Juan Antonio Botía

The paper evaluates antimicrobial peptide prediction tools and proposes a standardized evaluation framework to improve comparability and reproducibility.

go3 provides a fast and lightweight Rust-based library for calculating semantic similarity of GO terms and genes, achieving significant speed and memory improvements over existing tools.

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 uses long-read RNA-seq to study splicing changes in an Alzheimer's mouse model, identifying novel transcript isoforms and alternative splicing events in response to amyloid-beta.

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

The paper introduces scCoExpNets and CovCoExpNets to analyze cell-type specific gene co-expression networks from single-cell RNA-seq data, identifying iron accumulation as a factor in dopaminergic neuron vulnerability in Parkinson's disease.

The paper identifies and replicates epistatic variant-variant interactions in Parkinson's disease across genetically diverse populations using a new pipeline called VARI3.

The paper shows that a significant portion of gene expression regulation in the human brain occurs post-transcriptionally in the cytoplasm, particularly for synaptic genes.

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.

This paper develops an automated ML model to predict Parkinson's Disease using multi-modal data, achieving high AUC scores and constructing gene networks relevant to PD.

The paper identifies microglial activation as a factor contributing to cortical thinning in epilepsy by integrating neuroimaging and gene expression data.

PhenoExam is an R package and web tool that performs phenotype and disease enrichment analysis on gene sets, detecting significant phenotypic similarities and differences across databases.

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 identifies a genetic variant in OAS1 linked to increased Alzheimer's disease risk and severe COVID-19 outcomes, showing its role in microglial inflammation.

This study investigates how TREM2 influences microglial anti-inflammatory responses and shows that reduced TREM2 expression impairs anti-inflammatory gene expression and STAT6 levels.

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

The paper identifies pathway-specific polygenic risk factors and transcriptomic networks associated with Parkinson disease using large-scale genetic and expression data.

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.

The paper identifies disease-relevant regulatory loci in human basal ganglia using genomic and transcriptomic data from 117 brains, highlighting splicing eQTLs and ASE analyses as sources of cell-specific regulatory information.

Across 37,688 Parkinson's cases, 18,618 proxy-cases and 1.4M controls, 90 risk signals map to 78 loci (37 new); an 1805-variant polygenic score explains 26-36% of heritability.

This study conducts a GWAS of Parkinson disease in Spain, identifies a novel population-specific signal at PARK2 associated with age-at-onset, and highlights genetic substructure for future fine-mapping.

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

This paper integrates eQTL and Parkinson’s disease GWAS data to identify 11 disease genes and pathways involved in PD risk through colocalisation, TWAS, and network analysis.

This study connects Parkinson’s disease heritability to cell-type-specific gene regulation, finding enrichment in lysosomal genes in astrocytic and microglial subtypes rather than specific cell types or brain regions.