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

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Inhibition decorrelates visual feature representations in the inner retina

(2017) Katrin Franke et al.   NATURE

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Win–win data sharing in neuroscience

(2017) Giorgio A Ascoli et al.   NATURE METHODS

Effective detection of variation in single-cell transcriptomes using MATQ-seq

(2017) Kuanwei Sheng et al.   NATURE METHODS

In vivo imaging of neural activity

(2017) Weijian Yang et al.   NATURE METHODS

Multicut brings automated neurite segmentation closer to human performance

(2017) Thorsten Beier et al.   NATURE METHODS

In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain

(2017) Dimitre G Ouzounov et al.   NATURE METHODS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Video-rate volumetric functional imaging of the brain at synaptic resolution

(2017) Rongwen Lu et al.   NATURE NEUROSCIENCE

A molecular census of arcuate hypothalamus and median eminence cell types

(2017) John N Campbell et al.   NATURE NEUROSCIENCE

Genetically Distinct Parallel Pathways in the Entopeduncular Nucleus for Limbic and Sensorimotor Output of the Basal Ganglia

(2017) Michael L. Wallace et al.   NEURON

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus

(2016) Josh Lyskowski Morgan et al.   CELL

From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response

(2016) Eva A. Naumann et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Glutamatergic Monopolar Interneurons Provide a Novel Pathway of Excitation in the Mouse Retina

(2016) Luca Della Santina et al.   CURRENT BIOLOGY

Development of synaptic connectivity in the retinal direction selective circuit

(2016) Ryan D Morrie et al.   CURRENT OPINION IN NEUROBIOLOGY

Voltage imaging to understand connections and functions of neuronal circuits

(2016) Srdjan D. Antic et al.   JOURNAL OF NEUROPHYSIOLOGY

Decoding ALS: from genes to mechanism

(2016) J. Paul Taylor et al.   NATURE

The functional diversity of retinal ganglion cells in the mouse

(2016) Tom Baden et al.   NATURE

Anatomy and function of an excitatory network in the visual cortex

(2016) Wei-Chung Allen Lee et al.   NATURE

A multi-modal parcellation of human cerebral cortex

(2016) Matthew F. Glasser et al.   NATURE

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Nanoscale imaging of RNA with expansion microscopy

(2016) Fei Chen et al.   NATURE METHODS

Disentangling neural cell diversity using single-cell transcriptomics

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

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes

(2016) Roman A Romanov et al.   NATURE NEUROSCIENCE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

(2016) Suguna Rani Krishnaswami et al.   Nature Protocols

Visualization of cortical, subcortical and deep brain neural circuit dynamics during naturalistic mammalian behavior with head-mounted microscopes and chronically implanted lenses

(2016) Shanna L Resendez et al.   Nature Protocols

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases

(2016) Marta Costa et al.   NEURON

Congenital Nystagmus Gene FRMD7 Is Necessary for Establishing a Neuronal Circuit Asymmetry for Direction Selectivity

(2016) Keisuke Yonehara et al.   NEURON

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

GABAergic Interneurons in the Neocortex: From Cellular Properties to Circuits

(2016) Robin Tremblay et al.   NEURON

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

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level

(2016) Hui Gong et al.   Nature Communications

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2016) Benjamin Lacar et al.   Nature Communications

Calcium imaging of sleep–wake related neuronal activity in the dorsal pons

(2016) Julia Cox et al.   Nature Communications

Long-Term Optical Access to an Estimated One Million Neurons in the Live Mouse Cortex

(2016) Tony Hyun Kim et al.   Cell Reports

Analogous Convergence of Sustained and Transient Inputs in Parallel On and Off Pathways for Retinal Motion Computation

(2016) Matthew J. Greene et al.   Cell Reports

A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging

(2016) Nicholas James Sofroniew et al.   eLife

The wiring diagram of a glomerular olfactory system

(2016) Matthew E Berck et al.   eLife

A platform for brain-wide imaging and reconstruction of individual neurons

(2016) Michael N Economo 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

Reconstruction and Simulation of Neocortical Microcircuitry

(2015) Henry Markram et al.   CELL

Saturated Reconstruction of a Volume of Neocortex

(2015) Narayanan Kasthuri et al.   CELL

Molecular Identity of Human Outer Radial Glia during Cortical Development

(2015) Alex A. Pollen et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity

(2015) Chang-Lin Li et al.   CELL RESEARCH

Connectomics-Based Analysis of Information Flow in the Drosophila Brain

(2015) Chi-Tin Shih et al.   CURRENT BIOLOGY

Comprehensive imaging of cortical networks

(2015) Simon Peron et al.   CURRENT OPINION IN NEUROBIOLOGY

The Independent Probabilistic Firing of Transcription Factors: A Paradigm for Clonal Variability in the Zebrafish Retina

(2015) Henrik Boije et al.   DEVELOPMENTAL CELL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

High-resolution, high-throughput imaging with a multibeam scanning electron microscope

(2015) A.L. EBERLE et al.   JOURNAL OF MICROSCOPY

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

Neurotransmitter Switching? No Surprise

(2015) Nicholas C. Spitzer   NEURON

Three Types of Cortical Layer 5 Neurons That Differ in Brain-wide Connectivity and Function

(2015) Euiseok J. Kim et al.   NEURON

BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images

(2015) Hanchuan Peng et al.   NEURON

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Tuning of fast-spiking interneuron properties by an activity-dependent transcriptional switch

(2015) Nathalie Dehorter et al.   SCIENCE

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

(2015) A. Zeisel et al.   SCIENCE

Principles of connectivity among morphologically defined cell types in adult neocortex

