Huy Q. Dinh

Spatial Autocorrelation Aware Resampling Improves Cell-Cell Interaction Inference in Spatial Transcriptomics Data

SOAAR improves cell-cell interaction inference in spatial transcriptomics by accounting for spatial autocorrelation, reducing false positives and identifying consistent immune signatures in cancer patients.

Single-cell multi-omics analysis reveals heterogeneity and plasticity of neutrophil states in response to immunotherapies

This study identifies treatment-induced neutrophil states in tumors using single-cell multi-omics, showing ICAM1 as a marker of anti-tumor activity and potential biomarker for immunotherapy response.

SR2P: an efficient stacking method to predict protein abundance from gene expression in spatial transcriptomics data

SR2P predicts protein abundance from RNA expression in spatial transcriptomics data, improving immune cell identification in tumors.

Immune-mediated Engagement of T Regulatory Cells with Tumor Cells Results in Trogocytosis and Tumor Cell Killing.

The paper shows CD4 T regulatory cells can kill tumor cells through trogocytosis after immunocytokine treatment in a melanoma model.

Divergent role of CD8 T cells with distinct metabolic phenotypes during curative radio-immunotherapy in hot versus cold tumors

This study examines how CD8 T cells with different metabolic profiles contribute to tumor cure in hot versus cold murine tumors using radio-immunotherapy.

Fluoro-forest: A random forest workflow for cell type annotation in high-dimensional immunofluorescence imaging

Fluoro-forest improves cell type annotation in immunofluorescence imaging using a semi-supervised random forests workflow with cluster-based sampling and probabilistic outputs.

Integrated single-cell and spatial analysis identifies context-dependent myeloid-T cell interactions in head and neck cancer immune checkpoint blockade response

This study identifies context-dependent myeloid-T cell interactions in HNSCC ICB response using integrated single-cell and spatial omics data.

Single-cell transcriptional landscape of temporal neutrophil response to burn wound in larval zebrafish

This study maps the temporal neutrophil response to burn wounds in larval zebrafish, identifying distinct subsets and their interactions, and links zebrafish myeloid signatures to human burn severity.

A cellular and molecular portrait of endometriosis subtypes

This study profiles single-cell transcriptomes of endometriosis subtypes to identify transcriptional differences and associations with ovarian cancer.

Single-cell Transcriptomics Identifies Gene Expression Networks Driving Differentiation and Tumorigenesis in the Human Fallopian Tube

This study uses single-cell transcriptomics to identify gene expression networks in the human fallopian tube, revealing epithelial subtypes and their role in cancer progression.

StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation.

The paper introduces StateHub and StatePaintR to provide rapid, reproducible chromatin state annotations for genome annotation, supporting variant prioritization and analysis.