Publication list

Selected publications

  • 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: Workshop and Conference Proceedings, 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

  • 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]
  • 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: Workshop and Conference Proceedings, 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]

Articles under review

  • Stochastic quorum percolation and noise focusing in neuronal networks
    Orlandi, J.G. and Casademunt, J.
    Physical Review Letters, 2018.
  • Neuronal spatial arrangement shapes effective connectivity traits in in vitro cortical networks
    Tibau, E., Ludl, A., Rüdiger, S., Orlandi, J.G., and Soriano, J.
    IEEE Transactions on Network Science and Engineering, 2018.

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

  • 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

  • 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

  • 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]
  • 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]
  • 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]
  • 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, vol. 27, 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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