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‎joss/paper.bib‎

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@Article{bezanson_2017,
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author = {Jeff Bezanson and Alan Edelman and Stefan Karpinski and Viral B. Shah},
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journal = {SIAM Review},
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title = {Julia: A Fresh Approach to Numerical Computing},
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year = {2017},
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month = jan,
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number = {1},
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pages = {65--98},
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volume = {59},
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creationdate = {2024-10-29T12:38:15},
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doi = {10.1137/141000671},
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file = {:bezanson_2017.pdf:PDF},
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groups = {misc},
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publisher = {Society for Industrial \& Applied Mathematics (SIAM)},
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@article{bezanson_2017,
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author = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.},
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title = {Julia: A Fresh Approach to Numerical Computing},
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journal = {SIAM Review},
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volume = {59},
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number = {1},
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pages = {65-98},
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year = {2017},
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doi = {10.1137/141000671},
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URL = {https://doi.org/10.1137/141000671},
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eprint = {https://doi.org/10.1137/141000671},
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}
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@Article{bezanson_2018,
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author = {Bezanson, Jeff and Chen, Jiahao and Chung, Benjamin and Karpinski, Stefan and Shah, Viral B. and Vitek, Jan and Zoubritzky, Lionel},
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journal = {Proceedings of the ACM on Programming Languages},
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title = {Julia: dynamism and performance reconciled by design},
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year = {2018},
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issn = {2475-1421},
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month = oct,
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number = {OOPSLA},
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pages = {1--23},
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volume = {2},
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creationdate = {2024-10-29T12:50:02},
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doi = {10.1145/3276490},
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publisher = {Association for Computing Machinery (ACM)},
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@article{bezanson_2018,
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author = {Bezanson, Jeff and Chen, Jiahao and Chung, Benjamin and Karpinski, Stefan and Shah, Viral B. and Vitek, Jan and Zoubritzky, Lionel},
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journal = {Proceedings of the ACM on Programming Languages},
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title = {Julia: dynamism and performance reconciled by design},
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year = {2018},
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issn = {2475-1421},
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month = oct,
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number = {OOPSLA},
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pages = {1--23},
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volume = {2},
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creationdate = {2024-10-29T12:50:02},
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doi = {10.1145/3276490},
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publisher = {Association for Computing Machinery (ACM)},
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}
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@Misc{selvaraj_2022,
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author = {Selvaraj, Natassha},
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month = nov,
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title = {Meet {Julia}: {The} {Future} of {Data} {Science}},
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year = {2022},
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abstract = {The next big thing, or just massively overhyped?},
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creationdate = {2024-10-29T12:51:25},
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journal = {Medium},
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language = {en},
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shorttitle = {Meet {Julia}},
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url = {https://towardsdatascience.com/meet-julia-the-future-of-data-science-52414b29ebb},
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urldate = {2024-10-29},
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@misc{selvaraj_2022,
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author = {Selvaraj, Natassha},
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month = nov,
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title = {Meet {Julia}: {The} {Future} of {Data} {Science}},
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year = {2022},
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abstract = {The next big thing, or just massively overhyped?},
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creationdate = {2024-10-29T12:51:25},
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journal = {Medium},
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language = {en},
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shorttitle = {Meet {Julia}},
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url = {https://towardsdatascience.com/meet-julia-the-future-of-data-science-52414b29ebb},
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urldate = {2024-10-29},
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}
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@Article{delorme_2011,
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author = {Delorme, Arnaud and Mullen, Tim and Kothe, Christian and Akalin Acar, Zeynep and Bigdely-Shamlo, Nima and Vankov, Andrey and Makeig, Scott},
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journal = {Computational Intelligence and Neuroscience},
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title = {EEGLAB, SIFT, NFT, BCILAB, and ERICA: New Tools for Advanced EEG Processing},
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year = {2011},
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issn = {1687-5265, 1687-5273},
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pages = {1--12},
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volume = {2011},
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abstract = {We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments.},
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creationdate = {2024-10-29T14:14:01},
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doi = {10.1155/2011/130714},
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file = {:delorme_2011.pdf:PDF},
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groups = {EEG},
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langid = {english},
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shorttitle = {EEGLAB, SIFT, NFT, BCILAB, and ERICA},
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url = {http://www.hindawi.com/journals/cin/2011/130714/},
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urldate = {2021-07-01},
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@article{delorme_2011,
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author = {Delorme, Arnaud and Mullen, Tim and Kothe, Christian and Akalin Acar, Zeynep and Bigdely-Shamlo, Nima and Vankov, Andrey and Makeig, Scott},
