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Multi-omic deconvolution and DNA-RNA dynamics in cancer

Montierth MD*, Yan H*, Xie L*, Nemeth K, Pan X, Li R, Ercan C, Yang P, Sinjab A, Zhou T, Peng F, Singh M, Wang L, Kopetz S, Kadara H, Yuan Y, Calin GA, Wang W**. . Under review. bioRxiv [Preprint]. 2025 Nov 24:2025.11.21.689822. doi: 10.1101/2025.11.21.689822.

Dai Y, Pan X, Guo S, Ji S, Cao S, Montierth MD, Jiang Y, Shi L, Shalapour S, Echeverria GV, Yates L, Staaf J, Chang JT, Lim B, Yuan Y, Wang W**. Tumor Microenvironment Transcriptional Activity Enables Robust Stratification of Chemotherapy Response in Triple-Negative Breast Cancer. Accepted, Cell Reports Medicine.

Jiang Y*, Montierth M*, Yu K* , et al., Wang W**. . Under revision. bioRxiv [Preprint]. 2025 Jun 10:2024.07.03.601939. doi: 10.1101/2024.07.03.601939.

Risk prediction with machine learning and Bayesian semi-parametric models

Liu X, Yan H, Shi H, Montellier E, Chi E, Hainaut P, Wang W**. . Under revision, Journal of the American Statistics Association. bioRxiv [Preprint]. 2025 Oct 6:2025.10.06.680732. doi: 10.1101/2025.10.06.680732.
Proceedings of The Inaugural Workshop on Frontiers in Statistical Machine Learning (FSML) travel award

Corredor JL*, Li R*, Dodd-Eaton EB, Woodman-Ross J, Woodson A, Nguyen NH, Peng G, Green S, Gutierrez AM, Arun BK**, Wang W**. . Under revision, American Journal of Human Genetics. medRxiv [Preprint]. 2024 Jul 10:2024.07.09.24310095. doi: 10.1101/2024.07.09.24310095.

Collaboration Papers

Li S et al. PRECISE: A prognostic thyrocyte-derived gene signature for papillary thyroid carcinoma. Submitted.

Duan Y, Guo S, Yan H, Wang W, Mueller P. . Under second review, Bayesian Analysis. bioRxiv [Preprint]. 2025.04.16.649218; doi: 10.1101/2025.04.16.649218.

Multi-omic deconvolution and DNA-RNA dynamics in cancer

Dai Y, Guo S, Pan Y, Castignani C, Montierth MD, Van Loo P**, Wang W**. . Nat Rev Cancer. 2025 Dec 2. doi: 10.1038/s41568-025-00886-9.

Guo S*, Liu X*, Cheng X*, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Lee S, Sood AK, Kopetz S, Shen JP, Weinstein JN, Deangelis MM, Chen R, Wang W**. . Genome Res. 2025 Jan 22;35(1):147-161. doi: 10.1101/gr.278822.123.

Risk prediction with machine learning and Bayesian semi-parametric models

Nguyen NH*, Shin SJ*, Dodd-Eaton EB, Ning J, Wang W**. . Annals of Applied Statistics. 19(4): 3091-3112 (December 2025). doi: 10.1214/25-AOAS2083.

Stats Up AI

Zheng et al. . Harvard Data Science Review. 2025 Apr 30;7(2).

Collaboration Papers

Foutunno C, Fone MN, Mester J, et al. . Genome Medicine. 2025 Oct 22;17(1):128. doi: 10.1186/s13073-025-01536-3.

Bhinder B et al. . Scientific Reports. 2025 Jul 4;15(1):23921. doi: 10.1038/s41598-025-09075-y.

Lin C et al. . Cell Reports. 2025 Jun 24;44(6):115792. doi: 10.1016/j.celrep.2025.115792.

Chowdhury S, Ferri-Borgogno S, Yang P, Wang W, Peng J, Mok S, Wang P. . Briefings in Bioinformatics. 2025 Mar 4;26(2):bbaf085. doi: 10.1093/bib/bbaf085.

Ito I et al. . ESMO Gastrointest Oncol. 2025 Mar;7:100133. doi: 10.1016/j.esmogo.2025.100133.

Duan Y, Guo S, Wang W, Mueller P. . J Am Stat Assoc. 2025;120(550):671-684. doi: 10.1080/01621459.2024.2427936.

Multi-omic deconvolution and DNA-RNA dynamics in cancer

Ji S, Zhu T, Sethia A, Wang W. . Genome Res. 2024 May 15;34(4):633-641. doi: 10.1101/gr.278456.123.

