Convergence Circuit Mapping: Genetic Approaches From Structure to Function

Functional Electron Microscopy (“Flash and Freeze”) of Identified Cortical Synapses in Acute Brain Slices

(2020) Carolina Borges-Merjane et al.   NEURON

The Functional Organization of Cortical and Thalamic Inputs onto Five Types of Striatal Neurons Is Determined by Source and Target Cell Identities

(2020) Yvonne Johansson et al.   Cell Reports

Cell-type specific innervation of cortical pyramidal cells at their apical dendrites

(2020) Ali Karimi et al.   eLife

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

(2020) Quanxin Wang et al.   CELL

Synaptic Specificity and Application of Anterograde Transsynaptic AAV for Probing Neural Circuitry

(2020) Brian Zingg et al.   JOURNAL OF NEUROSCIENCE

The Temporal Association Cortex Plays a Key Role in Auditory-Driven Maternal Plasticity

(2020) Gen-ichi Tasaka et al.   NEURON

Whole-Neuron Synaptic Mapping Reveals Spatially Precise Excitatory/Inhibitory Balance Limiting Dendritic and Somatic Spiking

(2020) Daniel Maxim Iascone et al.   NEURON

Light Up the Brain: The Application of Optogenetics in Cell-Type Specific Dissection of Mouse Brain Circuits

(2020) Candice Lee et al.   Frontiers in Neural Circuits

Nucleus Accumbens Cell Type- and Input-Specific Suppression of Unproductive Reward Seeking

(2020) Christopher K. Lafferty et al.   Cell Reports

Layer 6b Is Driven by Intracortical Long-Range Projection Neurons

(2020) Timothy A. Zolnik et al.   Cell Reports

Anatomic resolution of neurotransmitter-specific projections to the VTA reveals diversity of GABAergic inputs

(2020) Marta E. Soden et al.   NATURE NEUROSCIENCE

Viral Vectors for Neural Circuit Mapping and Recent Advances in Trans-synaptic Anterograde Tracers

(2020) Xiangmin Xu et al.   NEURON

Hindbrain Double-Negative Feedback Mediates Palatability-Guided Food and Water Consumption

(2020) Rong Gong et al.   CELL

Pseudotyped lentiviral vectors for tract-targeting and application for the functional control of selective neural circuits

(2020) Shigeki Kato et al.   JOURNAL OF NEUROSCIENCE METHODS

An expanded palette of dopamine sensors for multiplex imaging in vivo

(2020) Tommaso Patriarchi et al.   NATURE METHODS

Imaging Neurotransmitter and Neuromodulator Dynamics In Vivo with Genetically Encoded Indicators

(2020) Bernardo L. Sabatini et al.   NEURON

A connectome and analysis of the adult Drosophila central brain

(2020) Louis K Scheffer et al.   eLife

Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning

(2020) Elizabeth K. Unger et al.   CELL

Cell-type-specific asynchronous modulation of PKA by dopamine in learning

(2020) Suk Joon Lee et al.   NATURE

A collicular visual cortex: Neocortical space for an ancient midbrain visual structure

(2019) Riccardo Beltramo et al.   SCIENCE

CAV-2 Vector Development and Gene Transfer in the Central and Peripheral Nervous Systems

(2019) Danila del Rio et al.   Frontiers in Molecular Neuroscience

Distinct Cortical-Thalamic-Striatal Circuits through the Parafascicular Nucleus

(2019) Gil Mandelbaum et al.   NEURON

Long-range inhibitory intersection of a retrosplenial thalamocortical circuit by apical tuft-targeting CA1 neurons

(2019) Naoki Yamawaki et al.   NATURE NEUROSCIENCE

A whole-brain atlas of monosynaptic input targeting four different cell types in the medial prefrontal cortex of the mouse

(2019) Sofie Ährlund-Richter et al.   NATURE NEUROSCIENCE

A hypothalamus-habenula circuit controls aversion

(2019) Iakovos Lazaridis et al.   MOLECULAR PSYCHIATRY

Rational Engineering of XCaMPs, a Multicolor GECI Suite for In Vivo Imaging of Complex Brain Circuit Dynamics

(2019) Masatoshi Inoue et al.   CELL

High-density multi-fiber photometry for studying large-scale brain circuit dynamics

