Jeremy M. Simon

Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories

The paper links early cell cycle gene expression in cortical organoids to interindividual variability in infant brain growth trajectories.

Single-cell transcriptomics predict novel potential regulators of acute epithelial restitution in the ischemia-injured intestine

The paper uses single-cell RNA sequencing to identify CSF-1 as a potential regulator of age-dependent intestinal epithelial restitution in a pig model.

The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice

The paper updates the MiniMUGA genotyping array's bioinformatic pipeline to enhance genetic QC in laboratory mice by improving marker annotation, consensus genotypes, and report usability.

Investigating cocaine- and abstinence-induced effects on astrocyte gene expression in the nucleus accumbens

This study identifies molecular changes in astrocytes of the nucleus accumbens in rats following cocaine self-administration and abstinence using RiboTag and RNA-seq.

Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids

This study shows that UBE3A loss affects both neuronal and non-neuronal cells in human cerebral organoids, altering cell composition and transcriptomes.

A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV infected cells

The paper identifies HDAC inhibitors as agents that prevent HIV latency by maintaining viral expression and altering memory T cell phenotypes in infected cells.

Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders

The paper shows environmental carcinogens like PAHs disproportionately mutate genes linked to neurodevelopmental disorders such as ASD and schizophrenia.

Distinct roles for canonical and variant histone H3 lysine 36 in Polycomb silencing

The paper shows that H3.2 and H3.3 K36 residues have distinct roles in maintaining Polycomb silencing of Hox genes through different mechanisms, enabling development.

Single-cell dynamics of core pluripotency factors in human pluripotent stem cells

This study uses CRISPR/Cas9 and microraft arrays to track OCT4, SOX2, and NANOG dynamics in human stem cells during differentiation, revealing spatiotemporal patterns in germ layer formation.

Basal forebrain cholinergic circuits orchestrate diverse cell types in the adult dentate gyrus to support neural stem cell function and spatial memory

This study identifies cholinergic circuits that regulate neural stem cell function and spatial memory by orchestrating diverse cell types in the dentate gyrus through transcriptomic and functional analyses.

Rescue of behavioral and electrophysiological phenotypes in a Pitt-Hopkins syndrome mouse model by genetic restoration of Tcf4 expression

This study shows that restoring Tcf4 expression in neurons of a PTHS mouse model improves behavioral and electrophysiological phenotypes.

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

The paper identifies genetic regulators of gene expression and chromatin accessibility across multiple tissues using a genetically diverse mouse population and proposes a causal model for gene regulation.

Single-cell transcriptomic catalog of mouse cortical development

This study creates a single-cell transcriptomic catalog of mouse cortical development, revealing cell types, states, and their relationships, and linking gene expression to disease subtypes.

Defects of myelination are common pathophysiology in syndromic and idiopathic autism spectrum disorders

The paper compares mouse models of syndromic ASD with human ASD brain data to identify shared myelination and axon development disruptions across both syndromic and idiopathic ASD.