Tim O. Nieuwenhuis

Monkeybread: A Python toolkit for the analysis of cellular niches in single-cell resolution spatial transcriptomics data

Monkeybread identifies cellular niches in spatial transcriptomics data, revealing immunogenic and tolerogenic macrophage populations in melanoma tumors.

Patterns of unwanted biological and technical expression variation across 49 human tissues

This study identifies biological and technical sources of expression variation across 49 human tissues using GTEx data, revealing 522 variable transcript clusters with varying confidence in their explanations.

Sex, age, tissue, and disease patterns of matrisome expression in GTEx transcriptome data

The paper analyzes matrisome gene expression patterns across tissues, age, sex, and disease using GTEx and TCGA data, finding that transcriptomics can recapitulate proteomic patterns and identify tissue-specific and sex/age-related expression variations.

Proteogenomic single cell analysis of skeletal muscle myocytes

The paper integrates proteomic and genomic data from skeletal muscle myocytes to identify gene and protein expression differences between slow and fast-twitch fiber types.

Basal Contamination of Sequencing: Lessons from the GTEx dataset

The paper identifies basal contamination in GTEx data, showing that highly expressed tissue-specific genes contaminate samples, affecting eQTL assignments and analysis accuracy.