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Xiaoqing Yu, PhD

Program: Biostatistics and Bioinformatics

Overview

Studying the immune-tumor interaction across cancer types and building predictive models for patients’ response to immunotherapy; and 2) Statistical and bioinformatics methods development to identify aberrant methylation patterns in tumors using bisulfite sequencing data.


Associations

    • Biostatistics and Bioinformatics
    • Immuno-Oncology
    • Immuno-Oncology

Education & Training

Research

Dr. Yu brings both experience in methodology development and collaborative research in bioinformatics, biostatistics and genomics. Her particular areas of research focus and interest include: 1) Studying the immune-tumor interaction across cancer types and building predictive models for patients’ response to immunotherapy; and 2) Statistical and bioinformatics methods development to identify aberrant methylation patterns in tumors using bisulfite sequencing data. Through her research experience she is poised to make significant contributions to addressing complex questions in cancer research by applying and developing modern statistical, bioinformatics and computational methods.

Publications

  • Biswas S, Mandal G, Payne KK, Anadon CM, Gatenbee CD, Chaurio RA, Costich TL, Moran C, Harro CM, Rigolizzo KE, Mine JA, Trillo-Tinoco J, Sasamoto N, Terry KL, Marchion D, Buras A, Wenham RM, Yu X, Townsend MK, Tworoger SS, Rodriguez PC, Anderson AR, Conejo-Garcia JR. IgA transcytosis and antigen recognition govern ovarian cancer immunity. Nature. 2021 Mar.591(7850):464-470. Pubmedid: 33536615. Pmcid: PMC7969354.
  • Yun S, Vincelette ND, Yu X, Watson GW, Fernandez MR, Yang C, Hitosugi T, Cheng CH, Freischel AR, Zhang L, Li W, Hou H, Schaub FX, Vedder AR, Cen L, McGraw KL, Moon J, Murphy DJ, Ballabio A, Kaufmann SH, Berglund AE, Cleveland JL. TFEB links MYC signaling to epigenetic control of myeloid differentiation and acute myeloid leukemia. Blood Cancer Discov. 2021 Mar.2(2):162-185. Pubmedid: 33860275. Pmcid: PMC8043621.
  • de Mingo Pulido Á, Hänggi K, Celias DP, Gardner A, Li J, Batista-Bittencourt B, Mohamed E, Trillo-Tinoco J, Osunmakinde O, Peña R, Onimus A, Kaisho T, Kaufmann J, McEachern K, Soliman H, Luca VC, Rodriguez PC, Yu X, Ruffell B. The inhibitory receptor TIM-3 limits activation of the cGAS-STING pathway in intra-tumoral dendritic cells by suppressing extracellular DNA uptake. Immunity. 2021 Jun.54(6):1154-1167.e7. Pubmedid: 33979578. Pmcid: PMC8192496.
  • Smalley I, Chen Z, Phadke MS, Li J, Yu X, Wyatt C, Evernden B, Messina JL, Sarnaik A, Sondak VK, Zhang C, Law V, Tran N, Etame A, Macaulay RJB, Eroglu Z, Forsyth PA, Rodriguez PC, Chen YA, Smalley KSM. Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases. Clin Cancer Res. 2021 Jul.27(14):4109-4125. Pubmedid: 34035069. Pmcid: PMC8282775.
  • El-Kenawi A, Dominguez-Viqueira W, Liu M, Awasthi S, Abraham-Miranda J, Keske A, Steiner KK, Noel L, Serna AN, Dhillon J, Gillies RJ, Yu X, Koomen JM, Yamoah K, Gatenby RA, Ruffell B. Macrophage-derived cholesterol contributes to therapeutic resistance in prostate cancer. Cancer Res. 2021 Jul. Pubmedid: 34301759.
  • Wilson CM, Fridley BL, Conejo-Garcia JR, Wang X, Yu X. Wide and deep learning for automatic cell type identification. Comput Struct Biotechnol J. 2021 Jan.19:1052-1062. Pubmedid: 33613870. Pmcid: PMC7878986.
