Publications

Under Review

Findling C., Hubert F., International Brain Laboratory, Acerbi L., Benson B., Benson J., Birman D., Bonacchi N., Bruijns S., Carandini M., Catarino J., Chapuis G., Churchland A., Dan Y., Davatolhagh F., DeWitt E., Engel T., Fabbri M., Faulkner M., Fiete I., Freitas-Silva L., Gerçek B., Harris K., Häusser M., Hofer S., Hu F., Huntenburg J., Khanal A., Krasniak C., Langdon C., Latham P., Lau P., Mainen Z., Meijer G., Miska N., Mrsic-Flogel T., Noel J., Nylund K., Pan-Vazquez A., Paninski L., Pillow J., Rossant C., Roth N., Schaeffer R., Schartner M., Shi Y., Socha K., Steinmetz N., Svoboda K., Tessereau C., Urai A., Wells M., West S., Whiteway M., Winter O., Witten I., Zador A., Zhang Y., Dayan P., Pouget A.
Brain-wide representations of prior information in mouse decision-making Nature [IN_REVIEW]
International Brain Laboratory, Benson B., Benson J., Birman D., Bonacchi N., Bougrova K., Bruijns S., Carandini M., Catarino J., Chapuis G., Churchland A., Dan Y., Davatolhagh F., Dayan P., DeWitt E., Engel T., Fabbri M., Faulkner M., Fiete I., Findling C., Freitas-Silva L., Gerçek B., Harris K., Häusser M., Hofer S., Hu F., Hubert F., Huntenburg J., Khanal A., Krasniak C., Langdon C., Lau P., Mainen Z., Meijer G., Miska N., Mrsic-Flogel T., Noel J., Nylund K., Pan-Vazquez A., Paninski L., Pouget A., Rossant C., Roth N., Schaeffer R., Schartner M., Shi Y., Socha K., Steinmetz N., Svoboda K., Urai A., Wells M., West S., Whiteway M., Winter O., Witten I.
A Brain-Wide Map of Neural Activity during Complex Behaviour Nature [IN_REVIEW]

2025

Seedat A., Lepauvre A., Jeschke J., Gorska-Klimowska U., Armendariz M., Bendtz K., Henin S., Hirschhorn R., Brown T., Jensen E., Kozma C., Mazumder D., Montenegro S., Yu L., Bonacchi N., Das D., Kahraman K., Sripad P., Taheriyan F., Devinsky O., Dugan P., Doyle W., Flinker A., Friedman D., Lake W., Pitts M., Mudrik L., Boly M., Devore S., Kreiman G., Melloni L. (2025).
Open multi-center intracranial electroencephalography dataset with task probing conscious visual perception. Nature Scientific Data, 12, 854 10.1038/s41597-025-04833-z
Cogitate Consortium, Ferrante O., Gorska-Klimowska U., Henin S., Hirschhorn R., Khalaf A., Lepauvre A., Liu L., Richter D., Vidal Y., Bonacchi N., Brown T., Sripad P., Armendariz M., Bendtz K., Ghafari T., Hetenyi D., Jeschke J., Kozma C., Mazumder D., Montenegro S., Seedat A., Sharafeldin A., Yang S., Baillet S., Chalmers D., Cichy R., Fallon F., Panagiotaropoulos T., Blumenfeld H., de Lange F., Devore S., Jensen O., Kreiman G., Luo H., Boly M., Dehaene S., Koch C., Tononi G., Pitts M., Mudrik L., Melloni L. (2025).
An adversarial collaboration to critically evaluate theories of consciousness Nature.
10.1038/s41586-025-08888-1
International Brain Laboratory, Kush Banga, Julius Benson, Jai Bhagat, Dan Biderman, Daniel Birman, Niccolò Bonacchi, Sebastian A Bruijns, Kelly Buchanan, Robert AA Campbell, Matteo Carandini, Gaelle A Chapuis, Anne K Churchland, M Felicia Davatolhagh, Hyun Dong Lee, Mayo Faulkner, Berk Gerçek, Fei Hu, Julia Huntenburg, Cole Lincoln Hurwitz, Anup Khanal, Christopher Krasniak, Petrina Lau, Christopher Langfield, Nancy Mackenzie, Guido T Meijer, Nathaniel J Miska, Zeinab Mohammadi, Jean-Paul Noel, Liam Paninski, Alejandro Pan-Vazquez, Cyrille Rossant, Noam Roth, Michael Schartner, Karolina Z Socha, Nicholas A Steinmetz, Karel Svoboda, Marsa Taheri, Anne E Urai, Shuqi Wang, Miles Wells, Steven J West, Matthew R Whiteway, Olivier Winter, Ilana B Witten, Yizi Zhang (2025) Reproducibility of in vivo electrophysiological measurements in mice eLife 13:RP100840
10.7554/eLife.100840.3

