Publications of the BRADY project
Publications
Barbora Rehák Bučková, Charlotte Fraza, Rastislav Rehák, Marián Kolenič, Christian Beckmann, Filip Španiel, Andre Marquand, Jaroslav Hlinka (2024). Using normative models pre-trained on cross-sectional data to evaluate longitudinal changes in neuroimaging data, eLife 13:RP95823. (preprint, publisher, permanent link).
David Kordek, Laura Young, Petr Voda, Jan Kremláček (2024). Motion onset VEPs can see through the blur. Scientific Reports, 14 (1) 21296. (preprint, publisher, permanent link).
Pavel Hok, Quang Thong Thai, Barbora Rehák Bučková, Martin Domin, Kamila Řasová, Jaroslav Tintěra, Martin Lotze, Matthias Grothe, Jaroslav Hlinka (2024). Global functional connectivity reorganization reflects cognitive processing speed deficits and fatigue in multiple sclerosis. European Journal of Neorology, e16421. (publisher, permanent link).
Josef Urbanec, Kateřina Chládková, Jan Kremláček (2024). Neural processing of speech sounds at premature and term birth: ERPs and MMR between 32 and 42 weeks of gestation. Developmental Cognitive Neuroscience, Volume 70 (preprint, publisher, permanent link).
David Berling, Luca Baroni, Antoine Chaffiol, Gregory Gauvain, Serge Picaud, Ján Antolík (2024). Optogenetic stimulation recruits cortical neurons in a morphology-dependent manner. Journal of Neuroscience 18 October 2024, e1215242024 (preprint, publisher, permanent link).
Jiří Hammer, Michaela Kajšová, Adam Kalina, David Krysl, Petr Fabera, Martin Kudr, Petr Ježdík, Radek Janča, Pavel Krsek, Petr Marusic (2024). Antagonistic behavior of brain networks mediated by low-frequency oscillations: electrophysiological dynamics during internal–external attention switching. Commun Biol 7, 1105 (preprint, publisher, permanent link).
McWhinney, S. R., Hlinka, J., Bakstein, E., Dietze, L. M. F., Corkum, E. L. V., Abé, C., Alda, M., Alexander, N., Benedetti, F., Berk, M., Bøen, E., Bonnekoh, L. M., Boye, B., Brosch, K., Canales-Rodríguez, E. J., Cannon, D. M., Dannlowski, U., Demro, C., Diaz-Zuluaga, A., … Hajek, T. (2024). Principal component analysis as an efficient method for capturing multivariate brain signatures of complex disorders—ENIGMA study in people with bipolar disorders and obesity. Human Brain Mapping, 45(8), e26682 (publisher, permanent link).
Jan Strobl, Vojtěch Viktorin, Marek Piorecký, Inga Griskova-Bulanova, Jan Hubený, Martin Brunovský, Tomáš Páleníček, Vlastimil Koudelka (2024). Unveiling stimulus transduction artifacts in auditory steady-state response experiments: Characterization, risks, and mitigation strategies. Biomedical Signal Processing and Control, Volume 101 (publisher, permanent link).
Stanislav Jiricek, Vlastimil Koudelka, Dante Mantini, Radek Marecek, Jaroslav Hlinka (2025). Spatial (Mis)match Between EEG and fMRI Signal Patterns Revealed by Spatio-Spectral Source-Space EEG Decomposition. Frontiers in Neuroscience (publisher, preprint).
Akbar Davoodi, Martin Holeňa, Martin Brunovský, Aditi Kathpalia, Jaroslav Hlinka, Martin Bareš, Milan Paluš (2025). Response prediction of antidepressants: Using graph theory tools for brain network connectivity analysis. Biomedical Signal Processing and Control, Volume 103 (publisher, permanent link, preprint).
Eva Výtvarová, Martin Lamoš, Jaroslav Hlinka et al. (2024). Revealing connectivity patterns of deep brain stimulation efficacy in Parkinson’s disease. Sci Rep 14, 31652 (publisher, permanent link, preprint).
Barbora Splítková, Kateřina Macková, Miroslav Koblížek, Zuzana Holubová, Martin Kyncl, Kateřina Bukacova et al. (2024). A new perspective on drug-resistant epilepsy in children with focal cortical dysplasia type 1: From challenge to favorable outcome. Epilepsia, 00: 1–16 (publisher, permanent link).
