Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

Spatially resolved single-cell genomics and transcriptomics by imaging

(2021) Xiaowei Zhuang   NATURE METHODS

Spatially resolved transcriptomics adds a new dimension to genomics

(2021) Ludvig Larsson et al.   NATURE METHODS

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

(2021) Zizhen Yao et al.   CELL

Morphological diversity of single neurons in molecularly defined cell types

(2021) Hanchuan Peng et al.   NATURE

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

(2021) Zizhen Yao et al.   NATURE

Cellular anatomy of the mouse primary motor cortex

(2021) Rodrigo Muñoz-Castañeda et al.   NATURE

Epigenomic diversity of cortical projection neurons in the mouse brain

(2021) Zhuzhu Zhang et al.   NATURE

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

(2020) Quanxin Wang et al.   CELL

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

The diversity of GABAergic neurons and neural communication elements

(2019) Z. Josh Huang et al.   NATURE REVIEWS NEUROSCIENCE

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Continuous and Discrete Neuron Types of the Adult Murine Striatum

(2019) Geoffrey Stanley et al.   NEURON

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

(2018) Guiping Wang et al.   Scientific Reports

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics

(2018) Kenneth D. Harris et al.   PLOS BIOLOGY

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

The logic of single-cell projections from visual cortex

(2018) Yunyun Han et al.   NATURE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Distinct descending motor cortex pathways and their roles in movement

(2018) Michael N. Economo et al.   NATURE

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Perspectives on defining cell types in the brain

(2018) Eran A Mukamel et al.   CURRENT OPINION IN NEUROBIOLOGY

Neuronal cell-type classification: challenges, opportunities and the path forward

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

(2017) Ed Lein et al.   SCIENCE

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Disentangling neural cell diversity using single-cell transcriptomics

(2016) Jean-Francois Poulin et al.   NATURE NEUROSCIENCE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Neural Networks of the Mouse Neocortex

(2014) Brian Zingg et al.   CELL

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A genuine layer 4 in motor cortex with prototypical synaptic circuit connectivity

(2014) Naoki Yamawaki et al.   eLife

Correlated Gene Expression and Target Specificity Demonstrate Excitatory Projection Neuron Diversity

(2013) Staci A. Sorensen et al.   CEREBRAL CORTEX

Corticostriatal connectivity and its role in disease

(2013) Gordon M. G. Shepherd   NATURE REVIEWS NEUROSCIENCE

The Organization of the Forelimb Representation of the C57BL/6 Mouse Motor Cortex as Defined by Intracortical Microstimulation and Cytoarchitecture

(2010) Kelly A. Tennant et al.   CEREBRAL CORTEX

Three groups of interneurons account for nearly 100% of neocortical GABAergic neurons

(2010) Bernardo Rudy et al.   Developmental Neurobiology

Sublayer-specific microcircuits of corticospinal and corticostriatal neurons in motor cortex

(2010) Charles T Anderson et al.   NATURE NEUROSCIENCE

Immunochemical characterization of inhibitory mouse cortical neurons: Three chemically distinct classes of inhibitory cells

(2009) Xiangmin Xu et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS