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Identification

Personal identification

Full name
Niccolò Bonacchi

Citation names

  • Bonacchi, Niccolò
  • Bonacchi, N.

Author identifiers

Ciência ID
0612-705C-8295
ORCID iD
0000-0001-5228-6918
Google Scholar ID
https://scholar.google.com/citations?hl=en&user=ii0Eww0AAAAJ
Scopus Author Id
56598047300

Languages

Language Speaking Reading Writing Listening Peer-review
Italian Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2017/07
Concluded
 Ph.D. in Biology | Neuroscience (Doutoramento)
Major in Especialidade: Neurociências
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
"Spatial goals and actions in the orbitofrontal cortex" (THESIS/DISSERTATION)
2014 - 2014
Concluded
 Computational and Cognitive Neuroscience Summer School (Outros)
New York University, United States
2012 - 2012
Concluded
 Course in Laboratory Animal Science - Cat B (Outros)
Direcção-Geral de Alimentação e Veterinária, Portugal
2010
Concluded
 M.Sc. in Psychobiology (Mestrado)
Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal
"BEHAVIORAL SUPPRESSION IN A MODIFIED CONFLICT PARADIGM A Framework to Test the Photostimulation of 5-HT" (THESIS/DISSERTATION)
 20
2004
Concluded
 Rehabilitation and Social Inclusion (Licenciatura)
Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal
"Attitudes towards people with disabilities - Comparative study between 1st and final year ISPA students. PT: Atitudes face à pessoa com deficiência - Estudo comparativo entre alunos do 1º e último ano do ISPA." (THESIS/DISSERTATION)
 16
Affiliation

Science

Category
Host institution 		Employer
2023/03/01 - Current Researcher (Research) Instituto Superior de Psicologia Aplicada Centro de Investigação William James, Portugal
Instituto Superior de Psicologia Aplicada Centro de Investigação William James, Portugal
2023 - Current Visiting Researcher (Research) Fundação Champalimaud, Portugal
Programa Champalimaud de Neurociências, Portugal
2023 - Current Visiting Researcher (Research) Max-Planck-Institut für empirische Ästhetik, Germany
Max-Planck-Institut für empirische Ästhetik, Germany
2019 - 2022/12/31 Coordinating Researcher (Research) Programa Champalimaud de Neurociências, Portugal
2018 - 2018/12/31 Coordinating Researcher (Research) University College London Wolfson Institute for Biomedical Research, United Kingdom
University College London Wolfson Institute for Biomedical Research, United Kingdom
2017/07/27 - 2018/03 Postdoc (Research) Programa Champalimaud de Neurociências, Portugal
2005 - 2007 Researcher (Research) ISCTE-Instituto Universitário de Lisboa Centro de Investigação e Intervenção Social, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2023 - Current Assistant Professor (University Teacher) Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal
Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal

Others

Category
Host institution 		Employer
2009/09/15 - 2017/07/26 PhD Student (International Neuroscience Doctoral Programme - INDP) Systems Neuroscience Lab, Programa Champalimaud de Neurociências, Portugal
2008/06/02 - 2009/09/14 MS Student / Assistant researcher Champalimaud Neuroscience Programme Instituto Gulbenkian de Ciência, Portugal
2005 - 2007 Junior Researcher - European Social Survey (P143B) Universidade de Lisboa Instituto de Ciências Sociais, Portugal
2005 - 2007 Junior Researcher EUROFOR (Daphne - EU) Berliner Institut für Vergleichende Sozialforschung eV, Germany
Projects

Grant

Designation Funders
2023 - Current ARC - COGITATE
TWCF 0389
Principal investigator
Programa Champalimaud de Neurociências, Portugal
 Templeton World Charity Foundation Inc
Ongoing
2018 - 2022/12/01 The International Brain Laboratory (IBL)
Wellcome 209558
Wellcome 216324
Researcher
University College London Wolfson Institute for Biomedical Research, United Kingdom

Programa Champalimaud de Neurociências, Portugal
Wellcome Trust

Simons Foundation
Ongoing
2010/10/01 - 2013/11/30 CONTEXT DEPENDENT MODULATION OF VALUE
SFRH/BD/51259/2010
 Fundação para a Ciência e a Tecnologia
Concluded
2010 - 2012 Context dependent modulation of value
SFRH / BD / 51259 / 2010
 Secretaria de Estado de Ciência Tecnologia e Ensino Superior
2009/10/01 - 2010/09/30 PROGRAMA GULBENKIAN CHAMPALIMAUD EM NEUROCIÊNCIAS - INTERNATIONAL NEUROSCIENCE DOCTORAL PROGRAM
SFRH/BI/33927/2009
 Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2018/10/01 - 2022/09/30 Odors and memory: neural mechanisms for encoding contextual information in olfactory cortex
PTDC/MED-NEU/28509/2017
Fundação Champalimaud, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2019/12/31 Champalimaud Neuroscience Programme
UID/NEU/04443/2019
Fundação Champalimaud, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference abstract
  1. Bougrova, Kcenia; Bonacchi, Niccolò; Catarino, Joana A; DeWitt, Eric; Meijer, Guido; Dayan, Peter; Mainen, Zachary; The International Brain Laboratory. "Comparison of neuromodulator signaling in a visual decision-making task". Paper presented in 51st Annual Meeting of the Society for Neuroscience, San Diego, CA, 2022.
    Published
  2. Bonacchi, Niccolò; Chapuis, G.A.; Anne K. Churchland; Kenneth D. Harris; Rossant, Cyrille; Olivier Winter; Miles J. Wells; Mainen, Zachary; The International Brain Laboratory. "The IBL data architecture: tools for storing and accessing divers databases collected at multiple sites". Paper presented in Society for Neuroscience (SfN), Chicago, 2019.
    Accepted
  3. Poo, Cindy; Agarwal, Gautam; Bonacchi, Niccolò; Mainen, Zachary. "Conjunctive map for odors and space in posterior piriform cortex". Paper presented in Society for Neuroscience (SfN), Lisbon, 2019.
    Accepted
  4. Cindy Poo; Bonacchi, Niccolò; Mainen, Zachary. "Spatial context modulates odor representations in posterior piriform cortex". Paper presented in 11th FENS Forum of Neuroscience, Berlin, 2018.
  5. Bonacchi, Niccolò; Cindy Poo; Cruz, AS; Mainen, Zachary. "Encoding of odor context in posterior piriform cortex". Paper presented in Computational and Systems Neuroscience (CoSyNe), Salt Lake City, 2016.
    Accepted
  6. Bonacchi, Niccolò; Cindy Poo; Cruz, AS; Mainen, Zachary. "Orbitofrontal cortex and outcome locations". Paper presented in Computationam ans Systems Neurosciecnc (CoSyNe), Salt Lake City, 2016.
    Accepted
  7. Bonacchi, Niccolò; Cindy Poo; Cruz, AS; Mainen, Zachary. "Posterior piriform cortex in an odor-guided spatial navigation task". Paper presented in Society for Neuroscience (SfN), San Diego, 2016.
  8. Bonacchi, Niccolò; Cindy Poo; Cruz, AS; Mainen, Zachary. "Orbitofrontal cortex, reversals, and locations". Paper presented in Society for Neuroscience (SfN), San Diego, 2016.
    Accepted
  9. Bonacchi, Niccolò; Cindy Poo; Mainen, Zachary F.. "Spatial goals and actions in the orbitofrontal cortex". Paper presented in Society fo Neuroscience (SfN), New Orleans, 2012.
    Accepted
  10. Bonacchi, Niccolò; Mainen, Zachary. "Context dependent modulation of value". Paper presented in Annual Meeting of Gulbenkian Students, Foz do Arelho, 2012.
    Accepted
  11. Correia, PA; Dugué, GP; MatiasS; Lörincz, ML; Bonacchi, Niccolò; Audero, E; Lottem, E; Mainen, Zachary. "Testing the link between serotonin and aversive behaviors using optogenetics". Paper presented in CNP-CRICM Meeting, Lisbon, 2011.
    Accepted
  12. Bonacchi, Niccolò; Dugué, Guillaume; Mainen, Zachary F.. "Behavioral suppression in a modified conflict paradigm". Paper presented in Associação Portuguesa de Psicologia Experimental, Lisbon, 2009.
    Accepted
Journal article
