Publication list

Selected publications

  • Distributed context-dependent choice information in mouse dorsal-parietal cortex
    Orlandi, J.G., Abdolrahmani, M., Aoki, R., Lyamzin, D.R., and Benucci, A.
    bioRxiv, 2021. [DOI]
  • Deficits in coordinated neuronal activity and network topology are striatal hallmarks in Huntington’s disease
    Fernández-García, S., Orlandi, J.G., {García-Díaz Barriga}, G.A., Rodríguez, M.J., Masana, M., Soriano, J., and Alberch, J.
    BMC Biol., vol. 18, iss.1, p. 58, 2020. [DOI]
  • NETCAL: An interactive platform for large-scale, NETwork and population dynamics analysis of CALcium imaging recordings
    Orlandi, J.G., Fernández-García, S., Comella-Bolla, A., Masana, M., {García-Díaz Barriga}, G., Yaghoubi, M., Kipp, A., Canals, J.M., Colicos, M.A., Davidsen, J., Alberch, J., and Soriano, J., Zenodo research data repository, 2017. [DOI]
  • First connectomics challenge: from imaging to connectivity
    Orlandi, J.G., Ray, B., Battaglia, D., Guyon, I., Lemaire, V., Saeed, M., Soriano, J., Statnikov, A., and Stetter, O.
    Journal of Machine Learning: WCP, vol. 46, pp. 1-22, 2015. [URL]
  • Transfer Entropy Reconstruction and Labeling of Neuronal Connections from Simulated Calcium Imaging
    Orlandi, J.G., Stetter, O., Soriano, J., Geisel, T., and Battaglia, D.
    PLoS ONE, vol. 9, iss.6, p. e98842, 2014. [DOI]
  • Noise focusing and the emergence of coherent activity in neuronal cultures
    Orlandi, J.G., Soriano, J., Alvarez-Lacalle, E., Teller, S., and Casademunt, J.
    Nature Physics, vol. 9, iss.9, pp. 582-590, 2013. [DOI]

