The Virtual Brain

Nature Communications

DOI: 0.1038/s41467-024-47860-x

Dominik P. Koller, Michael Schirner and Petra Ritter

Human connectome topology directs cortical traveling waves and shapes frequency gradients

Nature Communications (accepted)

Nanditha Rajamani, Helen Friedrich, Konstantin Butenko, […], Petra Ritter, […], Andreas Horn

Toward personalized deep brain stimulation

National Science Review

DOI: 10.1093/nsr/nwae079

Huifang E Wang, Paul Triebkorn, Martin Breyton, Borana Dollomaja, Jean-Didier Lemarechal, Spase Petkoski, Pierpaolo Sorrentino, Damien Depannemaecker, Meysam Hashemi, Viktor K Jirsa

Virtual brain twins: from basic neuroscience to clinical use

Nature Communications

DOI: 10.1038/s41467-023-38626-y

Michael Schirner, Gustavo Deco and Petra Ritter

Learning how network structure shapes decision-making for bio-inspired computing

The Lancet Neurology

DO: 10.1016/S1474-4422(23)00008-X

Viktor Jirsa, Huifang Wang, Paul Triebkorn, Meysam Hashemi, Jayant Jha, Jorge Gonzalez-Martinez, Maxime Guye, Julia Makhalova, Prof Fabrice Bartolomei

Personalised virtual brain models in epilepsy

Science Advances

DOI: 10.1126/sciadv.abq7547

Viktor Sip, Meysam Hashemi, Timo Dickscheid, Katrin Amunts, Spase Petkoski, Viktor Jirsa

Characterization of regional differences in resting-state fMRI with a data-driven network model of brain dynamics

Science Translational Medicine

DOI: 10.1126/scitranslmed.abp8982

Huifang E. Wang, Marmaduke Woodman, Paul Triebkorn, Jean-Didier Lemarechal, Jayant Jha, Borana Dollomaja, Anirudh Nihalani Vattikonda, Viktor Sip, Samuel Medina Villalon, Meysam Hashemi, Maxime Guye, Julia Makhalova, Fabrice Bartolomei, Viktor Jirsa

Delineating epileptogenic networks using brain imaging data and personalized modeling in drug-resistant epilepsy

Cerebral Cortex

DOI: 10.1093/cercor/bhac500/6972302

Spase Petkoski, Petra Ritter, Viktor K. Jirsa

White-matter degradation and dynamical compensation support age-related functional alterations in human brain

Frontiers Neuroinformatics

doi: 10.3389/fninf.2022.937790

Jorge Gulín-González, Maria L. Bringas-Vega, Eduardo Martínez-Montes, Petra Ritter, Ana Solodkin, Mitchell Joseph Valdes-Sosa and Pedro Antonio Valdes-Sosa

Brain Modeling of Neurogenerative Disorders

Neuroimage

https://doi.org/10.1016/j.neuroimage.2022.118973

Schirner, Domide, Perdikis, Triebkorn, Stefanovski, Pai, Prodan, Valean, Palmer, Langford, Blickensdörfer, van der Vlag, Diaz-Pier, Peyser, Klijn, Pleiter, Nahm, Schmid, Woodman, Zehl, Fousek, Petkoski, Kusch, Hashemi, Marinazzo, Mangin, Flöel, Akintoye, Stahl, Cepic, Johnson, Deco, McIntosh, Hilgetag, Morgan, Schuller, Upton, McMurtrie, Dickscheid, Bjaalie, Amunts, Mersmann, Jirsa, Ritter

Brain simulation as a cloud service: The Virtual Brain on EBRAINS

Experimental Neurology

DOI: 10.1016/j.expneurol.2022.114111

Meier JM, Perdikis D, Blickensdörfer A, Stefanovski L, Liu Q, Maith O, Dinkelbach HÜ, Baladron J, Hamker FH, Ritter P

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

Alzheimer’s Dement. Transl. Res. Clin. Interv.

doi: 10.1002/trc2.12303

Paul Triebkorn, Leon Stefanovski, Kiret Dhindsa, Margarita-Arimatea Diaz-Cortes, Patrik Bey, Konstantin Bülau, Roopa Kalsank Pai, Andreas Spiegler, Ana Solodkin, Viktor Jirsa, Randy McIntosh, Alzheimer's Disease Neuroimaging Initiative, Petra Ritter

Brain simulation augments machine-learning-based classification of dementia

eNeuro

doi: 10.1523/ENEURO.0075-21.2022

Tyler Good, Michael Schirner, Kelly Shen, Petra Ritter, Pratik Mukherjee, Brian Levine, and Anthony McIntosh

Personalized connectome-based modeling in patients with semi-acute phase mild TBI: relationship to acute neuroimaging and 6-month follow-up.

