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Yonghua Zhuang

TitleAsst Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-PEDS
ORCID ORCID Icon0000-0002-1822-2395 Additional info

    Collapse Biography 
    Collapse awards and honors
    2021Strother Walker Award for Outstanding PhD Student, University of Colorado Anschutz Medical Campus
    2020 - 2022NHLBI BioData Catalyst Fellowship, NIHBI
    2015Dr. Donald H. Gilden’s award, International Society for NeuroVirology

    Collapse Overview 
    Collapse overview
    My research interests are the development and application of statistical methods for analyzing high throughput omics data to better understand how key interactions between genes (or proteins) contribute to human diseases. My academic training and research experience have provided me with a strong integrated background in biostatistics, machine learning, and biology. I have received interdisciplinary training including immunology, molecular biology, statistics methods in genomics, network inference, bioinformatics, and deep learning. Recently I focuses on developing statistical methods for constructing protein-protein networks associated with phenotype and developing Graph Convolutional Neural Network algorithms in the field of genomics for classification. To date, my colleagues and I have developed several statistical methods including a novel tissue augmented Bayesian model for eQTL analysis, sparse multiple canonical correlation network analysis (smCCNet), and an augmented high-dimensional graphical Lasso method to incorporate prior biological knowledge for global network learning (ahGlasso).

