Publications

2020

  • Gabriela J. Jurkiewicz, Mark J. Hunt & Jarosław Żygierewicz Addressing Pitfalls in Phase-Amplitude Coupling Analysis with an Extended Modulation Index Toolbox, Neuroinformatics (2020) doi:10.1007/s12021-020-09487-3
  • Adam Messinger, Nikoloz Sirmpilatze, Katja Heuer, Kep Kee Loh, Rogier B. Mars, Julien Sein, Ting Xu, Daniel Glen, Benjamin Jung, Jakob Seidlitz, Paul Taylor, Roberto Toro, Eduardo A. Garza-Villarreal, Caleb Sponheim, Xindi Wang, R. Austin Benn, Bastien Cagna, Rakshit Dadarwal, Henry C. Evrard, Pamela Garcia-Saldivar, Steven Giavasis, Renée Hartig, Claude Lepage, Cirong Liu, Piotr Majka, Hugo Merchant, Michael P. Milham, Marcello G.P. Rosa, Jordy Tasserie, Lynn Uhrig, Daniel S. Margulies, P. Christiaan Klink. A collaborative resource platform for non-human primate neuroimaging. NeuroImage, to appear. bioRxiv, doi: 10.1101/2020.07.31.230185
  • Jacek Wróbel, Władysław Średniawa, Gabriela Bernatowicz, Jarosław Żygierewicz, Daniel K Wójcik, Miles Adrian Whittington, Mark Jeremy Hunt. Nasal respiration is necessary for ketamine-dependent high frequency network oscillations and behavioral hyperactivity in rats (2020) Scientific Reports, to appear. bioRxiv doi:10.1101/2020.07.22.213850
  • Władysław Średniawa, Jacek Wróbel, Ewa Kublik, Daniel Krzysztof Wójcik, Miles Adrian Whittington, Mark Jeremy Hunt. Network and synaptic mechanisms underlying high frequency oscillations in the rat and cat olfactory bulb under ketamine-xylazine anesthesia (2020) bioRxiv doi:10.1101/2020.07.23.217604
  • Jan Szczypiński, Anna Alińska, Marek Waligóra, Maciej Kopera, Aleksandra Krasowska, Aneta Michalska, Hubert Suszek, Andrzej Jakubczyk, Marek Wypych, Marcin Wojnar, Artur Marchewka. Familiarity with children improves the ability to recognize children’s mental states: an fMRI study using the Reading the Mind in the Eyes Task and the Nencki Children Eyes Test. Scientific Reports 10, 12964 (2020). doi:
  • Jacek Rogala, Beata Bajno, Andrzej Wróbel. A hidden message: Decoding artistic intent. PsyCH J. (2020) doi:10.1002/pchj.374
  • Jaroslav Lacik, Vlastimil Koudelka, David Kuratko, Zbynek Raida, Daniel K. Wójcik, Tomas Mikulasek, Jiri Vanek, Stanislav Jiricek, Cestmir Vejmola. Rat Head Phantom for Testing of Electroencephalogram Source Localization Techniques. IEEE Access (2020) doi: 10.1109/ACCESS.2020.3000581.
  • Joanna Jędrzejewska-Szmek, Daniel K. Wójcik. Oblicza neuroinformatyki. Kosmos 69:1 (2020) 157-167.
  • Piotr Majka, Sylwia Bednarek, Jonathan M. M. Chan, Natalia Jermakow, Cirong Liu, Gabriela Saworska, Katrina H. Worthy, Afonso C. Silva*, Daniel K. Wójcik*, Marcello G. P. Rosa*. Histology-Based Average Template of the Marmoset Cortex With Probabilistic Localization of Cytoarchitectural Areas. (2020) bioRxiv 2020.04.10.036632; doi:10.1101/2020.04.10.036632. *senior authors.
  • Katarzyna Kuc, Maksymilian Bielecki, Ewa Racicka-Pawlukiewicz, Michał B. Czerwiński, Anita Cybulska-Klosowicz. The SLC6A3 gene polymorphism is related to the development of attentional functions but not to ADHD. Scientific Reports 10, 6176 (2020). doi:10.1038/s41598-020-63296-x
  • Jacek Rogala, Ewa Kublik, Rafał Krauz, Andrzej Wróbel, Resting-state EEG activity predicts frontoparietal network reconfiguration and improved attentional performance. Scientific Reports 10, 5064 (2020). doi: 10.1038/s41598-020-61866-7
  • Panagiota Theodoni, Piotr Majka, David H Reser, Daniel K Wójcik, Marcello G P Rosa, Xiao-Jing Wang, Structural attributes and principles of the neocortical connectome in the marmoset monkey. (2020) bioRxiv preprint
  • Piotr Majka, Shi Bai, Sophia Bakola, Sylwia Bednarek, Jonathan Chan, Natalia Jermakow, Lauretta Passarelli, David Reser, Panagiota Theodoni, Katrina Worthy, Xiao-Jing Wang*, Daniel Wójcik*, Partha Mitra*, and Marcello Rosa* Open Access Resource for Cellular-Resolution Analyses of Corticocortical Connectivity in the Marmoset Monkey. Nature Communications, 11, 1133 (2020). doi: 10.1038/s41467-020-14858-0. *senior authors.
  • The PRIMatE Data Exchange (PRIME-DE) Global Collaboration Workshop and Consortium, Accelerating the Evolution of Nonhuman Primate Neuroimaging. Neuron 105(4) p. 600 – 603 (2020), doi: 10.1016/j.neuron.2019.12.023.
  • Hubert Dolezyczek, Szymon Tamborski, Piotr Majka, Danuta Sampson, Maciej Wojtkowski, Grzegorz Wilczyński, Maciej Szkulmowski, Monika Malinowska, In vivo brain imaging with multimodal optical coherence microscopy in a mouse model of thromboembolic photochemical stroke Neurophotonics (2020) 7(1), doi: 10.1038/s41593-019-0575-0
  • Cirong Liu, Frank Q. Ye, John D. Newman, Diego Szczupak, Xiaoguang Tian, Cecil Chern-Chyi Yen, Piotr Majka, Daniel Glen, Marcello G. P. Rosa, David A. Leopold & Afonso C. Silva A resource for the detailed 3D mapping of white matter pathways in the marmoset brain. Nature Neuroscience (2020) doi: 10.1117/1.NPh.7.1.015002