Neuroimage

doi: 10.1016/j.neuroimage.2022.118928

M Schirner; X Kong; T Yeo; G Deco, P Ritter

Dynamic primitives of brain network interaction

Alzheimer’s & Dementia

doi: 10.1002/alz.12311

Claudio Babiloni, Xianghong Arakaki, Hamed Azami, Karim Bennys, Katarzyna Blinowska, Laura Bonanni, Ana Bujan, Maria C Carrillo, Andrzej Cichocki, Jaisalmer de Frutos-Lucas, Claudio Del Percio, Bruno Dubois, Rebecca Edelmayer, Gary Egan, Stephane Epelbaum, Javier Escudero, Alan Evans, Francesca Farina, Keith Fargo, Alberto Fernández, Raffaele Ferri, Giovanni Frisoni, Harald Hampel, Michael G Harrington, Vesna Jelic, Jaeseung Jeong, Yang Jiang, Maciej Kaminski, Voyko Kavcic, Kerry Kilborn, Sanjeev Kumar, Alice Lam, Lew Lim, Roberta Lizio, David Lopez, Susanna Lopez, Brendan Lucey, Fernando Maestú, William J McGeown, Ian McKeith, Davide Vito Moretti, Flavio Nobili, Giuseppe Noce, John Olichney, Marco Onofrj, Ricardo Osorio, Mario Parra-Rodriguez, Tarek Rajji, Petra Ritter, Andrea Soricelli, Fabrizio Stocchi, Ioannis Tarnanas, John Paul Taylor, Stefan Teipel, Federico Tucci, Mitchell Valdes-Sosa, Pedro Valdes-Sosa, Marco Weiergräber, Gorsev Yener, Bahar Guntekin

Measures of Resting State EEG Rhythms for Clinical Trials in Alzheimer’s Disease Patients: Recommendations of an Expert Panel

PLoS computational biology

doi: 10.1371/journal.pcbi.1009129

Hashemi M, Vattikonda AN, Sip V, Diaz-Pier S, Peyser A, Wang H, Guye M, Bartolomei F, Woodman MM, Jirsa VK

On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread

eNeuro

doi: 10.1523/ENEURO.0475-20.2021

Arbabyazd L, Shen K, Wang Z, Hofmann-Apitius M, Ritter P, The Alzheimer’s Disease Neuroimaging Initiative, McIntosh AR, Battaglia D, Jirsa V

Virtual connectomic datasets in Alzheimer’s Disease and aging using wholebrain network dynamics modelling

BioRxiv

doi: 10.1101/2021.02.27.433161

Triebkorn P, Stefanovski L, Dhindsa K, Diaz-Cortes M, Bey P, Bülau K, Kalsank Pai R, Spiegler A, Solodkin A, Jirsa V, McIntosh R, Ritter P, Alzheimer's Disease Neuroimaging Initiative

Multi-scale brain simulation with integrated positron emission tomography yields hidden local field potential activity that augments machine-learning classification of Alzheimer's disease

arXiv

arXiv:2102.05888

M. Schirner, L. Domide, D. Perdikis, P. Triebkorn, L. Stefanovski, R. Pai, P. Popa, B. Valean, J. Palmer, C. Langford, A. Blickensdörfer, M. van der Vlag, S. Diaz-Pier, A. Peyser, W. Klijn, D. Pleiter, A. Nahm, O. Schmid, M. Woodman, L. Zehl, J. Fousek, S. Petkoski, L. Kusch, M. Hashemi, D. Marinazzo, J.-F. Mangin, A. Flöel, S. Akintoye, B. C. Stahl, M. Cepic, E. Johnson, G. Deco, A. R. McIntosh, C. C. Hilgetag, M. Morgan, B. Schuller, A. Upton, C. McMurtrie, T. Dickscheid, J. G. Bjaalie, K. Amunts, J. Mersmann, V. Jirsa, P. Ritter

