James W. MacDonald

Prenatal cannabis exposure affects human fetal neurodevelopment: anintegrated multi-omics study

This study investigates the molecular effects of prenatal cannabis exposure on human fetal brains, finding significant disruptions in male second trimester brains linked to neurodevelopmental disorders.

Voclosporin Preserves Mitochondrial Function Compared With Cyclosporine A in Perfused Human Proximal Tubule Microphysiological Systems

This study compares voclosporin and cyclosporine A in 3D kidney MPS, finding that voclosporin preserves mitochondrial function and reduces proteostatic stress compared to cyclosporine A.

EpiBrain: the brain's epigenetic landscape in a snapshot

EpiBrain visualizes whole-brain epigenetic changes in zebrafish following perturbations like brain activity and chemical exposure, revealing gadd45b's role in experience-induced epigenetic modifications.

From Home to Transcriptome: Comparing the transcriptomic profile of induced immune response via lipopolysaccharide stimulation in homeRNA and venous blood

This study compares the transcriptomic profiles of LPS-induced immune responses in homeRNA and venous blood samples, showing homeRNA captures comparable inflammatory responses.

The Placental Transcriptome Serves as a Mechanistic Link between Prenatal Phthalate Exposure and Placental Efficiency

This study identifies placental transcriptome genes and modules mediating the effect of prenatal phthalate exposure on placental efficiency and fetal growth.

Butyrate rescues chlorpyrifos-induced social deficits through inhibition of class I histone deacetylases

The paper shows that butyrate rescues CPF-induced social deficits in zebrafish by inhibiting class I HDACs, linking CPF exposure to gut microbiome, metabolome, and epigenetic changes.

Evaluation of toxicological mechanisms of ochratoxin-A in human primary proximal tubule epithelial cells

This study investigates OTA toxicity in human kidney cells, showing it causes mitochondrial dysfunction, oxidative stress, and reduced energy production, contributing to kidney disease.

Mitochondrial Calcium Signaling Regulates Branched-Chain Amino Acid Catabolism in Fibrolamellar Carcinoma

This study shows that mitochondrial calcium signaling regulates branched-chain amino acid catabolism and the urea cycle in fibrolamellar carcinoma through transcriptional control of metabolic genes.

Glucocerebrosidase deficiency leads to neuropathology via cellular immune activation

This study identifies macrophage activation as a key mechanism by which GBA mutations contribute to neuropathology in a Drosophila model.

Rigor and Reproducibility of Digital Spatial Profiling on Clinically Sourced Human Tissues

This study evaluates the rigor and reproducibility of digital spatial profiling in clinically sourced human tissues, finding it to be highly reliable.

Associations Between Prenatal Vitamin D and Placental Gene Expression

This study examines the association between prenatal vitamin D levels and placental gene expression, finding 25 differentially expressed genes linked to mid-pregnancy vitamin D levels.

RNAseqCovarImpute: a multiple imputation procedure that outperforms complete case and single imputation differential expression analysis

RNAseqCovarImpute improves differential expression analysis by handling missing covariate data through multiple imputation, outperforming complete case and single imputation methods.

A Genome Scale Transcriptional Regulatory Model of the Human Placenta

The paper constructs a genome-scale transcriptional regulatory network of the human placenta using genomic and transcriptomic data, identifying key regulators of preterm birth.

Transcriptomic comparison of in vitro models of the human placenta

This study compares transcriptomes of in vitro human placental models to bulk placental tissue, finding significant gene expression differences and developing a web tool for model selection.

Ancestry-specific maps of GRCh38 linkage disequilibrium blocks for human genome research

The paper creates ancestry-specific linkage disequilibrium block maps for GRCh38, providing updated LD blocks for four populations.