A multimodal cell census and atlas of the mammalian primary motor cortex

Spatially resolved transcriptomics in neuroscience

(2021) Jennie L. Close et al.   NATURE METHODS

Spatially resolved single-cell genomics and transcriptomics by imaging

(2021) Xiaowei Zhuang   NATURE METHODS

Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes

(2021) Ethan J. Armand et al.   NEURON

High-definition imaging using line-illumination modulation microscopy

(2021) Qiuyuan Zhong et al.   NATURE METHODS

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

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

(2021) Zizhen Yao et al.   CELL

Enhancer viruses for combinatorial cell-subclass-specific labeling

(2021) Lucas T. Graybuck et al.   NEURON

Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

(2021) John K. Mich et al.   Cell Reports

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

(2020) Quanxin Wang et al.   CELL

Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice

(2020) Matthew B. Veldman et al.   NEURON

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Innovations present in the primate interneuron repertoire

(2020) Fenna M. Krienen et al.   NATURE

A community-based transcriptomics classification and nomenclature of neocortical cell types

(2020) Rafael Yuste et al.   NATURE NEUROSCIENCE

Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans

(2020) Douglas Vormstein-Schneider et al.   NATURE NEUROSCIENCE

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

The diversity of GABAergic neurons and neural communication elements

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

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain

(2019) Johan Winnubst et al.   CELL

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

A scalable platform for the development of cell-type-specific viral drivers

(2019) Sinisa Hrvatin et al.   eLife

High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing

(2019) Xiaoyin Chen et al.   CELL

Hierarchical organization of cortical and thalamic connectivity

(2019) Julie A. Harris et al.   NATURE

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

The art of using t-SNE for single-cell transcriptomics

(2019) Dmitry Kobak et al.   Nature Communications

Continuous and Discrete Neuron Types of the Adult Murine Striatum

(2019) Geoffrey Stanley et al.   NEURON

Lhx2, an evolutionarily conserved, multifunctional regulator of forebrain development

(2018) Shen-Ju Chou et al.   BRAIN RESEARCH

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

(2018) Tanya L. Daigle et al.   CELL

Neural mechanisms of movement planning: motor cortex and beyond

(2018) Karel Svoboda et al.   CURRENT OPINION IN NEUROBIOLOGY

Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences

(2018) Arielle Baker et al.   JOURNAL OF NEUROSCIENCE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

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

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

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

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

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

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

Cancer chromatin accessibility landscape

(2018) Steve Mao   SCIENCE

Perspectives on defining cell types in the brain

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

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq

(2017) Cathryn R Cadwell et al.   Nature Protocols

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

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

(2017) Joseph R. Ecker et al.   NEURON

AAV-Mediated Anterograde Transsynaptic Tagging: Mapping Corticocollicular Input-Defined Neural Pathways for Defense Behaviors

(2017) Brian Zingg et al.   NEURON

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

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

(2017) Ed Lein et al.   SCIENCE

Cell Type-Specific Structural Organization of the Six Layers in Rat Barrel Cortex

(2017) Rajeevan T. Narayanan et al.   Frontiers in Neuroanatomy

LHX2 Interacts with the NuRD Complex and Regulates Cortical Neuron Subtype Determinants Fezf2 and Sox11

(2016) Bhavana Muralidharan et al.   JOURNAL OF NEUROSCIENCE

The mouse cortico-striatal projectome

(2016) Houri Hintiryan et al.   NATURE NEUROSCIENCE

A viral strategy for targeting and manipulating interneurons across vertebrate species

(2016) Jordane Dimidschstein et al.   NATURE NEUROSCIENCE

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex

(2016) Miao He et al.   NEURON

Rabies Virus CVS-N2c ΔG Strain Enhances Retrograde Synaptic Transfer and Neuronal Viability

(2016) Thomas R. Reardon et al.   NEURON

A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons

(2016) D. Gowanlock R. Tervo et al.   NEURON

MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders

(2016) Adam J Harrington et al.   eLife

The Types of Retinal Ganglion Cells: Current Status and Implications for Neuronal Classification

(2015) Joshua R. Sanes et al.   Annual Review of Neuroscience

fitdistrplus: AnRPackage for Fitting Distributions

(2015) Marie Laure Delignette-Muller et al.   Journal of Statistical Software

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes

(2015) János Fuzik et al.   NATURE BIOTECHNOLOGY

Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq

(2015) Cathryn R Cadwell et al.   NATURE BIOTECHNOLOGY

The neocortical circuit: themes and variations

(2015) Kenneth D Harris et al.   NATURE NEUROSCIENCE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Neural Networks of the Mouse Neocortex

(2014) Brian Zingg et al.   CELL

Cortical and Clonal Contribution of Tbr2 Expressing Progenitors in the Developing Mouse Brain

(2014) Navneet A. Vasistha et al.   CEREBRAL CORTEX

Area 4 has layer IV in adult primates

(2014) Miguel Ángel García-Cabezas et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex

(2014) Matthew J Eckler et al.   Neural Development

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

(2014) Naoki Yamawaki et al.   eLife

Genetic Approaches to Neural Circuits in the Mouse

(2013) Z. Josh Huang et al.   Annual Review of Neuroscience

Molecular logic of neocortical projection neuron specification, development and diversity

(2013) Luciano Custo Greig et al.   NATURE REVIEWS NEUROSCIENCE

GENSAT BAC Cre-Recombinase Driver Lines to Study the Functional Organization of Cerebral Cortical and Basal Ganglia Circuits

(2013) Charles R. Gerfen et al.   NEURON

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

The protein tyrosine phosphatases PTPRZ and PTPRG bind to distinct members of the contactin family of neural recognition molecules

(2010) S. Bouyain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Descending Pathways in Motor Control

(2008) Roger N. Lemon   Annual Review of Neuroscience

Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex

(2008)   NATURE REVIEWS NEUROSCIENCE