Tyler S. Mollenkopf

Iterative co-creation of harmonized human and non-human primate cellular and structural ontologies and 3D common coordinate frameworks for the basal ganglia

The paper describes the iterative creation of harmonized ontologies and 3D frameworks for the basal ganglia across human and non-human primates to enable cross-species comparisons of cellular and molecular data.

A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases

This paper introduces a standards framework for integrating single-cell and spatial omics data into brain cell atlases, enabling interoperable and reusable knowledge-ready resources.

MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies

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

A Cross-Species Enhancer-AAV Toolkit for Cell Type-Specific Targeting Across the Basal Ganglia

The paper develops a cross-species enhancer-AAV toolkit for targeting specific cell types in the basal ganglia across species, validated in mouse and macaque.

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

The paper presents an integrated single-cell and epigenomic resource for exploring basal ganglia datasets across species, enabling multi-omics and comparative analysis.

A curvilinear coordinate flatmap for visualizing hippocampal structure and development

This paper introduces a curvilinear coordinate flatmap method to visualize hippocampal structure and development, revealing topographic variations obscured in standard coordinate systems.

Cross-species consensus atlas of the primate basal ganglia

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

The paper develops a toolkit of transgenic mouse lines and enhancer AAVs for selective targeting of cortical cell populations using transcriptomic and epigenomic data.

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.

Brain Data Standards - A method for building data-driven cell-type ontologies

The paper introduces a data-driven method to extend cell ontologies for multi-modal single-cell omics data, focusing on the Primary Motor Cortex in humans, mice, and marmosets.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

The paper presents a dataset and analysis of spiking activity across multiple mouse visual areas, revealing that functional connectivity mirrors anatomical hierarchy.