Pavel Filip, Lubomír Vojtíšek, Anna Marie Jičínská, Zdeněk Valenta, Ondřej Horák, Matěj Hrunka, Silvia Mangia, Shalom Michaeli and Petr Jabandžiev (2024). Wide-spread brain alterations early after the onset of Crohn’s disease in children in remission—a pilot study. Front. Neurosci, 18:1491770 (publisher, permanent link, preprint).
Pavel Filip, J. Riley McCarten, Laura Hemmy, Jillian Crocker, Michael Wolf, Jeromy Thotland, Zuzan Cayci, Shalom Michaeli, Lynn E. Eberly, Melissa Terpstra, Silvia Mangia (2025). Different Grey Matter Microstructural Patterns in Cognitively Healthy Versus Typical Ageing. NMR in Biomedicine, 38: e5305 (publisher, permanent link, preprint).
Conference proceedings
Jaroslav Hlinka, David Tomeček, Marián Kolenič, Barbora Rehák Bučková, Jaroslav Tintěra, Jiří Horáček, Filip Španiel. Role of fMRI Denoising for Classification of Schizophrenia from Functional Brain Connectivity. Advances in Signal Processing and Artificial Intelligence: Proceedings of the 6th International Conference on Advances in Signal Processing and Artificial Intelligence. Barcelona: IFSA Publishing, 2024. (publisher, permanent link).
Preprints
Jakub Korenek, Pavel Sanda, Jaroslav Hlinka. Towards Definition of Higher Order Causality in Complex Systems. Submitted, arXiv preprint arXiv:2409.08295 (2024). Presented at CCS2024 as "Detection of Higher Order Causality in Complex Systems". (preprint).
Jan Strobl, Vojtech Viktorin, Marek Piorecky, Inga Griskova-Bulanova, Jan Hubeny, Martin Brunovsky, Tomas Palenicek, Vlastimil Koudelka. Unveiling Stimulus Transduction Artifacts in Auditory Steady-State Response Experiments: Characterization, Risks, and Mitigation Strategies. bioRxiv 2024.05.30.596610. (preprint)
Tereza Klučková, Marek Nikolič, Filip Tylš, Vojtěch Viktorin, Čestmír Vejmola, Michaela Viktorinová, Anna Bravermanová, Renáta Androvičová, Veronika Andrashko, Jakub Korčák, Peter Zach, Kateřina Hájková, Martin Kuchař, Marie Balíková, Martin Brunovský, Jiří Horáček, Tomáš Páleníček. The phenomenology of psilocybin’s experience mediates subsequent persistent psychological effects independently of sex, previous experience or setting. medRxiv 2024.08.26.24311611. (preprint)
Sofiia Moraresku, Jiri Hammer, Vasileios Dimakopoulos, Michaela Kajsova, Radek Janca, Petr Jezdik, Adam Kalina, Petr Marusic, Kamil Vlcek. Neural dynamics of visual streams interactions during memory-guided actions investigated by intracranial EEG. bioRxiv 2024.08.20.608807. (preprint)
Cheng Kang,Jindich Prokop, Lei Tong, Huiyu Zhou, Yong Hu, Daniel Novak. InA: Inhibition Adaption on Pre-Trained Language Models. Available at SSRN. (preprint)
Cheng Kang, Daniel Novak, Katerina Urbanova, Yuqing Cheng, Yong Hu. Domain-Specific Improvement on Psychotherapy Chatbot Using Assistant. arXiv:2404.16160 (2024). (preprint)
Yana Vella, Kateřina Syrová, Aneta Petrušková, Isis Koutrouli, Viera Kútna, Jan Pala, Marek Nikolič, Klára Šíchová, Vladimír Mazoch, Radek Jurok, Martin Kuchař, Zdeňka Bendová, Tomáš Páleníček. Effects of serotonergic psychedelics on synaptogenesis and immediate early genes expression – comparison with ketamine, fluoxetine and lithium. bioRxiv 2024.08.07.606965. (preprint)
Lucie Olejníková-Ladislavová, Michaela Fujáková-Lipski, Klára Šíchová, Hynek Danda, Kateřina Syrová, Jiří Horáček, Tomáš Páleníček. Behavioral pharmacology of mescaline - the role of serotonin 5-HT2A, 5-HT2B, 5-HT2C and 5-HT1A receptors. bioRxiv 2024.08.28.610032. (preprint)
