2022
The Cortex and the Critical Point: Understanding the Power of Emergence
JM Beggs
MIT Press
Revealing the Dynamics of Neural Information Processing with Multivariate Information Decomposition
EL Newman, TF Varley, VK Parakkattu, SP Sherrill, JM Beggs
Entropy 24 (7), 930
Self-organization of in vitro neuronal assemblies drives to complex network topology
PC Antonello, TF Varley, J Beggs, M Porcionatto, O Sporns, J Faber
Elife 11, e74921
Addressing skepticism of the critical brain hypothesis
J Beggs
Frontiers in computational neuroscience 16
A computational examination of the two-streams hypothesis: which pathway needs a longer memory?
A Alipour, JM Beggs, JW Brown, TW James
Cognitive Neurodynamics 16 (1), 149-165
JM Beggs
MIT Press
Revealing the Dynamics of Neural Information Processing with Multivariate Information Decomposition
EL Newman, TF Varley, VK Parakkattu, SP Sherrill, JM Beggs
Entropy 24 (7), 930
Self-organization of in vitro neuronal assemblies drives to complex network topology
PC Antonello, TF Varley, J Beggs, M Porcionatto, O Sporns, J Faber
Elife 11, e74921
Addressing skepticism of the critical brain hypothesis
J Beggs
Frontiers in computational neuroscience 16
A computational examination of the two-streams hypothesis: which pathway needs a longer memory?
A Alipour, JM Beggs, JW Brown, TW James
Cognitive Neurodynamics 16 (1), 149-165
2021
Partial information decomposition reveals that synergistic neural integration is greater downstream of recurrent information flow in organotypic cortical cultures
SP Sherrill, NM Timme, JM Beggs, EL Newman
PLoS computational biology 17 (7), e1009196
Evidence for quasicritical brain dynamics
LJ Fosque, RV Williams-García, JM Beggs, G Ortiz
Physical Review Letters 126 (9), 098101
Inhibition-dominated rich-club shapes dynamics in cortical microcircuits in awake behaving mice
H Hafizi, S Nigam, J Barnathan, N Ren, IH Stevenson, SC Masmanidis, ...
bioRxiv
SP Sherrill, NM Timme, JM Beggs, EL Newman
PLoS computational biology 17 (7), e1009196
Evidence for quasicritical brain dynamics
LJ Fosque, RV Williams-García, JM Beggs, G Ortiz
Physical Review Letters 126 (9), 098101
Inhibition-dominated rich-club shapes dynamics in cortical microcircuits in awake behaving mice
H Hafizi, S Nigam, J Barnathan, N Ren, IH Stevenson, SC Masmanidis, ...
bioRxiv
2020
Correlated activity favors synergistic processing in local cortical networks in vitro at synaptically-relevant timescales
SP Sherrill, NM Timme, JM Beggs, EL Newman
Network Neuroscience, 1-20
One-stop Microfluidic Assembly of Human Brain Organoids to Model Prenatal Cannabis Exposure
Z Ao, H Cai, DJ Havert, Z Wu, Z Gong, JM Beggs, K Mackie, F Guo
Analytical Chemistry 92 (6), 4630-4638
Differential effects of propofol and ketamine on critical brain dynamics
TF Varley, O Sporns, A Puce, J Beggs
PLoS computational biology 16 (12), e1008418
Model-based detection of putative synaptic connections from spike recordings with latency and type constraints
N Ren, S Ito, H Hafizi, JM Beggs, IH Stevenson
Journal of Neurophysiology 124 (6), 1588-1604
SP Sherrill, NM Timme, JM Beggs, EL Newman
Network Neuroscience, 1-20
One-stop Microfluidic Assembly of Human Brain Organoids to Model Prenatal Cannabis Exposure