Peer-reviewed articles

  • Stochastic quorum percolation and noise focusing in neuronal networks
    Orlandi, J.G. and Casademunt, J.
    arXiv (accepted Europhys. Lett.), 2021. [URL]
  • Human Pluripotent Stem Cell-Derived Neurons Are Functionally Mature In Vitro and Integrate into the Mouse Striatum Following Transplantation
    Comella-Bolla, A., Orlandi, J.G., Miguez, A., Straccia, M., García-Bravo, M., Bombau, G., Galofré, M., Sanders, P., Carrere, J., Segovia, J.C., Blasi, J., Allen, N.D., Alberch, J., Soriano, J., and Canals, J.M.
    Mol. Neurobiol., vol. 57, iss.6, pp. 2766-2798, 2020. [DOI]
  • Deficits in coordinated neuronal activity and network topology are striatal hallmarks in Huntington’s disease
    Fernández-García, S., Orlandi, J.G., {García-Díaz Barriga}, G.A., Rodríguez, M.J., Masana, M., Soriano, J., and Alberch, J.
    BMC Biol., vol. 18, iss.1, p. 58, 2020. [DOI]
  • Unraveling the hidden complexity of quasideterministic ratchets: Random walks, graphs, and circle maps
    Blanch-Mercader, C., Orlandi, J.G., and Casademunt, J.
    Phys. Rev. E, vol. 101, iss.1, p. 12203, 2020. [DOI]
  • Neuronal avalanche dynamics indicates different universality classes in neuronal cultures
    Yaghoubi, M., de Graaf, T., Orlandi, J.G., Girotto, F., Colicos, M.A., and Davidsen, J.
    Scientific Reports, vol. 8, iss.1, p. 3417, 2018. [DOI]
  • Neuronal spatial arrangement shapes effective connectivity traits of in vitro cortical networks
    {Tibau Martorell}, E., Ludl, A.A., Rudiger, S., Orlandi, J.G., and Soriano, J.
    IEEE Transactions on Network Science and Engineering, vol. early acc, pp. 1-1, 2018. [DOI]
  • Dominance of Metric Correlations in Two-Dimensional Neuronal Cultures Described through a Random Field Ising Model
    Hernández-Navarro, L., Orlandi, J.G., Cerruti, B., Vives, E., and Soriano, J.
    Physical Review Letters, vol. 118, iss.20, p. 208101, 2017. [DOI]
  • Noise focusing in neuronal tissues: Symmetry breaking and localization in excitable networks with quenched disorder
    Orlandi, J.G. and Casademunt, J.
    Physical Review E, vol. 95, iss.5, p. 52304, 2017. [DOI]
  • 7,8-dihydroxyflavone ameliorates cognitive and motor deficits in a Huntington’s disease mouse model through specific activation of the PLC$\gamma$1 pathway
    {García-Díaz Barriga}, G., Giralt, A., Anglada-Huguet, M., Gaja-Capdevila, N., Orlandi, J.G., Soriano, J., Canals, J., and Alberch, J.
    Human Molecular Genetics, vol. 26, iss.16, pp. 3144-3160, 2017. [DOI]
  • First connectomics challenge: from imaging to connectivity
    Orlandi, J.G., Ray, B., Battaglia, D., Guyon, I., Lemaire, V., Saeed, M., Soriano, J., Statnikov, A., and Stetter, O.
    Journal of Machine Learning: WCP, vol. 46, pp. 1-22, 2015. [URL]
  • Activity and High-Order Effective Connectivity Alterations in Sanfilippo C Patient-Specific Neuronal Networks
    Canals, I., Soriano, J., Orlandi, J.G., Torrent, R., Richaud-Patin, Y., Jiménez-Delgado, S., Merlin, S., Follenzi, A., Consiglio, A., Vilageliu, L., Grinberg, D., and Raya, A.
    Stem Cell Reports, vol. 5, iss.4, pp. 546-557, 2015. [DOI]
  • Transfer Entropy Reconstruction and Labeling of Neuronal Connections from Simulated Calcium Imaging
    Orlandi, J.G., Stetter, O., Soriano, J., Geisel, T., and Battaglia, D.
    PLoS ONE, vol. 9, iss.6, p. e98842, 2014. [DOI]
  • Noise focusing and the emergence of coherent activity in neuronal cultures
    Orlandi, J.G., Soriano, J., Alvarez-Lacalle, E., Teller, S., and Casademunt, J.
    Nature Physics, vol. 9, iss.9, pp. 582-590, 2013. [DOI]
  • Cooperativity of self-organized Brownian motors pulling on soft cargoes
    Orlandi, J.G., Blanch-Mercader, C., Brugués, J., and Casademunt, J.
    Physical review. E, Statistical, nonlinear, and soft matter physics, vol. 82, iss.6, p. 61903, 2010. [DOI]
  • Theoretical study of a membrane channel gated by ATP
    Orlandi, J.G. and Sancho, J.M.
    The European Physical Journal E, vol. 29, iss.3, pp. 329-336, 2009. [DOI]

Other peer-reviewed publications

  • Experimental approaches to assess connectivity in living neuronal networks
    Hernández-Navarro, L., Orlandi, J.G., Casademunt, J., and Soriano, J., ,” in Artificial Neural Networks and Machine Learning – ICANN 2016, Springer International Publishing, 2016, vol. 9886 LNCS.
  • The emergence of spontaneous activity in neuronal cultures
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Soriano, J., and Casademunt, J.
    American Institute of Physics: Conference Proceedings, vol. 1510, iss.25, pp. 25-27, 2013. [DOI]
  • The role of connectivity and noise in the emergence of spontaneous activity in cultured neuronal networks
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Casademunt, J., Soriano, J., and Casademunt, J.
    NOLTA 2012 International Symposium on Nonlinear Theory and its Applications, vol. 1, pp. 547-550, 2012. [DOI]

Software

  • NETCAL: An interactive platform for large-scale, NETwork and population dynamics analysis of CALcium imaging recordings
    Orlandi, J.G., Fernández-García, S., Comella-Bolla, A., Masana, M., {García-Díaz Barriga}, G., Yaghoubi, M., Kipp, A., Canals, J.M., Colicos, M.A., Davidsen, J., Alberch, J., and Soriano, J., Zenodo research data repository, 2017. [DOI]

Books

  • Neural Connectomics Challenge
    Battaglia, D., Guyon, I., Lemaire, V., Orlandi, J.G., Ray, B., and Soriano, J., , Battaglia, D., Guyon, I., Lemaire, V., Orlandi, J., Ray, B., and Soriano, J., Eds., Cham: Springer International Publishing, 2017. [DOI]

