Solving brain circuit function and dysfunction with computational modeling and optogenetic fMRI

Dissection of brain-wide resting-state and functional somatosensory circuits by fMRI with optogenetic silencing

(2022) Won Beom Jung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep brain stimulation in the subthalamic nucleus for Parkinson’s disease can restore dynamics of striatal networks

(2022) Elie M. Adam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virtual deep brain stimulation: Multiscale co-simulation of a spiking basal ganglia model and a whole-brain mean-field model with The Virtual Brain

(2022) Jil M. Meier et al.   EXPERIMENTAL NEUROLOGY

Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings

(2021) Nicholas A. Steinmetz et al.   SCIENCE

Brain-wide neural dynamics of poststroke recovery induced by optogenetic stimulation

(2021) Shahabeddin Vahdat et al.   Science Advances

Brain regions susceptible to alpha-synuclein spreading

(2021) Yu-Jie Guo et al.   MOLECULAR PSYCHIATRY

Repeated hippocampal seizures lead to brain-wide reorganization of circuits and seizure propagation pathways

(2021) ManKin Choy et al.   NEURON

Frequency modulation of entorhinal cortex neuronal activity drives distinct frequency-dependent states of brain-wide dynamics

(2021) Piergiorgio Salvan et al.   Cell Reports

Optogenetic activation of striatal D1R and D2R cells differentially engages downstream connected areas beyond the basal ganglia

(2021) Christina Grimm et al.   Cell Reports

Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature

(2020) Christoph Kirst et al.   CELL

Predicting Successful Generation and Inhibition of Seizure-like Afterdischarges and Mapping Their Seizure Networks Using fMRI

(2020) Ben A. Duffy et al.   Cell Reports

The microcircuits of striatum in silico

(2020) J. J. Johannes Hjorth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep brain stimulation-guided optogenetic rescue of parkinsonian symptoms

(2020) Sébastien Valverde et al.   Nature Communications

The globus pallidus orchestrates abnormal network dynamics in a model of Parkinsonism

(2020) Brice de la Crompe et al.   Nature Communications

Optogenetic Activation of Striatopallidal Neurons Reveals Altered HCN Gating in DYT1 Dystonia

(2020) Giuseppe Sciamanna et al.   Cell Reports

Neural activity during a simple reaching task in macaques is counter to gating and rebound in basal ganglia–thalamic communication

(2020) Bettina C. Schwab et al.   PLOS BIOLOGY

LRRK2 modifies α-syn pathology and spread in mouse models and human neurons

(2019) Gregor Bieri et al.   ACTA NEUROPATHOLOGICA

Predictive model of spread of Parkinson's pathology using network diffusion

(2019) S. Pandya et al.   NEUROIMAGE

Spread of α-synuclein pathology through the brain connectome is modulated by selective vulnerability and predicted by network analysis

(2019) Michael X. Henderson et al.   NATURE NEUROSCIENCE

Role of cerebellar GABAergic dysfunctions in the origins of essential tremor

(2019) Xu Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0

(2019) Venkatakaushik Voleti et al.   NATURE METHODS

Thalamic Input to Orbitofrontal Cortex Drives Brain-wide, Frequency-Dependent Inhibition Mediated by GABA and Zona Incerta

(2019) Andrew J. Weitz et al.   NEURON

Brain-wide Electrical Spatiotemporal Dynamics Encode Depression Vulnerability

(2018) Rainbo Hultman et al.   CELL

Optogenetic astrocyte activation evokes BOLD fMRI response with oxygen consumption without neuronal activity modulation

(2018) Norio Takata et al.   GLIA

Optogenetic fMRI and electrophysiological identification of region-specific connectivity between the cerebellar cortex and forebrain

(2018) Katrina Y. Choe et al.   NEUROIMAGE

Inferring multi-scale neural mechanisms with brain network modelling

(2018) Michael Schirner et al.   eLife

Diametric neural ensemble dynamics in parkinsonian and dyskinetic states

(2018) Jones G. Parker et al.   NATURE

Carbon monofilament electrodes for unit recording and functional MRI in same subjects

(2018) Miguel R. Chuapoco et al.   NEUROIMAGE

Inhibitory Basal Ganglia Inputs Induce Excitatory Motor Signals in the Thalamus

(2017) Jeongjin Kim et al.   NEURON

Studying Brain Circuit Function with Dynamic Causal Modeling for Optogenetic fMRI

(2017) David Bernal-Casas et al.   NEURON

Predictive Model of Spread of Progressive Supranuclear Palsy Using Directional Network Diffusion

(2017) Sneha Pandya et al.   Frontiers in Neurology

Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes

(2016) Nicolas Renier et al.   CELL

Combining optogenetic stimulation and fMRI to validate a multivariate dynamical systems model for estimating causal brain interactions

