journal articles

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]

Non-negative Matrix Factorization

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


  • 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]

book chapters

  • 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]