Z Ao, H Cai, DJ Havert, Z Wu, Z Gong, JM Beggs, K Mackie, F Guo
Analytical Chemistry 92 (6), 4630-4638
Differential effects of propofol and ketamine on critical brain dynamics
TF Varley, O Sporns, A Puce, J Beggs
PLoS computational biology 16 (12), e1008418
Model-based detection of putative synaptic connections from spike recordings with latency and type constraints
N Ren, S Ito, H Hafizi, JM Beggs, IH Stevenson
Journal of Neurophysiology 124 (6), 1588-1604
2019
Computation is concentrated in rich clubs of local cortical networks
SP Faber, NM Timme, JM Beggs, EL Newman
Network Neuroscience 3 (2), 384-404
The Critically Tuned Cortex
JM Beggs
Neuron 104 (4), 623-624
SP Faber, NM Timme, JM Beggs, EL Newman
Network Neuroscience 3 (2), 384-404
The Critically Tuned Cortex
JM Beggs
Neuron 104 (4), 623-624
2017
Cortical Circuits from Scratch: A Metaplastic Architecture for the Emergence of Lognormal Firing Rates and Realistic Topology
Z Tosi, JM Beggs
https://arxiv.org/pdf/1706.00133.pdf
Unveiling causal activity of complex networks
RV Williams-Garcia, JM Beggs, G Ortiz
Europhysics Letters, 119 (1)
Z Tosi, JM Beggs
https://arxiv.org/pdf/1706.00133.pdf
Unveiling causal activity of complex networks
RV Williams-Garcia, JM Beggs, G Ortiz
Europhysics Letters, 119 (1)
2016
Criticality maximizes complexity in neural tissue
NM Timme, N Marshall, N Bennett, M Ripp, E Lautzenhiser, JM Beggs
Frontiers in Physiology 7
A novel cross-frequency coupling detection method using the generalized Morse wavelets
A Nakhnikian, S Ito, LL Dwiel, LM Grasse, GV Rebec, LN Lauridsen, JM Beggs
Journal of neuroscience methods 269, 61-73
High-degree neurons feed cortical computations
NM Timme, S Ito, M Myroshnychenko, S Nigam, M Shimono, FC Yeh, P Hottowy, AM Litke, JM Beggs
PLoS Comput Biol 12 (5), e1004858
Rich-club organization in effective connectivity among cortical neurons
S Nigam, M Shimono, S Ito, FC Yeh, N Timme, M Myroshnychenko, CC Lapish, Z Tosi, P Hottowy, WC Smith, SC Masmanidis, AM Litke, O Sporns, JM Beggs
Journal of Neuroscience 36 (3), 670-684
Analysis of power laws, shape collapses, and neural complexity: new techniques and MATLAB support via the NCC toolbox
N Marshall, NM Timme, N Bennett, M Ripp, E Lautzenhiser, JM Beggs
Frontiers in Physiology 7
NM Timme, N Marshall, N Bennett, M Ripp, E Lautzenhiser, JM Beggs
Frontiers in Physiology 7
A novel cross-frequency coupling detection method using the generalized Morse wavelets
A Nakhnikian, S Ito, LL Dwiel, LM Grasse, GV Rebec, LN Lauridsen, JM Beggs
Journal of neuroscience methods 269, 61-73
High-degree neurons feed cortical computations
NM Timme, S Ito, M Myroshnychenko, S Nigam, M Shimono, FC Yeh, P Hottowy, AM Litke, JM Beggs
PLoS Comput Biol 12 (5), e1004858
Rich-club organization in effective connectivity among cortical neurons
S Nigam, M Shimono, S Ito, FC Yeh, N Timme, M Myroshnychenko, CC Lapish, Z Tosi, P Hottowy, WC Smith, SC Masmanidis, AM Litke, O Sporns, JM Beggs
Journal of Neuroscience 36 (3), 670-684
Analysis of power laws, shape collapses, and neural complexity: new techniques and MATLAB support via the NCC toolbox
N Marshall, NM Timme, N Bennett, M Ripp, E Lautzenhiser, JM Beggs
Frontiers in Physiology 7
2015
Editorial: Can there be a physics of the brain?