  • Harro CM, Perez-Sanz J, Costich TL, Payne KK, Anadon Galindo CM, Chaurio RA, Biswas S, Mandal G, Rigolizzo KE, Sprenger KB, Mine JA, Showe L, Yu X, Liu K, Rodriguez PC, Pinilla-Ibarz J, Sokol L, Conejo-Garcia JR. Methyltransferase inhibitors restore SATB1 protective activity against cutaneous T cell lymphoma in mice. J Clin Invest. 2021 Feb.131(3). Pubmedid: 33270606. Pmcid: PMC7843215.
  • 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.
  • Yu X, Abbas-Aghababazadeh F, Chen YA, Fridley BL. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments. Methods Mol Biol. 2020 Sep.2194:143-175. Pubmedid: 32926366. Pmcid: PMC7771369.
  • 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.
  • 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.
  • Biswas S, Mandal G, Roy Chowdhury S, Purohit S, Payne KK, Anadon C, Gupta A, Swanson P, Yu X, Conejo-Garcia JR, Bhattacharyya A. Exosomes Produced by Mesenchymal Stem Cells Drive Differentiation of Myeloid Cells into Immunosuppressive M2-Polarized Macrophages in Breast Cancer. J Immunol. 2019 Dec.203(12):3447-3460. Pubmedid: 31704881. Pmcid: PMC6994919.
  • Wilson CM, Li K, Yu X, Kuan PF, Wang X. Multiple-kernel learning for genomic data mining and prediction. BMC Bioinformatics. 2019 Aug.20(1):426. Pubmedid: 31416413. Pmcid: PMC6694479.
  • Rauniyar N, Yu X, Cantley J, Voss EZ, Belcher J, Colangelo CM, Stone KL, Dahl N, Parikh C, Lam TT, Cantley LG. Quantification of Urinary Protein Biomarkers of Autosomal Dominant Polycystic Kidney Disease by Parallel Reaction Monitoring. Proteom Clin Appl. 2018 Sep.12(5):e1700157. Pubmedid: 29573172. Pmcid: PMC6736530.
  • Chorzalska A, Ahsan N, Rao RSP, Roder K, Yu X, Morgan J, Tepper A, Hines S, Zhang P, Treaba DO, Zhao TC, Olszewski AJ, Reagan JL, Liang O, Gruppuso PA, Dubielecka PM. Overexpression of Tpl2 is linked to imatinib resistance and activation of MEK-ERK and NF-κB pathways in a model of chronic myeloid leukemia. Mol Oncol. 2018 May.12(5):630-647. Pubmedid: 29485707. Pmcid: PMC5928369.
  • Yu X, Wang X. Tumor immunity landscape in non-small cell lung cancer. PeerJ. 2018 Mar.6:e4546. Pubmedid: 29593943. Pmcid: PMC5868477.
  • Villarroel-Espindola F, Yu X, Datar I, Mani N, Sanmamed MF, Velcheti V, Syrigos KN, Toki MI, Zhao H, Chen L, Herbst RS, Schalper KA. Spatially Resolved and Quantitative Analysis of VISTA/PD-1H as a Novel Immunotherapy Target in Human Non-Small Cell Lung Cancer. Clin Cancer Res. 2018 Apr.24(7):1562-1573. Pubmedid: 29203588. Pmcid: PMC5884702.
  • Charkoftaki G, Chen Y, Han M, Sandoval M, Yu X, Zhao H, Orlicky DJ, Thompson DC, Vasiliou V. Transcriptomic analysis and plasma metabolomics in Aldh16a1-null mice reveals a potential role of ALDH16A1 in renal function. Chem Biol Interact. 2017 Oct.276:15-22. Pubmedid: 28254523. Pmcid: PMC5725231.
  • Chorzalska A, Kim JF, Roder K, Tepper A, Ahsan N, Rao RSP, Olszewski AJ, Yu X, Terentyev D, Morgan J, Treaba DO, Zhao TC, Liang O, Gruppuso PA, Dubielecka PM. Long-Term Exposure to Imatinib Mesylate Downregulates Hippo Pathway and Activates YAP in a Model of Chronic Myelogenous Leukemia. Stem Cells Dev. 2017 May.26(9):656-677. Pubmedid: 28103766. Pmcid: PMC5421616.
  • Goffredo M, Santoro N, Tricò D, Giannini C, D'Adamo E, Zhao H, Peng G, Yu X, Lam TT, Pierpont B, Caprio S, Herzog RI. A Branched-Chain Amino Acid-Related Metabolic Signature Characterizes Obese Adolescents with Non-Alcoholic Fatty Liver Disease. Nutrients. 2017 Jun.9(7). Pubmedid: 28640216. Pmcid: PMC5537762.
