Meng Xiao He

Systemic neoantigen-specific T cells reveal central determinants of PD-(L)1 blockade efficacy

The paper identifies coordinated neoantigen-specific CD8 T cell responses as key predictors of PD-(L)1 therapy efficacy in non-small cell lung cancer patients.

Single-cell epigenetic profiling reveals an interferon response-high program associated with BAP1 deficiency in kidney cancer

The paper identifies an IFN response-high epigenetic program linked to BAP1 deficiency in kidney cancer using single nucleus ATAC sequencing across multiple cohorts.

Epiregulon: Inference of single-cell transcription factor activity to predict drug response and drivers of cell state

Epiregulon infers single-cell TF activity using ATAC-seq and RNA-seq to predict drug response and identify drivers of cell state.

Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics

The paper introduces BEANIE, a nonparametric method to improve differential enrichment analysis in single-cell transcriptomics by accounting for sample-specific biology and robustness of signatures across cohorts.

Mutational footprint of platinum chemotherapy in a secondary thyroid cancer

This paper reports a case where platinum chemotherapy exposure was linked to the development of aggressive thyroid cancer through mutational signatures and genomic analysis.

Transcriptional mediators of treatment resistance in lethal prostate cancer

This study identifies transcriptional states in mCRPC that mediate treatment resistance, including AR splicing heterogeneity, TGF-β signaling, and immune infiltration patterns.

CoMut: Visualizing integrated molecular information with comutation plots

CoMut creates customizable comutation plots from user data to visualize genomic and phenotypic relationships in patient cohorts.

Germline features associated with immune infiltration in solid tumors

The paper identifies germline genetic features associated with immune infiltration in solid tumors using TCGA data and develops a framework for studying inherited factors influencing immune microenvironment.

Intron retention as a novel source of cancer neoantigens

This paper identifies intron retention as a new source of cancer neoantigens and shows that retained intron neoantigen burden correlates with immune checkpoint blockade response.