2019

  • C. Chintaluri, M. Kowalska, W. Średniawa, M.B. Czerwiński, J.M. Dzik, J. Jędrzejewska-Szmek, D.K. Wójcik kCSD-python, a tool for reliable current source density estimation. (2019) bioRxiv preprint
  • Goulas A, Majka P, Rosa MGP, Hilgetag CC A blueprint of mammalian cortical connectomes. PLOS Biology 17(3), (2019). doi: e2005346
  • J. Jędrzejewska-Szmek, K.T. Blackwell From membrane receptors to protein synthesis and actin cytoskeleton: Mechanisms underlying long lasting forms of synaptic plasticity. Seminars in Cell & Developmental Biology 95, 120-129 (2019). doi: 10.1016/j.semcdb.2019.01.006
  • M.J. Hunt, N.E. Adams, W. Średniawa, D.K. Wójcik, A. Simon, S. Kasicki & M.A. Whittington The olfactory bulb is a source of high-frequency oscillations (130–180 Hz) associated with a subanesthetic dose of ketamine in rodents. Neuropsychopharmacology 44, 435–442 (2019). doi:10.1038/s41386-018-0173-y
  • P. Majka, M.G.P. Rosa, S. Bai, J.M. Chan, B.-X. Huo, N. Jermakow, M.K. Lin, Y.S. Takahashi, I.H. Wolkowicz, K.H. Worthy, R. Rajan, D.H. Reser, D.K. Wójcik, H. Okano, P.P. Mitra: Unidirectional monosynaptic connections from auditory areas to the primary visual cortex in the marmoset monkey. Brain Structure and Function 224, 11-131 (2019), doi: 10.1007/s00429-018-1764-4