Risk prediction with machine learning and Bayesian semi-parametric models

Nguyen NH, Dodd-Eaton EB, Corredor JL, Woodman-Ross J, Green S, Gutierrez AM, Arun BK, Wang W. . J Clin Oncol. 2024 Apr 3;:JCO2301926. doi: 10.1200/JCO.23.01926.

Nguyen NH, Dodd-Eaton EB, Peng G, Corredor JL, Jiao W, Woodman-Ross J, Arun BK, Wang W**. . JCO Clinical Cancer Informatics. 2024 Feb 12. Volume 8. doi: 10.1200/CCI.23.00167.

Collaboration Papers

Yuan D, Zhang Y, Guo S, Wang W, Gaynanova I. . Preprint.

Yousef M, Yousef A, Chowdury S, Fanaeian M, Knafl M, Peterson J, Zeineddine M, Alfaro K, Zeineddine F, Godstein D, Horstein N, Dasari A, Huey R, Johnson B, Higbie V, Bent A, Kee B, Lee M, Morelli MP, Morris VK, Halperin D, Overman MJ, Parseghian C, Villar E, Wolff R, Raghav KP, White MG, Uppal A, Sun R, Wang W, Kopetz SK, Willis J, Shen JP. . JAMA Oncol. 2024 Nov 1;10(11):1519-1529. doi: 10.1001/jamaoncol.2024.3666.

Wang JR, Zafereo ME, Cabanillas ME, Wu CC, Xu L, Dai Y, Wang W, Lai SY, Henderson Y, Erasmus L, Williams MD, Joshu C, Ray D. . J Clin Endocrinol Metab. 2024 Aug 1:dgae532. doi: 10.1210/clinem/dgae532.

Aparicio AM, Tidwell RSS, Yadav SS, Chen JS, Zhang M, Liu J, Guo S, Pilie PG, Yu Y, Song X, Vundavilli H, Jindal S, Zhu K, Viscuse PV, Lebenthal JM, Hahn AW, Soundararajan R, Corn PG, Zurita AJ, Subudhi SK, Zhang J, Wang W, Huff C, Troncoso P, Allison JP, Sharma P, Logothetis CJ. . Clin Cancer Res. 2024 Apr 29;. doi: 10.1158/1078-0432.CCR-23-3740.

Bahrambeigi V, Lee JJ, Branchi V, Rajapakshe KI, Xu Z, Kui N, Henry JT, Wang K, Stephens BM, Dhebat S, Hurd MW, Sun R, Yang P, Ruppin E, Wang W, Kopetz S, Maitra A, Guerrero PA. . Cancer Res. 2024 Mar 7;. doi: 10.1158/0008-5472.CAN-23-4070.

Rangel R et al. . J Immunother Cancer. 2023 Aug;11(8):e006666. doi: 10.1136/jitc-2023-006666.

Wang JR, Zafereo ME, Wang W, Joshu C, Debashree R. . J Clin Endocrinol Metab. 2023 Dec 21;109(1):e306-e313. doi: 10.1210/clinem/dgad407.

Cermakova K, Tao L, Dejmek M, Sala M, Montierth MD, Chan YS, Patel I, Chambers C, Cabrera ML, Hoffman D, Parchem RJ, Wang W, Nencka R, Barbieri E, Hodges HC. . Nucleic Acids Res. 2024 Jan 11;52(1):4-21. doi: 10.1093/nar/gkad1081.
Selected by NAR as a "breakthrough article" of the journal issue!

Zheng C et al. . Nature Structural & Molecular Biology Nov 2023; 30, 1878¨C1892. doi:10.1038/s41594-023-01117-1.

Zheng C et al. . Science Advances, Aug 4;9(31):eadf3984. doi: 10.1126/sciadv.adf3984. Epub 2023 Aug 4.

Chachad D, Patel LR, Recio CV, Pourebrahim R, Whitley EM, Wang W, Su X, Xu A, Lee DF, Lozano G. . Cancer Research, 2023 May 19:CAN-22-3464. doi: 10.1158/0008-5472.CAN-22-3464.

Multi-omic deconvolution and DNA-RNA dynamics in cancer

Ji S, Montierth M, Wang W**. . Methods Mol Biol. 2022;2493:21-27. doi: 10.1007/978-1-0716-2293-3_2.

Cao S, et al., Wang W**. . Nat Biotechnol. 2022 Nov;40(11):1624-1633. doi: 10.1038/s41587-022-01342-x. Epub 2022 Jun 13.

