Chengwen Li

The paper curates a collection of transcriptome datasets from viral respiratory inoculation and vaccination studies to enable reanalysis of transcriptional responses in blood and nasal samples.

The paper constructs a temporal atlas of human blood leukocyte changes after respiratory virus infection, showing shared immune responses and virus-specific kinetics.

ARTdeConv improves cell type deconvolution by addressing limitations in existing methods, showing better performance in simulations and real data compared to other approaches.

The paper evaluates ten differential expression methods for metatranscriptomics data using real and simulated datasets, finding the logistic-beta test has highest sensitivity and reasonable type I error control.

The paper develops a bivariate zero-inflated negative binomial model and applies it to analyze zero-inflated count data from scRNA-seq and dental caries studies.