Publications

#3 Principles and Operation of Virtual Brain Twins

Hashemi M*†, Depannemaecker D†, Saggio M†, Triebkorn P, Rabuffo G, Fousek J, Ziaeemehr A, Sip V, Athanasiadis A, Breyton M, Woodman M, Wang H, Petkoski S, Sorrentino P, Jirsa V.

IEEE Reviews in Biomedical Engineering. 2025 Apr 21. DOI: 10.1109/RBME.2025.3562951

#2 Virtual brain twins: from basic neuroscience to clinical use

Wang HE, Triebkorn P, Breyton M, Dollomaja B, Lemarechal JD, Petkoski S, Sorrentino P, Depannemaecker D, Hashemi M, Jirsa V.

National Science Review. 2024 Feb 28;11(5):nwae079. DOI: 10.1093/nsr/nwae079

#1 Personalised virtual brain models in epilepsy

Jirsa V, Wang H, Triebkorn P, Hashemi M, Jha J, Gonzalez-Martinez J, Guye M, Makhalova J, Bartolomei F.

The Lancet Neurology. 2023 May;22(5):443–454. DOI: 10.1016/S1474-4422(23)00008-X

#30 High-resolution Bayesian Virtual Epileptic Patient using neural field models

Vattikonda AN†, Hashemi M†*, Woodman MM, Lemarechal JD, Daini D, Bartolomei F, Jirsa V†.

Network Neuroscience (accepted).

#29 Probabilistic inference of social presence across brain scales reveals enhanced synaptic efficacy

Esmaeili A, Demolliens M, Viersen M, Ziaeemehr A, Isbaine F, Huguet P, Zaal F, Jirsa V†, Boussaoud D†, Hashemi M†*.

Communication Biology. 2025 Nov 19;8(1):1608. DOI: 10.1038/s42003-025-08971-3

#28 Virtual Brain Inference (VBI), a flexible and integrative toolkit for efficient probabilistic inference on whole-brain models

Ziaeemehr A, Woodman M, Domide L, Petkoski S, Jirsa V†, Hashemi M†*.

eLife. 2025;14:RP106194. DOI: 10.7554/eLife.106194.4

#27 Dynamic Causal Modeling in Probabilistic Programming Languages

Baldy N, Woodman M, Jirsa V†, Hashemi M†*.

Journal of the Royal Society Interface. 2025 Jun;22(227):20240880. DOI: 10.1098/rsif.2024.0880

#25 The Virtual Parkinsonian Patient

Angiolelli M, Depannemaecker D, Agouram H, Régis J, Carron R, Woodman M, Chiodo L, Triebkorn P, Ziaeemehr A, Hashemi M, Eusebio A, Jirsa V, Sorrentino P.

NPJ Systems Biology and Applications. 2025 Apr 26;11(1):40. DOI: 10.1038/s41540-025-00516-y

#24 Mapping Brain Lesions to Conduction Delays: The Next Step for Personalized Brain Models in Multiple Sclerosis

Mazzara C, Ziaeemehr A, Troisi Lopez E, Cipriano L, Angiolelli M, Sparaco M, Quarantelli M, Granata C, Sorrentino G, Hashemi M, Jirsa V, Sorrentino P.

Human Brain Mapping. 2025 May;46(7):e70219. DOI: 10.1002/hbm.70219

#23 PLSKB: An Interactive Knowledge Base to Support Diagnosis, Treatment, and Screening of Lynch Syndrome on the Basis of Precision Oncology

Dehghani Soufi M, Shirkoohi R, Sanaat Z, Torkamannia A, Hashemi M, Jahandar-Lashaki S, Yousefpour Marzbali M, Vaez Y, Ferdousi R.

JCO Clinical Cancer Informatics. 2025 Mar;9:e2400246. DOI: 10.1200/CCI-24-00246

#22 Mapping global brain reconfigurations following local targeted manipulations

Rabuffo G, Lokossou HA, Li Z, Ziaee-Mehr A, Hashemi M, Quilichini PP, Ghestem A, Arab O, Esclapez M, Verma P, Raj A, Gozzi A, Sorrentino P, Chuang KH, Perles-Barbacaru TA, Viola A, Jirsa V, Bernard C.

Proc. Natl. Acad. Sci. U.S.A. 2025 Apr 22;122(16):e2405706122. DOI: 10.1073/pnas.2405706122

#21 Inference on the macroscopic dynamics of spiking neurons

Baldy N, Breyton M, Woodman MM, Jirsa VK†, Hashemi M†*.

Neural Computation. 2024 Sep 17;36(10):2030–2072. DOI: 10.1162/neco_a_01701

#20 Simulation-based inference on virtual brain models of disorders

Hashemi M*, Ziaeemehr A, Woodman MM, Fousek J, Petkoski S, Jirsa V.