(2019) Yaroslav Sych et al.   NATURE METHODS

A subcortical excitatory circuit for sensory-triggered predatory hunting in mice

(2019) Congping Shang et al.   NATURE NEUROSCIENCE

Whole-animal connectomes of both Caenorhabditis elegans sexes

(2019) Steven J. Cook et al.   NATURE

A genetically encoded fluorescent sensor for in vivo imaging of GABA

(2019) Jonathan S. Marvin et al.   NATURE METHODS

Kilohertz frame-rate two-photon tomography

(2019) Abbas Kazemipour et al.   NATURE METHODS

A whole-brain map of long-range inputs to GABAergic interneurons in the mouse medial prefrontal cortex

(2019) Qingtao Sun et al.   NATURE 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

Rabies virus-mediated connectivity tracing from single neurons

(2019) Martin K. Schwarz et al.   JOURNAL OF NEUROSCIENCE METHODS

A Student’s Guide to Neural Circuit Tracing

(2019) Christine Saleeba et al.   Frontiers in Neuroscience

Hierarchical organization of cortical and thalamic connectivity

(2019) Julie A. Harris et al.   NATURE

Dense connectomic reconstruction in layer 4 of the somatosensory cortex

(2019) Alessandro Motta et al.   SCIENCE

Complementary Roles for Ventral Pallidum Cell Types and Their Projections in Relapse

(2019) Asheeta A. Prasad et al.   JOURNAL OF NEUROSCIENCE

A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism

(2019) Marcus Davidsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

rAAV2-Retro Enables Extensive and High-Efficient Transduction of Lower Motor Neurons following Intramuscular Injection

(2019) Zhilong Chen et al.   Molecular Therapy-Methods & Clinical Development

Adeno-Associated Viral Vectors in Neuroscience Research

(2019) David L. Haggerty et al.   Molecular Therapy-Methods & Clinical Development

Genetically Encoded Glutamate Indicators with Altered Color and Topology

(2018) Jiahui Wu et al.   ACS Chemical Biology

Identification of a Corticohabenular Circuit Regulating Socially Directed Behavior

(2018) Madhurima Benekareddy et al.   BIOLOGICAL PSYCHIATRY

The use of chemogenetics in behavioural neuroscience: receptor variants, targeting approaches and caveats

(2018) Erin J Campbell et al.   BRITISH JOURNAL OF PHARMACOLOGY

A Fine-Scale Functional Logic to Convergence from Retina to Thalamus

(2018) Liang Liang et al.   CELL

Progress and remaining challenges in high-throughput volume electron microscopy

(2018) Jörgen Kornfeld et al.   CURRENT OPINION IN NEUROBIOLOGY

t-GRASP, a targeted GRASP for assessing neuronal connectivity

(2018) Harold K. Shearin et al.   JOURNAL OF NEUROSCIENCE METHODS

A genetically encoded fluorescent acetylcholine indicator for in vitro and in vivo studies

(2018) Miao Jing et al.   NATURE BIOTECHNOLOGY

Author Correction: High-speed volumetric imaging of neuronal activity in freely moving rodents

(2018) Oliver Skocek et al.   NATURE METHODS

Genetic Dissection of Neural Circuits: A Decade of Progress

(2018) Liqun Luo et al.   NEURON

Chemogenetic Tools for Causal Cellular and Neuronal Biology

(2018) Deniz Atasoy et al.   PHYSIOLOGICAL REVIEWS

Interregional synaptic maps among engram cells underlie memory formation

(2018) Jun-Hyeok Choi et al.   SCIENCE

Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors

(2018) Tommaso Patriarchi et al.   SCIENCE

Action Selection and Flexible Switching Controlled by the Intralaminar Thalamic Neurons

(2018) Shigeki Kato et al.   Cell Reports

The coding of valence and identity in the mammalian taste system

(2018) Li Wang et al.   NATURE

Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area

(2018) Bryan M. Hooks et al.   Nature Communications

Combining mGRASP and Optogenetics Enables High-Resolution Functional Mapping of Descending Cortical Projections

(2018) Jun Ho Song et al.   Cell Reports

Axonal synapse sorting in medial entorhinal cortex

(2017) Helene Schmidt et al.   NATURE

Whole-brain serial-section electron microscopy in larval zebrafish

(2017) David Grant Colburn Hildebrand et al.   NATURE

Fast high-resolution miniature two-photon microscopy for brain imaging in freely behaving mice

(2017) Weijian Zong et al.   NATURE METHODS

Integration of optogenetics with complementary methodologies in systems neuroscience

(2017) Christina K. Kim et al.   NATURE REVIEWS NEUROSCIENCE

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

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

Different Modes of Visual Integration in the Lateral Geniculate Nucleus Revealed by Single-Cell-Initiated Transsynaptic Tracing

(2017) Santiago B. Rompani et al.   NEURON

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

(2017) Brian Zingg et al.   NEURON

DREADDS: Use and application in behavioral neuroscience.

