Tom C. Freeman

This study identifies mitochondrial dysfunction and impaired mitophagy in CKD-MBD as contributors to renal osteodystrophy, showing reversible effects with rapamycin treatment.

This study uses scRNA-seq to identify cell types and gene signatures in developing worker honey bees, providing a first single-cell atlas of honey bee development.

The paper uses single-cell RNA sequencing to show that CD16- monocytes are key in the transcriptional response of human monocytes to Toxoplasma infection, revealing transcriptional heterogeneity and cytokine secretion patterns.

Graphia is an open-source platform for graph-based analysis of complex biomedical data, offering visualization, transformation, and analysis tools for high-dimensional datasets.

The paper constructs a computational model of the mammalian renal circadian clock and validates it against experimental data to understand its role in blood pressure regulation.

The paper defines a core transcriptional signature of human microglia through meta-analysis and shows its utility in identifying region-specific alterations in Alzheimer’s disease.

The paper identifies 701 genes associated with human mitotic phases through transcriptomics analysis, including 205 putative cell cycle genes and 53 uncharacterised ones, with some showing novel centrosomal localization or proliferation inhibition.

The paper develops a graph-based visualization method for RNA-Seq data to better understand transcript diversity and assembly issues.

The paper characterizes the metagenome of UK honey bee colonies, identifying microbial diversity and potential pathogens in their microbiota.

The paper introduces survivALL, an R package for continuous biomarker assessment through survival analysis, enabling reliable evaluation of gene expression cut-points across datasets.

This paper presents a high-resolution gene expression atlas for sheep, identifying transcriptional signatures and functional annotations across tissues and developmental stages.