Joshua Z. Levin

Single cell eQTL mapping reveals convergent glial-neuronal risk architecture in Parkinson's disease

The paper fine-maps PD GWAS signals across cell types, revealing convergent glial-neuronal risk genes and a shared vesiculopathy network.

Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data

This paper develops computational tools for allelic imbalance analysis using single-nucleus RNA-seq and demonstrates their application in a Parkinson's disease cohort.

Concordant transcriptional and morphological remodeling revealed by in vivo Perturb-CLEAR

The paper develops Perturb-CLEAR to study dendritic morphogenesis in the developing mouse cortex, revealing gene-specific multimodal phenotypes linked to NDD risk genes.

Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease

This study integrates long-read WGS and single-nucleus RNA-seq to identify structural variants affecting gene expression in Parkinson's disease with cell type resolution.

In vivo multiomic Perturb-seq with enhanced nuclear gRNA capture

This paper develops an in vivo multiomic Perturb-seq platform to improve gRNA recovery and applies it to study neurodevelopmental disorder risk genes in the cortex.

Disrupted Sleep-Dependent Neural Oscillations and Transcriptomic Changes in the Cacna1g Loss-of-Function Mouse Model Implicated in Schizophrenia

Loss of CACNA1G disrupts sleep rhythms and gene regulation, creating a mismatch between brain state and behavior linked to schizophrenia.

Elevated synaptic PKA activity and abnormal striatal dopamine signaling in Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder

This study investigates Akap11 mutant mice to explore the neurobiological effects of AKAP11 loss, finding increased PKA activity and transcriptomic changes linked to schizophrenia and bipolar disorder.

The G-protein coupled receptor GPR34 maintains the homeostatic state of microglia and restrains the disease-associated microglial response in an Alzheimers disease model

This study shows that GPR34 maintains microglial homeostasis and limits disease-associated microglial responses in Alzheimer's disease models.

Human brain organoids record the passage of time over multiple years in culture

This study shows human brain organoids can mature over 5 years in culture, transcriptionally aging and retaining memory of time spent in vitro.

Meta-analysis of the brain transcriptomes of multiple genetic mouse models of schizophrenia highlights dysregulation in striatum and thalamus

This study performs a meta-analysis of brain transcriptomes from genetic mouse models of schizophrenia, identifying dysregulation in striatum and thalamus with distinct patterns in different models.

A foundational neuronal protein network model unifying multimodal genetic, transcriptional, and proteomic perturbations in schizophrenia.

The paper identifies three neuron-specific schizophrenia protein networks enriched for genetic and transcriptional perturbations and validates their disruption in 22q11.2 deletion carriers.

Abnormal Lipid Metabolism and Altered Neuronal Support by Astrocytes Lacking Akap11, a Risk Gene for Schizophrenia and Bipolar Disorder

This study identifies AKAP11's role in regulating lipid metabolism and neuronal support in astrocytes, linking its dysfunction to schizophrenia and bipolar disorder risk.

Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.

This paper benchmarks multimodal single-cell data integration methods to improve kidney reference atlas quality by identifying adaptive states and rare cell types.

Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development

This study develops a high-throughput in vivo Perturb-seq platform to analyze gene function across diverse cell types in the brain and peripheral nervous system, identifying cell type-specific transcriptional networks.

Fetal brain response to maternal inflammation requires microglia

This study shows that microglia mediate fetal brain transcriptional responses to maternal inflammation, highlighting their role in neurodevelopmental outcomes.

Neuronal-class specific molecular cues drive differential myelination in the neocortex

The paper identifies neuron-class specific signals that drive differential myelination across cortical layers using single-cell data from mouse neocortex.

Multi-donor human cortical Chimeroids reveal individual susceptibility to neurotoxic triggers

The paper introduces a multi-donor brain organoid model called Chimeroids to study individual genetic variation in neurotoxin susceptibility.

Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types

This study uses single-cell transcriptomics to show that heterochronic parabiosis alters aging signatures in multiple brain cell types, with endothelial cells showing significant transcriptional changes.

The effect of background noise and its removal on the analysis of single-cell expression data

This study evaluates background noise in single-cell RNA-seq data and assesses methods for its removal, finding that CellBender performs best for marker gene detection.

Cell-type specific developmental defects in PTEN-mutant cortical organoids converge on abnormal circuit activity

The paper investigates how PTEN heterozygous mutations affect different cell types in human cortical organoids and shows that these effects lead to abnormal circuit activity regardless of genetic background.

Brain region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice

This study identifies brain region-specific changes and dopamine dysregulation in Grin2a mutant mice, supporting schizophrenia hypotheses and highlighting their utility as a genetic model.

Single cell RNA-seq by mostly-natural sequencing by synthesis

The paper benchmarks a new low-cost sequencing by synthesis method for scRNA-seq, showing comparable results to existing technologies and enabling cost-effective large-scale applications.

Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex

The paper presents a single-cell multiomics atlas of human cortical organoid development, revealing molecular programs of cellular diversification and identifying human-specific gene roles in lineage establishment.

Human-specific enrichment of schizophrenia risk-genes in callosal neurons of the developing neocortex

The paper identifies human-specific enrichment of schizophrenia risk genes in callosal neurons of the developing neocortex using comparative transcriptomic analysis across species and developmental stages.

Pluripotent stem cell derived models of neurological diseases reveal early transcriptional heterogeneity

The paper uses scRNA-seq to show increased transcriptional heterogeneity in neurodegenerative disease models, suggesting early regulatory imbalances.

A comprehensive fitness landscape model reveals the evolutionary history and future evolvability of eukaryotic cis-regulatory DNA sequences

The paper constructs a deep transformer model to predict gene expression from cis-regulatory DNA sequences in yeast, revealing evolutionary constraints and evolvability patterns.

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with Autism risk genes

This study uses in vivo Perturb-Seq to analyze the effects of 35 autism risk genes on neuronal and glial cells in the developing brain.

Human brain organoids reveal accelerated development of cortical neuron classes as a shared feature of autism risk genes

This study uses human brain organoids to show that ASD risk genes cause accelerated development of specific cortical neuron classes.

Temporally-Divergent Regulatory Mechanisms Govern Neuronal Development and Diversification in the Neocortex

This study identifies temporally divergent regulatory mechanisms in neuronal development and maturation across mouse and marmoset neocortex.

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.