2018

  • D. K. Wójcik The Kinematics of Spike Trains, Acta Phys. Pol. B, doi:10.5506/APhysPolB.49.2127 49 (2018) 2127-2138.
  • Nafiseh Atapour, Piotr Majka, Ianina H Wolkowicz, Daria Malamanova, Katrina H Worthy, Marcello G P Rosa; Neuronal Distribution Across the Cerebral Cortex of the Marmoset Monkey (Callithrix jacchus), Cerebral Cortex, bhy263
  • M.G.P. Rosa, J.G.M. Soares, T.A. Chaplin, P. Majka, S. Bakola, K.A. Phillips, D.H. Reser, R. Gattass: Cortical afferents of area 10 in Cebus monkeys: implications for the evolution of the frontal pole. Cerebral Cortex (2018) https://doi.org/10.1093/cercor/bhy044.
  • Z. Harda, J.M. Dzik, M. Nalberczak-Skóra, K. Meyza, K. Łukasiewicz, S. Łęski and K. Radwanska: Autophosphorylation of αCaMKII affects social interactions in mice. Genes, Brain and Behavior (2018), e12457. doi:10.1111/gbb.12457
  • P. Majka, N. Chlodzinska, K. Turlejski, T. Banasik, R. L. Djavadian, W. P. Węglarz, D. K. Wójcik: A three-dimensional stereotaxic atlas of the gray short-tailed opossum (Monodelphis domestica) brain. Brain Structure and Function 223 (2018) 1779-1795. doi:10.1007/s00429-017-1540-x. Article and Atlas
  • J.M. Dzik: Metody analizy zachowania myszy w systemie IntelliCage (Methods of analysis of mouse behaviour in the IntelliCage system) PhD thesis (2018) doi:10.13140/RG.2.2.32854.50243/2

2017

  • T. V. Gehring, M. J. Węsierska, D. K. Wójcik, E. Vasilaki: Analysis of behaviour in the Active Allothetic Place Avoidance task based on cluster analysis of the rat movement motifs. bioRxiv (2017), doi:10.1101/157859
  • D. Cserpan, D. Meszena, L. Wittner, K. Toth, I. Ulbert, Z. Somogyvari, D. K. Wójcik: Revealing The Distribution Of Transmembrane Currents Along The Dendritic Tree Of A Neuron With Known Morphology From Extracellular Recordings. eLife (2017) 6:e29384, doi:10.7554/eLife.2938.
  • S. Naess, C. Chintaluri, T. B. Ness, A. M. Dale, G. T. Einevoll, D. K. Wojcik: Corrected Four-Sphere Head Model for EEG Signals. Frontiers in Human Neuroscience, 11:490.(2017), doi: 10.3389/fnhum.2017.00490
  • J. M. Dzik, A. Puścian, Z. Mijakowska, K. Radwańska, S. Łęski: PyMICE – a Python library for analysis of IntelliCage data, Behavior Research Methods (2017) doi:10.3758/s13428-017-0907-5
  • M. Stefaniuk, A. Beroun, T. Lebitko, O. Markina, S. Łęski, K. Meyza, A. Grzywacz, J. Samochowiec, A. Samochowiec, K. Radwanska, L. Kaczmarek: Matrix metalloproteinase-9 and synaptic plasticity in the central amygdala in control of alcohol seeking behavior., Biological Psychiatry  81:11 (2017) 907–917, doi: 10.1016/j.biopsych.2016.12.026
  • D. H. Reser, P. Majka, S. Snell, J. Chan, K. Watkins, K. Worthy, M. Del Mar Quiroga, M. G. P. Rosa: Topography of claustrum and insula projections to medial prefrontal and anterior cingulate cortex of the common marmoset (Callithrix jacchus), Journal of Comparative Neurology 525 (2017) 1421–1441. doi:10.1002/cne.24009
  • B. Knauer, P. Majka, K. J Watkins, A. WR Taylor, D. Malamanova, B. Paul, H. Yu, A. Ian Bush, D. J. Hare, D. Reser Whole-brain metallomic analysis of the common marmoset (Callithrix jacchus)., Metallomics 9 (2017) 411-423, doi: 10.1039/C7MT00012J
  • H. Głąbska, C. Chintaluri, D.K. Wójcik Collection of simulated data from a thalamocortical network model., Neuroinformatics  15:87 (2017) , doi: 10.1007/s12021-016-9319-4
  • I. Kondratiuk, S. Łęski, M. Urbańska, J. Jaworski, P. Biecek, H. Devijver, B. Lechat, F. Van Leuven, L. Kaczmarek, T. Jaworski: GSK-3β and MMP-9 cooperate in control of dendritic spine morphology, Molecular Neurobiology 54:1 (2017) 200-211, doi:10.1007/s12035-015-9625-0
  • Z. Mijakowska, K. Łukasiewicz, M. Ziółkowska, M. Lipiński, A. Trąbczyńska, Z. Matuszek, S. Łęski, K. Radwanska: Autophosphorylation of alpha isoform of calcium/calmodulin-dependent kinase II regulates alcohol addiction-related behaviors, Addiction Biology 22:2 (2015) 331-341, doi:10.1111/adb.12327