J Beggs
Physical review letters 114 (22), 220001
Functional clusters, hubs, and communities in the cortical microconnectome
M Shimono, JM Beggs
Cerebral Cortex 25 (10), 3743-3757
J Beggs
Physical review letters 114 (22), 220001
Functional clusters, hubs, and communities in the cortical microconnectome
M Shimono, JM Beggs
Cerebral Cortex 25 (10), 3743-3757
2014
Multiplex networks of cortical and hippocampal neurons revealed at different timescales
N Timme, S Ito, M Myroshnychenko, FC Yeh, E Hiolski, P Hottowy, JM Beggs
PLoS One 9 (12), e115764
Quasicritical brain dynamics on a nonequilibrium widom line
RV Williams-García, M Moore, JM Beggs, G Ortiz
Physical Review E 90 (6), 062714
Large-scale, high-resolution multielectrode-array recording depicts functional network differences of cortical and hippocampal cultures
S Ito, FC Yeh, E Hiolski, P Rydygier, DE Gunning, P Hottowy, N Timme, AM Litke, JM Beggs
PloS one 9 (8), e105324
Network community, clusters and hubs in cortical micro circuits
M Shimono, JM Beggs
BMC Neurosci 15 (Suppl 1), F2
Synergy, redundancy, and multivariate information measures: an experimentalist’s perspective
N Timme, W Alford, B Flecker, JM Beggs
Journal of computational neuroscience 36 (2), 119-140
Behavior modulates effective connectivity between cortex and striatum
A Nakhnikian, GV Rebec, LM Grasse, LL Dwiel, M Shimono, JM Beggs
PLoS One 9 (3), e89443
N Timme, S Ito, M Myroshnychenko, FC Yeh, E Hiolski, P Hottowy, JM Beggs
PLoS One 9 (12), e115764
Quasicritical brain dynamics on a nonequilibrium widom line
RV Williams-García, M Moore, JM Beggs, G Ortiz
Physical Review E 90 (6), 062714
Large-scale, high-resolution multielectrode-array recording depicts functional network differences of cortical and hippocampal cultures
S Ito, FC Yeh, E Hiolski, P Rydygier, DE Gunning, P Hottowy, N Timme, AM Litke, JM Beggs
PloS one 9 (8), e105324
Network community, clusters and hubs in cortical micro circuits
M Shimono, JM Beggs
BMC Neurosci 15 (Suppl 1), F2
Synergy, redundancy, and multivariate information measures: an experimentalist’s perspective
N Timme, W Alford, B Flecker, JM Beggs
Journal of computational neuroscience 36 (2), 119-140
Behavior modulates effective connectivity between cortex and striatum
A Nakhnikian, GV Rebec, LM Grasse, LL Dwiel, M Shimono, JM Beggs
PLoS One 9 (3), e89443
2013
Neuronal networks: focus amidst the noise
JM Beggs
Nature Physics 9 (9), 533-534
Attaining and maintaining criticality in a neuronal network model
J Peng, JM Beggs
Physica A: Statistical Mechanics and its Applications 392 (7), 1611-1620
JM Beggs
Nature Physics 9 (9), 533-534
Attaining and maintaining criticality in a neuronal network model
J Peng, JM Beggs
Physica A: Statistical Mechanics and its Applications 392 (7), 1611-1620
2012
Dense arrays of micro-needles for recording and electrical stimulation of neural activity in acute brain slices
DE Gunning, JM Beggs, W Dabrowski, P Hottowy, CJ Kenney, A Sher, AM Litke, K Mathieson
Journal of neural engineering 10 (1), 016007
Method for suppressing and reversing epileptogenesis
DA Hsu, MA Hsu, JM Beggs, , JM Beggs
US Patent 8,301,257
Being critical of criticality in the brain
JM Beggs, N Timme
Frontiers in physiology 3, 163
Universal critical dynamics in high resolution neuronal avalanche data
N Friedman, S Ito, BAW Brinkman, M Shimono, RE Lee DeVille, KA Dahmen, JM Beggs, TC Butler
Physical review letters 108 (20), 208102
DE Gunning, JM Beggs, W Dabrowski, P Hottowy, CJ Kenney, A Sher, AM Litke, K Mathieson
Journal of neural engineering 10 (1), 016007
Method for suppressing and reversing epileptogenesis
DA Hsu, MA Hsu, JM Beggs, , JM Beggs
US Patent 8,301,257
Being critical of criticality in the brain
JM Beggs, N Timme
Frontiers in physiology 3, 163
Universal critical dynamics in high resolution neuronal avalanche data
N Friedman, S Ito, BAW Brinkman, M Shimono, RE Lee DeVille, KA Dahmen, JM Beggs, TC Butler
Physical review letters 108 (20), 208102
2011
Extending transfer entropy improves identification of effective connectivity in a spiking cortical network model
S Ito, ME Hansen, R Heiland, A Lumsdaine, AM Litke, JM Beggs
PloS one 6 (11), e27431
Partial information decomposition as a spatiotemporal filter
B Flecker, W Alford, JM Beggs, PL Williams, RD Beer
Chaos: An Interdisciplinary Journal of Nonlinear Science 21 (3), 037104