  • Heit C, Marshall S, Singh S, Yu X, Charkoftaki G, Zhao H, Orlicky DJ, Fritz KS, Thompson DC, Vasiliou V. Catalase deletion promotes prediabetic phenotype in mice. Free Radical Bio Med. 2017 Feb.103:48-56. Pubmedid: 27939935. Pmcid: PMC5513671.
  • Johnson RM, Bergmann KR, Manaloor JJ, Yu X, Slaven JE, Kharbanda AB. Pediatric Kawasaki Disease and Adult Human Immunodeficiency Virus Kawasaki-Like Syndrome Are Likely the Same Malady. Open Forum Infect Dis. 2016 Sep.3(3):ofw160. Pubmedid: 27704015. Pmcid: PMC5047405.
  • Delpech JC, Wei L, Hao J, Yu X, Madore C, Butovsky O, Kaffman A. Early life stress perturbs the maturation of microglia in the developing hippocampus. Brain Behav Immun. 2016 Oct.57:79-93. Pubmedid: 27301858. Pmcid: PMC5010940.
  • Li N, Subrahmanyan L, Smith E, Yu X, Zaidi S, Choi M, Mane S, Nelson-Williams C, Behjati M, Kazemi M, Hashemi M, Fathzadeh M, Narayanan A, Tian L, Montazeri F, Mani M, Begleiter ML, Coon BG, Lynch HT, Olson EN, Zhao H, Ruland J, Lifton RP, Mani A. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Am J Hum Genet. 2016 Oct.99(4):1000. Pubmedid: 27716515. Pmcid: PMC5065682.
  • 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.
  • Yu X, Sun S. HMM-DM: identifying differentially methylated regions using a hidden Markov model. Stat Appl Genet Mol Biol. 2016 Mar.15(1):69-81. Pubmedid: 26887041.
  • Sun S, Yu X. HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test. Stat Appl Genet Mol Biol. 2016 Mar.15(1):55-67. Pubmedid: 26854292.
  • Li N, Subrahmanyan L, Smith E, Yu X, Zaidi S, Choi M, Mane S, Nelson-Williams C, Bahjati M, Kazemi M, Hashemi M, Fathzadeh M, Narayanan A, Tian L, Montazeri F, Mani M, Begleiter ML, Coon BG, Lynch HT, Olson EN, Zhao H, Ruland J, Lifton RP, Mani A. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Am J Hum Genet. 2016 Jun.98(6):1082-1091. Pubmedid: 27181681. Pmcid: PMC4908195.
  • Yao J, Leng L, Sauler M, Fu W, Zheng J, Zhang Y, Du X, Yu X, Lee P, Bucala R. Transcription factor ICBP90 regulates the MIF promoter and immune susceptibility locus. J Clin Invest. 2016 Feb.126(2):732-744. Pubmedid: 26752645. Pmcid: PMC4731159.
  • Dong J, Yu X, Porter DW, Battelli LA, Kashon ML, Ma Q. Common and distinct mechanisms of induced pulmonary fibrosis by particulate and soluble chemical fibrogenic agents. Arch Toxicol. 2016 Feb.90(2):385-402. Pubmedid: 26345256. Pmcid: PMC4749430.
  • Yu X, Sun S. Comparing five statistical methods of differential methylation identification using bisulfite sequencing data. Stat Appl Genet Mol Biol. 2016 Apr.15(2):173-191. Pubmedid: 26910753.
  • 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.
  • Yu X, Sun S. Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics. 2013 Sep.14:274. Pubmedid: 24044377. Pmcid: PMC3848615.
  • Sun S, Noviski A, Yu X. MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment. BMC Bioinformatics. 2013 Aug.14:259. Pubmedid: 23968174. Pmcid: PMC3765750.
  • Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams MD, Sun S. How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?. BioData Min. 2012 Jun.5(1):6. Pubmedid: 22709551. Pmcid: PMC3414812.
  • Adams MD, Veigl ML, Wang Z, Molyneux N, Sun S, Guda K, Yu X, Markowitz SD, Willis J. Global mutational profiling of formalin-fixed human colon cancers from a pathology archive. Mod Pathol. 2012 Dec.25(12):1599-1608. Pubmedid: 22878650. Pmcid: PMC3697090.
  • Xu P, Lu J, Li Z, Yu X, Chen L, Xu T. Aggregation of STIM1 underneath the plasma membrane induces clustering of Orai1. Biochem Bioph Res Co. 2006 Dec.350(4):969-976. Pubmedid: 17045966.