(2016) Srikanth Ryali et al.   NEUROIMAGE

Activation of Direct and Indirect Pathway Medium Spiny Neurons Drives Distinct Brain-wide Responses

(2016) Hyun Joo Lee et al.   NEURON

Long-range projections coordinate distributed brain-wide neural activity with a specific spatiotemporal profile

(2016) Alex T. L. Leong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Striatal cholinergic interneurons generate beta and gamma oscillations in the corticostriatal circuit and produce motor deficits

(2016) Krishnakanth Kondabolu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-Dimensional Study of Alzheimer’s Disease Hallmarks Using the iDISCO Clearing Method

(2016) Thomas Liebmann et al.   Cell Reports

Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit

(2016) Marianne J Bezaire et al.   eLife

High spatial resolution compressed sensing (HSPARSE) functional MRI

(2015) Zhongnan Fang et al.   MAGNETIC RESONANCE IN MEDICINE

The connectomics of brain disorders

(2015) Alex Fornito et al.   NATURE REVIEWS NEUROSCIENCE

Direct in vivo assessment of human stem cell graft–host neural circuits

(2015) Blake Byers et al.   NEUROIMAGE

MRI compatible optrodes for simultaneous LFP and optogenetic fMRI investigation of seizure-like afterdischarges

(2015) Ben A. Duffy et al.   NEUROIMAGE

Optogenetic fMRI reveals distinct, frequency-dependent networks recruited by dorsal and intermediate hippocampus stimulations

(2015) Andrew J. Weitz et al.   NEUROIMAGE

Striatal cholinergic dysfunction as a unifying theme in the pathophysiology of dystonia

(2015) K.L. Eskow Jaunarajs et al.   PROGRESS IN NEUROBIOLOGY

Prefrontal cortical regulation of brainwide circuit dynamics and reward-related behavior

(2015) E. A. Ferenczi et al.   SCIENCE

Frequency-selective control of cortical and subcortical networks by central thalamus

(2015) Jia Liu et al.   eLife

Optogenetic Activation of CA1 Pyramidal Neurons at the Dorsal and Ventral Hippocampus Evokes Distinct Brain-Wide Responses Revealed by Mouse fMRI

(2015) Norio Takata et al.   PLoS One

iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging

(2014) Nicolas Renier et al.   CELL

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Direct and indirect pathways of basal ganglia: a critical reappraisal

(2014) Paolo Calabresi et al.   NATURE NEUROSCIENCE

Compressed sensing fMRI using gradient-recalled echo and EPI sequences

(2014) Xiaopeng Zong et al.   NEUROIMAGE

Great Expectations: Using Whole-Brain Computational Connectomics for Understanding Neuropsychiatric Disorders

(2014) Gustavo Deco et al.   NEURON

High-throughput optogenetic functional magnetic resonance imaging with parallel computations

(2013) Zhongnan Fang et al.   JOURNAL OF NEUROSCIENCE METHODS

Compressed sensing reconstruction improves sensitivity of variable density spiral fMRI

(2013) D. J. Holland et al.   MAGNETIC RESONANCE IN MEDICINE

CLARITY for mapping the nervous system

(2013) Kwanghun Chung et al.   NATURE METHODS

A DCM for resting state fMRI

(2013) Karl J. Friston et al.   NEUROIMAGE

Basal ganglia output to the thalamus: still a paradox

(2013) Jesse H. Goldberg et al.   TRENDS IN NEUROSCIENCES

Optogenetically Induced Behavioral and Functional Network Changes in Primates

(2012) Annelies Gerits et al.   CURRENT BIOLOGY

Three-dimensional imaging of solvent-cleared organs using 3DISCO

(2012) Ali Ertürk et al.   Nature Protocols

A Network Diffusion Model of Disease Progression in Dementia

(2012) Ashish Raj et al.   NEURON

Pathological  -Synuclein Transmission Initiates Parkinson-like Neurodegeneration in Nontransgenic Mice

(2012) K. C. Luk et al.   SCIENCE

Neocortical excitation/inhibition balance in information processing and social dysfunction

(2011) Ofer Yizhar et al.   NATURE

Global and local fMRI signals driven by neurons defined optogenetically by type and wiring

(2010) Jin Hyung Lee et al.   NATURE

Regulation of parkinsonian motor behaviours by optogenetic control of basal ganglia circuitry

(2010) Alexxai V. Kravitz et al.   NATURE

Neurophysiological and Computational Principles of Cortical Rhythms in Cognition

(2010) Xiao-Jing Wang   PHYSIOLOGICAL REVIEWS

Ten simple rules for dynamic causal modeling

(2009) K.E. Stephan et al.   NEUROIMAGE

Nonlinear dynamic causal models for fMRI

(2008) Klaas Enno Stephan et al.   NEUROIMAGE

The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields

(2008) Gustavo Deco et al.   PLoS Computational Biology