2024

International Brain Laboratory, Banga Kush, Benson Julius, Bhagat Jai, Biderman Dan, Birman Daniel, Bonacchi Niccolò, et al. (2024)
Reproducibility of in vivo electrophysiological measurements in mice eLife 13:RP100840
10.7554/eLife.100840.1

Datasets

Hal Blumenfeld; Bonacchi, N.; Tanya Brown; Diptyajit Das; Floris de Lange; Rony Hirschhorn; Kyle Sinan Taylan Kahraman; Aya Khalaf; Lucia Melloni; Liad Mudrik et al. (2024).
Cogitate fMRI BIDS data: Max Planck Institute for Empirical Aesthetics
10.17617/1.8ax5-t263
Hal Blumenfeld; Bonacchi, N.; Tanya Brown; Diptyajit Das; Floris de Lange; Rony Hirschhorn; Kyle Sinan Taylan Kahraman; Aya Khalaf; Lucia Melloni; Liad Mudrik et al. (2024).
Cogitate fMRI RAW data: Max Planck Institute for Empirical Aesthetics.
10.17617/1.dhjj-er02
Marcelo Armendariz; Katarina Bendtz; Melanie Boly; Bonacchi, N.; Tanya Brown; Diptyajit Das; Sasha Devore; Urszula Górska-Klimowska; Simon Henin; Rony Hirschhorn et al. (2024).
Cogitate iEEG BIDS data: Max Planck Institute for Empirical Aesthetics.
10.17617/1.6qpg-gz82
Marcelo Armendariz; Katarina Bendtz; Melanie Boly; Bonacchi, N.; Tanya Brown; Diptyajit Das; Sasha Devore; Urszula Górska-Klimowska; Simon Henin; Rony Hirschhorn et al. (2024).
Cogitate iEEG RAW data: Max Planck Institute for Empirical Aesthetics.
10.17617/1.cqyn-9a87
Bonacchi, N.; Tanya Brown; Diptyajit Das; Oscar Ferrante; Rony Hirschhorn; Ole Jensen; Kyle Sinan Taylan Kahraman; Ling Liu; Huan Luo; Lucia Melloni et al. (2024).
Cogitate MEEG BIDS data: Max Planck Institute for Empirical Aesthetics.
10.17617/1.wqa3-wk71
Bonacchi, N.; Tanya Brown; Diptyajit Das; Oscar Ferrante; Rony Hirschhorn; Ole Jensen; Kyle Sinan Taylan Kahraman; Ling Liu; Huan Luo; Lucia Melloni et al. (2024).
Cogitate MEEG RAW data: Max Planck Institute for Empirical Aesthetics.
10.17617/1.nzwp-7j89

2023

International Brain Laboratory; Bonacchi, N., Chapuis, G. A., Churchland, A. K., DeWitt, E. E. J., Faulkner, M., Harris, K. D., Huntenburg, J. M., ... Wells, M. J. (2023).
A modular architecture for organizing, processing and sharing neurophysiology data Nature Methods 20, 403–407.
10.1038/s41592-022-01742-6

2022

Snitz, K., Honigstein, D., Weissgross, R., Ravia, A., Mishor, E., Perl, O., Karagach, S., Medhanie, A., Harel, N., Shushan, S., Roth, Y., Iravani, B., Arshamian, A., Ernst, G., Okamoto, M., Poo, C., Bonacchi, N., Mainen, Z., Monteleone, E., … Sobel, N. (2022).
An olfactory self-test effectively screens for COVID-19. Communications Medicine, 2(34).
10.1038/s43856-022-00095-7

