About Myself

Michele Allegra

Me

I am a physicist with a broad interest for neuroscience. My main research topic is the analysis and modeling of functional networks in the brain.

Upon completing a Ph.D in quantum physics at the University of Turin and the ISI Foundation in Turin, I changed research field, moving into to data analysis for neuroscience. I joined the Statistical Biophysics sector of the International School for Advanced Studies (SISSA), Trieste, where I worked in Prof.~Alessandro Laio's group from 2015 to 2018. My research activity within Laio's group focused on advanced clustering techniques and their application to the study of dynamically changing brain networks.

I deepened my focus on neuroscience during my stay at the Timone Institute for Neuroscience in Marseilles (2018-2021), where I joined the BraiNets group led by Andrea Brovelli. In Marseilles I focused on the analysis of brain imaging data, with the goal of characterizing functional networks in the brain and their disruption in major diseases such as stroke.

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My current research at the Laboratory of Interdisciplinary Physics and the Padua Neuroscience Center , University of Padua, focuses on applying statistics, information theory, and complex system modeling to obtain new insights in neuroscience research.

Curriculum

CV.pdf

Publications

  • A. Nazzi, C. Favaretto, A. Vallesi, M. Corbetta, M. Allegra, Switching patterns of cortical-subcortical interaction in the human brain , bioRxiv, 2024.05. 10.593351 (2024) PDF
  • M. Allegra, M. Gilson, A. Brovelli Directed neural interactions in fMRI: a comparison between Granger Causality and Effective Connectivity , bioRxiv, 2024.02. 22.581068 (2024) PDF
  • S. Idesis, G.Patow, M. Allegra, J. Vohryzek, Y. Sanz Perl, M.V. Sanchez-Vives, M. Massimini, M. Corbetta & G. Deco Whole-brain model replicates sleep-like slow-wave dynamics generated by stroke lesions , Neurobiology of Disease, 200, 106613 (2024) PDF
  • V. Rotondi, M. Allegra, R. Kashyap, N. Barban, M. Sironi, C. Reverberi, Enduring maternal brain changes and their role in mediating motherhood’s impact on well-being, Scientific Reports 14, 1 (2024) PDF
  • S. Idesis, M. Allegra, J. Vohryzek, Y. Sanz Perl, N.V. Metcalf, J.C. Griffis, M. Corbetta, G.L. Shulman, G. Deco Generative whole-brain dynamics models from healthy subjects predict functional alterations in stroke at the level of individual patients, Brain Communications 6, 1 (2024) PDF
  • K. K. H. Manjunatha, G. Baron, D. Benozzo, E. Silvestri, M. Corbetta, A. Chiuso, A. Bertoldo, S. Suweis, M. Allegra, Controlling target brain regions by optimal selection of input nodes, PLOS Computational Biology 20 (1), e1011274 (2024) PDF
  • C. Favaretto, M. Allegra, G. Deco, N.V. Metcalf, J.C. Griffis, G. L. Shulman, A. Brovelli, M. Corbetta, Subcortical-cortical dynamical states of the human brain and their breakdown in stroke, Nature Communications, 13(1), 1-17 (2022) PDF
  • S. Idesis, M. Allegra, J. Vohryzek, Y. Sanz Perl, J. Faskowitz, O. Sporns, M. Corbetta, G. Deco A low dimensional embedding of brain dynamics enhances diagnostic accuracy and behavioral prediction in stroke , Scientific Reports 13, 1 (2023) PDF
  • E. Combrisson, M. Allegra, R. Basanisi, R. A. Ince, B. Giordano, J. Bastin, A. Brovelli, Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data. NeuroImage 258 119347 (2022) PDF
  • M. Allegra, C. Favaretto, N. Metcalf, M. Corbetta, A. Brovelli, Stroke-related alterations in inter-areal communication revealed via Granger causality analysis, NeuroImage: Clinical 32, 102812 (2021) PDF
  • D. Mouillot, N. Loiseau, M. Grenié, A. C. Algar, M. Allegra, M. W. Cadotte, N. Casajus, P. Denelle, M. Guéguen, A. Maire, B. Maitner, B. McGill, M. McLean, N. Mouquet, F. Munoz, W. Thuiller, S. Villéger, C. Violle, Arnaud Auber, The dimensionality and structure of species trait spaces, Ecology Letters, accepted, in press (2021) PDF
  • M. Allegra, E. Facco, F. Denti, A. Laio, A. Mira, Data segmentation based on the local intrinsic dimension, Scientific Reports 10,16449 (2020) PDF
  • M. Allegra, S. Seyed-Allaei, N.W. Schuck, D. Amati, A. Laio, C. Reverberi, Brain network dynamics during spontaneous strategy shifts and incremental task optimization, NeuroImage, 116854 (2020) PDF
  • N. I. Ilieva, N. Galvanetto, M. Allegra, M. Brucale, and A. Laio, Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples, Bioinformatics, btaa626 (2020) PDF
  • M. Allegra, S. Seyed‐Allaei, F. Pizzagalli, F. Baftizadeh, M. Maieron, Carlo Reverberi, Alessandro Laio, Daniele Amati, fMRI single trial discovery of spatio‐temporal brain activity patterns, Human brain mapping 38 (3), 1421-1437 (2017) PDF
  • P. Giorda, M. Allegra, Coherence in quantum estimation, Journal of Physics A: Mathematical and Theoretical 51 (2), 025302 (2017) PDF
  • P. Giorda, M. Allegra, Two-qubit correlations revisited: average mutual information, relevant (and useful) observables and an application to remote state preparation, Journal of Physics A: Mathematical and Theoretical 50 (29), 295302 (2017) PDF
  • M. Allegra, P. Giorda, S. Lloyd, Global coherence of quantum evolutions based on decoherent histories: theory and application to photosynthetic quantum energy transport, Physical Review A 93 (4), 042312 (2016) PDF
  • X. Wang, M. Allegra, K. Jacobs, S. Lloyd, C. Lupo, M. Mohseni, Quantum brachistochrone curves as geodesics: Obtaining accurate minimum-time protocols for the control of quantum systems, Physical Review Letters 114 (17), 170501(2015) PDF
  • C.D. Aiello, M. Allegra, B. Hemmerling, X. Wan, P. Cappellaro, Algebraic synthesis of time-optimal unitaries in SU (2) with alternating controls, Quantum Information Processing 14 (9), 3233-3256 (2015) PDF
  • M. Allegra, Gain and loss of information by decoherence, PhD thesis, University of Turin (2014) PDF
  • M. Allegra, P. Giorda, M.G.A. Paris, Quantum discord for Gaussian states with non-Gaussian measurements, Physical Review A 86 (5), 052328 (2012) PDF
  • M. Allegra, P. Giorda, Topology and energy transport in networks of interacting photosynthetic complexes, Physical Review E 85 (5), 051917 (2012) PDF
  • M. Allegra, P. Giorda, A. Montorsi, Quantum discord and classical correlations in the bond-charge Hubbard model: Quantum phase transitions, off-diagonal long-range order, and violation of the monogamy property, Physical Review B 84 (24), 245133 (2011) PDF
  • M. Allegra, P. Giorda, M.G.A. Paris, Role of initial entanglement and non-Gaussianity in the decoherence of photon-number entangled states evolving in a noisy channel, Physical Review Letters 105 (10), 100503 (2010) PDF

