Kunal Rai

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.

This study compares canine and human peripheral nerve sheath tumors, finding that H3K27me3 loss and H3K27ac gain drive tumor progression in both species.

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.

The paper identifies a fasting-induced microbiome-metabolite-chromatin axis that primes intestinal stem cells for regeneration after radiation injury.

This study identifies Med4 as a regulator of metastatic dormancy in breast cancer, showing its role in maintaining chromatin structure and suppressing enhancer activation.

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.

This study clarifies that NOTCH1 acts as a tumor suppressor in head and neck cancer, reducing cancer stem cells and improving prognosis, despite conflicting prior reports.

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.

This study identifies Bhlhe40 as a key regulator of T cell effector differentiation, showing distinct roles in CD4 and CD8 T cells for anti-PD-1 and anti-CTLA-4 therapies.

The paper identifies a mature dendritic cell subtype associated with improved immune response and prognosis in melanoma patients treated with anti-PD-1 checkpoint inhibitors.

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.

This study shows that disrupting the WRAD core in pancreatic cancer leads to DNA replication errors, immune response activation, and improved response to immune checkpoint inhibitors.

The paper introduces a method to construct gene-specific methylation profiles for integrative methylation-expression analysis in cancer, showing improved explanation of expression variability and identification of methylation differences across cancer subtypes.

The paper shows that MLL4 loss in lung cancer promotes glycolysis and that inhibiting glycolysis selectively targets MLL4-mutant lung tumors.