Xiaoqing Yu, PhD
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Xiaoqing Yu, PhD

Academic Rank: Assistant Member

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.

Discipline

    • Biostatistics and Bioinformatics
    • Immunology

Education & Training

    • Case Western University, PhD - Biostatistics and Epidemiology
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

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.