Rui Fu

DECONVersation uses single-cell foundation model embeddings to improve bulk RNA-seq deconvolution by reducing batch effects and eliminating marker gene selection.

This study shows that elevated intraocular pressure compromises the blood-retinal barrier, leading to vascular leakage and retinal ganglion cell death in glaucoma models.

This paper identifies a NGF variant that selectively biases TrkA signaling towards neurotrophic functions without triggering pain, revealing mechanisms for therapeutic targeting of the NGF-TrkA pathway.

This study uses multi-omics approaches to analyze pediatric low-grade glioma and identifies immune-related differences linked to BRAF mutations.

The paper identifies the amino acid preceding a premature termination codon as a key determinant of nonsense-mediated mRNA decay efficiency.

This study uses spatial transcriptomics to analyze human adrenal tissue, supporting the centripetal differentiation model and characterizing aldosterone-producing micronodules.

The paper shows that inhibiting NMD in FSHD leads to widespread production of truncated RNA-binding proteins, some of which are toxic and can be detected in patient samples.

The paper introduces scraps, a pipeline for high-resolution APA detection in scRNA-seq, showing it outperforms existing methods and enables assessment of internal priming events.

This study identifies Srsf3 as a regulator of alternative RNA splicing downstream of PDGFRα signaling, which is critical for craniofacial development.

The paper identifies RNA-binding proteins and RNA decay factors that regulate aldosterone production kinetics in steroidogenic cells through coordinated transcription and decay mechanisms.

This paper highlights the issue of insufficient metadata in scRNA-seq studies, hindering data reuse and reproducibility, and advocates for improved documentation standards.

clustifyr assigns cell types to scRNA-seq clusters using diverse reference data and provides tools for exploratory analysis.

The paper develops a method to recover and analyze targeted transcriptome subsets from scRNA-seq libraries, improving sequencing depth and gene detection.