Md Ishtyaq Mahmud

This paper introduces a counterfactual framework to analyze directional cell-cell interactions in spatial transcriptomics, identifying significant asymmetric influences between tumor, immune, and stromal compartments in cholangiocarcinoma tissue.

The paper introduces an ambiguity-aware framework for spatial cell-type annotation, reducing cluster and cell-level ambiguity in cholangiocarcinoma data.

NanoCellAnnotator improves spatial transcriptomics cell-type annotation by combining biological constraints and LLMs, identifying canonical cell populations and flagging ambiguous clusters.

HyperNiche improves clustering and biological interpretability of spatial transcriptomics data by modeling higher-order cellular niches with hypergraph neural networks.

The paper develops a framework to integrate spatial transcriptomics with single-cell multiome data to infer spatially resolved regulatory programs in melanoma.