Yonghua Zhuang, PhD

Professional Titles

• Assistant Professor

Recognitions

• Strother Walker Award for Outstanding PhD Student, University of Colorado Anschutz Medical Campus (2021)
• NHLBI BioData Catalyst Fellowship, NHLBI (2020)

Research Interests

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).

Publications

• 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. Author Correction: Elective nodal irradiation mitigates local and systemic immunity generated by combination radiation and immunotherapy in head and neck tumors. Nat Commun. 2024 Oct 10;15(1):8781. PubMed PMID: 39389942
• Goldstein NB, Berk ZBK, Tomb LC, Hu J, Hoaglin LG, Roop DR, Adiri R, Zhuang Y, Canosa JM, Sanders P, Norris DA, Nocka K, Cha A, Birlea SA. Phosphodiesterase-4 Inhibitors Increase Pigment Cell Proliferation and Melanization in Cultured Melanocytes and within a 3-Dimensional Skin Equivalent Model. J Invest Dermatol. 2024 Sep 7. [Epub ahead of print] PubMed PMID: 39182565
• Liu W, Vu T, R Konigsberg I, A Pratte K, Zhuang Y, Kechris KJ. Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization. BMC Bioinformatics. 2024 Aug 24;25(1):276. PubMed PMID: 39179997
• L. Willems, K.B. Kurakula, V. Geudens, J. Verhaegen, M. Vermant, Y. Zhuang, Y.-R.A. Yu, S. Rajagopal, F. Klok, M. Delcroix, M.-J. Goumans, and R. Quarck. PIN1 Is Increased in Endothelial Cells Derived From Patients With Chronic Thromboembolic Pulmonary Hypertension (CTEPH) (abstract). Am J Respir Crit Care Med 2024;209:A5137.
• CPI203, a BET inhibitor, down-regulates a consistent set of DNA synthesis genes across a wide array of glioblastoma lines Matthew C. Garrett, Troy Carnwath, Rebecca Albano, Yonghua Zhuang, Catherine A. Behrmann, Merissa Pemberton, Farah Barakat, Robert Lober, Mark Hoeprich, Anthony Paravati, Marilyn Reed, Hailey Spry, Daniel Woo, Eric O’Brien, Brett VanCauwenbergh, John Perentesis, Rani Nasser, Mario Medvedovic, David R. Plas bioRxiv 2024.06.26.600837; doi: https://doi.org/10.1101/2024.06.26.600837
• Profiling FMR1 repeat expansion mosaicism in the human brain. Anna Dischler, Yonghua Zhuang, Abigail Lukowicz, Cristina Lau, Susana Lopez-Ignacio, Caroline Dias. ASHG Annual meeting, 2024.
• Hu J, Alami V, Zhuang Y, Alzofon N, Jimeno A, Gao D. Integrated variant allele frequency analysis pipeline and R package: easyVAF. Mol Carcinog. 2023 Dec;62(12):1877-1887. PubMed PMID: 37606183
• Chi C, Knight WE, Riching AS, Zhang Z, Tatavosian R, Zhuang Y, Moldovan R, Rachubinski AL, Gao D, Xu H, Espinosa JM, Song K. Interferon hyperactivity impairs cardiogenesis in Down syndrome via downregulation of canonical Wnt signaling. iScience. 2023 Jul 21;26(7):107012. PubMed PMID: 37360690
• Donson AM, Bertrand KC, Riemondy KA, Gao D, Zhuang Y, Sanford B, Norris GA, Chapman RJ, Fu R, Willard N, Griesinger AM, Ribeiro de Sousa G, Amani V, Grimaldo E, Hankinson TC, Booker F, Sill M, Grundy RG, Pajtler KW, Ellison DW, Foreman NK, Ritzmann TA. Significant increase of high-risk chromosome 1q gain and 6q loss at recurrence in posterior fossa group A ependymoma: A multicenter study. Neuro Oncol. 2023 Oct 3;25(10):1854-1867. PubMed PMID: 37246777
• Elias AD, Spoelstra NS, Staley AW, Sams S, Crump LS, Vidal GA, Borges VF, Kabos P, Diamond JR, Shagisultanova E, Afghahi A, Mayordomo J, McSpadden T, Crawford G, D'Alessandro A, Zolman KL, van Bokhoven A, Zhuang Y, Gallagher RI, Wulfkuhle JD, Petricoin Iii EF, Gao D, Richer JK. Phase II trial of fulvestrant plus enzalutamide in ER /HER2- advanced breast cancer. NPJ Breast Cancer. 2023 May 20;9(1):41. PubMed PMID: 37210417
