publications

Methodology work:

Z Guo$^\dag$, D Duan$^\dag$, W Tang, J Zhu, W S Bush, L Zhang, X Zhu, F Jin, H Feng, magpie: a power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing, major revision at PLOS Computational Biology, 2023.
D Duan, W Tang, R Shu, Z Guo^, H Feng^, Evaluation of Epitranscriptome-wide N6-methyladenosine Differential Analysis Methods. Briefings in Bioinformatics, 24 (3), bbad139, 2023.
Z Guo, A M Shafik, P Jin, H Wu Differential RNA Methylation Analysis for MeRIP-seq Data under General Experimental Design. Bioinformatics, (2022). [link]
Z Guo, Andrew M Shafik, Peng Jin, Zhijin Wu, Hao Wu, Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing. Bioinformatics, (2021). [link]

L Chen, Z Guo, T Deng, H Wu, scCTS: identifying the cell type specific marker genes from population-level single-cell RNA-seq . Under review at Genome Biology, 2023.
Bulk RNA-seq
Z Guo, Y Cui, X Shi, JA Birchler, I Albizua, SL Sherman, ZS Qin, T Ji. An empirical bayesian approach for testing gene expression fold change and its application in detecting global dosage effects. NAR Genomics and Bioinformatics, (2020), 2(3):lqaa072. [Link]
Z Li, Z Guo, Y Cheng, P Jin, H Wu. Robust partial reference-free cell composition estimation from tissue expression. Bioinformatics, (2020), 36(11): 3431-3438. [Link]

Z. Guo, S Zhang. Sparse deep nonnegative matrix factorization. Big Data Mining and Analytics, (2019), 3(1):13-28.
[Link]

Collaborations

Y. Pan, K. Kathleen, Z. Guo, Y. Yang, G. Khalil, R. Kelly, B. Switzer (202x) Simulation Study for Improving Efficacy Estimates for New HIV Treatments. In preparation.
M. C. Runnstrom1, A. Morrison-Porter, M. Ravindran, H. Quehl, R. Ramonell, M. Woodruff, M. Kuruvilla, F. Anam, R. Swerlick, C. Swenson, C. Polito, W. Neveu, R. Patel, C. Kim, l. Hentenaar, Z. Guo, H. Wu, N. S. Haddad, J. L. Daiss, I. Sanz, F. E. Lee*. Reduced SARS-CoV-2 Vaccine Response in Patients Treated with Biologic Therapies for Asthma. Journal of Allergy and Clinical Immunology, (2022), 149(2):AB319. [link]
A. M. Shafik, F. Zhang, Z. Guo, Q. Dai, K. Pajdzik, Y. Li, Y. Kang, B. Yao, H. Wu, C. He, E. G. Allen, R. Duan, P. Jin. N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer’s disease. Genome Biology, (2021), 22(1):1-19. [link]

Z. Guo, A. Shafik, P. Jin, Z. Wu, H. Wu (2023) Analyzing mRNA Epigenetic Sequencing Data with TRESS. In: H. Oliveira, P. (eds) Computational Epigenomics and Epitranscriptomics. Methods in Molecular Biology, vol 2624. Humana, New York, NY. [link]