Joseph R. Ecker

This study shows that maternal immune activation disrupts DNA methylation and transcriptome of cortical excitatory neurons, delaying their maturation and affecting synapse-related genes.

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.

This paper creates a multimodal single-cell atlas of the human basal ganglia, revealing epigenomic and 3D genome features across cell types and linking them to disease-associated genetic risk.

The paper shows transient cell states in plants encode positional information to direct asymmetric growth through gene regulatory networks and hormonal signaling.

This paper develops a platform for longitudinal imaging and transcriptomics of live cells, revealing adaptive drug-resistant states and key drivers of cellular function through integrated analysis.

The paper presents a cross-species, multimodal atlas of the basal ganglia using single-cell transcriptomics and integrates epigenomic and spatial genomic data to enable cross-species comparisons.

The paper maps gene expression responses to loss of 1,947 disease-associated genes across the mouse brain using Perturb-seq, revealing cell-type-specific essentiality and transcriptional programs.

The paper uses single-cell epigenomics to study brain aging in mice, finding heterochromatin instability and transcription factor dysfunction across multiple brain regions and cell types.

This paper presents a single-cell multiome atlas of the human basal ganglia, linking chromatin states and transcriptomes to cell-type identity and disease-associated variants.

The paper creates a single-cell atlas of transcription and chromatin states in the human brain, identifying regulatory programs and linking them to neuropsychiatric disorders.

The paper presents an integrated single-cell and epigenomic resource for exploring basal ganglia datasets across species, enabling multi-omics and comparative analysis.

The paper introduces a coefficient of variation-based filter for RNAseq data to retain low-variation genes, enabling better identification of cell populations in Arabidopsis snRNAseq data.

This study identifies how genetic and environmental factors shape the human immune cell epigenome through differential methylation and chromatin accessibility changes.

The paper describes a multi-institutional program for collecting neurotypical human brains to support multiomic brain cell atlas studies, highlighting challenges and opportunities for donor recruitment.

The paper defines major axes of human basal ganglia astrocyte specialization using a multimodal atlas and identifies enhancer code for targeted viral tools.

This paper creates a high-resolution spatial transcriptomic atlas of the human basal ganglia, identifying 60 cell types and their spatial organization across multiple nuclei.

This study presents a single-cell multi-omic atlas of Alzheimer's disease brain regions, revealing region-specific epigenomic changes and altered cell states.

The paper analyzes the epigenomic changes in innate immune cells after influenza virus infection and finds coordinated rewiring of the epigenetic landscape.

The paper presents a multimodal epigenome atlas of human immune cells exposed to viral and chemical agents, revealing epigenetic changes in transcription factor binding sites and cytokine networks.

The paper identifies cell type-specific aneuploidy in the adult mouse brain, finding a strong enrichment of chromosome 16 trisomy in non-neuronal cells.

The paper evaluates computational methods for predicting cell type-specific enhancers in the mouse cortex using in vivo validation data and finds that open chromatin and sequence models improve prediction accuracy.

This study examines DNA methylation changes in blood and muscle across different training programs and timepoints, identifying DMRs linked to exercise adaptation, sex, and physiological functions.

The paper maps epigenetic and spatial transcriptomic changes in aging mouse brain using single-cell multi-omic data and develops deep-learning models to predict age-related gene expression changes.

The paper shows drought stress accelerates leaf maturation transcriptional responses in Arabidopsis, and demonstrates targeted upregulation of FERRIC REDUCTION OXIDASE 6 can increase leaf growth under stress.

The paper introduces BAllC, a binary format for single-cell DNA methylation data, and BAllCools, a toolkit to improve storage and operational efficiency.

The paper examines age and sex effects on human cortical neurons using multiomic data, finding age-related changes in gene expression and DNA methylation, and sex differences in gene expression and X-inactivation escape.

This paper introduces scPRS, a deep learning model that deconvolves polygenic risk scores at the single-cell level to uncover cellular and molecular disease mechanisms in complex human diseases.