Eddie L. Imada

The paper shows TFE3 fusions upregulate CD44 and SPP1 in tRCC, with potential therapeutic implications.

This study creates a mouse model of SFPQ-TFE3-driven renal tumors and shows it induces lineage plasticity through mTORC1 activation.

This study identifies rare germline variants associated with metastatic prostate cancer using an extreme phenotype cohort and validates their functional impact.

CALANGO identifies genotype-phenotype associations across species by integrating genomic, evolutionary, and phenotypic data to uncover biologically relevant molecular mechanisms.

The paper develops mechanistic classifiers using biological constraints to improve the robustness and interpretability of gene signatures in cancer prediction.

This study identifies multi-omics prognostic signatures for prostate cancer using transcriptomics and metabolomics data, showing their ability to stratify patients into distinct risk groups.

The paper introduces REPAC, a framework for analyzing alternative polyadenylation from RNA-sequencing data, showing it identifies APA changes in B cell activation and is faster than existing methods.

recount3 provides uniformly processed RNA-seq data and tools for querying and analyzing large-scale human and mouse expression and splicing data.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.