Invited talks

  • Network interactions in the mouse visual cortex are predictive of perceptual decisions
    Orlandi, J.G.
    8th RIEC Int. Symp. Brain Funct. Brain Comput., Sendai, Japan, 2020. [URL]
  • Detecting neuron-glia communication through optic flow and synaptic stabilization in neuronal cultures
    Orlandi, J.G.
    The 7th RIEC International Symposium on Brain Functions and Brain Computer, Sendai, Japan, 2019. [URL]
  • Emergent behaviour in Neuronal Cultures. From activity to connectivity and back
    Orlandi, J.G.
    RIKEN Center for Brain Science, Wakoshi, Japan, 2018.
  • Emergent behaviour in neuronal cultures
    Orlandi, J.G.
    International Symposium on Complexity Science Approaches to Brain Dynamics, Calgary, Canada, 2018. [URL]
  • Inferring structural and functional neuronal networks from calcium imaging recordings
    Orlandi, J.G.
    Instituto de Neurociencias de Alicante, Alicante, Spain, 2017. [URL]
  • Noise focusing and the emergence of coherent activity in neuronal cultures
    Orlandi, J.G.
    Complexity Science Seminar, University of Calgary, Calgary, Canada, 2016. [URL]
  • First connectomics challenge in neuronal cultures. Crowdsourcing network reconstruction
    Orlandi, J.G.
    Connectome Workbench, University of Cambridge, Cambridge, United Kingdom, 2015. [URL]

Contributed talks

  • Network inference in neuroscience with Causal Deep Learning
    Orlandi, J.G.
    ICCS 2018 – 9th International Conference on Complex Systems, Boston, MA, 2018. [URL]
  • Neuronal avalanche dynamics leading to diverse universality classes in neuronal cultures
    Orlandi, J.G.
    ICCS 2018 – 9th International Conference on Complex Systems, Boston, MA, 2018. [URL]
  • Transfer entropy reconstruction of neuronal networks from calcium imaging data
    Orlandi, J.G.
    Causality, Information Transfer and Dynamical Networks, Dresden, Germany, 2014. [URL]
  • Noise focusing: unfolding coherent activity in neuronal cultures
    Orlandi, J.G.
    Anacapri Workshop – The Brain: Criticality, Dynamics, Networks and Function, Anacapri, Italy, 2013. [URL]
  • The emergence of spontaneous activity in neuronal cultures, coherence from noise
    Orlandi, J.G., Soriano, J., Alvarez-Lacalle, E., Teller, S., Casademunt, J., Soriano, J., and Casademunt, J.
    CNS 2013, 22nd Anual Computational Neuroscience Meeting, Barcelona, Spain, 2013, pp. 25-27. [DOI]
  • The role of connectivity and noise in the emergence of spontaneous activity in cultured neuronal networks
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Casademunt, J., Soriano, J., and Casademunt, J.
    NOLTA 2012 International Symposium on Nonlinear Theory and its Applications, vol. 1, pp. 547-550, 2012. [DOI]
  • The emergence of coherent activity in living neuronal networks
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Soriano, J., and Casademunt, J.
    FisEs ’12 XVIII Congreso de Física Estadística, Palma de Mallorca, Spain, 2012. [URL]
  • The emergence of spontaneous activity in neuronal cultures
    Orlandi, J.G.
    Physics, Computation, and the Mind – Advances and Challenges at Interfaces, La Herradura, Spain, 2012. [URL]
  • Neuronal Cultures: Synchronization, Forcing, and the Mechanisms behind Spontaneous Activity
    Orlandi, J.G.
    IBERSINC: Red sobre Dinámica y Sincronización en Redes, Barcelona, Spain, 2011.
  • Unraveling Spontaneous Activity in Neuronal Cultures
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Soriano, J., and Casademunt, J.
    BARCSYN: 2011 Barcelona Computational and Systems Neuroscience Meeting, Barcelona, Spain, 2011. [URL]

