Selected Publications After 2010

  • Yao S, Cao B, Li T, Kalos D, Yuan Y, Wang X. Prediction-oriented prognostic biomarker discovery with survival machine learning methods. NAR Genom Bioinform. 2023 Jun.5(2):lqad055. Pubmedid: 37332657. Pmcid: PMC10273194.
  • Cao B, Patel KB, Li T, Yao S, Chung CH, Wang X. A subnetwork-based framework for prioritizing and evaluating prognostic gene modules from cancer transcriptome data. iScience. 2023 Feb.26(2):105915. Pubmedid: 36685033. Pmcid: PMC9845797.
  • Byrd DA, Fan W, Greathouse KL, Wu MC, Xie H, Wang X. The intratumor microbiome is associated with microsatellite instability. J Natl Cancer Inst. 2023 Aug.115(8):989-993. Pubmedid: 37192013. Pmcid: PMC10407713.
  • Patel KB, Padhya TA, Huang J, Hernandez-Prera JC, Li T, Chung CH, Wang L, Wang X. Plasma cell-free DNA methylome profiling in pre- and post-surgery oral cavity squamous cell carcinoma. Mol Carcinogen. 2023 Apr.62(4):493-502. Pubmedid: 36636912. Pmcid: PMC10023468. (Featured on the cover)
  • Rose KM, Huelster HL, Meeks JJ, Faltas BM, Sonpavde GP, Lerner SP, Ross JS, Spiess PE, Grass GD, Jain RK, Kamat AM, Vosoughi A, Wang L, Wang X, Li R. Circulating and urinary tumour DNA in urothelial carcinoma - upper tract, lower tract and metastatic disease. Nat Rev Urol. 2023 Jul.20(7):406-419. Pubmedid: 36977797.
  • Patel KB, Turner K, Alishahi Tabriz A, Gonzalez BD, Oswald LB, Nguyen OT, Hong YR, Jim HSL, Nichols AC, Wang X, Robinson E, Naso C, Spiess PE. Estimated Indirect Cost Savings of Using Telehealth Among Nonelderly Patients With Cancer. JAMA Netw Open. 2023 Jan.6(1):e2250211. Pubmedid: 36626174. Pmcid: PMC9856804.
  • Patel KB, Gonzalez BD, Turner K, Alishahi Tabriz A, Rollison DE, Robinson E, Naso C, Wang X, Spiess PE. Estimated Carbon Emissions Savings With Shifts From In-Person Visits to Telemedicine for Patients With Cancer. JAMA Netw Open. 2023 Jan.6(1):e2253788. Pubmedid: 36719682. Pmcid: PMC9890284.
  • Liu J, Wang X, Sahin IH, Imanirad I, Felder SI, Kim RD, Xie H. Tumor Response-speed Heterogeneity as a Novel Prognostic Factor in Patients With Metastatic Colorectal Cancer. Am J Clin Oncol. 2023 Feb.46(2):50-57. Pubmedid: 36606664.
  • Wang X, Fridley BL. Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications. Methods Mol Biol. 2023 Mar.2629:1-9. Pubmedid: 36929070.
  • Lester DK, Burton C, Gardner A, Innamarato P, Kodumudi K, Liu Q, Adhikari E, Ming Q, Williamson DB, Frederick DT, Sharova T, White MG, Markowitz J, Cao B, Nguyen J, Johnson J, Beatty M, Mockabee-Macias A, Mercurio M, Watson G, Chen PL, McCarthy S, MoranSegura C, Messina J, Thomas KL, Darville L, Izumi V, Koomen JM, Pilon-Thomas SA, Ruffell B, Luca VC, Haltiwanger RS, Wang X, Wargo JA, Boland GM, Lau EK. Fucosylation of HLA-DRB1 regulates CD4+ T cell-mediated anti-melanoma immunity and enhances immunotherapy efficacy. Nat Cancer. 2023 Feb.4(2):222-239. Pubmedid: 36690875. Pmcid: PMC9970875. (News) 
  • Yu X, Cen L, Chen YA, Markowitz J, Shaw TI, Tsai KY, Conejo-Garcia JR, Wang X. Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures. Cancer Res. 2022 May.82(9):1724-1735. Pubmedid: 35176128. Pmcid: PMC9064917. (Featured on the cover)
  • Wang X, Muzaffar J, Kirtane K, Song F, Johnson M, Schell MJ, Li J, Yoder SJ, Conejo-Garcia JR, Guevara-Patino JA, Bonomi M, Bhateja P, Rocco JW, Steuer CE, Saba NF, Chung CH. T cell repertoire in peripheral blood as a potential biomarker for predicting response to concurrent cetuximab and nivolumab in head and neck squamous cell carcinoma. J Immunother Cancer. 2022 Jun.10(6). Pubmedid: 35676062. Pmcid: PMC9185557.
