Hongzhe Li

RICE improves causal gene network estimation in single-cell CRISPR screens by addressing confounding, count data, and high-MOI designs, outperforming existing methods in synthetic and real data.

The paper introduces cosmoDA, a differential abundance testing method for compositional sequencing data that reduces false positives by modeling feature interactions and covariates.

RCANE predicts whole-genome somatic copy number aberrations across cancers using RNA-seq data, outperforming existing methods on TCGA and DepMap datasets.

The paper introduces a quantitative method to measure and predict microbiome responses to antibiotics using a Microbiome Response Index (MiRIx) and applies it to human microbiome data.

This study maps expression and splicing QTLs in East Africans and finds population-specific genetic variation related to immunity, metabolism, and pigmentation.

The paper develops random-effects copula models to identify temporally conserved microbial co-variation networks in longitudinal microbiome data, showing that antibiotic treatment alters network stability.

The paper develops a sparse compositional mediation model to estimate causal effects in microbiome studies and applies it to investigate fat intake's effect on BMI through gut microbiome composition.

The paper identifies PPP1R3A as a central cardioprotective factor in pressure overload heart failure by analyzing gene network rewiring in human hearts.