Collaboration Papers

Wang JR, Montierth M, Li X, Goswami M, Zhao X, Cote G, Wang W, Iyer P, Dadu R, Busaidy NL, Lai SY, Grosss ND, Ferrarotto R, Lu C, Gunn GB, Williams MD, Routbort M, Zafereo ME, Cabanillas ME. . JCO Precis Oncol. 2022 Aug;6:e2100504. doi: 10.1200/PO.21.00504.

Bondaruk J et al., Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. . iScience 2022 Jun 7; 25(7):104551. doi: 10.1016/j.isci.2022.104551. eCollection 2022 Jul 15.

Wang Z, Baladandayuthapani V, Kaseb AO, Amin HM, Hassan MM, Wang W, Morris JS. . J Am Stat Assoc. 2022;117(538):533-546. doi: 10.1080/01621459.2021.2000866. Epub 2022 Jan 5.

Taavitsainen S et al., Wang W, Nykter M, Urbanucci A. . Nat Commun 2021 Sep 6;12(1):5307. doi: 10.1038/s41467-021-25624-1.

Cao L et al. Clinical Proteomic Tumor Analysis Consortium. . Cell 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023.

Morris JS, Hassan MM, Zohner YE, Wang Z, Xiao L, Rashid A, Haque A, Abdel-Wahab R, Mohamded YI, Ballard KL, Wolff RA, George B, Li L, Allen G, Weylandt M, Li D, Wang W, Raghav K, Yao J, Amin HM, Kaseb AO. . 2021 Jun;73(6):2278-2292. doi: 10.1002/hep.31555. Epub 2021 Jun 15.

Dentro S*, Leshchiner I*, Haase K*, Tarabichi M*, Wintersinger J*, Deshwar A*, Yu K*, Rubanova Y*, Mcintyre G*, et al. . Cell. 2021 Apr 15;184(8):2239-2254.e39. doi: 10.1016/j.cell.2021.03.009. Epub 2021 Apr 7.
Wang is a co-last author.
Selected for the MD Anderson Wall of Science and Research Excellence webpage.

Haider H*, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W*, Demichelis F*, Loda M*, Boutros PC*, TCGA Research Network. . JCO Precis Oncol. 2020 Sep 4;4:PO.20.00016. doi: 10.1200/PO.20.00016.

Gao F*, Pan X*, Dodd EB, Vera Recio C, Bojadzieva J, Mai PL, Johnson VE, Zelley K, Kim E. Nichols KE, Garber JE, Savage SA, Strong LC, Wang W**. . Genome Res. 2020 Aug;30(8):1170-1180. doi: 10.1101/gr.249599.119. Epub 2020 Aug 18.

Nikooienejad A, Wang W, Johnson V. . Ann Appl Stat. 2020 Jun;14(2):809-828. doi: 10.1214/20-AOAS1325. Epub 2020 Jun 29.

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. . Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5.

McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R, HipSci Consortium, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. . Nat Methods 2020 Apr;17(4):414-421. doi: 10.1038/s41592-020-0766-3. Epub 2020 Mar 16.

Wu CC, Beird H, Livingston JL, Advani S, Cao S, Reuben A, Ingram D, Ju Z, Wang WL, Leung CH, Zheng Y, Mitra A, Lin H, Roszik J, Wang W, Patel S, Benjamin R, Gordon M, Hwu P, Gorlick R, Lazar A, Daw N, Lewis V, Futreal PA. . Nat Commun 2020 Feb 21;11(1):1008. doi: 10.1038/s41467-020-14646-w.

Salcedo A, et al. . Nat Biotechnol. 2020 Jan;38(1):97-107. doi: 10.1038/s41587-019-0364-z. Epub 2020 Jan 9.

Shin SJ, Dodd E, Peng G, Bojadzieva J, Chen J, Amos C, Mai PL, Savage SA, Ballinger ML, Thomas DM, Yuan Y, Strong LC, Wang W**. . Cancer Res. 2020 Jan 15;80(2):354-360. doi: 10.1158/0008-5472.CAN-19-0728. Epub 2019 Nov 12.

Shin SJ, Dodd EB, Gao F, Bojadzieva J, Chen J, Kong X, Amos C, Ning J, Strong LC, Wang W**. . Cancer Res. 2020 Jan 15;80(2):347-353. doi: 10.1158/0008-5472.CAN-19-0725. Epub 2019 Nov 12.

