Evan Z. Macosko

This study shows that reduced Satb2 gene dosage in cortical projection neurons leads to chromatin and circuit defects, causing cognitive and sensory impairments in a mouse model of SATB2-associated syndrome.

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.

MapMyCells maps unlabeled single-cell datasets to reference brain taxonomies, enabling cross-study integration and reproducible cell-type annotation.

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.

The paper introduces Synapse-seq, a method to link transcriptomes to synaptic architecture by using protein-guided RNA barcoding, revealing new insights into neural connectivity and cell type-specific dendritic structures.

The paper identifies a circuit involving DLS Pdyn neurons that links contextual cues to feeding regulation through inhibition of LHA GABAergic neurons.

This study identifies IL13 as a survival factor for Hodgkin lymphoma cells by analyzing the tumor microenvironment with spatial and single-cell resolution.

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.

Cassini enables cost-effective, multiplexed profiling of mRNA and protein in tissue samples with high sensitivity and speed.

The paper presents a multi-modal atlas of human kidney disease, identifying cellular and spatial mechanisms of injury resolution or failure and linking them to clinical outcomes.

This study uses spatial transcriptomics and single-nucleus RNA-seq to analyze remyelination dynamics, identifying an interferon-responsive glial state that coordinates immune infiltration and oligodendrocyte differentiation.

This paper introduces an imaging-free spatial transcriptomics method using molecular diffusion patterns and UMAP to reconstruct spatial data with high fidelity and scalability.

The paper shows pyramidal neurons influence the survival and identity of specific interneuron subtypes through non-synaptic mechanisms.

The paper identifies neurexin gene expression patterns in olfactory sensory neurons that guide axonal targeting to specific glomeruli through interactions with neuroligins in mitral/tufted cells.

The paper identifies a Purkinje cell to parabrachial nucleus pathway that enables cerebellar influence over forebrain regions involved in nonmotor functions, distinct from the traditional deep cerebellar nuclei pathway.

The paper identifies two MLI subtypes with distinct connectivity and functional roles in cerebellar circuits, showing how disinhibition gates cerebellar-dependent learning.

This study shows thyroid hormone remodels cortical circuits in adult mice, linking metabolic state to exploratory behavior through transcriptional changes in neurons and glia.

This paper develops a platform to model and manipulate human microglial states in vitro using single-cell RNA sequencing and genetic tools, identifying disease-associated transcriptional signatures.

The paper creates a high-resolution cellular atlas of healthy and injured kidney cell states and niches using single-cell and spatial technologies, identifying molecular signatures and pathways related to kidney injury.

This study identifies somatic copy number variants (sCNVs) in schizophrenia cases, revealing their contribution to risk and specific NRXN1 disruptions.

The paper identifies a transient hyperactive neuronal state in early Alzheimer's disease using single-nucleus transcriptomics from living patients.

The paper develops a computational framework to study division of labor in tissues by analyzing cell interactions and spatial cues using single-cell RNA-seq and spatial transcriptomics data.

Slide-tags enables spatial localization of single nuclei for multi-modal spatial genomics, achieving high-resolution mapping and multiomic profiling in various tissues.

Whole-brain snRNA-seq paired with Slide-seq assigns cell types to each mouse neuroanatomical structure; most clusters need at least three markers to be defined uniquely.

HiDDEN refines case-control labels in single-cell transcriptomics to detect disease-relevant cell populations, improving detection of subtle perturbations in simulated and real datasets.

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.

The paper introduces a statistical method to detect cell type-specific differential gene expression in spatial transcriptomics data and validates it using simulations and real datasets.

This study uses Slide-seqV2 to identify disease-specific cell neighborhoods and pathways in human and mouse kidneys.

The paper shows enzymatic dissociation causes gene expression changes in microglia and proposes a protocol to reduce these artifacts in scRNA-seq.

The paper identifies cell-type specific circuits formed by subtypes of somatostatin interneurons in the cortex through genetic targeting and connectivity analysis.