journal articles

Methodology work:

MeRIP-seq

• D. Duan, W. Tang, R. Shu, Z. Guo, H. Feng (2023+) Evaluation of Differential Epitranscriptome Analysis Methods. Briefings in Bioinformatics, Under revision.
• 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]

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.
  [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]

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]