Jonathan S. Mill

The paper introduces PIPPA, a pipeline for processing large-scale ATAC-seq data, showing that peak calling performance varies by dataset and recommending parameters for high-confidence chromatin accessibility profiles.

The paper identifies seven sex-dependent differentially methylated positions in ALS blood samples, suggesting sex-specific biological mechanisms in the disease.

The paper introduces optimized fluorescence-activated nuclei sorting (FANS) protocols to isolate cell-type-specific nuclei from human and mouse brain tissue for multi-omic analysis.

The paper integrates multiomic data from human brain nuclei with GWAS statistics to prioritize neural cell types associated with brain-related traits.

The paper identifies cell-type-specific DNA methylation differences in autism, revealing female-specific X chromosome alterations in microglia.

The paper identifies neuron-specific DNA methylation differences in schizophrenia using cell type-resolved epigenome-wide association study in prefrontal cortex nuclei.

The paper shows miR-146a regulates multiple aspects of motor neuron degeneration in ALS, with genetic deletion extending survival and causing age-related paralysis and inflammation.

This study investigates the role of ZNF804A in human neurodevelopment, finding it regulates excitatory synapse formation through increased local protein translation in developing cortical glutamatergic neurons.

The paper identifies DNA methylation changes in transgenic mouse models of Alzheimer's disease, showing distinct patterns for tau and amyloid-beta pathology and some overlap with human AD data.

The paper identifies RNA-binding proteins (RBPs) whose regulation of synaptic mRNAs is enriched for schizophrenia genetic risk variants.

This study identifies neuron-specific DNA methylation changes in Parkinson's disease prefrontal cortex, revealing hypermethylation at seven novel loci and highlighting the importance of cell-type-specific analysis.

This study identifies 5'UTR exons containing uORFs as targets for splice-switching to increase protein translation in haploinsufficient disease genes.

This study investigates JAKMIP1's role in neuronal IL-6/STAT3 signaling and its implications for Dup15q syndrome, finding that JAKMIP1 deficiency impairs signaling and neuritogenesis.

The paper identifies SENP7 and UTF1/VENTX as new loci influencing cPCDH methylation in blood and brain through a genome-wide association study.

This study develops a human model of TDP43 proteinopathy by inducing endogenous TDP43 mislocalization in iPSC-derived neurons, revealing its role in neurodegeneration and splicing defects.

The paper identifies proteomic differences in cerebrospinal fluid between sporadic and familial ALS subtypes using network analysis and validates biomarkers across neurodegenerative diseases.

The paper shows that epigenetic variation recorded in mice during development predicts seizure susceptibility, with specific loci linked to human epilepsy genes.

The paper re-annotates the EPICv2 methylation array manifest to improve compatibility with previous versions and provide more comprehensive annotations for DNA methylation data.

The paper identifies sex-associated DNA methylation differences in ALS using a large-scale epigenome-wide association study and links them to survival outcomes.

The paper provides guidance for designing and analyzing cell-type specific epigenetic epidemiology studies using DNA methylation data from purified cell populations.

The paper examines sex differences in brain structure at birth in newborns, finding larger brain volumes in males and specific regional differences in gray and white matter volumes between sexes.

The paper develops a multivariate methylation risk score using blood DNA methylation data to predict dementia risk and cognitive impairment in Alzheimer's and Parkinson's disease cohorts.

The paper compares DNA methylation patterns in white matter of MSA, PD, and PSP to identify shared and disease-specific alterations.

The paper develops a computational framework to classify blood cell types from long-read sequencing data using DNA methylation patterns, showing accurate classification for some regions and cell types.

The paper characterizes expressed transcripts in the human cortex across development, identifying novel coding sequences with clinical relevance.

The paper investigates epigenetic age acceleration in schizophrenia, finding age- and sex-specific effects and associations with polygenic risk scores.

The paper develops and validates deconvolution models using DNA methylation data to estimate cell-type proportions in the human cortex, finding glial cells are twice as abundant as neurons and linking cell-type proportions to Alzheimer's disease neuropathology.

This study uses human naive PSC models to show FGF signaling is critical for hypoblast specification, revealing conservation with mouse lineage specification.

The paper quantifies DNA methylation changes in human fetal pancreas development, identifying developmental differentially methylated positions and their genomic distribution.

The paper uses long-read transcript sequencing to identify differential isoform expression in the entorhinal cortex of tau transgenic mice, revealing novel isoforms and transcript associations with tau pathology.