Joshua J. Waterfall

The paper shows EWSR1::FLI1 fusion drives the production of cancer-specific neoproteins in Ewing sarcoma, revealing a reversible dark proteome with therapeutic potential.

This paper introduces an alignment-last approach to transcriptomic analysis, enabling rapid biomarker discovery by using reads directly and revealing new transposable-element signatures and prognostic reads in cancer.

The paper demonstrates that TCR-T cells targeting neogene-encoded antigens can specifically kill Ewing sarcoma cells in vitro and in vivo.

Yomix is an interactive tool for exploring low-dimensional embeddings in omics data, allowing users to define subsets, compute feature signatures, and compare distributions.

The paper introduces a PDX platform for pediatric cancers, providing in vivo drug testing models and molecular data to aid in therapy development.

This study shows that poly(I:C) reprograms myeloid cells in rhabdoid tumors, enhancing CD8+ T cell infiltration and improving response to PD-1 blockade.

This study shows that combining PD-L1 and TIGIT blockade in a mouse model of rhabdoid tumors leads to tumor regression by promoting immune cell recruitment and vascular changes.

The paper identifies a common origin for effector and regulatory CD4+ T cells in non-small cell lung cancer through single-cell analysis, revealing their plasticity and role in immune responses.

pyALRA provides a Python implementation of ALRA for imputing dropouts in single-cell RNA-seq with improved speed and memory efficiency.

The paper evaluates deconvolution methods for inferring immune infiltration from bulk gene expression using a DREAM Challenge, finding that some community-contributed methods, especially deep learning-based ones, perform well.

The paper uses multi-omics analysis to compare malignant and normal uveal melanocytes, identifying genomic instability and a BAP1 promoter deletion as key features of uveal melanoma.