Brain Modelling as a Service: The Virtual Brain on EBRAINS

Cerebral Cortex

doi: 10.1093/cercor/bhaa339

Klein PC, Ettinger U, Schirner M, Ritter P, Rujescu D, Falkai P, Koutsouleris N, Kambeitz-Ilankovic L, Kambeitz J

Brain Network Simulations Indicate Effects of Neuregulin-1 Genotype on Excitation-Inhibition Balance in Cortical Dynamics

Front. Neuroinform

doi: 10.3389/fninf.2021.630172

Stefanovski L, Meier JM, Pai R, Triebkorn P, Lett T, Martin L, Bülau K, Hofmann-Apitius M, Solodkin A, McIntosh A, Ritter P

Bridging Scales in Alzheimer's Disease: Biological Framework for Brain Simulation With The Virtual Brain

Springer, New York, NY

doi: 10.1007/978-1-4614-7320-6

Viktor Jirsa, Marmaduke Woodman, Lia Domide

The Virtual Brain (TVB): Simulation Environment for Large-Scale Brain Networks

Front Cell Neurosci.

doi:10.3389/fncel.2020.00240

Palesi F, Lorenzi RM, Casellato C, Ritter P, Jirsa V, Gandini Wheeler- Kingshott CAM, D'Angelo E.

The Importance of Cerebellar Connectivity on Simulated Brain Dynamics

J Neurosci.

doi:10.1523/JNEUROSCI.0905-19.2020

Courtiol J, Guye M, Bartolomei F, Petkoski S, Jirsa VK.

Dynamical Mechanisms of Interictal Resting-State Functional Connectivity in Epilepsy

Neuroimage

doi:10.1101/752931

Aerts H, Schirner M, Hollander T, Jeurissen B, Achten E, Van Roost D, Ritter P, Marinazzo D

Modeling brain dynamics after tumor resection using The Virtual Brain

BioRxiv

doi: 10.1101/2020.03.26.009795

Triebkorn P, Zimmermann J, Stefanovski L, Roy D, Solodkin A, Jirsa V, Deco G, Breakspear M, McIntosh AR, Ritter P

Identifying optimal working points of individual Virtual Brains: A large-scale brain network modelling study

PNAS

doi:10.1073/pnas.1906694116

Melozzi F, Bergmann E, Harris JA, Kahn I, Jirsa V, Bernard C

Individual structural features constrain the mouse functional connectome

Network Neuroscience

doi:10.1162/netn_a_00120

Ryan JD, Shen K, Kacollja A, Tian H, Griffiths J, Bezgin G, McIntosh AR

Modeling the influence of the hippocampal memory system on the oculomotor system

Computational Brain & Behaviour

doi:10.1007/s42113-019-00062-x

Poldrack RA, Feingold F, Frank MJ, Gleeson P, de Hollander G, Huys QJM, Love BC, Markiewicz CJ, Moran R, Ritter P, Rogers TT, Turner BM, Yarkoni T, Zhan M, Cohen JD

The Importance of Standards for Sharing of Computational Models and Data

Network Neuroscience

doi:10.1162/netn_a_00107

McIntosh AR, Jirsa VK

The hidden repertoire of brain dynamics and dysfunction

Nature Scientific Data

doi: 10.1038/s41597-019-0129-z

Shen K, Bezgin G, Schirner M, Ritter P, Everling S, McIntosh AR

A macaque connectome for large-scale network simulations in The Virtual Brain

PLoS Comput Biol.

doi:10.1371/journal.pcbi.1007051

An S, Bartolomei F, Guye M, Jirsa V

Optimization of surgical intervention outside the epileptogenic zone in the Virtual Epileptic Patient (VEP)

Frontiers Computational Neuroscience

doi:10.3389/fncom.2019.00054

Stefanovski L, Triebkorn P, Spiegler A, Diaz-Cortes MA, Solodkin A, Jirsa VK, McIntosh AR, Ritter P, The Alzheimer's Disease Neuroimaging Initiative

Linking molecular pathways and large-scale computational modeling to assess candidate disease mechanisms and pharmacodynamics in Alzheimer's disease