(2015) X. Jiang et al.   SCIENCE

Design principles and developmental mechanisms underlying retinal mosaics

(2014) Benjamin E. Reese et al.   BIOLOGICAL REVIEWS

Space–time wiring specificity supports direction selectivity in the retina

(2014) Jinseop S. Kim et al.   NATURE

Interneuron cell types are fit to function

(2014) Adam Kepecs et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

Maintenance of postmitotic neuronal cell identity

(2014) Evan S Deneris et al.   NATURE NEUROSCIENCE

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Retinal bipolar cells: elementary building blocks of vision

(2014) Thomas Euler et al.   NATURE REVIEWS NEUROSCIENCE

The Stimulus Selectivity and Connectivity of Layer Six Principal Cells Reveals Cortical Microcircuits Underlying Visual Processing

(2014) Mateo Vélez-Fort et al.   NEURON

Neuronal Cell Types and Connectivity: Lessons from the Retina

(2014) H. Sebastian Seung et al.   NEURON

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Anatomical characterization of Cre driver mice for neural circuit mapping and manipulation

(2014) Julie A. Harris et al.   Frontiers in Neural Circuits

Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits

(2014) Kenneth J. Hayworth et al.   Frontiers in Neural Circuits

Genetic Approaches to Neural Circuits in the Mouse

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

A visual motion detection circuit suggested by Drosophila connectomics

(2013) Shin-ya Takemura et al.   NATURE

Ultrasensitive fluorescent proteins for imaging neuronal activity

(2013) Tsai-Wen Chen et al.   NATURE

Connectomic reconstruction of the inner plexiform layer in the mouse retina

(2013) Moritz Helmstaedter et al.   NATURE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Whole-brain functional imaging at cellular resolution using light-sheet microscopy

(2013) Misha B Ahrens et al.   NATURE METHODS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Long-term dynamics of CA1 hippocampal place codes

(2013) Yaniv Ziv et al.   NATURE NEUROSCIENCE

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Molecular logic of neocortical projection neuron specification, development and diversity

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

Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution

(2013) Hui Gong et al.   NEUROIMAGE

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

Membrane Potential Dynamics of Neocortical Projection Neurons Driving Target-Specific Signals

(2013) Takayuki Yamashita et al.   NEURON

Chronic Cellular Imaging of Entire Cortical Columns in Awake Mice Using Microprisms

(2013) Mark L. Andermann et al.   NEURON

The Neuron Identity Problem: Form Meets Function

(2013) Gord Fishell et al.   NEURON

The Subthalamic Nucleus Is One of Multiple Innervation Sites for Long-Range Corticofugal Axons: A Single-Axon Tracing Study in the Rat

(2012) T. Kita et al.   JOURNAL OF NEUROSCIENCE

MEGF10 and MEGF11 mediate homotypic interactions required for mosaic spacing of retinal neurons

(2012) Jeremy N. Kay et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

From Functional Architecture to Functional Connectomics

(2012) R. Clay Reid   NEURON

The Neuronal Organization of the Retina

(2012) Richard H. Masland   NEURON

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

A Resource for Manipulating Gene Expression and Analyzing cis-Regulatory Modules in the Drosophila CNS

(2012) Laurina Manning et al.   Cell Reports

A GAL4-Driver Line Resource for Drosophila Neurobiology

(2012) Arnim Jenett et al.   Cell Reports

Mechanisms of Inhibition within the Telencephalon: “Where the Wild Things Are”

(2011) Gord Fishell et al.   Annual Review of Neuroscience

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Network anatomy and in vivo physiology of visual cortical neurons

(2011) Davi D. Bock et al.   NATURE

Wiring specificity in the direction-selectivity circuit of the retina

(2011) Kevin L. Briggman et al.   NATURE

Miniaturized integration of a fluorescence microscope

(2011) Kunal K Ghosh et al.   NATURE METHODS

A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex

(2011) Hiroki Taniguchi et al.   NEURON

Chemoaffinity Revisited: Dscams, Protocadherins, and Neural Circuit Assembly

(2010) S. Lawrence Zipursky et al.   CELL

Three-Dimensional Reconstruction of Brain-wide Wiring Networks in Drosophila at Single-Cell Resolution

(2010) Ann-Shyn Chiang et al.   CURRENT BIOLOGY

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

(2010) Bernardo Rudy et al.   Developmental Neurobiology

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson et al.   NATURE METHODS

Design Principles of Insect and Vertebrate Visual Systems

(2010) Joshua R. Sanes et al.   NEURON

From Progenitors to Differentiated Cells in the Vertebrate Retina

(2009) Michalis Agathocleous et al.   Annual Review of Cell and Developmental Biology

Cone Contacts, Mosaics, and Territories of Bipolar Cells in the Mouse Retina

(2009) H. Wassle et al.   JOURNAL OF NEUROSCIENCE

Genetic address book for retinal cell types

(2009) Sandra Siegert et al.   NATURE NEUROSCIENCE

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Serial Section Scanning Electron Microscopy of Adult Brain Tissue Using Focused Ion Beam Milling

(2008) G. Knott et al.   JOURNAL OF NEUROSCIENCE

Molecular identification of a retinal cell type that responds to upward motion

(2008) In-Jung Kim et al.   NATURE

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

(2008)   NATURE REVIEWS NEUROSCIENCE

ExplorEnz: the primary source of the IUBMB enzyme list

(2008) A. G. McDonald et al.   NUCLEIC ACIDS RESEARCH

Neuronal Diversity and Temporal Dynamics: The Unity of Hippocampal Circuit Operations

(2008) T. Klausberger et al.   SCIENCE