Shu Dan

PIANO integrates single-cell data across species and modalities, models gene expression, and scales to 100 million cells for drug perturbation analysis.

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

This paper creates a cross-species spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, revealing conserved molecular organization and cell type-specific compartments.

The paper presents a spatially resolved transcriptomic and gene regulatory atlas of primate subcortical regions, revealing spatially tuned transcriptional and regulatory programs across cell types.

The paper introduces PIANO, a variational autoencoder for multi-omics integration, showing improved performance on single-species and multi-atlas datasets.

GASTON-Mix identifies spatial domains and gradients in SRT data more accurately than existing methods, revealing biological insights in brain and tumor tissues.

This study develops a clinically relevant murine model of electroconvulsive stimulation to investigate its effects on social behavior and gene expression after chronic social defeat stress.

This paper develops two epigenetic clocks for rhesus macaques and finds that early life adversity, specifically infant maltreatment, is associated with epigenetic age acceleration.

This study uses spatial transcriptomics to show gene expression changes across brain regions in mice after auditory threat conditioning, revealing altered transcriptional connectivity involving steroidogenic factor 1.

This study analyzes the morphology of praying mantis forelegs to determine how their structure relates to prey capture ability and camouflage.

The paper uses natural language processing on post-mortem electronic health records to derive RDoC cognitive scores and associates them with Alzheimer's disease neuropathology.