S Ito, ME Hansen, R Heiland, A Lumsdaine, AM Litke, JM Beggs
PloS one 6 (11), e27431
Partial information decomposition as a spatiotemporal filter
B Flecker, W Alford, JM Beggs, PL Williams, RD Beer
Chaos: An Interdisciplinary Journal of Nonlinear Science 21 (3), 037104
2010 and prior
Aberrant neuronal avalanches in cortical tissue removed from juvenile epilepsy patients
JP Hobbs, JL Smith, JM Beggs
Journal of Clinical Neurophysiology 27 (6), 380-386
(2010)
512-electrode MEA system for spatio-temporal distributed stimulation and recording of neural activity
P Hottowy, JM Beggs, EJ Chichilnisky, W Dąbrowski, T Fiutowski, DE Gunning, J Hobbs, L Jepson, S Kachiguine, K Mathieson, P Rydygier, A Sher, A Skoczeń, A Litke
Proceedings of the 7th International Meeting on Substrate-Proceedings of the 7th International Meeting on Substrate-Integrated Microelectrode Arrays, Reutlingen, Germany (Stett, A ed), June
(2010)
Maximum entropy approaches to living neural networks
FC Yeh, A Tang, JP Hobbs, P Hottowy, W Dabrowski, A Sher, A Litke, JM Beggs
Entropy 12 (1), 89-106
(2010)
A few strong connections: optimizing information retention in neuronal avalanches
W Chen, JP Hobbs, A Tang, JM Beggs
BMC neuroscience 11 (1), 3
(2010)
An open hypothesis: is epilepsy learned, and can it be unlearned?
D Hsu, W Chen, M Hsu, JM Beggs
Epilepsy & Behavior 13 (3), 511-522
(2008)
The criticality hypothesis: how local cortical networks might optimize information processing
JM Beggs
Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences
(2008)
A maximum entropy model applied to spatial and temporal correlations from cortical networks in vitro
A Tang, D Jackson, J Hobbs, W Chen, JL Smith, H Patel, A Prieto, D Petrusca, MI Grivich, A Sher, P Hottowy, W Dabrowski, AM Litke, JM Beggs
Journal of Neuroscience 28 (2), 505-518
(2008)
Theoretical neuroscience: How to build a critical mind
JM Beggs
Nature Physics 3 (12), 834-835
(2007)
Simple spontaneously active Hebbian learning model: homeostasis of activity and connectivity, and consequences for learning and epileptogenesis
D Hsu, A Tang, M Hsu, JM Beggs
Physical Review E 76 (4), 041909
(2007)
Neuronal avalanches and criticality: A dynamical model for homeostasis
D Hsu, JM Beggs
Neurocomputing 69 (10), 1134-1136
(2006)
Critical branching captures activity in living neural networks and maximizes the number of metastable states
C Haldeman, JM Beggs
Physical review letters 94 (5), 058101
(2005)
(Beggs and Haldeman Reply, JM Beggs, C Haldeman, Phys. Rev. Lett. 94, 219802)
Neuronal avalanches are diverse and precise activity patterns that are stable for many hours in cortical slice cultures
JM Beggs, D Plenz
Journal of neuroscience 24 (22), 5216-5229
(2004)
Neuronal avalanches in neocortical circuits
JM Beggs, D Plenz
Journal of neuroscience 23 (35), 11167-11177
(2003)
Analysis of spontaneous activity in cultured brain tissue using the discrete wavelet transform
JD Johnson, D Plenz, J Beggs, W Li, M Mieier, N Miltner, K Owen
Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium
(2003)
A statistical theory of long-term potentiation and depression
JM Beggs
Neural computation 13 (1), 87-111
(2001)
Prolonged synaptic integration in perirhinal cortical neurons
JM Beggs, JR Moyer, JP McGann, TH Brown
Journal of Neurophysiology 83 (6), 3294-3298
(2000)
Electrophysiology and morphology of neurons in rat perirhinal cortex
JM Beggs, EW Kairiss
Brain research 665 (1), 18-32
(1994)
JP Hobbs, JL Smith, JM Beggs
Journal of Clinical Neurophysiology 27 (6), 380-386
(2010)
512-electrode MEA system for spatio-temporal distributed stimulation and recording of neural activity
P Hottowy, JM Beggs, EJ Chichilnisky, W Dąbrowski, T Fiutowski, DE Gunning, J Hobbs, L Jepson, S Kachiguine, K Mathieson, P Rydygier, A Sher, A Skoczeń, A Litke
Proceedings of the 7th International Meeting on Substrate-Proceedings of the 7th International Meeting on Substrate-Integrated Microelectrode Arrays, Reutlingen, Germany (Stett, A ed), June
(2010)
Maximum entropy approaches to living neural networks
FC Yeh, A Tang, JP Hobbs, P Hottowy, W Dabrowski, A Sher, A Litke, JM Beggs
Entropy 12 (1), 89-106
(2010)
A few strong connections: optimizing information retention in neuronal avalanches
W Chen, JP Hobbs, A Tang, JM Beggs
BMC neuroscience 11 (1), 3
(2010)
An open hypothesis: is epilepsy learned, and can it be unlearned?
