Veena Kochat

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 identifies enhancer subtypes in cancer cell lines and tumors, revealing distinct epigenetic patterns and potential therapeutic targets.

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.

This study identifies two epigenetically distinct cell states in leiomyosarcoma using single-nucleus multiome sequencing and spatial transcriptomics, linking them to clinical outcomes and therapeutic vulnerabilities.

This study identifies stemness features in luminal hormone-responsive cells within DCIS that correlate with invasive progression and shows that targeting FOXA1 reduces tumor growth.

This study shows BET + MAPK inhibitors improve efficacy against BRAFV600E CRC by inducing epigenetic reprogramming and cellular plasticity through enhancer dynamics disruption.

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

This study uses single-nucleus multiome sequencing and spatial transcriptomics to analyze liposarcoma subtypes, revealing distinct cellular states, immune features, and gene regulatory circuits.

The paper creates a poly(A) isoform-aware single-cell and spatial atlas of the human bladder, identifying fibroblast niches and their spatial relationships.

This study shows ATRX loss in sarcomas correlates with poor outcomes and identifies TEAD inhibition as a potential therapy for ATRX-deficient tumors.

The paper investigates how alternative polyadenylation (APA) regulates urothelial differentiation using single-cell RNA-seq and spatial imaging, showing APA's role in shaping cell state-specific polyadenylation sites and transcriptome diversity.