Niccolò Bonacchi

Niccolò Bonacchi
Integrated Member
Social Cognitive and Applied Neuroscience Team

Niccolò Bonacchi is an assistant professor at ISPA – Instituto Universitário where he teaches graduate-level courses in experimental programming and neurobiology. He holds a Ph.D. in Neuroscience from the Nova University of Lisbon (UNL) and an M.Sc. in Psychobiology from the Higher Institute of Applied Psychology (ISPA). His doctoral work at the Champalimaud Center for the Unknown (CCU) examined how brains represent spatial objectives, olfactory cues, the results they anticipate, and how these expectations affect both behavior and brain function. During his Ph.D., he also contributed to the development of the Bonsai-RX programming language, which is now utilized in research laboratories all around the world. His work at the International Brain Laboratory (IBL) as Data Architect focused on the development of the experimental data acquisition system and procedures. He recently moved on to another international collaboration researching consciousness in humans, the COGITATE consortium. His work at the COGITATE Consortium focuses on the development of an experimental metadata ontology used to describe cognitive and systems neuroscience experiments, and on data curation and data release procedures that enable FAIR data-sharing practices. Niccolò Bonacchi is interested in bridging the gap between mechanistic explanations of brain processes and the emergent cognitive constructs that underpin them. To do this, he has concentrated his efforts on developing ever more precise and accurate approaches to behavioral quantification and data analysis, which he believes are critical for contextualizing and interpreting any type of experimental or (neuro)physiological measurements. He is also enthusiastic about the open movement in its various forms, particularly in regard to open science and its potential to improve experimental reproducibility.

Main 5 publications

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.. doi: 10.1038/s41592-022-01742-6
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(1). doi: 10.1038/s43856-022-00095-7
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. doi: 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. doi: 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. doi: 10.7554/elife.63711