Posters and other conference contributions

  • Low-dimensional representations of perceptual decision making across the mouse dorso-parietal cortex
    Javier G. Orlandi, Abdolrahmani, M., Aoki, R., Lyamzin, D.R., and Benucci, A.
    Int. Symp. Artif. Intell. Brain Sci., 2020.
  • Network interactions in the mouse visual cortex are predictive of perceptual decisions
    Orlandi, J.G., Grzelkowski, S., Abdolrahmani, M., Aoki, R., Lyamzin, D.R., and Benucci, A.
    Soc. Neurosci. SFN 2019, Chicago, USA, 2019.
  • Functional connectivity and dynamics in Huntington’s disease striatal cultures revealed through large-scale calcium imaging
    Fernández-García, S., Masana, M., Orlandi, J.G., {García-Díaz Barriga}, G., Soriano, J., and Alberch, J.
    Neuroscience 2017, Washington DC, USA, 2017. [URL]
  • NETCAL: An interactive platform for large-scale, NETwork and population dynamics analysis of CALcium imaging recordings
    Orlandi, J.G., Fernández-García, S., Comella-Bolla, A., Masana, M., {García-Díaz Barriga}, G., Yaghoobi, M., Canals, J., Colicos, M.A., Davidsen, J., Alberch, J., and Soriano, J.
    Neuroscience 2017, Washington DC, USA, 2017. [URL]
  • Deciphering Huntington’s disease striatal network dynamics using high-speed high-resolution calcium imaging
    Fernández-García, S., Masana, M., Orlandi, J.G., {García-Díaz Barriga}, G., Soriano, J., and Alberch, J.
    10th FENS Forum of Neuroscience, Copenhagen, Denmark, 2016. [URL]
  • First connectomics challenge: fostering research in network inference and its applications
    Orlandi, J.G., Battaglia, D., Stetter, O., Canals, I., Guyon, I., Ray, B., Saeed, M., and Soriano, J.
    10th FENS Forum of Neuroscience, Copenhagen, Denmark, 2016. [URL]
  • Spontaneous activity in cultures with dictated connectivity
    Hernández-Navarro, L., Orlandi, J.G., and Soriano, J.
    10th FENS Forum of Neuroscience, Copenhagen, Denmark, 2016. [URL]
  • Differentiation of human iPSC toward postmitotic forebrain neurons achieved a mature phenotype with spontaneous network activity
    Comella-Bolla, A., Straccia, M., Miguez, A., Sanders, P., Orlandi, J.G., Bombau, G., Carrere, J., Kemp, P.J., Alberch, J., Soriano, J., Allen, N.D., and Canals, J.M.
    10th FENS Forum of Neuroscience, Copenhagen, Denmark, 2016. [URL]
  • Characterization of neuronal network structure and dynamics in striatal cultures
    Masana, M., Orlandi, J.G., Fernández-García, S., {García-Díaz Barriga}, G., Alberch, J., and Soriano, J.
    10th FENS Forum of Neuroscience, Copenhagen, Denmark, 2016. [URL]
  • Altered functional activity in vmDA neurons derived from Parkinson’s disease-induced pluripotent stem cells (iPSC)
    Carola, G., Puxan, B.N., Orlandi, J.G., Faella, A., Soriano, J., Raya, A., and Consiglio, A.
    Human Gene Therapy 2016, 2016.
  • First connectomics challenge: fostering research in network inference and its applications
    Orlandi, J.G., Battaglia, D., Stetter, O., Canals, I., Guyon, I., Saeed, M., and Soriano, J.
    Brain Dynamics and Statistics: Simulation versus Data, Banff, Canada, 2016. [URL]
  • First neuronal connectomics challenge: From imaging to connectivity: From design to result harvesting and crowdpublishing
    Orlandi, J.G., Ray, B., Saeed, M., Soriano, J., Statnikov, A., Stetter, O., Guyon, I., and Battaglia, D.
    Society for Neuroscience SFN 2014, Washington DC, USA, 2014. [URL]
  • Design of the first neuronal connectomics challenge: From imaging to connectivity
    Guyon, I., Battaglia, D., Guyon, A., Lemaire, V., Orlandi, J.G., Ray, B., Saeed, M., Soriano, J., Statnikov, A., and Stetter, O.
    IEEE WCCI 2014, Beijing, China, 2014, pp. 2600-2607. [DOI]
  • Network reconstruction from calcium imaging data of spontaneously bursting neuronal activity
    Stetter, O., Orlandi, J.G., Soriano, J., Battaglia, D., and Geisel, T.
    CNS 2013, 22nd Anual Computational Neuroscience Meeting, vol. 14, iss.Suppl 1, p. 139, 2013. [DOI]