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Darragh LB, Gadwa J, Pham TT, Van Court B, Neupert B, Olimpo NA, Nguyen K, Nguyen D, Knitz MW, Hoen M, Corbo S, Joshi M, Zhuang Y, Amann M, Wang XJ, Dow S, Kedl RM, Samedi V, Boss MK, Karam SD. Elective nodal irradiation mitigates local and systemic immunity generated by combination radiation and immunotherapy in head and neck tumors. Nat Commun. 2022 11 16; 13(1):7015. PMID: 36385142.
      View in: PubMed
    2. Abdel-Hafiz M, Najafi M, Helmi S, Pratte KA, Zhuang Y, Liu W, Kechris KJ, Bowler RP, Lange L, Banaei-Kashani F. Significant Subgraph Detection in Multi-omics Networks for Disease Pathway Identification. Front Big Data. 2022; 5:894632. PMID: 35811829.
      View in: PubMed
    3. Zhuang Y, Xing F, Ghosh D, Banaei-Kashani F, Bowler RP, Kechris K. An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning. Front Genet. 2021; 12:760299. PMID: 35154240.
      View in: PubMed
    4. Zhuang Y, Hobbs BD, Hersh CP, Kechris K. Identifying miRNA-mRNA Networks Associated With COPD Phenotypes. Front Genet. 2021; 12:748356. PMID: 34777474.
      View in: PubMed
    5. Gillenwater LA, Helmi S, Stene E, Pratte KA, Zhuang Y, Schuyler RP, Lange L, Castaldi PJ, Hersh CP, Banaei-Kashani F, Bowler RP, Kechris KJ. Multi-omics subtyping pipeline for chronic obstructive pulmonary disease. PLoS One. 2021; 16(8):e0255337. PMID: 34432807.
      View in: PubMed
    6. Gillenwater LA, Pratte KA, Hobbs BD, Cho MH, Zhuang Y, Halper-Stromberg E, Cruickshank-Quinn C, Reisdorph N, Petrache I, Labaki WW, O'Neal WK, Ortega VE, Jones DP, Uppal K, Jacobson S, Michelotti G, Wendt CH, Kechris KJ, Bowler RP. Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules. Netw Syst Med. 2020 Dec 01; 3(1):159-181. PMID: 33987620.
      View in: PubMed
    7. Mastej E, Gillenwater L, Zhuang Y, Pratte KA, Bowler RP, Kechris K. Identifying Protein-metabolite Networks Associated with COPD Phenotypes. Metabolites. 2020 Mar 25; 10(4). PMID: 32218378.
      View in: PubMed
    8. Shi WJ, Zhuang Y, Russell PH, Hobbs BD, Parker MM, Castaldi PJ, Rudra P, Vestal B, Hersh CP, Saba LM, Kechris K. Unsupervised discovery of phenotype-specific multi-omics networks. Bioinformatics. 2019 11 01; 35(21):4336-4343. PMID: 30957844.
      View in: PubMed
    9. Halper-Stromberg E, Gillenwater L, Cruickshank-Quinn C, O'Neal WK, Reisdorph N, Petrache I, Zhuang Y, Labaki WW, Curtis JL, Wells J, Rennard S, Pratte KA, Woodruff P, Stringer KA, Kechris K, Bowler RP. Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma. Metabolites. 2019 Jul 25; 9(8). PMID: 31349744.
      View in: PubMed
    10. Clarke P, Zhuang Y, Berens HM, Leser JS, Tyler KL. Interferon Beta Contributes to Astrocyte Activation in the Brain following Reovirus Infection. J Virol. 2019 05 15; 93(10). PMID: 30814290.
      View in: PubMed
    11. Zhuang Y, Berens-Norman HM, Leser JS, Clarke P, Tyler KL. Mitochondrial p53 Contributes to Reovirus-Induced Neuronal Apoptosis and Central Nervous System Injury in a Mouse Model of Viral Encephalitis. J Virol. 2016 09 01; 90(17):7684-91. PMID: 27307572.
      View in: PubMed
    12. Chen Z, Wang S, Erekosima N, Li Y, Hong J, Qi X, Merkel P, Nagabhushanam V, Choo E, Katial R, Alam R, Trikha A, Chu HW, Zhuang Y, Jin M, Bai C, Huang H. IL-4 confers resistance to IL-27-mediated suppression on CD4+ T cells by impairing signal transducer and activator of transcription 1 signaling. J Allergy Clin Immunol. 2013 Oct; 132(4):912-21.e1-5. PMID: 23958647.
      View in: PubMed
    13. Qi X, Hong J, Chaves L, Zhuang Y, Chen Y, Wang D, Chabon J, Graham B, Ohmori K, Li Y, Huang H. Antagonistic regulation by the transcription factors C/EBPa and MITF specifies basophil and mast cell fates. Immunity. 2013 Jul 25; 39(1):97-110. PMID: 23871207.
      View in: PubMed
    14. Nishida J, Li Y, Zhuang Y, Huang Z, Huang H. IFN-? suppresses permissive chromatin remodeling in the regulatory region of the Il4 gene. Cytokine. 2013 Apr; 62(1):91-5. PMID: 23490416.
      View in: PubMed
    15. Zhuang Y, Dreskin SC. Redefining the major peanut allergens. Immunol Res. 2013 Mar; 55(1-3):125-34. PMID: 22948807.
      View in: PubMed
    16. Dionne KR, Zhuang Y, Leser JS, Tyler KL, Clarke P. Daxx upregulation within the cytoplasm of reovirus-infected cells is mediated by interferon and contributes to apoptosis. J Virol. 2013 Mar; 87(6):3447-60. PMID: 23302889.
      View in: PubMed
    17. Chen X, Wang Q, El-Mezayen R, Zhuang Y, Dreskin SC. Ara h 2 and Ara h 6 have similar allergenic activity and are substantially redundant. Int Arch Allergy Immunol. 2013; 160(3):251-8. PMID: 23075924.
      View in: PubMed
    18. Zhuang Y, Durrani S, Hodges BD, Dreskin SC, Chen X. Expression of recombinant Ara h 6 in Pichia pastoris but not in Escherichia coli preserves allergic effector function and allows assessment of specific mutations. Mol Nutr Food Res. 2012 Jun; 56(6):986-95. PMID: 22707273.
      View in: PubMed
    19. Goplen N, Karim Z, Guo L, Zhuang Y, Huang H, Gorska MM, Gelfand E, Pag?s G, Pouyss?gur J, Alam R. ERK1 is important for Th2 differentiation and development of experimental asthma. FASEB J. 2012 May; 26(5):1934-45. PMID: 22262639.
      View in: PubMed
    20. Chen X, Zhuang Y, Wang Q, Moutsoglou D, Ruiz G, Yen SE, Dreskin SC. Analysis of the effector activity of Ara h 2 and Ara h 6 by selective depletion from a crude peanut extract. J Immunol Methods. 2011 Sep 30; 372(1-2):65-70. PMID: 21777590.
      View in: PubMed
    21. Zhuang Y, Huang Z, Nishida J, Brown M, Zhang L, Huang H. A continuous T-bet expression is required to silence the interleukin-4-producing potential in T helper type 1 cells. Immunology. 2009 Sep; 128(1):34-42. PMID: 19689734.
      View in: PubMed
    22. Zhuang Y, Huang Z, Nishida J, Zhang L, Huang H. Signaling pathways that lead to the silencing of the interleukin-4-producing potential in Th1 cells. J Interferon Cytokine Res. 2009 Jul; 29(7):399-406. PMID: 19450151.
      View in: PubMed
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