2016

  • A. Puścian, S. Łęski, G. Kasprowicz, M. Winiarski, J. Borowska, T. Nikolaev, PM. Boguszewski, H-P. Lipp, E. Knapska: Eco-HAB – fully automated and ecologically relevant assessment of social impairments in mouse models of autism. eLife (2016), doi: 10.7554/eLife.19532
  • H. GłąbskaC. ChintaluriD.K. Wójcik (2016)Thalamocortical network simulated data. RepOD. http://dx.doi.org/10.18150/repod.6394793
  • M. Jasińska, J. Miłek, I. A. Cymerman, S. Łęski, L. Kaczmarek, M. Dziembowska: miR-132 regulates dendritic spine structure by direct targeting of matrix metalloproteinase 9 mRNA, Molecular Neurobiology 53 (2016) 4701 – 4712, doi:10.1007/s12035-015-9383-z, pdf
  • P. Majka, D.K. Wojcik: Possum – a framework for three-dimensional reconstruction of brain images from serial sections, Neuroinformatics 14:3 (2016) 265-278, doi:10.1007/s12021-015-9286-1
  • P. Majka, T. A. Chaplin, Hsin-Hao Yu, A. Tolpygo, P. P. Mitra, D. K. Wójcik, M. G. P. Rosa: Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. Journal of Comparative Neurology 11 (2016) 2161-81, doi: 10.1002/cne.24023.
  • S. Ray, C. Chintaluri, U. S. Bhalla, D.K. Wójcik: NSDF: Neuroscience Simulation Data Format, Neuroinformatics 14:2 (2016) 147-167, doi:10.1007/s12021-015-9282-5
  • H. Głąbska, E. Norheim, A. Devor, A.M. Dale, G.T. Einevoll, D.K. Wójcik: Generalized Laminar Population Analysis (gLPA) for interpretation of multielectrode data from cortex, Frontiers in Neuroinformatics (2016) 10:1. doi: 10.3389/fninf.2016.00001