  • Li K, Yao S, Zhang Z, Cao B, Wilson CM, Kalos D, Kuan PF, Zhu R, Wang X. Efficient gradient boosting for prognostic biomarker discovery. Bioinformatics. 2022 Jan. Pubmedid: 34978570.
  • Boucher JC, Li G, Kotani H, Cabral ML, Morrissey D, Lee SB, Spitler K, Beatty NJ, Cervantes EV, Shrestha B, Yu B, Kazi A, Wang X, Sebti SM, Davila ML. CD28 Costimulatory Domain-Targeted Mutations Enhance Chimeric Antigen Receptor T-cell Function. Cancer Immunol Res. 2021 Jan.9(1):62-74. Pubmedid: 33188139. Pmcid: PMC7864379.
  • Zhao X, Wang MY, Jiang H, Lwin T, Park PM, Gao J, Meads MB, Ren Y, Li T, Sun J, Fahmi NA, Singh S, Sehgal L, Wang X, Silva AS, Sotomayor EM, Shain KH, Cleveland JL, Wang M, Zhang W, Qi J, Shah BD, Tao J. Transcriptional programming drives Ibrutinib-resistance evolution in mantle cell lymphoma. Cell Rep. 2021 Mar.34(11):108870. Pubmedid: 33730585. Pmcid: PMC8057695.
  • Wilson CM, Li K, Sun Q, Kuan PF, Wang X. Fenchel duality of Cox partial likelihood with an application in survival kernel learning. Artif Intell Med. 2021 Jun.116:102077. Pubmedid: 34020756. Pmcid: PMC8159024.
  • Valderrabano P, Wang X, McIver B. Concerns About Methodology in Study of Thyroid Nodule Gene Expression Classifier-Reply. JAMA Otolaryngol Head Neck Surg. 2020 Mar.146(3):313-314. Pubmedid: 31917407.
  • Valderrabano P, Hallanger-Johnson JE, Thapa R, Wang X, McIver B. Comparison of Postmarketing Findings vs the Initial Clinical Validation Findings of a Thyroid Nodule Gene Expression Classifier: A Systematic Review and Meta-analysis. JAMA Otolaryngol Head Neck Surg. 2019 Sep.145(9):783-792. Pubmedid: 31318389. Pmcid: PMC6647006.
  • Wang X, Yu X, Krauthammer M, Hugo W, Duan C, Kanetsky PA, Teer JK, Thompson ZJ, Kalos D, Tsai KY, Smalley KSM, Sondak VK, Chen YA, Conejo-Garcia JR. The Association of MUC16 Mutation with Tumor Mutation Burden and Its Prognostic Implications in Cutaneous Melanoma. Cancer Epidemiol Biomarkers Prev. 2020 Sep.29(9):1792-1799. Pubmedid: 32611582. Pmcid: PMC7483810.
  • Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, Koomen JM, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gray NS, Cleveland JL, Qi J, Tao J. BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models. Cancer Cell. 2019 May;35(5):752-766.e9. Pubmedid: 31085176.
  • Li Q, Yu X, Chaudhary R, Slebos RJC, Chung CH, Wang X. lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA. BMC Genomics. 2019 Jul;20(1):539. Pubmedid: 31266446. Pmcid: PMC6604377.