  1. The International Brain Laboratory; Bonacchi, Niccolò; Gaelle Chapuis; Anne K. Churchland; DeWitt, Eric; Mayo Faulkner; Kenneth D. Harris; et al. Corresponding author: Kenneth D. Harris. "A modular architecture for organizing, processing and sharing neurophysiology data". Nature Methods (2023): http://dx.doi.org/10.1038/s41592-022-01742-6.
    10.1038/s41592-022-01742-6
  2. Kobi Snitz; Danielle Honigstein; Reut Weissgross; Aharon Ravia; Eva Mishor; Ofer Perl; Shiri Karagach; et al. "An olfactory self-test effectively screens for COVID-19". Communications Medicine (2022): https://publons.com/wos-op/publon/52618386/.
    10.1038/S43856-022-00095-7
  3. Poo, Cindy; Agarwal, Gautam; Bonacchi, Niccolo; Mainen, Zachary F.. "Spatial maps in piriform cortex during olfactory navigation". Nature (2022): https://publons.com/wos-op/publon/53522782/.
    10.1038/S41586-021-04242-3
  4. Aguillon, Valeria; Angelaki, Dora E.; Bayer, Hannah; Bonacchi, Niccolo; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle; et al. "Standardized and reproducible measurement of decision-making in mice (vol 10, e63711, 2021)". eLife (2022): https://publons.com/wos-op/publon/56762446/.
    10.7554/ELIFE.84310
  5. Matthew R. Whiteway; Frédéric E. Theunissen; Dan Biderman; Yoni Friedman; Mario Dipoppa; E. Kelly Buchanan; Anqi Wu; et al. "Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders". PLOS Computational Biology 17 9 (2021): e1009439-e1009439. https://doi.org/10.1371/journal.pcbi.1009439.
    10.1371/journal.pcbi.1009439
  6. Kobi Snitz; Danielle Honigstein; Reut Weissgross; Aharon Ravia; Eva Mishor; Ofer Perl; Shiri Karagach; et al. "Smelling Household-Odorants Effectively Screens for COVID-19". MedRxiv (2021): https://publons.com/wos-op/publon/40807612/.
    10.1101/2021.02.18.21251422
  7. Aguillon-Rodriguez, Valeria; Angelaki, Dora; Bayer, Hannah; Bonacchi, Niccolo; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle; et al. "Standardized and reproducible measurement of decision-making in mice". eLife (2021): https://publons.com/wos-op/publon/46523116/.
    10.7554/ELIFE.63711
  8. Poo, Cindy; Agarwal, Gautam; Bonacchi, Niccolo; Mainen, Zachary. "A map for odors and space in posterior piriform cortex". Chemical Senses (2020): https://publons.com/wos-op/publon/53522783/.
  9. Bonacchi, Niccolò. "Data architecture and visualization for a large-scale neuroscience collaboration". Biorxiv (2019): https://www.biorxiv.org/content/10.1101/827873v1.
    Open access
  10. Lopes, G.; Bonacchi, N.; Frazão, J.; Neto, J.P.; Atallah, B.V.; Soares, S.; Moreira, L.; et al. "Bonsai: An event-based framework for processing and controlling data streams". Frontiers in Neuroinformatics 9 APR (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84928034273&partnerID=MN8TOARS.
    10.3389/fninf.2015.00007
Preprint
  1. Brandon Benson; Julius Benson; Daniel Birman; Niccolò Bonacchi; Matteo Carandini; Joana A Catarino; Gaelle A Chapuis; et al. "A Brain-Wide Map of Neural Activity during Complex Behaviour". 2023. https://doi.org/10.1101/2023.07.04.547681.
    10.1101/2023.07.04.547681
  2. Oscar Ferrante; Urszula Gorska-Klimowska; Simon Henin; Rony Hirschhorn; Aya Khalaf; Alex Lepauvre; Ling Liu; et al. "An adversarial collaboration to critically evaluate theories of consciousness". 2023. https://doi.org/10.1101/2023.06.23.546249.
    10.1101/2023.06.23.546249
  3. Findling, Charles; Hubert, Felix; Acerbi, Luigi; Benson, Brandon; Benson, Julius; Birman, Daniel; Bonacchi, Niccolò; et al. "Brain-wide representations of prior information in mouse decision-making". 2023. http://dx.doi.org/10.1101/2023.07.04.547684.
    10.1101/2023.07.04.547684
Thesis / Dissertation
  1. Bonacchi, Niccolò. "Spatial goals and actions in the orbitofrontal cortex". PhD, Universidade Nova de Lisboa, 2017. http://hdl.handle.net/10362/76957.