• Zhuang Y, Xing F, Ghosh D, Hobbs BD, Hersh CP, Banaei-Kashani F, Bowler RP, Kechris K. Deep learning on graphs for multi-omics classification of COPD. PLoS One. 2023;18(4):e0284563. PubMed PMID: 37083575
• Viswanathan G, Kirshner HF, Nazo N, Ali S, Ganapathi A, Cumming I, Zhuang Y, Choi I, Warman A, Jassal C, Almeida-Peters S, Haney J, Corcoran D, Yu YR, Rajagopal S. Single-Cell Analysis Reveals Distinct Immune and Smooth Muscle Cell Populations that Contribute to Chronic Thromboembolic Pulmonary Hypertension. Am J Respir Crit Care Med. 2023 May 15;207(10):1358-1375. PubMed PMID: 36803741
• 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. PubMed PMID: 35811829
• 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. 2022 Jan 27;12:760299. doi: 10.3389/fgene.2021.760299. PMID: 35154240; PMCID: PMC8829118.
• Zhuang Y, Hobbs BD, Hersh CP, Kechris K. Identifying miRNA-mRNA Networks Associated With COPD Phenotypes. Front Genet. 2021;12:748356. PubMed PMID: 34777474
• 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. PubMed PMID: 34432807
• 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. PubMed PMID: 35154240
• Zhuang Y, Hobbs BD, Hersh CP, Kechris K. Identifying miRNA-mRNA Networks Associated With COPD Phenotypes. Front Genet. 2021;12:748356. PubMed PMID: 34777474
• 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. PubMed PMID: 34432807
• 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 1;3(1):159-181. PubMed PMID: 33987620
• 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 Nov 1;35(21):4336-4343. PubMed PMID: 30957844
• 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 May 15;93(10). PubMed PMID: 30814290
• 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 Sep 1;90(17):7684-91. PubMed PMID: 27307572
• 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. PubMed PMID: 23958647
• 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. PubMed PMID: 23302889
• Zhuang Y, Dreskin SC. Redefining the major peanut allergens. Immunol Res. 2013 Mar;55(1-3):125-34. PubMed PMID: 22948807
• 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. PubMed PMID: 23871207
• 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. PubMed PMID: 23490416
• 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. PubMed PMID: 23075924
• Goplen N, Karim Z, Guo L, Zhuang Y, Huang H, Gorska MM, Gelfand E, Pagés G, Pouysségur J, Alam R. ERK1 is important for Th2 differentiation and development of experimental asthma. FASEB J. 2012 May;26(5):1934-45. PubMed PMID: 22262639
• 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. PubMed PMID: 22707273
• 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. PubMed PMID: 21777590
• 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. PubMed PMID: 19689734
• 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. PubMed PMID: 19450151
• Laurel Darragh, Jacob Gadwa, Tiffany Pham, Benjamin Van Court, Brooke Neupert, Nicholas Olimpo, Khoa Nguyen, Diemmy Nguyen, Michael Knitz, Maureen Hoen, Sophia Corbo, Molishree Joshi, Yonghua Zhuang, Maria Amann, X.J. Wang, Steven Dow, Ross Kedl, Von Samedi, Mary-Keara Boss, and Sana Karam. Elective nodal irradiation mitigates local and systemic immunity generated by combination radiation and immunotherapy in head and neck tumors. Nature communications. 2022 (Accepted)
• Susana Lopez-Ignacio, Anna Dischler, Yonghua Zhuang, Caroline Dias. Characterizing Mosaicism of the FMR1 Gene in Fragile X Brains. Keystone Conference on Somatic Mosaicism in Human Development, Aging, and Diseases.2025.