  • Saglam O, Zhou J, Wang X, Conejo-Garcia JR. PD-L1 Expression Correlates With Young Age and CD8+ TIL Density in Poorly Differentiated Cervical Squamous Cell Carcinoma. Int J Gynecol Pathol. 2019 Jul. Pubmedid: 31274701.
  • Valderrabano P, Hallanger-Johnson JE, Thapa R, Wang X, McIver B. Comparison of Postmarketing Findings vs the Initial Clinical Validation Findings of a Thyroid Nodule Gene Expression Classifier: A Systematic Review and Meta-analysis. JAMA Otolaryngol Head Neck Surg. 2019 Jul. Pubmedid: 31318389. Pmcid: PMC6647006.
  • Yu X, Chen YA, Conejo-Garcia JR, Chung CH, Wang X. Estimation of immune cell content in tumor using single-cell RNA-seq reference data. BMC Cancer. 2019 Jul;19(1):715. Pubmedid: 31324168. Pmcid: PMC6642583.
  • Li E, Zhang Y, Tian X, Wang X, Gathungu G, Wolber A, Shiekh SS, Sartor RB, Davidson NO, Ciorba MA, Zhu W, Nelson LM, Robertson CE, Frank DN. Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome. PLoS One. 2019 Feb;14(2):e0213108. Pubmedid: 30818349. Pmcid: PMC6395037.
  • Wang X, Chen H, Zhang NR. DNA copy number profiling using single-cell sequencing. Brief Bioinform. 2018 Sep;19(5):731-736. Pubmedid: 28159966. Pmcid: PMC6171490.
  • Li G, Boucher JC, Kotani H, Park K, Zhang Y, Shrestha B, Wang X, Guan L, Beatty N, Abate-Daga D, Davila ML. 4-1BB enhancement of CAR T function requires NF-κB and TRAFs. JCI Insight. 2018 Sep;3(18). Pubmedid: 30232281. Pmcid: PMC6237232.
  • Yu X, Wang X. Tumor immunity landscape in non-small cell lung cancer. PeerJ. 2018 Mar;6:e4546. Pubmedid: 29593943. Pmcid: PMC5868477.
  • Ren Y, Bi C, Zhao X, Lwin T, Wang C, Yuan J, Silva AS, Shah BD, Fang B, Li T, Koomen JM, Jiang H, Chavez JC, Pham L, Sudalagunta PR, Wan L, Wang X, Dalton WS, Moscinski LC, Shain KH, Vose J, Cleveland JL, Sotomayor EM, Fu K, Tao J. PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas. J Clin Invest. 2018 Dec;128(12):5517-5530. Pubmedid: 30260324. Pmcid: PMC6264635.
  • Chen L, Reeve J, Zhang L, Huang S, Wang X, Chen J. GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ. 2018 Apr;6:e4600. Pubmedid: 29629248. Pmcid: PMC5885979.
  • Wang X, Zhang Z, Morris N, Cai T, Lee S, Wang C, Yu TW, Walsh CA, Lin X. Rare variant association test in family-based sequencing studies. Brief Bioinform. 2017 Nov;18(6):954-961. Pubmedid: 27677958. Pmcid: PMC5862290.
  • Wang H, Choi Y, Tayo B, Wang X, Morris N, Zhang X, Broeckel U, Hanis C, Kardia S, Redline S, Cooper RS, Tang H, Zhu X. Genome-wide survey in African Americans demonstrates potential epistasis of fitness in the human genome. Genet Epidemiol. 2017 Feb;41(2):122-135. Pubmedid: 27917522. Pmcid: PMC5226866.
  • Yue L, Bartenstein M, Zhao W, Ho WT, Han Y, Murdun C, Mailloux AW, Zhang L, Wang X, Budhathoki A, Pradhan K, Rapaport F, Wang H, Shao Z, Ren X, Steidl U, Levine RL, Zhao ZJ, Verma A, Epling-Burnette PK. Efficacy of ALK5 inhibition in myelofibrosis. JCI Insight. 2017 Apr;2(7):e90932. Pubmedid: 28405618. Pmcid: PMC5374075.