Other

Dataset
  1. Marcelo Armendariz; Katarina Bendtz; Melanie Boly; Bonacchi, Niccolò; Tanya Brown; Diptyajit Das; Sasha Devore; et al. Cogitate iEEG Data. 2024.
    10.17617/1.cqyn-9a87
  2. Hal Blumenfeld; Bonacchi, Niccolò; Tanya Brown; Diptyajit Das; Floris de Lange; Rony Hirschhorn; Kyle Sinan Taylan Kahraman; et al. Cogitate fMRI Data. 2024.
    10.17617/1.dhjj-er02
  3. Bonacchi, Niccolò; Tanya Brown; Diptyajit Das; Oscar Ferrante; Rony Hirschhorn; Ole Jensen; Kyle Sinan Taylan Kahraman; et al. Cogitate M-EEG Data. 2024.
    10.17617/1.wqa3-wk71
  4. Marcelo Armendariz; Katarina Bendtz; Melanie Boly; Bonacchi, Niccolò; Tanya Brown; Diptyajit Das; Sasha Devore; et al. Cogitate iEEG BIDS data. 2024.
    10.17617/1.6qpg-gz82
  5. Bonacchi, Niccolò; Tanya Brown; Diptyajit Das; Oscar Ferrante; Rony Hirschhorn; Ole Jensen; Kyle Sinan Taylan Kahraman; et al. Cogitate MEEG BIDS data. 2024.
    10.17617/1.nzwp-7j89
  6. Hal Blumenfeld; Bonacchi, Niccolò; Tanya Brown; Diptyajit Das; Floris de Lange; Rony Hirschhorn; Kyle Sinan Taylan Kahraman; et al. Cogitate fMRI BIDS data. 2024.
    10.17617/1.8ax5-t263
  7. Cogitate Consortium; Oscar Ferrante; Urszula Górska-Klimowska; Simon Henin; Rony Hirschhorn; Aya Khalaf; Alex Lepauvre; et al. Cogitate XNAT Data Release. 2024.
    10.17617/1.k278-n152
Other output
  1. Reproducibility of in-vivo electrophysiological measurements in mice. 2022. Laboratory, I.B.; Banga, K.; Benson, J.; Bonacchi, Niccolò; Bruijns, S.A.; Campbell, R.; Chapuis, G.A.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85133002014&partnerID=MN8TOARS.
    10.1101/2022.05.09.491042
  2. Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders. 2021. Matthew R Whiteway; Dan Biderman; Yoni Friedman; Mario Dipoppa; E Kelly Buchanan; Anqi Wu; John Zhou; et al. https://doi.org/10.1101/2021.02.22.432309.
    10.1101/2021.02.22.432309
  3. Spatial maps in olfactory cortex during olfactory navigation. 2020. Cindy Poo; Gautam Agarwal; Niccolò Bonacchi; Zachary Mainen. https://doi.org/10.1101/2020.02.18.935494.
    10.1101/2020.02.18.935494
  4. Standardized and reproducible measurement of decision-making in mice. 2020. Valeria Aguillon-Rodriguez; Dora E. Angelaki; Hannah M. Bayer; Niccolò Bonacchi; Matteo Carandini; Fanny Cazettes; Gaelle A. Chapuis; et al. https://doi.org/10.1101/2020.01.17.909838.
    10.1101/2020.01.17.909838
  5. Data architecture for a large-scale neuroscience collaboration. 2019. Niccolò Bonacchi; Gaelle Chapuis; Anne Churchland; Kenneth D. Harris; Max Hunter; Cyrille Rossant; Maho Sasaki; et al. https://doi.org/10.1101/827873.
    10.1101/827873
Software
  1. Cogitate Consortium; Oscar Ferrante; Urszula Górska-Klimowska; Rony Hirschhorn; Aya Khalaf; Alex Lepauvre; Ling Liu (¿¿); David Richter; Bonacchi, Niccolò. "Cogitate-consortium/cogitate-experiment-code: v1.0". 2024.
    10.5281/zenodo.14362839
  2. Cogitate Consortium; Oscar Ferrante; Urszula Górska-Klimowska; Rony Hirschhorn; Aya Khalaf; Alex Lepauvre; Ling Liu (¿¿); David Richter; Bonacchi, Niccolò. "Cogitate-consortium/cogitate-experiment-code: v1.0". 2024.
    10.5281/zenodo.14362838
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/06/21 The International Brain Laboratory: A distributed network for reproducible neuroscience Conference Cycle in Cognitive and Behavioral Sciences
Ispa - Instituto Universitário (Lisbon, Portugal)
2021/06/15 The International Brain Laboratory: A distributed network for reproducible neuroscience Methods and Models in Biomedical Sciences: Building bridges
European Commission - EU Science Hub (Online, EU)

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023 An Olfactory Virtual Reality System for Spatial Behaviors in Mice
(Thesis) Main arguer
 José Miguel Gomes Teixeira (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2023 - 2023 PLOS Computational Biology (1553-7358) PLOS
2021/03 - 2021/03 Nature Methods (1548-7091) Springer Nature

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023 - Current Experimental Neuroscience PhD in Integrative Biology (Doutoramento) Instituto Gulbenkian de Ciência, Portugal
2023 - Current Innate Behavior and Learning PhD in Biology (Doutoramento) Instituto Universitário de Ciências Psicológicas Sociais e da Vida, Portugal
2022 - Current Behavior Quantification PhD in Integrative Biology (Doutoramento) Instituto Gulbenkian de Ciência, Portugal
2021 - 2022 CAJAL Advanced Neuroscience Training Neurokit - Visual Reactive Programming - Bonsai 1022 Visual Reactive Programming - Bonsai 1022 (Outros) World Federation of Neurosurgical Societies, Switzerland

International Brain Research Organization, France
2011 - 2012 Scientific Hardware and Software INDP (Doutoramento) Programa Champalimaud de Neurociências, Portugal
Distinctions

Award

2009 Merit Diploma
Instituto Superior de Psicologia Aplicada Centro de Investigacao, Portugal