Gerstung M, et al. PCAWG Evolution and Heterogeneity Working Group. . Nature. 2020 Feb;578(7793):122-128. doi: 10.1038/s41586-019-1907-7. Epub 2020 Feb 6.

Maura F, Agnelli L, Leongamornlert D, Bolli N, Chan J, Dodero A, Carniti C, Heavican T, Pellegrinelli A, Pruneri G, Butler A, Bhosle S, Chiappella A, Rocco AD, Zinzani PL, Zaja F, Piva R, Inghirami G, Wang W, Palomero T, Iqbal J, Neri A, Campbell PJ, Corradini P. . Am J Hematol. 2019 Jun;94(6):628-634. doi: 10.1002/ajh.25450. Epub 2019 Mar 19.

Cao S, Wang Z, Gao F, Chen J, Zhang F, Frigo DE, Efstathiou E, Kopetz S, Wang W**. . bioRxiv [Preprint]. 566075; doi: 10.1101/566075.

Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F; PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjaerde OC, Wedge DC, Van Loo P.  Nature Genetics 2018 Dec;50(12):1630-1633. doi: 10.1038/s41588-018-0258-x.

Shin SJ, Li J, Ning J, Bodjadzieva J, Strong LC, Wang W**. . Biostatistics. 2020 Jul 1;21(3):467-482. doi: 10.1093/biostatistics/kxy066.

Wang Z, Morris JS, Cao S, Ahn J, Liu R, Tyekucheva S, Li B, Lu W, Tang X, Wistuba II, Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang W** . . iScience. 2018 Nov 30;9:451-460. doi: 10.1016/j.isci.2018.10.028.

Shin SJ, Yuan Y**, Strong LC, Bojadzieva J, Wang W**. . J Am Stat Assoc. 2019;114(526):541-552. doi: 10.1080/01621459.2018.1482749.

Li J, Fu C, Speed TP, Wang W**, Symmans WF**. . JCO Precis Oncol. 2018;2018:PO.17.00091. doi: 10.1200/PO.17.00091.
One of the most accessed articles on JCO PO in 2018

Peng G, Bojadzieva J, Ballinger ML, Thomas DM, Strong LC, Wang W**. . Cancer Epidemiol Biomarkers Prev. 2017 Jun;26(6):837-844. doi: 10.1158/1055-9965.EPI-16-0695.

Ahn J, Morita S, Wang W**, Yuan Y**. . Stat Methods Med Res. 2019 Jan;28(1):70-83. doi: 10.1177/0962280217715051.

Fan Y, Xi L, Hughes DST, Zhang J, Zhang J, Futreal PA, Wheeler DA, Wang W**. . Genome Biol. 2016 Aug 24;17(1):178. doi: 10.1186/s13059-016-1029-6.

Nikooienejad A, Wang W**, Johnson VE**. . Bioinformatics. 2016 May 1;32(9):1338-45. doi: 10.1093/bioinformatics/btv764. Epub 2016 Jan 6.

Holik AZ, Law CW, Liu R, Wang Z, Wang W, Ahn J, Asselin-Labat ML, Smyth GK, Ritchie ME. . Nucleic Acids Res. 2017 Mar 17;45(5):e30. doi: 10.1093/nar/gkw1063.

Palculict TB, Ruteshouser EC, Fan Y, Wang W, Strong LC, Huff V. . J Med Genet. 2016 Jun;53(6):385-8. doi: 10.1136/jmedgenet-2015-103311. Epub 2015 Nov 13.

Lefterova MI*, Shen P*, Odegaard JI*, Fung E, Chiang T, Peng G, Davis RW, Wang W, Schrijver I, Scharfe C. . J Mol Diagn. 2016 Mar;18(2):267-82. doi: 10.1016/j.jmoldx.2015.11.005. Epub 2016 Feb 1.

The Cancer Genome Atlas Research Network. . Cell, 2015 Nov 5;163(4):1011-25. doi: 10.1016/j.cell.2015.10.025.

Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC. . Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18.

Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY. . Genome Biology. 2015 Sep 17;16(1):197. doi: 10.1186/s13059-015-0758-2.

2014

Peng G, Fan Y, Wang W**. . PLoS Comput Biol. 2014 Oct 30;10(10):e1003880. doi: 10.1371/journal.pcbi.1003880.

Davis CF et al., The Cancer Genome Atlas Research Network. . Cancer Cell. 2014 Sep 8;26(3):319-330. doi: 10.1016/j.ccr.2014.07.014.