  • Canli T, Wen R, Wang X, Mikhailik A, Yu L, Fleischman D, Wilson RS, Bennett DA. Differential transcriptome expression in human nucleus accumbens as a function of loneliness. Mol Psychiatry. 2016 Nov. Pubmedid: 27801889. Pmcid: PMC5411331.
  • Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers RS, Krauthammer M. Global copy number profiling of cancer genomes. Bioinformatics. 2016 Mar;32(6):926-928. Pubmedid: 26576652. Pmcid: PMC4907391.
  • Wang X, Ji P, Zhang Y, LaComb JF, Tian X, Li E, Williams JL. Aberrant DNA Methylation: Implications in Racial Health Disparity. PLoS One. 2016 Apr;11(4):e0153125. Pubmedid: 27111221. Pmcid: PMC4844165.
  • Wang X, Xing EP, Schaid DJ. Kernel methods for large-scale genomic data analysis. Brief Bioinform. 2015 Mar;16(2):183-192. Pubmedid: 25053743. Pmcid: PMC4375394.
  • Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J. A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics. 2015 Jun;31(12):2040-2042. Pubmedid: 25681254. Pmcid: PMC4481698.
  • Wang X, Biernacka JM. Assessing the effects of multiple markers in genetic association studies. Front Genet. 2015 Feb;6:66. Pubmedid: 25759719. Pmcid: PMC4338793.
  • Wang X. Firth logistic regression for rare variant association tests. Front Genet. 2014 Jun;5:187. Pubmedid: 24995013. Pmcid: PMC4063169.
  • Tian X, Wang X, Chen J. Network-constrained group lasso for high-dimensional multinomial classification with application to cancer subtype prediction. Cancer Inform. 2014 Jan;13(Suppl 6):25-33. Pubmedid: 25635165. Pmcid: PMC4295837.
  • Wang X, Morris NJ, Zhu X, Elston RC. A variance component based multi-marker association test using family and unrelated data. BMC Genet. 2013 Mar;14:17. Pubmedid: 23497289. Pmcid: PMC3614458.
  • Wang X, Lee S, Zhu X, Redline S, Lin X. GEE-based SNP set association test for continuous and discrete traits in family-based association studies. Genet Epidemiol. 2013 Dec;37(8):778-786. Pubmedid: 24166731. Pmcid: PMC4007511.
  • Tang ZX, Wang XF, Zhang MZ, Zhang YH, Deng DX, Xu CW. The maternal cytoplasmic environment may be involved in the viability selection of gametes and zygotes. Heredity (Edinb). 2013 Apr;110(4):331-337. Pubmedid: 23169560. Pmcid: PMC3607179.
  • Wang X, Morris NJ, Schaid DJ, Elston RC. Power of single- vs. multi-marker tests of association. Genet Epidemiol. 2012 Jul;36(5):480-487. Pubmedid: 22648939. Pmcid: PMC3708310.
  • Wang X, Elston RC, Zhu X. The meaning of interaction. Hum Hered. 2012 Feb;70(4):269-277. Pubmedid: 21150212. Pmcid: PMC3025890.
  • Wang X, Qin H, Morris NJ, Zhu X, Elston RC. Testing gene-environment interactions in gene-based association studies. BMC Proc. 2011 Nov;5 Suppl 9:S26. Pubmedid: 22373316. Pmcid: PMC3287861.
  • Bickeböller H, Houwing-Duistermaat JJ, Wang X, Yan X. Dealing with high dimensionality for the identification of common and rare variants as main effects and for gene-environment interaction. Genet Epidemiol. 2011 Nov;35 Suppl 1:S35-S40. Pubmedid: 22128056.
  • Wang X, Elston RC, Zhu X. Statistical interaction in human genetics: how should we model it if we are looking for biological interaction?. Nat Rev Genet. 2011 Jan;12(1):74. Pubmedid: 21102529. Pmcid: PMC5189671.