Recounting the FANTOM Cage Associated Transcriptome

Long non-coding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes including human diseases. We …

recount-brain: a curated repository of human brain RNA-seq datasets metadata

recount-brain: a curated repository of human brain RNA-seq datasets metadata

The usability of publicly-available gene expression data is often limited by the availability of high-quality, standardized biological phenotype and experimental condition information (“metadata”). We released the recount2 project, which involved …

Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells

Understanding the molecular profile of every human cell type is essential for understanding its role in normal physi-ology and disease. Technological advancements in DNA sequencing, mass spectrometry, and computational methodsallow us to carry out …

Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information

Genome-wide association studies have generated an increasing number of common genetic variants that affect neurological and psychiatric disease risk. Given that many causal variants are likely to operate by regulating gene expression, an improved …

Reproducible RNA-seq analysis with recount2

Junior Research Symbiont Award Presentation for Excellence in Data Sharing at PSB2019

Reproducible RNA-seq analysis with recount2 and recount-brain

Work in progress presentation on recount-brain for the Joint Genomics Meeting

Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses

Background: Antibody class switch recombination (CSR) to IgG, IgA or IgE is a hallmark of adaptive immunity, allowing antibody function diversification beyond IgM. CSR involves a deletion of the IgM/IgD constant region genes placing a new acceptor …

From learning to using to teaching to developing R

Keynote to kickoff the CDSB Mexico 2018 R/Bioconductor workshop

Reproducible RNA-seq analysis with recount2 and recount-brain

Guest lecture for LCG-UNAM spanning some recent research