Humphries Lab Neural data science

Publications

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2024

Motor Cortex Latent Dynamics Encode Spatial and Temporal Arm Movement Parameters Independently
Motor Cortex Latent Dynamics Encode Spatial and Temporal Arm Movement Parameters Independently
Andrea Colins Rodriguez, Matt G. Perich, Lee E. Miller, Mark D. Humphries
The Journal of Neuroscience  ·  26 Jul 2024  ·  doi:10.1523/JNEUROSCI.1777-23.2024
Tracking subjects’ strategies in behavioural choice experiments at trial resolution
Tracking subjects’ strategies in behavioural choice experiments at trial resolution
Silvia Maggi, Rebecca M Hock, Martin O’Neill, Mark Buckley, Paula M Moran, Tobias Bast, Musa Sami, Mark D Humphries
eLife  ·  01 Mar 2024  ·  doi:10.7554/eLife.86491

2022

Activity Subspaces in Medial Prefrontal Cortex Distinguish States of the World
Activity Subspaces in Medial Prefrontal Cortex Distinguish States of the World
Silvia Maggi, Mark D. Humphries
The Journal of Neuroscience  ·  14 Apr 2022  ·  doi:10.1523/JNEUROSCI.1412-21.2022

2021

Bayesian Mapping of the Striatal Microcircuit Reveals Robust Asymmetries in the Probabilities and Distances of Connections
Bayesian Mapping of the Striatal Microcircuit Reveals Robust Asymmetries in the Probabilities and Distances of Connections
François Cinotti, Mark D. Humphries
The Journal of Neuroscience  ·  10 Dec 2021  ·  doi:10.1523/jneurosci.1487-21.2021
Making decisions in the dark basement of the brain: A look back at the GPR model of action selection and the basal ganglia
Making decisions in the dark basement of the brain: A look back at the GPR model of action selection and the basal ganglia
Mark D. Humphries, Kevin Gurney
Biological Cybernetics  ·  17 Jul 2021  ·  doi:10.1007/s00422-021-00887-5
Spectral estimation for detecting low-dimensional structure in networks using arbitrary null models
Spectral estimation for detecting low-dimensional structure in networks using arbitrary null models
Mark D. Humphries, Javier A. Caballero, Mat Evans, Silvia Maggi, Abhinav Singh
PLOS ONE  ·  02 Jul 2021  ·  doi:10.1371/journal.pone.0254057
Strong and weak principles of neural dimension reduction
Strong and weak principles of neural dimension reduction
Mark D Humphries
Neurons, Behavior, Data analysis, and Theory  ·  17 Jun 2021  ·  doi:10.51628/001c.24619
The spike: an epic journey through the brain in 2.1 seconds
The spike: an epic journey through the brain in 2.1 seconds
Mark Humphries
Princeton University Press  ·  01 Jan 2021  ·  isbn:9780691195889

2019

On the use of calcium deconvolution algorithms in practical contexts
On the use of calcium deconvolution algorithms in practical contexts
Mathew H. Evans, Rasmus S. Petersen, Mark D. Humphries
Cold Spring Harbor Laboratory  ·  11 Dec 2019  ·  doi:10.1101/871137
Maladaptive striatal plasticity and abnormal reward‐learning in cervical dystonia
Maladaptive striatal plasticity and abnormal reward‐learning in cervical dystonia
Tom Gilbertson, Mark Humphries, J. Douglas Steele
European Journal of Neuroscience  ·  14 May 2019  ·  doi:10.1111/ejn.14414
Prediction of Choice from Competing Mechanosensory and Choice-Memory Cues during Active Tactile Decision Making
Prediction of Choice from Competing Mechanosensory and Choice-Memory Cues during Active Tactile Decision Making
Dario Campagner, Mathew H. Evans, Katarina Chlebikova, Andrea Colins-Rodriguez, Michaela S.E. Loft, Sarah Fox, David Pettifer, Mark D. Humphries, Karel Svoboda, Rasmus S. Petersen
The Journal of Neuroscience  ·  08 Mar 2019  ·  doi:10.1523/JNEUROSCI.2217-18.2019
Medial prefrontal cortex population activity is plastic irrespective of learning
Medial prefrontal cortex population activity is plastic irrespective of learning
Abhinav Singh, Adrien Peyrache, Mark D. Humphries
The Journal of Neuroscience  ·  27 Feb 2019  ·  doi:10.1523/jneurosci.1370-17.2019