Lucia Jajcay, David Tomeček, Renáta Androvičová, Iveta Fajnerová, Filip Děchtěrenko, Jan Rydlo, Jaroslav Tintěra, Jiří Lukavský, Jiří Horáček, Jaroslav Hlinka. Deviation from typical brain activity during naturalistic stimulation predicts personality traits. bioRxiv 2024.04.23.586759. (preprint)
Stanislav Jiricek, Vlastimil Koudelka, Dante Mantini, Radek Marecek, Jaroslav Hlinka. Spatial (Mis)match Between EEG and fMRI Signal Patterns Revealed by Spatio-Spectral Source-Space EEG Decomposition. bioRxiv 2024.07.26.605087. (preprint)
Jiakun Fu, Suhas Shrinivasan, Luca Baroni, Zhuokun Ding, Paul G. Fahey, Paweł A. Pierzchlewicz, Kayla Ponder, Rachel Froebe, Lydia Ntanavara, Taliah Muhammad, Konstantin F. Willeke, Eric Wang, Zhiwei Ding, Dat T. Tran, Stelios Papadopoulos, Saumil Patel, Jacob Reimer, Alexander S. Ecker, Xaq Pitkow, Jan Antolik, Fabian H. Sinz, Ralf M. Häfner, Andreas S. Tolias, Katrin Franke. Pattern completion and disruption characterize contextual modulation in the visual cortex. bioRxiv 2023.03.13.532473. (preprint)
Barbora Splitkova, Katerina Mackova, Miroslav Koblizek, Zuzana Holubova, Martin Kyncl, Katerina Bukacova, Alice Maulisova, Barbora Straka, Martin Kudr, Matyas Ebel, Alena Jahodova, Anezka Belohlavkova, Gonzalo Alonso Ramos Rivera, Martin Hermanovsky, Petr Liby, Michal Tichy, Josef Zamecnik, Radek Janca, Pavel Krsek. Multi-layered Diagnostic Protocol Improves Postsurgical Outcomes in Children with Drug-resistant Epilepsy And Focal Cortical Dysplasia Type 1. medRxiv 2024.09.24.24314277. (preprint)
Kudr Martin, Janča Radek, Jahodová Alena, Bělohlávková Anežka, Ebel Matyáš, Maulisová Alice, Bukačová Kateřina, Tichý Michal, Libý Petr, Kynčl Martin, Holubová Zuzana, Šanda Jan, Ježdík Petr, Ramos Rivera Gonzalo Alonso, Kopač Luka, Kršek Pavel. Epilepsy surgery in children with operculo-insular epilepsy: Results of a large unicentric cohort. medRxiv 2024.05.15.24307360. (preprint)
Marek Nikolic, Pedro Mediano, Tom Froese, David Reydellet, Tomas Palenicek. Psilocybin alters brain activity related to sensory and cognitive processing in a time-dependent manner. medRxiv 2024.09.09.24313316. (preprint)
Saptarshi Ghosh, Isa Dallmer-Zerbe, Barbora Rehak Buckova, Jaroslav Hlinka. Amplitude entropy to capture chimera-like behavior in the altered brain dynamics during seizures. bioRxiv 2024.05.26.595969. (preprint)
Giulio Tani Raffaelli, Stanislav Jiříček, Jaroslav Hlinka. Nonlinear brain connectivity from neurons to networks: quantification, sources and localization. bioRxiv 2024.11.17.623635. (preprint)
Viktória Kokošová, Lubomír Vojtíšek, Marek Baláž, Silvia Mangia, Shalom Michaeli, Pavel Filip. Sleep quality and the integrity of ascending reticular activating system – a multimodal MRI study. Zenodo. (preprint)
Martina Bockova, Eva Vytvarova, Martin Lamos, Jaroslav Hlinka, Sabina Goldemundova, Ivan Rektor. Revealing Connectivity Patterns of Deep Brain Stimulation Efficacy in Parkinson’s Disease. ASEP. (preprint)
Data
BRADY project repository on Zenodo (both for data and final publications).
Code
BRADY project repository on Github contains the published source codes.
Christian G. Fink, Pavel Sanda, Logan Bayer, Eroma Abeysinghe, Maxim Bazhenov, Giri P. Krishnan. Python/NEURON code for simulating biophysically realistic thalamocortical dynamics during sleep. Software Impacts. 21, 100667, 2024. (preprint, publisher, permanent link, code).