2021

Whiteway, M. R., Biderman, D., Friedman, Y., Dipoppa, M., Buchanan, E. K., Wu, A., Zhou, J., Bonacchi, N., Miska, N. J., Noel, J.-P., Rodriguez, E., Schartner, M., Socha, K., Urai, A. E., Salzman, C. D., Cunningham, J. P., & and, L. P. (2021).
Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders. PLOS Computational Biology, 17(9), e1009439.
10.1371/journal.pcbi.1009439
Poo, C., Agarwal, G., Bonacchi, N., & Mainen, Z. F. (2021).
Spatial maps in piriform cortex during olfactory navigation. Nature, 601(7894), 595–599.
10.1038/s41586-021-04242-3
Aguillon-Rodriguez, and V., Angelaki, D., Bayer, H., Bonacchi, N., Carandini, M., Cazettes, F., Chapuis, G., Churchland, A. K., Dan, Y., Dewitt, E., Faulkner, M., Forrest, H., Haetzel, L., Häusser, M., Hofer, S. B., Hu, F., Khanal, A., Krasniak, C., Laranjeira, I., … Zador, A. M. (2021).
Standardized and reproducible measurement of decision-making in mice. ELife, 10:e63711.
10.7554/elife.63711

2015

Lopes, G., Bonacchi, N., Frazão, J., Neto, J. P., Atallah, B. V., Soares, S., Moreira, L., Matias, S., Itskov, P. M., Correia, P. A., Medina, R. E., Calcaterra, L., Dreosti, E., Paton, J. J., & Kampff, A. R. (2015).
Bonsai: An event-based framework for processing and controlling data streams. Frontiers in Neuroinformatics, 9:7.
10.3389/fninf.2015.00007

Preprints

Benson, B., Benson, J., Birman, D., … Winter, O., Bonacchi, N., Witten, I. B. (2023).
A Brain-Wide Map of Neural Activity during Complex Behaviour. bioRxiv.
10.1101/2023.07.04.547681
Findling, C., Hubert, F., Acerbi, L., … Dayan, P., Pouget, A., Bonacchi, N. (2023).
Brain-wide representations of prior information in mouse decision-making. bioRxiv.
10.1101/2023.07.04.547684
Melloni, L., Consortium, C., Ferrante, O., … Pitts, M., Mudrik, L., Bonacchi, N. (2023).
An adversarial collaboration to critically evaluate theories of consciousness. Research Square.
10.21203/rs.3.rs-3101836/v1
Ferrante, O., Gorska-Klimowska, U., Henin, S., … Mudrik, L., Melloni, L., Bonacchi, N. (2023).
An adversarial collaboration to critically evaluate theories of consciousness. bioRxiv.
10.1101/2023.06.23.546249
Banga, K., Benson, J., Bhagat, J., … Witten, I. B., Zhang, Y., Bonacchi, N. (2022).
Reproducibility of in vivo electrophysiological measurements in mice. bioRxiv.
10.1101/2022.05.09.491042
Whiteway, M. R., Biderman, D., Friedman, Y., … Cunningham, J. P., Paninski, L., Bonacchi, N. (2021).
Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders. bioRxiv.
10.1101/2021.02.22.432309
Snitz, K., Honigstein, D., Weissgross, R., … Lundström, J. N., Sobel, N., Bonacchi, N. (2021).
A novel olfactory self-test effectively screens for COVID-19. medRxiv.
10.1101/2021.02.18.21251422
Poo, C., Agarwal, G., Bonacchi, N., Mainen, Z. (2020).
Spatial maps in piriform cortex during olfactory navigation. bioRxiv.
10.1101/2020.02.18.935494
Bonacchi, N., Chapuis, G., Churchland, A., … Winter, O., Wells, M. (2019).
Data architecture for a large-scale neuroscience collaboration. bioRxiv.
10.1101/827873