2018

An ensemble code in medial prefrontal cortex links prior events to outcomes during learning
An ensemble code in medial prefrontal cortex links prior events to outcomes during learning
Silvia Maggi, Adrien Peyrache, Mark D. Humphries
Nature Communications  ·  07 Jun 2018  ·  doi:10.1038/s41467-018-04638-2
Insights into Parkinson’s disease from computational models of the basal ganglia
Insights into Parkinson’s disease from computational models of the basal ganglia
Mark D Humphries, Jose Angel Obeso, Jakob Kisbye Dreyer
Journal of Neurology, Neurosurgery & Psychiatry  ·  17 Apr 2018  ·  doi:10.1136/jnnp-2017-315922
A probabilistic, distributed, recursive mechanism for decision-making in the brain
A probabilistic, distributed, recursive mechanism for decision-making in the brain
Javier A. Caballero, Mark D. Humphries, Kevin N. Gurney
PLOS Computational Biology  ·  03 Apr 2018  ·  doi:10.1371/journal.pcbi.1006033

2017

Dynamical networks: Finding, measuring, and tracking neural population activity using network science
Dynamical networks: Finding, measuring, and tracking neural population activity using network science
Mark D. Humphries
Network Neuroscience  ·  01 Dec 2017  ·  doi:10.1162/NETN_a_00020
A spiral attractor network drives rhythmic locomotion
A spiral attractor network drives rhythmic locomotion
Angela M Bruno, William N Frost, Mark D Humphries
eLife  ·  07 Aug 2017  ·  doi:10.7554/eLife.27342

2016

The Goldilocks zone in neural circuits
The Goldilocks zone in neural circuits
Mark D Humphries
eLife  ·  02 Dec 2016  ·  doi:10.7554/eLife.22735

2015

Modular Deconstruction Reveals the Dynamical and Physical Building Blocks of a Locomotion Motor Program
Modular Deconstruction Reveals the Dynamical and Physical Building Blocks of a Locomotion Motor Program
Angela M. Bruno, William N. Frost, Mark D. Humphries
Neuron  ·  01 Apr 2015  ·  doi:10.1016/j.neuron.2015.03.005
Finding communities in sparse networks.
Finding communities in sparse networks.
Abhinav Singh, Mark D Humphries
Scientific reports  ·  06 Mar 2015  ·  pmid:25742951
A new framework for cortico-striatal plasticity: behavioural theory meets in vitro data at the reinforcement-action interface.
A new framework for cortico-striatal plasticity: behavioural theory meets in vitro data at the reinforcement-action interface.
Kevin N Gurney, Mark D Humphries, Peter Redgrave
PLoS biology  ·  06 Jan 2015  ·  pmid:25562526

2014

Early hypersynchrony in juvenile PINK1(-)/(-) motor cortex is rescued by antidromic stimulation.
Early hypersynchrony in juvenile PINK1(-)/(-) motor cortex is rescued by antidromic stimulation.
Romain Carron, Anton Filipchuk, Romain Nardou, Abhinav Singh, Francois J Michel, Mark D Humphries, Constance Hammond
Frontiers in systems neuroscience  ·  21 May 2014  ·  pmid:24904316
Striatal disorders dissociate mechanisms of enhanced and impaired response selection - Evidence from cognitive neurophysiology and computational modelling.
Striatal disorders dissociate mechanisms of enhanced and impaired response selection - Evidence from cognitive neurophysiology and computational modelling.
Christian Beste, Mark Humphries, Carsten Saft
NeuroImage. Clinical  ·  12 Apr 2014  ·  pmid:24936413
Slaves to the rhythm: coupling of the subthalamic nucleus-globus pallidus network in Parkinsonian oscillations.
Slaves to the rhythm: coupling of the subthalamic nucleus-globus pallidus network in Parkinsonian oscillations.
Mark D Humphries
The Journal of physiology  ·  01 Apr 2014  ·  pmid:24692460
Transient and steady-state selection in the striatal microcircuit.
Transient and steady-state selection in the striatal microcircuit.
Adam Tomkins, Eleni Vasilaki, Christian Beste, Kevin Gurney, Mark D Humphries
Frontiers in computational neuroscience  ·  20 Jan 2014  ·  pmid:24478684