  • The emergence of spontaneous activity in neuronal cultures, coherence from noise
    Orlandi, J.G., Soriano, J., Alvarez-Lacalle, E., Teller, S., Casademunt, J., Soriano, J., and Casademunt, J.
    CNS 2013, 22nd Anual Computational Neuroscience Meeting, Barcelona, Spain, 2013, pp. 25-27. [DOI]
  • The emergence of coherent activity in neuronal cultures
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Soriano, J., and Casademunt, J.
    8th FENS forum of European Neuroscience Societies, Barcelona, Spain, 2012. [URL]
  • Experiments on clustered neuronal cultures
    Teller, S., Orlandi, J.G., Alvarez-Lacalle, E., Casademunt, J., and Soriano, J.
    8th FENS forum of European Neuroscience Societies, Barcelona, Spain, 2012. [URL]
  • Self-similarity and chaos in coupled ratchets. Unfolding the complexity of cooperative Brownian motors
    Blanch-Mercader, C., Orlandi, J.G., and Casademunt, J.
    FisEs’11 XVII Congreso de Física Estadística, Barcelona, Spain, 2011. [URL]
  • Experiments on Patterned Neuronal Cultures
    Teller, S., Orlandi, J.G., Alvarez-Lacalle, E., Casademunt, J., Moses, E., and Soriano, J.
    FisEs’11 XVII Congreso de Física Estadística, Barcelona, Spain, 2011. [URL]
  • Spontaneous Activity in Neuronal Cultures: Experiments and Model
    Soriano, J., Teller, S., Orlandi, J.G., Álvarez, E., Casademunt, J., and Moses, E.
    XI Congreso de la Sociedad de Biofísica de España, Murcia, Spain, 2011. [URL]
  • Local noise amplification and synaptic depression control the spontaneous activity in neuronal cultures
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Soriano, J., and Casademunt, J.
    Ninth Göttingen Meeting of the German Neuroscience Society, Göttingen, Germany. March 23-27, 2011, G{\{}ö{\}}ttingen, Germany, 2011. [URL]
  • Unraveling Spontaneous Activity in Neuronal Cultures
    Orlandi, J.G., Alvarez-Lacalle, E., Teller, S., Soriano, J., and Casademunt, J.
    BARCSYN: 2011 Barcelona Computational and Systems Neuroscience Meeting, Barcelona, Spain, 2011. [URL]
  • Monitoring Dynamics in Living Neuronal Networks
    Teller, S., Orlandi, J.G., Alvarez-Lacalle, E., Casademunt, J., and Soriano, J.
    BARCSYN: 2011 Barcelona Computational and Systems Neuroscience Meeting, 2011. [URL]
  • Nucleation and front propagation in patterned neuronal networks.
    Orlandi, J.G., Alvarez-Lacalle, E., Amigó, N., Soriano, J., and Casademunt, J.
    7th FENS forum of European Neuroscience, Amsterdam, The Netherlands, 2010. [URL]
  • Modelling Spontaneous Activity in Neuronal Cultures
    Orlandi, J.G., Alvarez-Lacalle, E., Amigó, N., Soriano, J., and Casademunt, J.
    IV Spanish Portuguese Biophysical Congress, Zaragoza, Spain, 2010. [URL]
  • Cooperativity of single-headed kinesin motors in axonal transport
    Orlandi, J.G. and Casademunt, J.
    IV Spanish Portuguese Biophysical Congress, London, UK, 2010. [URL]
  • Quasi-deterministic collective ratchets. Some exact results.
    Blanch-Mercader, C., Orlandi, J.G., and Casademunt, J.
    FiSeS ’09 XVI Congreso de Física Estadística, Huelva, Spain, 2009.
  • Collective dynamics of interacting Brownian motors under unequal loading
    Orlandi, J.G., Blanch-Mercader, C., Brugués, J., and Casademunt, J.
    FiSeS ’09 XVI Congreso de Física Estadística, Huelva, Spain, 2009.
  • Cooperativity of single-headed kinesin motors
    Orlandi, J.G., Blanch-Mercader, C., and Casademunt, J.
    FiSeS ’09 XVI Congreso de Física Estadística, Huelva, Spain, 2009.

Popular science

  • Dinámica colectiva de las redes neuronales
    Casademunt, J., Orlandi, J.G., and Soriano, J.
    Mente y Cerebro – Investigación y Ciencia (Spanish Scientific American), vol. 67, pp. 49-50, 2014. [URL]
  • Avalanchas mentales
    Orlandi, J.G.
    Revista Española de Física (Journal of the Spanish Royal Society of Physics), vol. 28, iss.1, pp. 43-44, 2014. [URL]

Research coverage (editorals, news and views)

  • Focus amidst the noise
    Beggs, J.M.
    Nature Physics, vol. 9, iss.9, pp. 533-534, 2013. [DOI]

PhD thesis