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journal = {Computational Intelligence and Neuroscience},
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title = {EEGLAB, SIFT, NFT, BCILAB, and ERICA: New Tools for Advanced EEG Processing},
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year = {2011},
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issn = {1687-5265, 1687-5273},
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pages = {1--12},
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volume = {2011},
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creationdate = {2024-10-29T14:14:01},
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doi = {10.1155/2011/130714},
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file = {:delorme_2011.pdf:PDF},
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groups = {EEG},
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langid = {english},
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shorttitle = {EEGLAB, SIFT, NFT, BCILAB, and ERICA},
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url = {http://www.hindawi.com/journals/cin/2011/130714/},
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urldate = {2021-07-01},
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}
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@Article{oostenveld_2011,
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author = {Oostenveld, Robert and Fries, Pascal and Maris, Eric and Schoffelen, Jan-Mathijs},
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journal = {Computational Intelligence and Neuroscience},
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title = {FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data},
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year = {2011},
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issn = {1687-5265, 1687-5273},
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pages = {1--9},
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volume = {2011},
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abstract = {This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.},
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creationdate = {2024-10-29T14:15:03},
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doi = {10.1155/2011/156869},
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file = {:oostenveld_2011.pdf:PDF},
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groups = {EEG},
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langid = {english},
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shorttitle = {FieldTrip},
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url = {http://www.hindawi.com/journals/cin/2011/156869/},
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urldate = {2020-09-13},
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@article{oostenveld_2011,
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author = {Oostenveld, Robert and Fries, Pascal and Maris, Eric and Schoffelen, Jan-Mathijs},
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journal = {Computational Intelligence and Neuroscience},
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title = {FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data},
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year = {2011},
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issn = {1687-5265, 1687-5273},
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pages = {1--9},
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volume = {2011},
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creationdate = {2024-10-29T14:15:03},
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doi = {10.1155/2011/156869},
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file = {:oostenveld_2011.pdf:PDF},
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groups = {EEG},
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langid = {english},
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shorttitle = {FieldTrip},
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url = {http://www.hindawi.com/journals/cin/2011/156869/},
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urldate = {2020-09-13},
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}
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@Article{gramfort_2013,
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author = {Gramfort, Alexandre},
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journal = {Frontiers in Neuroscience},
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title = {MEG and EEG data analysis with MNE-Python},
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year = {2013},
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issn = {1662-453X},
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volume = {7},
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creationdate = {2024-10-29T14:15:34},
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doi = {10.3389/fnins.2013.00267},
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file = {:gramfort_2013.pdf:PDF},
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groups = {EEG},
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langid = {english},
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urldate = {2021-10-18},
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@article{gramfort_2013,
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author = {Gramfort, Alexandre},
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journal = {Frontiers in Neuroscience},
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title = {MEG and EEG data analysis with MNE-Python},
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year = {2013},
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issn = {1662-453X},
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volume = {7},
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creationdate = {2024-10-29T14:15:34},
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doi = {10.3389/fnins.2013.00267},
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file = {:gramfort_2013.pdf:PDF},
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groups = {EEG},
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langid = {english},
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urldate = {2021-10-18},
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}
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@Article{bezanson_2014,
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author = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.},
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title = {Julia: {A} Fresh Approach to Numerical Computing},
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journal = {CoRR},
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volume = {abs/1411.1607},
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year = {2014},
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url = {http://arxiv.org/abs/1411.1607},
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eprinttype = {arXiv},
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eprint = {1411.1607},
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timestamp = {Mon, 13 Aug 2018 16:47:09 +0200},
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biburl = {https://dblp.org/rec/journals/corr/BezansonEKS14.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{bezanson_2014,
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author = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.},
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title = {Julia: {A} Fresh Approach to Numerical Computing},
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journal = {CoRR},
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volume = {abs/1411.1607},
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year = {2014},
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url = {http://arxiv.org/abs/1411.1607},
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eprinttype = {arXiv},
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eprint = {1411.1607},
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timestamp = {Mon, 13 Aug 2018 16:47:09 +0200},
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biburl = {https://dblp.org/rec/journals/corr/BezansonEKS14.bib},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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}
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@article{pal_2024,
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title = {A next-generation dynamic programming language Julia: Its features and applications in biological science},
