James C. Nemesh

Sibling chimerism among microglia in marmosets

The paper identifies sibling-derived chimerism in microglia and macrophages across marmoset tissues using single-cell RNA-seq, showing hematopoietic origin and regional variation in brain microglia.

Common variation of cell abundances and gene expression in the human striatum

The paper analyzes single-nucleus RNA-seq data from the human striatum and prefrontal cortex to study inter-individual variation in cell abundances and gene expression, finding age-related changes and genetic associations.

Mesoscale molecular architecture of the human striatum across cell types and lifespan

The paper maps a mesoscale molecular architecture of the human striatum across cell types and age, revealing zonal differences in gene expression and aging effects.

Concerted neuron-astrocyte gene expression declines in aging and schizophrenia

The paper identifies a neuron-astrocyte gene expression program, SNAP, that declines in aging and schizophrenia, linking it to cognitive function and genetic risk factors.

A marmoset brain cell census reveals influence of developmental origin and functional class on neuronal identity

The paper analyzes single-nucleus RNA sequencing data from marmoset brain cells to show that neuronal identity is more influenced by developmental origin than functional class.

Efficient generation of lower induced Motor Neurons by coupling Ngn2 expression with developmental cues

This study combines Ngn2 overexpression with small molecule patterning to efficiently generate lower induced Motor Neurons (liMoNes) from hPSCs, achieving high yields and functional characteristics.

Ascertaining cells' synaptic connections and RNA expression simultaneously with massively barcoded rabies virus libraries

The paper introduces SBARRO, a method that maps synaptic connections and RNA expression in neurons using barcoded rabies virus and single-cell RNA sequencing, revealing cell-type-specific synaptic networks in mouse brain cells.

Natural variation in gene expression and Zika virus susceptibility revealed by villages of neural progenitor cells

The paper identifies a common genetic variant in IFITM3 that explains most inter-individual variation in neural progenitor cell susceptibility to Zika virus using natural genetic variation and synthetic perturbations.

Innovations in Primate Interneuron Repertoire

The paper profiles interneurons in primates and rodents to identify evolutionary innovations in brain cell types and their molecular features.

Mapping genetic effects on cellular phenotypes with "cell villages"

Census-seq pools cells from >100 human donors into "cell villages" and quantifies donor DNA before and after selection to map genetic effects on cellular traits.

Insights about variation in meiosis from 31,228 human sperm genomes

The paper analyzes 31,228 human sperm genomes to study meiotic variation, finding differences in aneuploidy rates and crossover patterns across donors and gametes.

Complex cell-state changes revealed by single cell RNA sequencing of 76,149 microglia throughout the mouse lifespan and in the injured brain

This study identifies nine distinct microglial states in mice across lifespan and after injury using single-cell RNA sequencing, revealing persistent and age-related changes.

A Single-Cell Atlas of Cell Types, States, and Other Transcriptional Patterns from Nine Regions of the Adult Mouse Brain

This paper constructs a single-cell atlas of the adult mouse brain, identifying 565 transcriptionally distinct cell groups and revealing new insights into neuronal specialization and brain organization.