Sonia García-Ruiz

IsoMatch integrates transcript models across references, showing how reference choice affects estimates of transcript novelty.

SALRR provides a scalable platform for long-read RNA-seq analysis, identifying novel splice variants in human brain tissue.

Isopedia reduces apparent isoform novelty by up to 26-fold in HG002 benchmarks and provides a reference-agnostic framework for population-scale isoform annotation.

The paper identifies splicing dysregulation in Parkinson's disease linked to TDP-43 loss of function and shows its association with genetic mutations and cellular models.

The paper shows that astrocytic RNA editing via ADAR1 modulates immune responses to alpha-synuclein, contributing to neuroinflammation in Parkinson's disease.

The paper examines mis-splicing across human introns, tissues, and age using RNA-sequencing data, finding correlations with spliceosome components and age-related neurodegenerative disease genes.

This study uses bulk and single nuclear RNA-sequencing to analyze transcriptomic changes in repeat expansion ataxias, revealing distinct non-neuronal cell type-specific disease signatures across the human brain.

The paper shows that sequencing ambiguity between GBA1 and its pseudogene GBAP1 affects transcriptomic analysis, revealing non-lysosomal functions in the brain and widespread annotation inaccuracies.

The paper investigates ligand-receptor interactions (LRIs) in neurological diseases and finds that 96.8% of disease-associated LRIs are interconnected, highlighting their role in disease comorbidity and potential drug targets.

The paper identifies 88 novel rare disease-gene associations using a burden analysis framework on whole genome sequencing data from the 100,000 Genomes Project, with potential clinical impact for undiagnosed cases.

The paper investigates the regulatory role of the NSL complex in Parkinson's disease by analyzing gene expression and regulatory networks in brain tissues.

ggtranscript is an R package that visualizes and compares transcript isoforms using ggplot2, offering flexibility and ease of use for analyzing long-read sequencing data.

The paper identifies 1,513 unannotated 3'UTRs across 39 human tissues using a machine learning framework, highlighting their enrichment in brain and synaptic function.

The paper identifies 38 genes regulating a-synuclein cell-to-cell transfer using an siRNA screen and shows genetic overlap with Parkinson's disease.

The paper identifies human-lineage-specific genomic elements, called CNCRs, and shows their enrichment in neurological disease genes and APOE intron-3 retention transcripts in Alzheimer's disease.

This paper introduces dasper, an R/Bioconductor package that detects pathogenic splicing events from RNA-sequencing data with higher accuracy than existing methods.

The paper introduces GMSCA, a tool to enhance gene multifunctionality predictions in bulk-tissue co-expression networks, revealing new roles for genes like SNCA in oligodendrocytes.

The paper examines mitochondrial-nuclear gene relationships in human brain tissue, finding cell-type specific variations and disruptions in Alzheimer’s disease.

CoExp Web provides a web tool and software for analyzing and sharing co-expression network models.

This study identifies cell-type-specific expression of dystonia-associated genes and links them to shared genetic and biological mechanisms with psychiatric disorders.

The paper identifies and validates novel transcription regions across tissues, improving gene annotation for 63% of OMIM-morbid genes and highlights tissue-specific and functionally significant variants.

ERASE assesses enrichment of GWAS risk loci in ASE data and identifies splicing-related ASEs associated with Parkinson's disease.