The Cancer Genome Atlas Research Network. . Nature. 2014 Mar 20;507(7492):315-22. doi: 10.1038/nature12965. Epub 2014 Jan 29.

2013

Ahn J, Liu S, Wang W**, Yuan Y**. . Biometrics. 2013 Dec;69(4):914-24. doi: 10.1111/biom.12100. Epub 2013 Nov 6.

Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W** . . Bioinformatics. 2013 Aug 1;29(15):1865-71. doi: 10.1093/bioinformatics/btt301. Epub 2013 May 27.

Shen P*, Wang W* , Chi AK, Fan Y, Davis RW, Scharfe C. . Genome Med. 2013 May 29;5(5):50. doi: 10.1186/gm454.
Highly accessed

Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW, Huff V, Scharfe C, Wang W** . . Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3985-90. doi: 10.1073/pnas.1222158110. Epub 2013 Feb 20.

The Cancer Genome Atlas Research Network. . Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764.

Srivastava S, Wang W, Manyem G, Ordonez C, Baladandayuthapani V. . EURASIP J Bioinform Syst Biol. 2013 Jun 28;2013(1):9. doi: 10.1186/1687-4153-2013-9.

2012

Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C, Wang W** . . Bioinformatics. 2012 Jul 15;28(14):1928-30. doi: 10.1093/bioinformatics/bts286. Epub 2012 May 10.

Hua Y, Gorshkov K, Yang Y, Wang W, Zhang N, Hughes DPM. . Cancer. 2012 Oct 15;118(20):5140-54. doi: 10.1002/cncr.27496. Epub 2012 Mar 13.

Rubio JP, Wilkins EJ, Kostchet K, Cowie TC, O'Hely M, Burfoot R, Wang W, Speed TP, Stankovich J, Horne M. . Parkinsonism Relat Disord. 2012 May;18(4):386-90. doi: 10.1016/j.parkreldis.2011.12.012. Epub 2012 Jan 12.

2011

Shen P*, Wang W*, Krishnakumar S, Chi AK, Palm C, Enns GM, Davis RW, Speed TP, Mindrinos M, Scharfe C. . Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6549-54. doi: 10.1073/pnas.1018981108. Epub 2011 Apr 5.
Listed among Most-Read Articles during Apr 2011

2010

Lin S*, Wang W*, Palm C, Davis RW, Juneau K. . BMC Genomics. 2010 Dec 17;11:712. doi: 10.1186/1471-2164-11-712.

Wang W, Shen P, Thyagarajan S, Lin S, Palm C, Horvath R, Klopstock T, Cutler D, Pique L, Schrijver I, Davis RW, Mindrinos M, Speed TP, Scharfe C. . Nucleic Acids Res. 2011 Jan;39(1):44-58. doi: 10.1093/nar/gkq750. Epub 2010 Sep 15.

Wang W, Niendorf KB, Patel D, Blackford A, Marroni F, Sober AJ, Parmigiani G and Tsao H. . Cancer Res. 2010 Jan 15;70(2):552-9. doi: 10.1158/0008-5472.CAN-09-2653. Epub 2010 Jan 12.

2008

Wang W, Carvalho B, Miller N, Pevsner J, Chakaravarti A and Irizarry RA. . J Comput Biol. 2008 Sep;15(7):857-66. doi: 10.1089/cmb.2007.0148.

2007

Wang W, Chen S, Brune KA, Hruban RH, Parmigiani G and Klein AP. . J Clin Oncol. 2007 Apr 10;25(11):1417-22. doi: 10.1200/JCO.2006.09.2452.

Nicodemus KK, Wang W, Shugart YY. . BMC Proc. 2007;1 Suppl 1(Suppl 1):S58. doi: 10.1186/1753-6561-1-s1-s58. Epub 2007 Dec 18.

2006

Chen S, Wang W, Lee S, Nafa K, Lee J, Romans K, Watson P, Gruber SB, Euhus D, Kinzler KW, Jass J, Gallinger S, Lindor N, Casey G, Ellis N, Giardiello FM, the Colon Cancer Family Registry, Offit K, Parmigiani G. . JAMA. 2006 Sep 27;296(12):1479-87. doi: 10.1001/jama.296.12.1479.

Gonzalez JR, Wang W, Ballana E, Estivill X. . Hum Mutat. 2006 Nov;27(11):1135-42. doi: 10.1002/humu.20390.

2004

Chen S, Wang W, Broman K, Parmigiani G. . Stat Appl Genet Mol Biol. 2004;3:Article21. doi: 10.2202/1544-6115.1063. Epub 2004 Sep 17.