Neurophysiologie Clinique

doi:10.1016/j.neucli.2018.06.036

Jirsa VK, Sip V

On generalized notions of the Epileptogenic Zone

Molecular-Genetic and Statistical Techniques for Behavioral and Neural Research; Elsevier

doi:10.1016/B978-0-12-804078-2.00001-5

Solodkin A, Zimmermann J, McIntosh AR, Stefanovski L, Ritter P

Neurological Biomarkers and Neuroinformatics: The Role of The Virtual Brain

Nature Communications

doi:10.1038/s41467-018-02973-y

Proix T, Jirsa VK, Bartolomei F, Guye M, Truccolo W

Predicting the spatiotemporal diversity of seizure propagation and termination in human focal epilepsy

Neuroimage Clinical

doi:10.1101/277624

Zimmermann J, Perry A, Breakspear M, Schirner, Sachdev P, Wen W, Kochan NA, Capstone M, Ritter P, McIntosh AR, Solodkin A

Differentiation of Alzheimer’s disease based on local and global parameters in personalized Virtual Brain models

Network Neuroscience

doi:10.1101/277590

Zimmermann J, Griffiths J, Schirner M, Ritter P, McIntosh AR

Subject-specificity of the correlation between large-scale structural and functional connectivity

eNeuro

doi:10.1101/265637

Aerts H, Schirner M, Jeurissen B, Van Roost D, Achten E, Ritter P, Marinazzo D

Modeling brain dynamics in brain tumor patients using The Virtual Brain

eLife 2018

doi:10.7554/eLife.28927

Schirner M, McIntosh AR, Jirsa V, Deco G, Ritter P

Inferring multi-scale neural mechanisms with brain network modelling

NeuroImage

doi.org/10.1016/j.neuroimage.2017.07.046

Díaz-Parra A, Osborn Z, Canals S, Moratal D, Sporns O

Structural and functional, empirical and modeled connectivity in the cerebral cortex of the rat

eNeuro

doi.org/10.1523/ENEURO.0111-17.2017

Melozzi F, Woodman MM, Jirsa VK and Bernard C

The Virtual Mouse Brain: A Computational Neuroinformatics Platform to Study Whole Mouse Brain Dynamics

Scientific Reports, 7: 3095

doi:10.1038/s41598-017-03073-5

Deco G, Kringelbach ML, Jirsa VK & Ritter P

The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core

Neuron

doi.org/10.1016/j.neuron.2017.05.013

Pillai AS and Jirsa VK

Symmetry Breaking in Space-Time Hierarchies Shapes Brain Dynamics and Behaviour

bioRxiv

doi:10.1101/123406

Melozzi F, Woodman MM, Jirsa VK, Bernard C

The Virtual Mouse Brain: a computational neuroinformatics platform to study whole mouse brain dynamics

Brain, 2017

doi:10.1093/awx018

Proix T, Bartolomei F, Guye M, Jirsa VK

Individual brain structure and modelling predict seizure propagation

Human Brain Mapping, 2017

doi:10.1002/hbm.23506

Bezgin G, Solodkin A, Bakker, Ritter P, McIntosh AR

Mapping complementary features of cross-species structural connectivity to construct realistic "Virtual Brains"

Neuroimage, 2016

doi: 10.1016/j.neuroimage.2016.06.016

Prix T, Spiegler A, Schirner M, Rothmeier S, Ritter P, Jirsa VK

How do parcellation size and short-range connectivity affect dynamics in large-scale brain network models?

e-Neuroforum, 2016

doi:10.1007/s13295-016-0027-1

Stefanovski L, Ghani A, McIntosh AR, Ritter P

Linking connectomics and dynamics in the human brain: Big data need big theories!

Neuroimage, 2016

doi:10.1016/j.neuroimage.2016.04.049

Jirsa VK, Proix T, Perdikis D, Woodman MM, Wang H, Gonzalez-Martinez J, Bernard C, Bénar C, Guye M, Chauvel P, Bartolomei F

The Virtual Epileptic Patient: Individualized whole-brain models of epilepsy spread

eneuro. Mar 2016;3(2)

doi:10.1523/ENEURO.0158-15.2016

Falcon MI, Riley JD, Jirsa VK, McIntosh AR, Shereen AD, Chen EE, Solodkin A

Functional mechanisms of recovery after chronic stroke: modelling with The Virtual Brain