Code

Coherence Density Peak Clustering

code

Heterogeneous Intrinsic Dimension Estimation

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Single Molecule Force Spectroscopy Clustering

code

covariance-based Granger causality fMRi for

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Talks

  • 25/01/2018: invited talk at the Monthly Neuroimaging Meeting, Aix-Marseille Université, Marseilles (France) PDF ODP
  • 04/17/2018: invited talk at the Institute for Computational Science, Università della Svizzera Italiana, Lugano (Switzerland) PDF ODP
  • 06/08/2018 invited talk at the CECAM Workshop on Machine Learning at Interfaces, CECAM-HQ-EPFL, Lausanne (Switzerland) PDF ODP
  • 06/22/2018: invited talk at the 49. Meeting of the Italian Statistical Society, Palermo (Italy) PDF ODP
  • 09/04/2019: invited talk at the Theoretical Neuroscience group meeting, Institut de Neurosciences de Systèmes, Marseilles (France) PDF
  • 05/09/2019: invited talk at the Young Researcher’s Workshop on Machine Learning for Materials Science 2019, Helsinki (Finland) PDF ODP Video
  • 06/11/2019: invited talk at the CINaM, Aix-Marseille Université, Marseilles (France) ODP
  • 16/05/2020: invited talk at Department of Physics, Università di Padova (Italy) PDF ODP
  • 16/05/2020: invited talk at Department of Physics, Università di Padova (Italy) PDF ODP
  • 02/02/2022: invited virtual talk at the Institute for Research in Fundamental Sciences (IPM), Tehran (Iran) PDF ODP
  • 09/05/2022: invited talk at the Data Science Sector, SISSA, Trieste (Italy) PDF ODP
  • 06/06/2022: invited talk at the Neuroscience and Statistical Physics Workshop, SISSA, Trieste (Italy) PDF ODP

Contact

Info

Email: micheleallegra85@gmail.com, michele.allegra@unipd.it
Phone: +39 3516258520, +33 767423968
Skype: michele.allegra
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