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journal = {Journal of Advanced Research},
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volume = {64},
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pages = {143-154},
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year = {2024},
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issn = {2090-1232},
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doi = {https://doi.org/10.1016/j.jare.2023.11.015},
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url = {https://www.sciencedirect.com/science/article/pii/S2090123223003521},
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author = {Pal, Soumen and Bhattacharya, Manojit and Dash, Snehasish and Lee, Sang-Soo and Chakraborty, Chiranjib},
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}
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title = {A next-generation dynamic programming language Julia: Its features and applications in biological science},
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journal = {Journal of Advanced Research},
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volume = {64},
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pages = {143-154},
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year = {2024},
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issn = {2090-1232},
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doi = {10.1016/j.jare.2023.11.015},
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url = {https://www.sciencedirect.com/science/article/pii/S2090123223003521},
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author = {Pal, Soumen and Bhattacharya, Manojit and Dash, Snehasish and Lee, Sang-Soo and Chakraborty, Chiranjib},
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}
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@article{wysokinski_2023,
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title = {Improved cognitive performance, increased theta, alpha, beta and decreased delta powers after cognitive rehabilitation augmented with {tDCS} in a patient with post-{COVID}-19 cognitive impairment (brain-fog)},
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volume = {2},
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url = {https://www.semanticscholar.org/paper/de5938b95d5967e75b9d5c746c1ba98f1d75b294},
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doi = {10.1016/j.psycr.2023.100164},
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number = {2},
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journal = {Psychiatry Research Case Reports},
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author = {Wysokiński, Adam and Szczepocka, Ewa and Szczakowska, Adrianna},
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month = aug,
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year = {2023},
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pages = {100164-100164},
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}
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@article{sochal_2024a,
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title = {The {Relationship} between {Sleep} {Parameters} {Measured} by {Polysomnography} and {Selected} {Neurotrophic} {Factors}},
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volume = {13},
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url = {https://www.mdpi.com/2077-0383/13/3/893},
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doi = {10.3390/jcm13030893},
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number = {3},
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journal = {Journal of Clinical Medicine},
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author = {Sochal, Marcin and Binienda, Agata and Tarasiuk, Aleksandra and Gabryelska, Agata and Białasiewicz, Piotr and Ditmer, Marta and Turkiewicz, Szymon and Karuga, Filip Franciszek and Fichna, Jakub and Wysokiński, Adam},
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month = jan,
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year = {2024},
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pages = {893-893},
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}
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@article{sochal_2024b,
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title = {Circadian {Rhythm} {Genes} and {Their} {Association} with {Sleep} and {Sleep} {Restriction}},
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volume = {25},
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doi = {10.3390/ijms251910445},
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number = {19},
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journal = {International Journal of Molecular Sciences},
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author = {Sochal, Marcin and Ditmer, Marta and Tarasiuk-Zawadzka, Aleksandra and Binienda, Agata and Turkiewicz, Szymon and Wysokiński, Adam and Karuga, Filip Franciszek and Białasiewicz, Piotr and Fichna, Jakub and Gabryelska, Agata},
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month = sep,
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year = {2024},
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pages = {10445-10445},
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}
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@article{datseris_2024,
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title = {Physiological signal analysis and open science using the {Julia} language and associated software},
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volume = {4},
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issn = {2674-0109},
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doi = {10.3389/fnetp.2024.1478280},
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language = {eng},
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journal = {Frontiers in Network Physiology},
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author = {Datseris, George and Zelko, Jacob S.},
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year = {2024},
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pmid = {39569020},
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pages = {1478280},
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}

‎joss/paper.md‎

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# Research projects using the software
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NeuroAnalyzer has been used in the preparation of the following publications:
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1. Wysokiński A, Szczepocka E, Szczakowska A. Improved cognitive performance, increased theta, alpha, beta and decreased delta powers after cognitive rehabilitation augmented with tDCS in a patient with post-COVID-19 cognitive impairment (brain-fog). Psychiatry Research Case Reports. 2023 DOI: 10.1016/j.psycr.2023.100164
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2. Sochal M. et al. The relationship between sleep quality measured by polysomnography and selected neurotrophic factors. Journal of Clinical Medicine. 2024 DOI: 10.3390/jcm13030893
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3. Sochal M. et al. Circadian Rhythm Genes and Their Association with Sleep and Sleep Restriction. International Journal of Molecular Sciences. 2024 DOI: 10.3390/ijms251910445
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4. Datseris G, Zelko J. Physiological signal analysis and open science using the Julia language and associated software. Frontiers in Network Physiology. 2024 DOI: 10.3389/fnetp.2024.1478280
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5. Wysokiński A, Pazdrak M. Complete resolution of auditory verbal hallucinations (AVH) in a patient with schizophrenia after transcranial direct current stimulation (tDCS) therapy. Psychiatria i Psycholologia Kliniczna. 2024 (in press)
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NeuroAnalyzer has been used in the preparation of the following publications: Wysokiński et al. [@wysokinski_2023], Sochal M. et al. [@sochal_2024a], Sochal et al. [@sochal_2024b], Datseris & Zelko [@datseris_2024] and Wysokiński & Pazdrak (in press).
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In the Department of Old Age Psychiatry and Psychotic Disorders (Medical University of Lodz, Poland) we are using NeuroAnalyzer for analyzing EEG data to analyze EEG data from our research projects on functional (EEG-based) connectivity in schizophrenia and EEG markers of tDCS stimulation.
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