Sudin Bhattacharya

A high-fat hypertensive diet induces a coordinated perturbation signature across cell types in thoracic perivascular adipose tissue

This study uses single nucleus RNA-sequencing to show that a high-fat hypertensive diet induces coordinated gene expression changes across cell types in thoracic perivascular adipose tissue in Dahl SS rats.

A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers

The paper uses snRNAseq to analyze thoracic aortic perivascular adipose tissue (taPVAT) and subscapular brown adipose tissue (BAT) in rats, identifying cell-specific gene expression and highlighting PIEZO1 as a key mechanotransducer in taPVAT.

A multiscale model of the mammalian liver circadian clock supports synchronization of autonomous oscillations by intercellular communication.

The paper develops a multiscale model of the mammalian liver circadian clock to show that intercellular communication is necessary for sustained circadian oscillations with a near 24-hour period.

Generative Modeling of Single Cell Gene Expression for Dose-Dependent Chemical Perturbations

This paper introduces scVIDR, a variational autoencoder for predicting dose-dependent gene expression in single cells across different cell types and tissues, showing improved performance over existing methods.

Predictive Models of Genome-wide Aryl Hydrocarbon Receptor DNA Binding Reveal Tissue Specific Binding Determinants

The paper develops predictive models to identify tissue-specific AhR binding determinants using machine learning on genomic features.

Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs.

This study benchmarks Bayesian and frequentist methods for differential gene expression analysis in dose-response scRNA-seq studies, finding that multi-group methods outperform two-group approaches.

Application of single nuclei RNA sequencing to assess the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin

This study uses single nuclei RNA sequencing to identify cell-specific transcriptional changes and population shifts in mouse liver exposed to TCDD, revealing increased macrophages and RAS signaling in nonparenchymal cells.

Gene Coregulation and Coexpression in the Aryl Hydrocarbon Receptor-mediated Transcriptional Regulatory Network in the Mouse Liver

The paper maps the AHR-mediated gene regulatory network in mouse liver using gene expression and TF binding data, showing distinct expression patterns and biological process enrichments among AHR-bound and unbound genes.