Li Ma

The Urogenital Lactobacillus Axis Across Menopause: Connections Between the Vagina, Bladder, and Urinary Metabolome

The paper examines how vaginal estrogen affects the urinary microbiome and metabolome in postmenopausal women, finding that it increases lactobacilli and alters metabolite profiles.

An Exponential Scale Mixture Model for Metatranscriptomics Data with Application to Inflammatory Bowel Disease

The paper introduces a scale mixture model for metatranscriptomics data to improve differential expression analysis in inflammatory bowel disease, identifying new candidate genes not found by Gaussian methods.

From external-input sensitivity to resident persistence: community assembly in a sink p-trap model

The paper shows that microbial communities in retentive habitats shift from being sensitive to external input to being shaped by local history over time.

A negative binomial latent factor model for paired microbiome sequencing data

The paper introduces a negative binomial latent factor model for paired microbiome data to account for cross-site correlations and improve statistical analysis of microbial compositions.

Quantitative occupancy of myriad transcription factors from one DNase experiment enables efficient comparisons across conditions

The paper introduces TOP, a Bayesian framework that quantifies TF occupancy across many conditions using a single DNase-seq experiment, showing changes in 1500 TF motifs across cell types, hormone exposure, and genetic backgrounds.