Machine Learning: Science and Technology. 2024 Jul 19;5(3):035019. DOI: 10.1088/2632-2153/ad6230

#19 The virtual multiple sclerosis patient

Sorrentino P, Pathak A, Ziaeemehr A, Troisi Lopez E, Cipriano L, Romano A, Sparaco M, Quarantelli M, Banerjee A, Sorrentino G, Jirsa† V, Hashemi M†*.

iScience. 2024 May 24;27(7):110101. DOI: 10.1016/j.isci.2024.110101

#18 Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers

Penas DR†, Hashemi M†, Jirsa V, Banga JR.

PLOS Computational Biology. 2024 Jul 11;20(7):e1011642. DOI: 10.1371/journal.pcbi.1011642

#17 Effects of the spatial resolution of the Virtual Epileptic Patient on the identification of epileptogenic networks

Lemaréchal JD, Triebkorn P, Vattikonda AN, Hashemi M, Woodman M, Guye M, Bartolomei F, Wang HE, Jirsa V.

Imaging Neuroscience. 2024 May 8;2:imag-2-00153. DOI: 10.1162/imag_a_00153

#16 Hierarchical Bayesian pharmacometrics analysis of Baclofen for alcohol use disorder

Baldy N, Simon N, Jirsa V, Hashemi M†*.

Machine Learning: Science and Technology. 2023 Sep 14;4(3):035048. DOI: 10.1088/2632-2153/acf6aa

#15 The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging

Lavanga M, Stumme J, Yalcinkaya BH, Fousek J, Jockwitz C, Sheheitli H, Bittner N, Hashemi M, Petkoski S, Caspers S, Jirsa V.

NeuroImage. 2023 Dec 1;283:120403. DOI: 10.1016/j.neuroimage.2023.120403

#14 Amortized Bayesian inference on generative dynamical network models of epilepsy using deep neural density estimators

Hashemi M*, Vattikonda AN, Jha J, Sip V, Woodman M, Bartolomei F, Jirsa V.

Neural Networks. 2023 Jun;163:178–194. DOI: 10.1016/j.neunet.2023.03.040

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

Wang H, Woodman M, Triebkorn P, Lemarechal JD, Jha J, Dollomaja B, Vattikonda AN, Sip V, Medina Villalon S, Hashemi M, Guye M, Makhalova J, Bartolomei F, Jirsa V.

Science Translational Medicine. 2023 Jan 25;15(680):eabp8982. DOI: 10.1126/scitranslmed.abp8982

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

Sip V, Hashemi M, Dickscheid T, Amunts K, Petkoski S, Jirsa V.

Science Advances. 2023 Mar 15;9(11):eabq7547. DOI: 10.1126/sciadv.abq7547

#11 Fully Bayesian estimation of virtual brain parameters with self-tuning Hamiltonian Monte Carlo

Jha J, Hashemi M, Vattikonda AN, Wang H, Jirsa V.

Machine Learning: Science and Technology. 2022 Sep 26;3(3):035016. DOI: 10.1088/2632-2153/ac9037

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

Schirner M... Hashemi M... Ritter P.

NeuroImage. 2022 May 1;251:118973. DOI: 10.1016/j.neuroimage.2022.118973

#9 Identifying spatio-temporal seizure propagation patterns in epilepsy using Bayesian inference

Vattikonda AN, Hashemi M, Sip V, Woodman MM, Bartolomei F, Jirsa V.

Communications Biology. 2021 Nov 1;4(1):1244. DOI: 10.1038/s42003-021-02751-5

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

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

PLoS Computational Biology. 2021 Jul 14;17(7):e1009129. DOI: 10.1371/journal.pcbi.1009129

#7 Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography

Sip V, Hashemi M, Vattikonda AN, Woodman MM, Wang H, Scholly J, Medina Villalon S, Guye M, Bartolomei F, Jirsa V.

PLoS Computational Biology. 2021 Feb 17;17(2):e1008689. DOI: 10.1371/journal.pcbi.1008689

#6 The Bayesian Virtual Epileptic Patient: A probabilistic framework designed to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread

Hashemi M*, Vattikonda AN, Sip V, Guye M, Bartolomei F, Woodman MM, Jirsa V.

NeuroImage. 2020 Aug 15;217:116839. DOI: 10.1016/j.neuroimage.2020.116839

#5 Optimal model parameter estimation from EEG power spectrum features observed during general anesthesia

Hashemi M*, Hutt A, Buhry L, Sleigh J.

Neuroinformatics. 2018 Apr;16(2):231–251. DOI: 10.1007/s12021-018-9369-x (View PDF)

#4 Anesthetic action on the transmission delay between cortex and thalamus explains the beta-buzz observed under propofol anesthesia

Hashemi M*, Hutt A, Hight D, Sleigh J.

PLoS One. 2017 Jun 16;12(6):e0179286. DOI: 10.1371/journal.pone.0179286

#3 How the cortico-thalamic feedback affects the EEG power spectrum over frontal and occipital regions during propofol-induced sedation

Hashemi M*, Hutt A, Sleigh J.

Journal of Computational Neuroscience. 2015 Oct;39(2):155–179. DOI: 10.1007/s10827-015-0569-1 (View PDF)

#2 Anesthetic action on extra-synaptic receptors: effects in neural population models of EEG activity

Hashemi M*, Hutt A, Sleigh J.