2013

Population-wide distributions of neural activity during perceptual decision-making
Population-wide distributions of neural activity during perceptual decision-making
Adrien Wohrer, Mark D. Humphries, Christian K. Machens
Progress in Neurobiology  ·  01 Apr 2013  ·  doi:10.1016/j.pneurobio.2012.09.004
Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
Romain Daniel Cazé, Mark Humphries, Boris Gutkin
PLoS Computational Biology  ·  28 Feb 2013  ·  doi:10.1371/journal.pcbi.1002867

2012

Network effects of subthalamic deep brain stimulation drive a unique mixture of responses in basal ganglia output
Network effects of subthalamic deep brain stimulation drive a unique mixture of responses in basal ganglia output
Mark D. Humphries, Kevin Gurney
European Journal of Neuroscience  ·  01 Jul 2012  ·  doi:10.1111/j.1460-9568.2012.08085.x
Dopaminergic Control of the Exploration-Exploitation Trade-Off via the Basal Ganglia.
Dopaminergic Control of the Exploration-Exploitation Trade-Off via the Basal Ganglia.
Mark D Humphries, Mehdi Khamassi, Kevin Gurney
Frontiers in neuroscience  ·  06 Feb 2012  ·  pmid:22347155
Integrating cortico-limbic-basal ganglia architectures for learning model-based and model-free navigation strategies
Integrating cortico-limbic-basal ganglia architectures for learning model-based and model-free navigation strategies
Mehdi Khamassi, Mark D. Humphries
Frontiers in Behavioral Neuroscience  ·  01 Jan 2012  ·  doi:10.3389/fnbeh.2012.00079
Dopaminergic control of the exploration-exploitation trade-off via the basal ganglia
Dopaminergic control of the exploration-exploitation trade-off via the basal ganglia
Mark Humphries
Frontiers in Neuroscience  ·  01 Jan 2012  ·  doi:10.3389/fnins.2012.00009

2011

The medial reticular formation: a brainstem substrate for simple action selection?
The medial reticular formation: a brainstem substrate for simple action selection?
Mark D. Humphries, Kevin N. Gurney, Tony J Prescott
Modelling Natural Action Selection  ·  10 Nov 2011  ·  doi:10.1017/CBO9780511731525.018
Spike-Train Communities: Finding Groups of Similar Spike Trains
Spike-Train Communities: Finding Groups of Similar Spike Trains
Mark D. Humphries
The Journal of Neuroscience  ·  09 Feb 2011  ·  doi:10.1523/JNEUROSCI.2853-10.2011
Onset of pup locomotion coincides with loss of NR2C/D-mediated cortico-striatal EPSCs and dampening of striatal network immature activity
Onset of pup locomotion coincides with loss of NR2C/D-mediated cortico-striatal EPSCs and dampening of striatal network immature activity
Nathalie Dehorter
Frontiers in Cellular Neuroscience  ·  01 Jan 2011  ·  doi:10.3389/fncel.2011.00024