2015

  • Z. Setkowicz, A. Gaździńska, J. J. Osoba, K. Karwowska, P. Majka, J. Orzeł, B. Kossowski, P. Bogorodzki, K. Janeczko, M. Wyleżoł, S. P. Gazdzinski: Does Long-Term High Fat Diet Always Lead to Smaller Hippocampi Volumes, Metabolite Concentrations, and Worse Learning and Memory? A Magnetic Resonance and Behavioral Study in Wistar Rats, PLOS ONE 10 (2015), e0139987
  • I. Laskowska, L. Gawryś, S. Łęski, D. Koziorowski:Emotional processing in Parkinson’s disease and schizophrenia: Evidence for response bias deficits in PD, Frontiers in Psychology 6:1417 (2015)
  • T. Górski, M. Sandström: 12th INCF Nodes Workshop Node Communication and Collaborative Neuroinformatics, pdf
  • I.M. Zakiewicz, P. Majka, D.K. Wojcik, J.G. Bjaalie, T.B. Leergaard Three-dimensional histology volume reconstruction of axonal tract tracing data: exploring topographical organization in subcortical projections from rat barrel cortex, PLOS ONE 10 (2015), e0137571
  • S. ŁęskiLinking extracellular electric potential in the brain to neural activity — a review of source localisation and component identification methods, Acta Neurobiologiae Experimentalis 75 (2015), 117–125
  • T.V. Ness, C. Chintaluri, J. Potworowski, S. ŁęskiH. Głąbska, D.K. Wójcik, G.T. Einevoll: Modelling and analysis of neural electrical potentials recorded in microelectrode arrays (MEAs), Neuroinformatics 13:4 (2015), 403-426
  • T. Górski, K. Rzążewski: Classical fields and quantum measurement for Bose–Einstein condensate, Journal of Physics B: Atomic, Molecular and Optical Physics 48:3 (2015), 035303

2014

  • A. Wróbel, C. Radzewicz, L. Mankiewicz, P. Hottowy, E. Knapska, W. Konopka, E. Kublik, K. Radwańska, W.J. Waleszczyk, D.K. Wójcik: Neuroengineering control and regulation of behavior, Proc. of SPIE 9290 (2014), pdf
  • M. Denker, G. Einevoll, F. Franke, S. Grün, E. Hagen, J. Kerr, M. Nawrot, T. B. Ness, R. Ritz, L. Smith, T. Wachtler, D. Wójcik: 1st INCF workshop on validation on analysis methods, pdf
  • H. Głąbska, J. Potworowski, S. Łęski, D. K. Wójcik: Independent components of neural activity carry information on individual populations, PLOS ONE 9 (2014), e105071
  • A. Puścian, S. Łęski, T. Górkiewicz, K. Meyza, H.-P. Lipp, E. A. Knapska: A novel automated behavioral test battery assessing cognitive rigidity in two genetic mouse models of autism, Frontiers in Behavioral Neuroscience 8:140 (2014)
  • D.K. Wójcik: Current Source Density (CSD) Analysis. In: Jaeger D., Jung R. (Ed.) Encyclopedia of Computational Neuroscience: SpringerReference. Springer-Verlag Berlin Heidelberg, 2013. 2014-02-10 17:39:21 UTC, preprint
  • H. Lindén, E. Hagen, S. Łęski, E. S. Norheim, K. H. Pettersen, G. T. Einevoll: LFPy: A tool for biophysical simulation of extracellular potentials generated by detailed model neurons, Frontiers in Neuroinformatics 7:41 (2014)

2013

  • P. Majka, J. Kowalski, N. Chlodzinska, D. K. Wójcik: 3D Brain Atlas Reconstructor service – online repository of three-dimensional models of brain structures, Neuroinformatics 11 (2013) 507–518
  • E. Knapska, V. Lioudyno, A. Kiryk, M. Mikosz, T. Gorkiewicz, P. Michaluk, M. Gawlak, M. Chaturvedi, G. Mochol, M. Balcerzyk, D. K. Wójcik, G. M. Wilczyński, L. Kaczmarek: Reward learning requires activity of matrix metalloproteinase-9 in the central amygdala,
    Journal of Neuroscience 33 (2013), 14591–14600
  • S. Łęski, H. Lindén, T. Tetzlaff, K. H. Pettersen, G. T. Einevoll:
    Frequency dependence of signal power and spatial reach of the local field potential, PLOS Computational Biology 9 (2013), e1003137,
    preprint: arXiv:1302.4559 [q-bio.NC]
  • J. Rogala, W. J. Waleszczyk, S. Łęski, A. Wróbel, D. K. Wójcik:
    Reciprocal inhibition and slow calcium decay in perigeniculate interneurons explain changes of spontaneous firing of thalamic cells caused by cortical inactivation, Journal of Computational Neuroscience 34 :3(2013), 461–476, pdfsupplementary material
  • G. T. Einevoll, H. Lindén, T. Tetzlaff, S. Łęski, K. H. Pettersen: Local Field Potentials: Biophysical Origin and Analysis, in Principles of Neural Coding, CRC Press (2013)