Frontiers in Systems Neuroscience. 2014 Dec 10;8:232. DOI: 10.3389/fnsys.2014.00232

#1 Effect of duration of synaptic activity on spike rate of a Hodgkin-Huxley neuron with delayed feedback

Hashemi M, Valizadeh A, Azizi Y.

Physical Review E—Statistical, Nonlinear, and Soft Matter Physics. 2012 Feb;85(2 Pt 1):021917. DOI: 10.1103/PhysRevE.85.021917 (View PDF)

#4 A deformable attractor manifold organizes human resting-state brain dynamics

Athanasiadis A, Woodman M, Hashemi M, Triebkorn P, Petkoski S, Jirsa V.

bioRxiv. 2025. DOI: 10.64898/2025.12.02.691788

#3 Data-driven mean-field within whole-brain models

Breyton M, Sip V, Woodman M, Hashemi M, Petkoski S, Jirsa V.

arXiv. 2025. DOI: 10.48550/arXiv.2509.02799

#2 Degeneracy in neuronal bifurcation landscapes: equivalent bifurcation sequences across distinct parameter sets

Cafaro G, Bernard C, Hashemi M, Depannemaecker D.

bioRxiv. 2025. DOI: 10.1101/2025.08.04.668451

#1 Personalized virtual brains of Alzheimer’s Disease link dynamical biomarkers of fMRI with increased local excitability

Yalçınkaya BH, Ziaeemehr A, Fousek J, Hashemi M, Lavanga M, Solodkin A, McIntosh AR, Jirsa VK, Petkoski S.

medRxiv. 2023. DOI: 10.1101/2023.01.11.23284438

#1 Bridging the Gap Between Neuroscience and Artificial Intelligence

Kim CE, Sora AN, Hashemi M, Kang J.

Frontiers in Computational Neuroscience, 2023. (See here)

#2 How to render Neural Fields more realistic

Hutt A, Hashemi M, Graben P.

In: Validating Neuro-Computational Models... Springer. 2015; pp. 141–159. DOI: 10.1007/978-3-319-20037-8_6 (View PDF)

#1 A thalamocortical model to explain EEG during anaesthesia

Hashemi M, Hutt A.

In: Self-Organization in Complex Systems... Springer. 2015; pp. 305–312. DOI: 10.1007/978-3-319-27635-9_20 (View PDF)

#4 A Method for Inferring Epileptogenicity of a Brain Region

Hashemi M, Sip V, Vattikonda AN, Woodman M, Jirsa V.

WO/2021/197612, PCT/EP2020/059511. (See here)

#3 Method for Inferring a Change in a Whole-brain Network and System with Stimulation

Hashemi M, Arbabyazd L, Williamson A, Jirsa V.

WO/2024/218403, PCT/EP2024/060977. (See here)

#2 Computer-Implemented Method for Inferring a Conduction Velocity of a Subject's Brain

Hashemi M, Sorrentino P, Jirsa V.

WO/2025/114407, PCT/EP2024/083847. (See here)

#1 Bayesian Inversion of Whole-Brain Model of Epilepsy based on Real SEEG Recording

Hashemi M, Jha J, Jirsa V.

Submitted. Réf/AMU: 21D051.

#7 Mapping brain lesions to conduction delays: the next step for personalized brain models in Multiple Sclerosis

Mazzara C... Hashemi M*.

CNS 2024. (See here)

#6 Model inversion techniques for seizure spread in individual brain networks

Sip V, Jirsa V, Hashemi M, Vattikonda AN, Jha J.

BMC Neuroscience, CNS 2021. (See here)

#5 Inferring the dynamic of personalized large-scale brain network models using Bayesian framework

Hashemi M*... Jirsa V.

BMC Neuroscience, CNS 2019. (See here)

#4 Fitting a thalamo-cortical model to EEG power spectrum using evolutionary algorithm

Hashemi M*, Hutt A, Sleigh J.

ICMNS 2015. (See here)

#3 Thalamo-cortical mechanisms of the observed specific changes in frontal and occipital EEG rhythms...

Hashemi M*, Hutt A, Sleigh J.

BMC Neuroscience CNS, 2015. (See here)

#2 Reproduction of EEG power spectrum over frontal region during the propofol-induced general anesthesia

Hashemi M*... Graben P.

BMC Neuroscience, CNS 2014. (See here)

#1 A thalamocortical model to explain EEG during anesthesia

Hashemi M*, Hutt A.

BMC Neuroscience, CNS 2013. (See here)

PhD Thesis: Analytical and numerical studies of thalamo-cortical neural population models during general anesthesia

M. Hashemi (2016)

Université de Lorraine, Computer Science. (View PDF)

Master Thesis: Effect of the duration of the synaptic activity on a delayed recurrent neuronal loop

M. Hashemi (2012)

IASBS, Physics. (View PDF)

Review Articles

Accepted Peer-Reviewed Articles

Submitted Original Articles

Editorial

Book Chapters

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Theses