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Message 1559 - Posted: 22 May 2019, 12:35:43 UTC
Last modified: 22 May 2019, 12:37:43 UTC

Thanks to the invaluable contribution of the gene@home volunteers, we were able to perform a wide number of 'virtual experiments' using two different algorithms: PC-IM (PC Iterative Method) which is done with BOINC and NESRA (Network Expansion by Subsetting and Ranking Aggregation) which further analyzes BOINC results. The experiments were made on various organisms (among them Escherichia coli, Arabidopsis thaliana and Vitis vinifera), expanding different Local Gene Networks. We also did analysis for optimizing the whole computing system and the algorithms' parameters.

After having organized and analyzed the results we started to present some of them to the international scientific community. Here follows the current list of our contributions, links to papers will be provided when published.


  • Discovering Candidates for Gene Network Expansion by Variable Subsetting and Ranking Aggregation
    Luca Erculiani, Francesca Galante, Caterina Gallo, Francesco Asnicar, Luca Masera, Paolo Morettin, Nadir Sella, Thomas Tolio, Giulia Malacarne, Kristof Engelen, Andrea Argentini, Valter Cavecchia, Claudio Moser, Enrico Blanzieri

    Poster, Network Biology SIG on July 10, 2015, preceding the main ISMB conference in Dublin (Ireland). http://f1000research.com/posters/4-562

  • Discovering Candidates for Gene Network Expansion by Distributed Volunteer Computing
    Francesco Asnicar, Luca Erculiani, Francesca Galante, Caterina Gallo, Luca Masera, Paolo Morettin, Nadir Sella, Stanislau Semeniuta, Thomas Tolio, Giulia Malacarne, Kristof Engelen, Andrea Argentini, Valter Cavecchia, Claudio Moser, Enrico Blanzieri

    Paper, The 13th IEEE International Symposium on Parallel and Distributed Processing with Applications (IEEE ISPA-15), 20-22 August 2015 in Helsinki, Finland, Published in 2015 IEEE Trustcom/BigDataSE/ISPA, https://ieeexplore.ieee.org/document/7345656/

  • TN-Grid and gene@home project: Volunteer Computing for Bioinformatics
    Francesco Asnicar, Nadir Sella, Luca Masera, Paolo Morettin, Thomas Tolio, Stanislau Semeniuta, Claudio Moser, Enrico Blanzieri and Valter Cavecchia

    Paper, BOINC:FAST 2015 (BOINC: Fundamental & Applied Science & Technology), Second International Conference, 14-18 September, 2015, Petrozavodsk, Republic of Karelia (Russia).

    Presentation: http://gene.disi.unitn.it/test/documents/Gene@Home.@BF15.pdf
    Proceedings: http://ceur-ws.org/Vol-1502/

  • NES2RA: Network expansion by stratified variable subsetting and ranking aggregation
    Francesco Asnicar, Luca Masera, Emanuela Coller, Caterina Gallo, Nadir Sella, Thomas Tolio, Paolo Morettin, Luca Erculiani, Francesca Galante, Stanislau Semeniuta, Giulia Malacarne, Kristof Engelen, Andrea Argentini, Valter Cavecchia, Claudio Moser and Enrico Blanzieri

    Paper, International Journal of High Performance Computing Applications, August 22, 2016 (doi:10.1177/1094342016662508, http://hpc.sagepub.com/content/early/2016/08/17/1094342016662508.full.pdf+html)

  • Discovering causal relationships in grapevine expression data to expand gene networks. a case study: Four networks related to climate change
    Malacarne, G., Pilati, S., Valentini, S., Asnicar, F., Moretto, M., Sonego, P., Masera, L. Cavecchia, V., Blanzieri, E. & Moser, C.

    Frontiers in plant science, 2018, 9.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161569/

  • OneGenE: Regulatory Gene Network Expansion via Distributed Volunteer Computing on BOINC
    Asnicar, F., Masera, L., Pistore, D., Valentini, S., Cavecchia, V., & Blanzieri, E. (2019, February).

    In 2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP) (pp. 315-322). IEEE. https://ieeexplore.ieee.org/abstract/document/8671629/



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