(2016) Kyle S. Smith et al.   BEHAVIORAL NEUROSCIENCE

The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus

(2016) Josh Lyskowski Morgan et al.   CELL

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

Simultaneous fast measurement of circuit dynamics at multiple sites across the mammalian brain

(2016) Christina K Kim et al.   NATURE METHODS

Genetically encoded indicators of neuronal activity

(2016) Michael Z Lin et al.   NATURE NEUROSCIENCE

Orientation selectivity and the functional clustering of synaptic inputs in primary visual cortex

(2016) Daniel E Wilson et al.   NATURE NEUROSCIENCE

Distributed and Mixed Information in Monosynaptic Inputs to Dopamine Neurons

(2016) Ju Tian 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

DREADDs for Neuroscientists

(2016) Bryan L. Roth   NEURON

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

(2016) Hui Gong et al.   Nature Communications

Improved Monosynaptic Neural Circuit Tracing Using Engineered Rabies Virus Glycoproteins

(2016) Euiseok J. Kim 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

A comprehensive excitatory input map of the striatum reveals novel functional organization

(2016) Barbara J Hunnicutt et al.   eLife

Sensitive red protein calcium indicators for imaging neural activity

(2016) Hod Dana et al.   eLife

Clusters of synaptic inputs on dendrites of layer 5 pyramidal cells in mouse visual cortex

(2016) Onur Gökçe et al.   eLife

Saturated Reconstruction of a Volume of Neocortex

(2015) Narayanan Kasthuri et al.   CELL

CAV-2—why a canine virus is a neurobiologist's best friend

(2015) Felix Junyent et al.   CURRENT OPINION IN PHARMACOLOGY

Dual-Channel Circuit Mapping Reveals Sensorimotor Convergence in the Primary Motor Cortex

(2015) B. M. Hooks et al.   JOURNAL OF NEUROSCIENCE

Mapping Synapses by Conjugate Light-Electron Array Tomography

(2015) F. Collman et al.   JOURNAL OF NEUROSCIENCE

Monosynaptic Circuit Tracing with Glycoprotein-Deleted Rabies Viruses

(2015) E. M. Callaway et al.   JOURNAL OF NEUROSCIENCE

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

(2015) Leonard Kuan et al.   METHODS

Optogenetics: 10 years of microbial opsins in neuroscience

(2015) Karl Deisseroth   NATURE NEUROSCIENCE

A New DREADD Facilitates the Multiplexed Chemogenetic Interrogation of Behavior

(2015) Eyal Vardy et al.   NEURON

Dynamic labelling of neural connections in multiple colours by trans-synaptic fluorescence complementation

(2015) Lindsey J. Macpherson et al.   Nature Communications

Neuroanatomy goes viral!

(2015) Jonathan J. Nassi et al.   Frontiers in Neuroanatomy

Double Virus Vector Infection to the Prefrontal Network of the Macaque Brain

(2015) Mineki Oguchi et al.   PLoS One

Chemogenetic Tools to Interrogate Brain Functions

(2014) Scott M. Sternson et al.   Annual Review of Neuroscience

Neural Networks of the Mouse Neocortex

(2014) Brian Zingg et al.   CELL

Systematic comparison of adeno-associated virus and biotinylated dextran amine reveals equivalent sensitivity between tracers and novel projection targets in the mouse brain

(2014) Quanxin Wang et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Improved transduction efficiency of a lentiviral vector for neuron-specific retrograde gene transfer by optimizing the junction of fusion envelope glycoprotein

(2014) Shigeki Kato et al.   JOURNAL OF NEUROSCIENCE METHODS

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Erratum: Addendum: Independent optical excitation of distinct neural populations

(2014) Nathan C Klapoetke et al.   NATURE METHODS

Rational design of a high-affinity, fast, red calcium indicator R-CaMP2

(2014) Masatoshi Inoue et al.   NATURE METHODS

A comprehensive thalamocortical projection map at the mesoscopic level

(2014) Barbara J Hunnicutt et al.   NATURE NEUROSCIENCE

The big data challenges of connectomics

(2014) Jeff W Lichtman et al.   NATURE NEUROSCIENCE

A Whole-Brain Atlas of Inputs to Serotonergic Neurons of the Dorsal and Median Raphe Nuclei

(2014) Iskra Pollak Dorocic et al.   NEURON

Structured Synaptic Connectivity between Hippocampal Regions

(2014) Shaul Druckmann et al.   NEURON

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

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

Cell-Type-Specific Circuit Connectivity of Hippocampal CA1 Revealed through Cre-Dependent Rabies Tracing

