Publications

You can find all lab publications here. Below are some main publications:

  • Chen Y and Wang X (2022) Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection. Bioinformatics. 38(23):5175–5181.
  • Tang G, Cho M, Wang X (2022) OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer, Nucleic Acids Research.50(D1):D1334-D1339
  • Huang X, Tang G, Ismail N, Wang X (2022) Developing RT-LAMP assays for rapid diagnosis of SARS-CoV-2 in saliva.EBioMedicine.75:103736
  • Liu X, Liu P, Chernock RD, Lang Kuhs KA, Lewis JS Jr, Li H, Gay HA, Thorstad WL, Wang X (2022). Impact of human papillomavirus on the tumor microenvironment in oropharyngeal squamous cell carcinoma. Int J Cancer.1;150(3):521-531 
  • Liu X, Liu P, Chernock, RD, Yang Z, Kuhs KA, Lewis Jr. JS, Luo J, Li H, Gay HA, Thorstad, WL, Wang X (2021) A microRNA expression signature as prognostic marker for oropharyngeal squamous cell carcinoma. JNCI: Journal of the National Cancer Institute.113(6):752-759.
  • Liu X, Liu P, Chernock, RD, Kuhs KA, Lewis Jr. JS, Luo J, Gay HA, Thorstad, WL, Wang X (2020) A prognostic gene expression signature for oropharyngeal squamous cell carcinoma. EBioMedicine.2020;61:102805.
  •  Tong F, Andress A, Tang G, Liu P, Wang X (2020) Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis. Scientific Reports. 10(1):19450.
  • Hiranniramol K, Chen Y, Liu W, Wang X (2020) Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency. Bioinformatics. 36(9):2684-2689.
  • Hiranniramol K, Chen Y, Wang X (2020) CRISPR/Cas9 Guide RNA Design Rules for Predicting Activity. Methods in Molecular Biology. 2115:351-364.
  • Cosper PF, McNair C, Ivan Gonzalez, Wong N, Knudsen KE, Chen JJ, Markovina S, Schwarz JK, Grigsby PW, Wang X (2020) Decreased local immune response and retained HPV gene expression during chemoradiotherapy are associated with treatment resistance and death from cervical cancer. International Journal of Cancer. 146(7):2047–2058.
  • Chen Y and Wang X (2020) miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Research. 48(D1):D127-D131.
  • Liu W, Wang X (2019) Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. Genome Biology. 20:18 1-10.
  • Wong N, Chen Y, Chen S, Wang X (2018) OncomiR: An online resource for exploring pan-cancer microRNA dysregulation. Bioinformatics. 34(4):713-715.
  • Liu W, Chen H, Wong N, Haynes W, Baker CM, Wang X (2017) Pseudohypoxia induced by miR-126 deactivation promotes migration and therapeutic resistance in renal cell carcinoma. Cancer Letters. 394:65-75.
  • Wang X (2016) Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-Ligation studies. Bioinformatics. 32(9):1316-1322.
  • Khwaja SS, Baker C, Haynes W, Spencer CR, Gay H, Thorstad W, Adkins DR, Nussenbaum B, Chernock RD, Lewis Jr. JS, Wang X (2016) High E6 gene expression predicts for distant metastasis and poor survival in patients with HPV-positive oropharyngeal squamous cell carcinoma. Int J Radiat Oncol Biol Phys. 95(4): 1132-1141.
  • Wong N, Khwaja SS, Baker CM, Gay HA, Thorstad WL, Daly MD, Lewis JS Jr, Wang X (2016) Prognostic microRNA signatures derived from The Cancer Genome Atlas for head and neck squamous cell carcinomas. Cancer Medicine. 5(7):1619-1628.
  • Wong N, Liu W, Wang X (2015) WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biology. 16(1):218 1-8.
  • Wong N, Wang X (2015) miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Research. 43(D1):D146-152.
  • Liu W, Gao G, Hu X, Wang Y, Schwarz JK, Chen JJ, Grigsby PW, Wang X (2014) Activation of miR-9 by human papillomavirus in cervical cancer. Oncotarget. 5(22):11620-11630.
  • Wang X (2014) Composition of seed sequence is a major determinant of microRNA targeting patterns. Bioinformatics 30(10):1377-1383.
  • Jiang Z, Liu W, Wang Y, Gao Z, Gao G, Wang X (2013) Rational design of microRNA-siRNA chimeras for multi-functional target suppression. RNA 19(12):1745-1754.
  • Gao G, Gay HA, Chernock RD, Zhang TR, Luo J, Thorstad WL, Lewis JS, Wang X (2013) A microRNA expression signature for the prognosis of oropharyngeal squamous cell carcinoma. Cancer 119(1):72-80.
  • Gao G, Chernock RD, Gay HA, Thorstad WL, Zhang TR, Wang H, Ma XJ, Luo Y, Lewis JS, Wang X (2013) A novel RT-PCR method for quantification of human papillomavirus transcripts in archived tissues and its application in oropharyngeal cancer prognosis. International Journal of Cancer 132(4):882-90.
  • Wang X, Spandidos A, Wang H, Seed B (2012) PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. Nucleic Acids Research 40(1):D1144-1149.
  • Nelson PT, Wang WX, Mao G, Wilfred BR, Xie K, Jennings MH, Gao Z, Wang X (2011) Specific sequence determinants of miR-15/107 microRNA gene group targets. Nucleic Acids Research 39(18):8163-8172.
  • Hu X, Schwarz JK, Lewis JS., Huettner PC, Rader JS, Deasy JO, Grigsby PW, Wang X (2010) A microRNA expression signature for cervical cancer prognosis. Cancer Research 70(4):1441-1448.
  • Wang X (2010) Computational prediction of microRNA targets. Methods in Molecular Biology 667:283-295.
  • Wang X, Wang XH, Varma RK, Beauchamp L, Magdaleno S, Sendera TJ (2009) Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Research 37(22):e152 1-9.
  • Hu X, Macdonald DM, Huettner PC, Feng Z, El Naqa IM, Schwarz JK, Mutch DG, Grigsby PW, Powell SN, Wang X (2009) A miR-200 microRNA cluster as prognostic marker in advanced ovarian cancer. Gynecologic Oncology 114(3):457-464.
  • Wang X (2009) A PCR-based platform for microRNA expression profiling studies. RNA 15(4):716-723.
  • Wang X (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14(6):1012-1017.
  • Wang X and El Naqa IM (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24(3):325-332.