Zefang Tang

Computational reconstruction of hierarchical cis-regulatory networks reveals synergistic transcription control and disease-associated rewiring

ORIGAMI reconstructs cis-regulatory networks using multi-omics data and deep learning, revealing synergistic transcription control and disease-associated rewiring.

In Situ Graphene-Seq: Spatial Transcriptomics and Chronic Electrophysiological Characterization of Tissue Microenvironments

This paper introduces in situ graphene-seq, a platform integrating chronic electrophysiology with spatial transcriptomics to analyze tissue microenvironments, showing how spatial heterogeneity affects cell function and gene expression.

Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks

This paper develops Deep-STARmap and Deep-RIBOmap for 3D spatial transcriptomics and translatomics in thick tissue blocks, enabling analysis of gene expression and immune interactions in human skin cancer.

Search and Match across Spatial Omics Samples at Single-cell Resolution

CAST enables spatial-to-spatial searching and matching of single-cell spatial omics data across technologies and conditions, identifying disease-associated pathways and translational efficiency variations.

Towards a universal spatial molecular atlas of the mouse brain

The paper introduces FuseMap, a deep-learning framework for spatial transcriptomics that creates a comprehensive molecular spatial reference atlas of the mouse brain.

Spatial Atlas of the Mouse Central Nervous System at Molecular Resolution

The paper creates a high-resolution spatial atlas of the mouse CNS by combining in situ sequencing with scRNA-seq data to map cell types and gene expression across the brain and spinal cord.

Spatially Resolved Single-cell Translatomics at Molecular Resolution

The paper introduces RIBOmap, a 3D in situ method to profile mRNA translation at single-cell and spatial resolutions, revealing translation dependencies on cell cycle and subcellular localization in brain tissue.

Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in an Alzheimer's disease model

The paper introduces STARmap PLUS to map single-cell transcriptional states and disease markers in AD mouse models, revealing spatial relationships between cell types and pathological features.

Disease Network Delineates the Disease Progression Profile of Cardiovascular Diseases

This study constructs a disease network from EHR data to map cardiovascular disease progression and identifies age-associated progression paths and risk models.