID: PMC8357309.

Zhu M, Li L, Lu T, Yoo H, Zhu J, Gopal P, Wang SC, Porembka MR, Rich NE, Kagan S, Odewole M, Renteria V, Waljee AK, Wang T, Singal AG, Yopp AC, Zhu H. Uncovering Biological Factors That Regulate Hepatocellular Carcinoma Growth Using Patient-Derived Xenograft Assays. Hepatology. 2020 Sep;72(3):1085-1101. doi: 10.1002/hep.31096. Epub 2020 Sep 2. PMID: 31899548; PMCID: PMC7332388.

Hsiehchen D, Hsieh A, Samstein RM, Lu T, Beg MS, Gerber DE, Wang T, Morris LGT, Zhu H. DNA Repair Gene Mutations as Predictors of Immune Checkpoint Inhibitor Response beyond Tumor Mutation Burden. Cell Rep Med. 2020 Jun 23;1(3):100034. doi: 10.1016/j.xcrm.2020.100034. PMID: 32676589; PMCID: PMC7365618.

Wang S, Rong R, Yang DM, Fujimoto J, Yan S, Cai L, Yang L, Luo D, Behrens C, Parra ER, Yao B, Xu L, Wang T, Zhan X, Wistuba II, Minna J, Xie Y, Xiao G. Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer. Cancer Res. 2020 May 15;80(10):2056-2066. doi: 10.1158/0008-5472.CAN-19-1629. Epub 2020 Jan 8. PMID: 31915129; PMCID: PMC7919065.

Lin YH, Zhang S, Zhu M, Lu T, Chen K, Wen Z, Wang S, Xiao G, Luo D, Jia Y, Li L, MacConmara M, Hoshida Y, Singal AG, Yopp A, Wang T, Zhu H. Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury. Gastroenterology. 2020 May;158(6):1698-1712.e14. doi: 10.1053/j.gastro.2020.01.026. Epub 2020 Jan 20. PMID: 31972235; PMCID: PMC8902703.

Singla N, Xie Z, Zhang Z, Gao M, Yousuf Q, Onabolu O, McKenzie T, Tcheuyap VT, Ma Y, Choi J, McKay R, Christie A, Torras OR, Bowman IA, Margulis V, Pedrosa I, Przybycin C, Wang T, Kapur P, Rini B, Brugarolas J. Pancreatic tropism of metastatic renal cell carcinoma. JCI Insight. 2020 Apr 9;5(7):e134564. doi: 10.1172/jci.insight.134564. PMID: 32271170; PMCID: PMC7205259.

Lu T, Wang S, Xu L, Zhou Q, Singla N, Gao J, Manna S, Pop L, Xie Z, Chen M, Luke JJ, Brugarolas J, Hannan R, Wang T. Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes. Sci Immunol. 2020 Feb 21;5(44):eaaz3199. doi: 10.1126/sciimmunol.aaz3199. PMID: 32086382; PMCID: PMC7239327.

Courtney KD, Ma Y, Diaz de Leon A, Christie A, Xie Z, Woolford L, Singla N, Joyce A, Hill H, Madhuranthakam AJ, Yuan Q, Xi Y, Zhang Y, Chang J, Fatunde O, Arriaga Y, Frankel AE, Kalva S, Zhang S, McKenzie T, Reig Torras O, Figlin RA, Rini BI, McKay RM, Kapur P, Wang T, Pedrosa I, Brugarolas J. HIF-2 Complex Dissociation, Target Inhibition, and Acquired Resistance with PT2385, a First-in-Class HIF-2 Inhibitor, in Patients with Clear Cell Renal Cell Carcinoma. Clin Cancer Res. 2020 Feb 15;26(4):793-803. doi: 10.1158/1078-0432.CCR-19-1459. Epub 2019 Nov 14. PMID: 31727677; PMCID: PMC7024660.

Zhang M, Wang T, Xiao G, Xie Y. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes (Basel). 2020 Jan 3;11(1):54. doi: 10.3390/genes11010054. PMID: 31947823; PMCID: PMC7016857.