(2014) Yanjun Sun et al.   Cell Reports

Monitoring activity in neural circuits with genetically encoded indicators

(2014) Gerard J. Broussard et al.   Frontiers in Molecular Neuroscience

Concurrent activation of striatal direct and indirect pathways during action initiation

(2013) Guohong Cui 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

An optimized fluorescent probe for visualizing glutamate neurotransmission

(2013) Jonathan S Marvin et al.   NATURE METHODS

ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation

(2013) John Y Lin et al.   NATURE NEUROSCIENCE

The WU-Minn Human Connectome Project: An overview

(2013) David C. Van Essen 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

Permanent Genetic Access to Transiently Active Neurons via TRAP: Targeted Recombination in Active Populations

(2013) Casey J. Guenthner et al.   NEURON

Fast GCaMPs for improved tracking of neuronal activity

(2013) Xiaonan R. Sun et al.   Nature Communications

Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging

(2012) J. Akerboom et al.   JOURNAL OF NEUROSCIENCE

Serial two-photon tomography for automated ex vivo mouse brain imaging

(2012) Timothy Ragan et al.   NATURE METHODS

A half century of experimental neuroanatomical tracing

(2011) José L. Lanciego et al.   JOURNAL OF CHEMICAL NEUROANATOMY

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

mGRASP enables mapping mammalian synaptic connectivity with light microscopy

(2011) Jinhyun Kim et al.   NATURE METHODS

Miniaturized integration of a fluorescence microscope

(2011) Kunal K Ghosh et al.   NATURE METHODS

New Rabies Virus Variants for Monitoring and Manipulating Activity and Gene Expression in Defined Neural Circuits

(2011) Fumitaka Osakada et al.   NEURON

A Cre-Dependent, Anterograde Transsynaptic Viral Tracer for Mapping Output Pathways of Genetically Marked Neurons

(2011) Liching Lo et al.   NEURON

Optogenetics in Neural Systems

(2011) Ofer Yizhar et al.   NEURON

Genetic visualization with an improved GCaMP calcium indicator reveals spatiotemporal activation of the spinal motor neurons in zebrafish

(2011) A. Muto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Expanded Palette of Genetically Encoded Ca2+ Indicators

(2011) Y. Zhao et al.   SCIENCE

A Lentiviral Strategy for Highly Efficient Retrograde Gene Transfer by Pseudotyping with Fusion Envelope Glycoprotein

(2010) Shigeki Kato et al.   HUMAN GENE THERAPY

High-performance genetically targetable optical neural silencing by light-driven proton pumps

(2010) Brian Y. Chow et al.   NATURE

Single-Synapse Analysis of a Diverse Synapse Population: Proteomic Imaging Methods and Markers

(2010) Kristina D. Micheva et al.   NEURON

Monosynaptic circuit tracing in vivo through Cre-dependent targeting and complementation of modified rabies virus

(2010) N. R. Wall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators

(2009) Lin Tian et al.   NATURE METHODS

The cell biology of rabies virus: using stealth to reach the brain

(2009) Matthias J. Schnell et al.   NATURE REVIEWS MICROBIOLOGY

Remote Control of Neuronal Activity in Transgenic Mice Expressing Evolved G Protein-Coupled Receptors

(2009) Georgia M. Alexander et al.   NEURON

Motor Control in a Drosophila Taste Circuit

(2009) Michael D. Gordon et al.   NEURON

Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design

(2008) Jasper Akerboom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A FLEX Switch Targets Channelrhodopsin-2 to Multiple Cell Types for Imaging and Long-Range Circuit Mapping

(2008) D. Atasoy et al.   JOURNAL OF NEUROSCIENCE

In Vitro and In Vivo Gene Therapy Vector Evolution via Multispecies Interbreeding and Retargeting of Adeno-Associated Viruses

(2008) D. Grimm et al.   JOURNAL OF VIROLOGY

High-speed, miniaturized fluorescence microscopy in freely moving mice

(2008) Benjamin A Flusberg et al.   NATURE METHODS

Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri

(2008) Feng Zhang et al.   NATURE NEUROSCIENCE

GFP Reconstitution Across Synaptic Partners (GRASP) Defines Cell Contacts and Synapses in Living Nervous Systems

(2008) Evan H. Feinberg et al.   NEURON

High-Resolution Labeling and Functional Manipulation of Specific Neuron Types in Mouse Brain by Cre-Activated Viral Gene Expression

(2008) Sandra J. Kuhlman et al.   PLoS One