Gabriela Balderrama-Gutierrez

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper introduces Topyfic, a reproducible LDA method, to identify cellular programs in single-cell data and shows sex-specific differences in microglial activation in Alzheimer's disease mouse models.

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper shows that C5aR1 antagonism reduces amyloid load and dystrophic neurites in a mouse model of Alzheimer's disease, shifting microglial polarization toward a neuroprotective phenotype.

This study shows that modulating C5a-C5aR1 signaling in Alzheimer's disease models affects cognitive decline and gene expression related to inflammation and astrocyte activation.

The paper performs a comprehensive phenotypic analysis of the 5xFAD mouse model across its lifespan, identifying novel age-related pathological features.

The paper introduces LR-Split-seq, a long-read single-cell RNA-seq method, to study differential RNA isoform expression and validates it using mouse myoblast differentiation data.

The paper uses single-cell and nucleus RNA-seq to analyze glial subpopulations in AD mouse models, finding differences in astrocyte activation and microglia subtypes between 3xTg-AD and 5xFAD models.

This study compares the inflammatory responses of two rodent species to LPS, finding differences in cytokine profiles and metabolic pathways that suggest infection tolerance mechanisms in the deermouse.

This paper introduces Long-TUC-seq, a method combining metabolic labeling with long-read sequencing to reliably detect isoform-level transcription dynamics.

TALON annotates and counts full-length reads from PacBio or Nanopore in one framework; in mouse brain, 422 genes showed more novel-isoform reads than annotated ones.