D Hsu, W Chen, M Hsu, JM Beggs
Epilepsy & Behavior 13 (3), 511-522
(2008)
The criticality hypothesis: how local cortical networks might optimize information processing
JM Beggs
Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences
(2008)
A maximum entropy model applied to spatial and temporal correlations from cortical networks in vitro
A Tang, D Jackson, J Hobbs, W Chen, JL Smith, H Patel, A Prieto, D Petrusca, MI Grivich, A Sher, P Hottowy, W Dabrowski, AM Litke, JM Beggs
Journal of Neuroscience 28 (2), 505-518
(2008)
Theoretical neuroscience: How to build a critical mind
JM Beggs
Nature Physics 3 (12), 834-835
(2007)
Simple spontaneously active Hebbian learning model: homeostasis of activity and connectivity, and consequences for learning and epileptogenesis
D Hsu, A Tang, M Hsu, JM Beggs
Physical Review E 76 (4), 041909
(2007)
Neuronal avalanches and criticality: A dynamical model for homeostasis
D Hsu, JM Beggs
Neurocomputing 69 (10), 1134-1136
(2006)
Critical branching captures activity in living neural networks and maximizes the number of metastable states
C Haldeman, JM Beggs
Physical review letters 94 (5), 058101
(2005)
(Beggs and Haldeman Reply, JM Beggs, C Haldeman, Phys. Rev. Lett. 94, 219802)
Neuronal avalanches are diverse and precise activity patterns that are stable for many hours in cortical slice cultures
JM Beggs, D Plenz
Journal of neuroscience 24 (22), 5216-5229
(2004)
Neuronal avalanches in neocortical circuits
JM Beggs, D Plenz
Journal of neuroscience 23 (35), 11167-11177
(2003)
Analysis of spontaneous activity in cultured brain tissue using the discrete wavelet transform
JD Johnson, D Plenz, J Beggs, W Li, M Mieier, N Miltner, K Owen
Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium
(2003)
A statistical theory of long-term potentiation and depression
JM Beggs
Neural computation 13 (1), 87-111
(2001)
Prolonged synaptic integration in perirhinal cortical neurons
JM Beggs, JR Moyer, JP McGann, TH Brown
Journal of Neurophysiology 83 (6), 3294-3298
(2000)
Electrophysiology and morphology of neurons in rat perirhinal cortex
JM Beggs, EW Kairiss
Brain research 665 (1), 18-32
(1994)
Book Chapters
Connectivity and dynamics in local cortical networks
JM Beggs, J Klukas, W Chen
Chapter 3, pp. 91-116,
Handbook of Brain Connectivity, (eds., V Jirsa and R MacIntosh), Springer, 2007
Learning and memory: Basic mechanisms
JM Beggs, TH Brown, JH Byrne, T Crow, JE LeDoux, K LeBar, RF Thompson
Chapter 55, pp. 1411-1454
Fundamental Neuroscience.(Eds: F Bloom, S Landis, J Roberts, L Squire, and M Zigmond), 1999.
JM Beggs, J Klukas, W Chen
Chapter 3, pp. 91-116,
Handbook of Brain Connectivity, (eds., V Jirsa and R MacIntosh), Springer, 2007
Learning and memory: Basic mechanisms
JM Beggs, TH Brown, JH Byrne, T Crow, JE LeDoux, K LeBar, RF Thompson
Chapter 55, pp. 1411-1454
Fundamental Neuroscience.(Eds: F Bloom, S Landis, J Roberts, L Squire, and M Zigmond), 1999.