Catherine J. Wu

This paper introduces APC-ms, a platform that expands rare tumor-antigen-specific T cells from peripheral blood, achieving higher enrichment and functional properties compared to conventional methods.

PAIR-Scan identifies potent TCR-neoantigen pairs from tumor samples through library-on-library screening, enabling efficient analysis of T cell reactivity.

This paper develops LIME, a bacterial platform that engagers T and NK cells to target tumors, showing enhanced cytotoxicity and immune response in preclinical models.

The paper shows that inhibiting the CoREST complex with corin alters RNA splicing, increases neoantigen expression, and enhances tumor immunity in melanoma.

The paper identifies recipient stem-cell persistence and T-cell dysregulation as predictors of relapse after HSCT in AML/MDS by analyzing single-cell RNA and TCR sequencing data.

This study identifies ASXL1 truncating mutations as a driver of leukemic resistance to T cell attack and proposes EZH2 inhibition as a therapeutic strategy to overcome this resistance.

The paper analyzes single-cell data from bone marrow samples to identify immune cell interactions that predict response to adoptive cellular therapy in myeloid leukemia.

DIISCO infers dynamic intercellular interactions from time-series single-cell data using a Bayesian framework, showing its ability to capture time-dependent communication patterns in simulated and CAR-T cell data.

STAPLER is a transformer model that predicts TCR-pMHC specificity by learning from TCR and peptide sequences, outperforming existing methods in antigen recognition prediction.

Slide-tags enables spatial localization of single nuclei for multi-modal spatial genomics, achieving high-resolution mapping and multiomic profiling in various tissues.

FLAIR3 integrates SNV, fusion, and isoform analysis using long-read RNA-seq to better understand cancer drivers by capturing full-length molecules and their variant interactions.

This study developed a DNA origami-based cancer vaccine that co-delivers antigen and CpG immune adjuvant with an optimal nanospacing for Th1 immune polarization.

This paper introduces cyCombine, a method for integrating single-cell cytometry datasets to reduce technical variance and maintain biological structure, enabling robust and scalable analysis.

The paper develops a toolbox for scRNA-Seq and snRNA-Seq of fresh and frozen human tumors, testing it across eight tumor types and optimizing protocols for different tissue characteristics.

The paper uses nanopore sequencing to analyze full-length transcripts in CLL samples with and without SF3B1 mutations, revealing altered intron retention and splicing patterns.

PhylogicNDT statistically reconstructs cancer driver timing, subclonal phylogenies, and population dynamics from single- or multi-timepoint sequencing, revealing subtype-specific trajectories and therapy resistance evolution across 498 lung adenocarcinomas.

The paper identifies cancer-associated T cells using TCR repertoire and gene expression data, revealing novel regulators and antigens with potential for immune monitoring and immunotherapy.

Filtering STAR's chimeric alignments against gene annotations outscored 15 other fusion callers on 60 cancer cell lines and ran fastest, averaging 2.3 single-core hours per sample.