For linear model design (i.e., continuous covariates)
Liu K, Shen L, Jiang H (2018) A Unified Model for Robust Differential Expression Analysis of RNA-Seq data
Proceedings of the 2018 IEEE International Conference on Bioinformatics and Biomedicine, 437-442.
Liu K, Shen L, Jiang H (2019) Joint Between-Sample Normalization and Differential Expression Detection through L0 Regularized Linear Regression
For binary or categorical model design (e.g., two- or multiple-group comparison)
Jiang H, Zhan T (2017) Unit-Free and Robust Detection of Differential Expression from RNA-Seq Data
Statistics in Biosciences, 9:178-199. [online][arXiv][The R program for generating the results in this paper]