2010

Reconstructing the Three-Dimensional GABAergic Microcircuit of the Striatum
Reconstructing the Three-Dimensional GABAergic Microcircuit of the Striatum
Mark D. Humphries, Ric Wood, Kevin Gurney
PLoS Computational Biology  ·  24 Nov 2010  ·  doi:10.1371/journal.pcbi.1001011
The ventral basal ganglia, a selection mechanism at the crossroads of space, strategy, and reward.
The ventral basal ganglia, a selection mechanism at the crossroads of space, strategy, and reward.
Mark D. Humphries, Tony J. Prescott
Progress in Neurobiology  ·  01 Apr 2010  ·  doi:10.1016/j.pneurobio.2009.11.003

2009

Dopamine-modulated dynamic cell assemblies generated by the GABAergic striatal microcircuit
Dopamine-modulated dynamic cell assemblies generated by the GABAergic striatal microcircuit
Mark D. Humphries, Ric Wood, Kevin Gurney
Neural Networks  ·  01 Oct 2009  ·  doi:10.1016/j.neunet.2009.07.018
Technical integration of hippocampus, basal ganglia and physical models for spatial navigation
Technical integration of hippocampus, basal ganglia and physical models for spatial navigation
Charles Fox
Frontiers in Neuroinformatics  ·  01 Jan 2009  ·  doi:10.3389/neuro.11.006.2009
Capturing dopaminergic modulation and bimodal membrane behaviour of striatal medium spiny neurons in accurate, reduced models
Capturing dopaminergic modulation and bimodal membrane behaviour of striatal medium spiny neurons in accurate, reduced models
Mark Humphries
Frontiers in Computational Neuroscience  ·  01 Jan 2009  ·  doi:10.3389/neuro.10.026.2009

2008

Network ‘Small-World-Ness’: A Quantitative Method for Determining Canonical Network Equivalence
Network ‘Small-World-Ness’: A Quantitative Method for Determining Canonical Network Equivalence
Mark D. Humphries, Kevin Gurney
PLoS ONE  ·  30 Apr 2008  ·  doi:10.1371/journal.pone.0002051

2007

Solution Methods for a New Class of Simple Model Neurons
Solution Methods for a New Class of Simple Model Neurons
Mark D. Humphries, Kevin Gurney
Neural Computation  ·  01 Dec 2007  ·  doi:10.1162/neco.2007.19.12.3216
Is there a brainstem substrate for action selection?
Is there a brainstem substrate for action selection?
M D Humphries, K Gurney, T J Prescott
Philosophical transactions of the Royal Society of London. Series B, Biological sciences  ·  29 Sep 2007  ·  pmid:17428776

2006

A Physiologically Plausible Model of Action Selection and Oscillatory Activity in the Basal Ganglia
A Physiologically Plausible Model of Action Selection and Oscillatory Activity in the Basal Ganglia
Mark D. Humphries, Robert D. Stewart, Kevin N. Gurney
The Journal of Neuroscience  ·  13 Dec 2006  ·  doi:10.1523/JNEUROSCI.3486-06.2006
The brainstem reticular formation is a small-world, not scale-free, network.
The brainstem reticular formation is a small-world, not scale-free, network.
M D Humphries, K Gurney, T J Prescott
Proceedings. Biological sciences  ·  22 Feb 2006  ·  pmid:16615219
A robot model of the basal ganglia: Behavior and intrinsic processing
A robot model of the basal ganglia: Behavior and intrinsic processing
Tony J. Prescott, Fernando M. Montes González, Kevin Gurney, Mark D. Humphries, Peter Redgrave
Neural Networks  ·  01 Jan 2006  ·  doi:10.1016/j.neunet.2005.06.049

2002

The role of intra-thalamic and thalamocortical circuits in action selection
The role of intra-thalamic and thalamocortical circuits in action selection
M.D. Humphries, K.N. Gurney
Network: Computation in Neural Systems  ·  01 Jan 2002  ·  doi:10.1088/0954-898X/13/1/305

2001

A pulsed neural network model of bursting in the basal ganglia
A pulsed neural network model of bursting in the basal ganglia
Mark D. Humphries, Kevin N. Gurney
Neural Networks  ·  01 Jul 2001  ·  doi:10.1016/S0893-6080(01)00060-0