Roger Pique-Regi

Traumatic brain injury causes retention of long introns in metabolic genes via regulation of intronic Histone 3 lysine 36 methylation levels in the sub-acute phase of injury

This paper investigates how traumatic brain injury (TBI) affects alternative splicing in Drosophila by increasing retention of long introns in metabolic genes through regulation of H3K36me3 levels.

Genetic and transcriptional analysis of human host response to healthy gut microbiome

This study identifies gene expression changes and host SNPs influenced by the gut microbiome in human cells, linking them to microbiome-related diseases.

Efficient Integrative Multi-SNP Association Analysis using Deterministic Approximation of Posteriors

This paper introduces DAP, a method for efficient integrative multi-SNP association analysis that improves computational efficiency and rigor in incorporating genomic annotations into GWAS and molecular QTL mapping.

A high-throughput RNA-seq approach to profile transcriptional responses

The paper introduces a two-step RNA-seq approach to efficiently profile transcriptional responses to multiple treatments across cell lines.

Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells

This study shows that bacterial infection rapidly alters DNA methylation in human dendritic cells, affecting enhancer elements and gene expression related to immune responses.

Cross-population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

This study improves eQTL discovery and fine mapping by analyzing data across multiple populations, finding that variants disrupting transcription factor binding are enriched in eQTLs.

Which genetic variants in DNase I sensitive regions are functional?

The paper identifies functional genetic variants in DNase I sensitive regions by integrating sequence and footprinting data, finding they are enriched for allele-specific binding and GWAS traits.

QuASAR: Quantitative Allele Specific Analysis of Reads

QuASAR jointly infers genotypes and allele-specific expression while accounting for sequencing errors and allelic over-dispersion, showing effectiveness when genotypes are unavailable.