2012

  • J. Potworowski, W. Jakuczun, S. Łęski, D. K. WójcikKernel Current Source Density Method, Neural Computation 24 (2012), 541–575, pdf
  • P. Majka, E. Kublik, G. Furga, D. K. WójcikCommon Atlas Format and 3D Brain Atlas Reconstructor, the infrastructure for constructing 3D brain atlases, Neuroinformatics 10 (2012), 181–197

2011

  • S. Łęski, K. H. Pettersen, B. Tunstall, G. T. Einevoll, J. Gigg, D. K. WójcikInverse Current Source Density method in two dimensions: Inferring neural activation from multielectrode recordings,
    Neuroinformatics 9 (2011), 401–425, pdf, MATLAB toolbox available through INCF Software Center
  • A. Kiryk, G. Mochol, R. K. Filipkowski, M. Wawrzyniak, V. Lioudyno, E. Knapska, T. Gorkiewicz, M. Balcerzyk, S. Łęski, F. Van Leuven, H.-P. Lipp, D. K. Wójcik, L. Kaczmarek: Cognitive abilities of Alzheimer’s disease transgenic mice are modulated by social context and circadian rhythm, Current Alzheimer Research 8 (2011), 883–892, pdf
  • M. J. Hunt, M. Falińska, S. Łęski, D. K. Wójcik, S. Kasicki: Differential effects produced by ketamine on oscillatory activity recorded in the rat hippocampus, dorsal striatum and nucleus accumbens, Journal of Psychopharmacology 25 (2011), 808–821, pdf

2010

  • G. T. Einevoll, D. K. Wójcik, A. Destexhe: Modeling extracellular potentials, Journal of Computational Neuroscience 29 (2010) 367–369
  • S. Łęski, E. Kublik, D. A. Świejkowski, A. Wróbel, D. K. Wójcik:
    Extracting functional components of neural dynamics with Independent Component Analysis and inverse Current Source Density, Journal of Computational Neuroscience 29 (2010), 459–473, pdf
  • A. Sobolewski, E. Kublik, D. A. Świejkowski, S. Łęski, J. K. Kamiński, A. Wróbel: Cross-trial correlation analysis of evoked potentials reveals arousal related attenuation of thalamo-cortical coupling, Journal of Computational Neuroscience 29 (2010), 485–493, pdf
  • D. K. Wójcik, S. ŁęskiCurrent source density reconstruction from incomplete data, Neural Computation 22 (2010), 48–60,
    arXiv:0903.2379 [q-bio.QM], pdf
  • G. Mochol, D. K. Wójcik, M. Wypych, A. Wróbel, W. Waleszczyk: Variability of visual responses of superior colliculus neurons corresponds to their velocity preferences, Journal of N10.1016/j.semcdb.2019.01.006euroscience 30:9 (2010) 3199–3209

Older

  • D. K. Wójcik, G. Mochol, W. Jakuczun, M. Wypych, W. Waleszczyk: Direct estimation of inhomogenous Markov interval models of spike-trains, Neural Computation 21 (2009), 2105–2113
  • S. Łęski, D. K. WójcikInferring coupling strength from event-related dynamicsPhysical Review E 78, 041918 (2008), arXiv:0805.0532 [q-bio.NC], pdf
  • S. Łęski, D. K. Wójcik, J. Tereszczuk, D. A. Świejkowski, E. Kublik, A. Wróbel: Inverse Current-Source Density method in 3D: reconstruction fidelity, boundary effects, and influence of distant sources,
    Neuroinformatics 5 (2007), 207–222, pdf
  • W. Jakuczun, E. Kublik, D. K. Wójcik, A. Wróbel: Local classifiers for evoked potentials recorded from behaving rats, Acta Neurobiologiae Experimentalis 65 (2005), 425–434

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