Neuroimage, 2016

doi:10.1016/j.neuroimage.2016.02.015

Kunze T, Hunold A, Haueisen J, Jirsa VK, Spiegler A

Transcranial direct current stimulation changes resting state functional connectivity: A large-scale brain network modelling study

Front Neurol. 2015 Nov 2;6:228

doi:10.3389/fneur.2015.00228. eCollection 2015. PubMed PMID: 26579071; PubMed Central PMCID: PMC4629463

Falcon MI, Riley JD, Jirsa V, McIntosh AR, Shereen AD, Chen EE, Solodkin A

The Virtual Brain: Modeling Biological Correlates of Recovery after Chronic Stroke

Front Neuroinform. 2015 Nov 25;9:27

doi: 10.3389/fninf.2015.00027. eCollection 2015. PubMed PMID: 26635597; PubMed Central PMCID: PMC4658631

Matzke H, Schirner M, Vollbrecht D, Rothmeier S, Llarena A, Rojas R, Triebkorn P, Domide L, Mersmann J, Solodkin A, Jirsa VK, McIntosh AR, Ritter P

TVB-EduPack - An Interactive Learning and Scripting Platform for The Virtual Brain

PLoS Computational Biology

doi:10.1371/journal.pcbi.1004352

Becker R, Knock S, Ritter P, Jirsa V

Relating alpha power and phase to population firing and hemodynamic activity using a thalamo-cortical neural mass model

Neuroimage, 2015 Aug 15;117:343-357

doi:10.1016/j.neuroimage.2016.03.055

Schirner M, Rothmeier S, Jirsa VK, McIntosh AR, Ritter P

An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data

Trends in Cognitive Science, 19(10): 616-628

doi:10.1016/j.tics.2015.07.011

Kringelbach M, McIntosh AR, Ritter P, Jirsa V, Deco G.

The rediscovery of slowness: exploring the timing of cognition

J Neurosci. 2015 Jun 10;35(23):8914-24

doi: 10.1523/JNEUROSCI.4560-14.2015. PubMed PMID: 26063923; PubMed Central PMCID: PMC4589568

Adhikari MH, Raja Beharelle A, Griffa A, Hagmann P, Solodkin A, McIntosh AR, Small SL, Deco G

Computational modeling of resting-state activity demonstrates markers of normalcy in children with prenatal or perinatal stroke

Front Comput Neurosci. 2015 Jun 23;9:77

doi: 10.3389/fncom.2015.00077. eCollection 2015. PubMed PMID: 26157384; PubMed Central PMCID: PMC4477138

Ritter P, Jirsa VK, McIntosh AR, Breakspear M

Editorial: State-dependent brain computation

Neuroimage. 2015 May 1;111:385-430

doi: 10.1016/j.neuroimage.2015.01.002. Epub 2015 Jan 13. PubMed PMID: 25592995

Sanz-Leon P, Knock SA, Spiegler A, Jirsa VK

Mathematical framework for large-scale brain network modeling in The Virtual Brain

Brain Connect. 2014 Dec;4(10):791-811

doi:10.1089/brain.2014.0252. PubMed PMID: 25131838

Roy D, Sigala R, Breakspear M, McIntosh AR, Jirsa VK, Deco G, Ritter P

Using The Virtual Brain to reveal the role of oscillations and plasticity in shaping brain's dynamical landscape

Front Comput Neurosci 8: 36

doi:10.3389/fncom.2014.00036

Sigala, R, Haufe S, Roy D, Dinse HR, Ritter P.

The role of alpha-rhythm states in perceptual learning: insights from experiments and computational models

Front. Neuroinform. 8:36

doi: 10.3389/fninf.2014.00036

Woodman MM, Pezard L, Domide L, Knock S, Sanz Leon P, Mersmann J, McIntosh AR, Jirsa VK

Integrating Neuroinformatics Tools in The Virtual Brain

Neuroimage. 2013 Jun 3;83:704-725

doi:10.1016/j.neuroimage.2013.06.018

Spiegler A, Jirsa VK

Systematic approximations of neural fields through networks of neural masses in The Virtual Brain

Brain Connect 3(2): 121-145

doi:10.1089/brain.2012.0120

Ritter, P., M. Schirner, A. R. McIntosh and V. K. Jirsa

The Virtual Brain integrates computational modeling and multimodal neuroimaging