Publications
For a full 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. . 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. . 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. . 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, Sj?str?m 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. 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.
Yang Y, Wang K, Lu Z, Wang T, Wang X. . Genome Biol. 2023 Nov 16;24(1):262. doi: 10.1186/s13059-023-03099-1. PMID: 37974276; PMCID: PMC10652542.
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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . 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. . Genes (Basel). 2020 Jan 3;11(1):54. doi: 10.3390/genes11010054. PMID: 31947823; PMCID: PMC7016857.