Zhi‐Jie Cao

CASCADE is a framework for causal regulatory inference and rational transcriptomic reprogramming design, enabling causal discovery and intervention design for targeted cells.

PASSAGE identifies phenotype-associated spatial signatures in spatial transcriptomics data using a deep learning framework.

DECIPHER generates high-fidelity disentangled embeddings for large-scale heterogeneous spatial omics data, outperforming existing methods and enabling global analysis.

SLAT aligns heterogeneous spatial omics data by integrating omics profiles and spatial context, improving cell-typing resolution and regulatory inference.

This paper introduces GLUE, a framework for integrating unpaired single-cell multi-omics data using regulatory knowledge, showing improved accuracy and scalability across various tasks.

A NeurIPS 2021 benchmarking competition evaluated over 2600 submissions from 280 competitors across three multimodal single-cell integration tasks using a purpose-built benchmarking dataset and cloud evaluation pipeline.

Cell BLAST provides a tool for querying and annotating scRNA-seq data using a reference database and web interface.

The paper introduces GeACT, a genomic database for human mid-gestation fetus cells, linking gene expression to chromatin states and identifying key transcription factors.