Michael Kunst

SCALPEL: A pipeline for processing large-scale spatial transcriptomics data

SCALPEL processes large-scale spatial transcriptomics data with improved 3D segmentation, doublet detection, and spatial alignment, showing better performance than previous methods.

A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

This paper creates a cross-species spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, revealing conserved molecular organization and cell type-specific compartments.

The ANTsX Ecosystem for Mapping the Mouse Brain

The paper demonstrates the use of ANTsX for precise spatial mapping of the mouse brain using standardized coordinate systems and presents novel workflows for longitudinal trajectory analysis and automated morphological measurements.

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The paper analyzes the transcriptomic and spatial organization of GABAergic neurons in the mouse telencephalon, revealing complex developmental and spatial relationships across multiple brain regions.

Data-driven fine-grained region discovery in the mouse brain with transformers

This paper introduces CellTransformer, a self-supervised framework for detecting fine-grained spatial domains in mouse brain spatial transcriptomics data, achieving high consistency across large datasets.

MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

The paper introduces MerQuaCo, an open-source tool to automatically detect and quantify imperfections in spatial transcriptomics data, improving quality assessment.

Integrated multimodal cell atlas of Alzheimer's disease

This study creates an integrated multimodal cell atlas of Alzheimer's disease by analyzing single nuclei transcriptomes, epigenomes, and spatial coordinates across AD stages.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.

Transcriptomic cytoarchitecture reveals principles of human neocortex organization

The paper uses single nucleus RNA-sequencing to analyze human cortical areas, revealing cell type proportions and gene expression patterns that correlate with functional connectivity and areal specialization.

Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

The paper identifies transcriptomic and morpho-electric diversity in human neocortical layer 1 interneurons, revealing greater subclass distinction compared to mouse.

Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex

The paper uses viral labeling and Patch-seq to define morpho-electric properties of GABAergic interneurons in human neocortex, revealing functional insights and reclassifying some SST neurons into PVALB subclass.

Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species

The paper develops AAV-based genetic tools to specifically target astrocytes and oligodendrocytes across species, revealing functional roles in reward-dependent acetylcholine responses.

A single-cell resolution gene expression atlas of the larval zebrafish brain

The paper creates a single-cell gene expression atlas of the larval zebrafish brain using HCR, identifies a novel cerebellar cell type, and integrates gene expression with functional activity maps.

Neural assemblies uncovered by generative modeling explain whole-brain activity statistics and reflect structural connectivity

The paper uses a generative model to uncover neural assemblies in zebrafish brains, showing it can replicate activity statistics and reveal functional connectivity.