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).
- 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.
- 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/
- A Computing System for Discovering Causal Relationships among Human Genes to Improve Drug Repositioning.
Blanzieri, E.; Tebaldi, T.; Cavecchia, V.; Asnicar, F.; Masera, L.; Tomè, G.; Nigro, E.; Colasurdo, E.; Ciciani, M.; Mazzoni, C.; Pilati, S.
IEEE Transactions on Emerging Topics in Computing. 2020. doi: 10.1109/TETC.2020.3031024 https://ieeexplore.ieee.org/document/9224179
If you don't have access to any of the above papers, please send a message to me and I will send it to you by e-mail.
For comments please use this thread: https://gene.disi.unitn.it/test//forum_thread.php?id=112