Jeremy J. Day

nf_xpatial provides a standardized Nextflow pipeline for preprocessing and clustering Xenium spatial transcriptomics data, enabling reproducible analysis and parameter comparison.

The paper identifies a rare striatal neuron population, Chst9-MSNs, that is critical for opioid reward and distinct from canonical pathways.

The paper functionally characterizes two transcriptionally distinct VTA dopamine neuron subtypes using single nucleus RNA sequencing and AAV-based cell-type-specific analysis.

This study shows that adolescent amphetamine exposure causes sex-specific changes in mesolimbic dopamine axons and PFC dopamine transporter expression in adulthood, with males showing increased vulnerability to drug effects.

This study demonstrates using sex-dependent gene expression patterns to accurately deconvolve pooled snRNA-seq data, achieving 93-95% accuracy in cell sex classification.

This study identifies morphine-induced transcriptional changes in VTA glial cells and dopamine neurons, revealing glucocorticoid-mediated regulation of Fkbp5 in astrocytes.

This study identifies Reelin as a marker of cocaine-activated neuronal ensembles in the rat nucleus accumbens and shows its role in cocaine reward and neuronal excitability.

The paper identifies a novel population of Oprm1-expressing neurons in the NAc marked by Chst9 expression, showing spatial and transcriptional distinctiveness across species.

This study investigates the functional roles of Bdnf I and Bdnf IV transcript variants in hippocampal neurons using CRISPRa, finding distinct effects on dendritic growth and fear behavior.

This study shows that amphetamine exposure in adolescence causes sex-specific changes in dopamine axon growth via Netrin-1/DCC signaling, with male mice showing increased vulnerability.

The paper identifies a conserved enhancer upstream of Pdyn that is regulated by activity-dependent transcription factors and required for Pdyn expression in neurons.

The paper uses snRNA-seq to identify distinct D1-MSN subpopulations with differential transcriptional responses to cocaine in rats.

The paper generates a transcriptional atlas of the rat ventral tegmental area using snRNA-seq, identifying 16 cell types, including neurons co-expressing multiple neurotransmitter systems and associated with neuropsychiatric disorders.

The paper develops a Cre-dependent CRISPR-dCas9 system for gene regulation in neurons, showing improved specificity over traditional methods.

This paper improves CRISPR/dCas9 interference for neuronal gene suppression by using a dual lentivirus system and dCas9-KRAB-MeCP2 construct, showing superior repression of the Bdnf gene in rat neurons.

This study investigates the role of Gadd45b in dopamine-dependent transcription and cocaine reward, showing its necessity for cocaine-induced behavioral and epigenetic changes.

The paper identifies enhancer-gene regulatory links using eRNAs and shows their functional importance in neuronal systems.

This study shows that increased BIN1 expression in neurons leads to hyperexcitability, which is modulated by Tau, suggesting a role for BIN1 in Alzheimer's disease pathogenesis.

This study identifies a dopamine-induced gene expression signature in the nucleus accumbens that drives cocaine-induced physiological and behavioral adaptations in rats.

This study shows blue light exposure alters gene expression in cultured neurons, but this effect is due to phototoxic interactions between light and culture media, not direct neuronal activation.

This paper develops a neuron-optimized CRISPRa system for efficient and specific gene regulation in neurons and the adult brain.