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.

This study investigates how the gut microbiome interacts with aging and dietary restriction in mice, finding that host genetics significantly influence microbiome features and that dietary restriction does not rejuvenate the microbiome.

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.