Research
Topics
Graph algorithms applied to protein sequence annotation
Integration of bioinformatics tools
Multi-agent systems
Expert systems using fuzzy logic
Papers - Journals
2019
Zhou et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol 20, 244, 2019. https://doi.org/10.1186/s13059-019-1835-8 [Q1, IF 10.806]
E. Capriotti, L. Montanucci, G. Profiti, I. Rossi, D. Giannuzzi, L. Aresu, P. Fariselli, Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome, Nucleic Acids Res. 2019. DOI: 10.1093/nar/gkz420 [Q1, IF 11.501]
2018
C. Savojardo, P.L. Martelli, P. Fariselli, G. Profiti, Rita Casadio. BUSCA: an integrative web server to predict subcellular localization of proteins. Nucleic Acids Res. 2018. DOI: 0.1093/nar/gky320 [Q1, IF 11.147]
2017
G. Babbi, P. L. Martelli, G. Profiti, S. Bovo, C. Savojardo, and R. Casadio, eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes, BMC Genomics 18(Suppl 5):554, 2017. DOI: 10.1186/s12864-017-3911-3 [Q1, IF 3.730]
G. Profiti, P. L. Martelli, and R. Casadio, The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation, Nucleic Acids Res. 45 (W1): W285-W290, 2017 DOI: 10.1093/nar/gkx330 [Q1, IF 11.561]
2016
Jiang et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, 17:184, 2016. DOI: 10.1186/s13059-016-1037-6 [Q1, IF 11.908]
Sazzini et al. Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations. Genes & Nutrition, 11:15, 2016. DOI: 10.1186/s12263-016-0532-4 [Q2, IF 2.797]
Ison, et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res, 44 (D1): D38-D47, 2016. doi: 10.1093/nar/gkv1116 PubMed PMID: 26538599. [Q1, IF 10.162]
2015
G. Profiti, P. Fariselli, and R. Casadio. "AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints". Bioinformatics, 31 (23): 3841-3843, 2015. doi: 10.1093/bioinformatics/btv451 [Q1, IF 5.766]
G. Profiti, D. Piovesan, P.L. Martelli, P. Fariselli, and R. Casadio. "Protein sequence annotation by means of community detection". Current Bioinformatics, 10(2):139-143, 2015 [Q4, IF 0.77]
2013
D. Piovesan, G. Profiti, P. L. Martelli, P. Fariselli, and R. Casadio, "Extended and robust protein sequence annotation over conservative non hierarchical clusters: the case study of the ABC transporters.," Emerging Technologies in Computing Systems, ACM Journal on, vol. 9, no. 4, Nov. 2013. [Q3=2/3, Q4=1/3, IF 0.833]
D. Piovesan , G. Profiti, P.L. Martelli, et al. " SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation". Database, Vol. 2013, doi:10.1093/database/bat065 [Q1, IF 4.457]
D. Piovesan, P. L. Martelli, P. Fariselli, G. Profiti, A. Zauli, I. Rossi and R. Casadio. "How to inherit statistically validated annotation within BAR+ protein clusters," BMC Bioinformatics, vol. 14, no. Suppl 3, p. S4, 2013. [Q1=1/3, Q2=2/3, IF 2.672]
2012
D. Piovesan, G. Profiti, P. L. Martelli, and R. Casadio, "The human ‘magnesome’: detecting magnesium binding sites on human proteins," BMC Bioinformatics, vol. 13, no. Suppl 14, p. S10, 2012. doi:10.1186/1471-2105-13-S14-S10 [Q1=1/3, Q2=2/3, IF 3.024]
Papers and posters - Conferences
2018
Martelli PL, Profiti G, Casadio R and Savojardo C. Integrating ELIXIR Italy with ELIXIR Interoperability platform activities [version 1; not peer reviewed]. F1000Research 2018, 7(ELIXIR):763 (poster) (doi: 10.7490/f1000research.1115554.1)
2017
G. Babbi, P. L. Martelli, G. Profiti, S. Bovo, C. Savojardo, R. Casadio (2017)." Analysing the relations among genes and polygenic diseases with eDGAR". In: F1000Research. (poster) doi: 10.7490/f1000research.1114767.1
Goble C, Jimenez R, Gray A et al. Bioschemas.org [version 1; not peer reviewed]. F1000Research 2017, 6:1226 (poster) (doi: 10.7490/f1000research.1114493.1)
2016
A. Via, F. Zambelli, D. Carnevali, T. Castrignanò, A. Cattani, G. Chillemi, G. Cuccuru, G. Della Vedova, G. Donvito, A. Facchiano, M. Fondi, F. Galeazzi, L. Licata, A. Marabotti, L. Milanesi, E. Picardi, G. Profiti, S. Tomassini, S. Tosatto and G. Pesole. "ELIXIR-IIB: a growing support to national and international research in life sciences", NETTAB 2016 (doi: 10.7490/f1000research.1111432.1)
G. Profiti, P. L. Martelli, R. Casadio. "The Bologna Annotation Resource (BAR 3.0): improving the functional annotation of protein sequences", Function-SIG at ISMB 2016
2015
G. Profiti, P. Fariselli, P.L. Martelli, F. Aggazio, R. Casadio. "A graph-based approach for predicting protein function: challenges in interconnected data". BITS 2015
2014
G. Profiti, P.L. Martelli, and R. Casadio. "A pipeline for predicting the function of the AFP/CAFA 2014 targets at the Bologna Biocomputing Group". In 22nd Annual Conference on Intelligent Systems for Molecular Biology Automated Function Prediction Special Interest Group, 2014
2013
G. Profiti, D. Piovesan, P.L. Martelli, P. Fariselli and R. Casadio. "Protein Sequence Annotation by means of Community Detection". In Proceedings IWBBIO 2013 International Work-Conference on Bioinformatics and Biomedical Engineering. p. 753-755, 2013.
G. Profiti, D. Piovesan, P.L. Martelli, P. Fariselli, R. Casadio. "Community Detection within clusters helps large scale protein annotation - Preliminary Results of Modularity Maximization for the BAR+ Database". In Proceedings of the 4th International Conference on Bioinformatics Models, Methods and Algorithms. p. 328-332, 2013
Papers - Others
2017
P. L. Martelli, G. Profiti and R. Casadio, "Protein Functional Annotation", In Reference Module in Life Sciences, Elsevier, 2017, ISBN: 978-0-12-809633-8, DOI: 10.1016/B978-0-12-809633-8.12364-7
2010
D. Guidi, M. Gaspari, G. Profiti, "Web Services integration in Multi-Agent Systems" in Developing Advanced Web Services through P2P Computing and Autonomous Agents: Trends and Innovation, K. Ragab, A.-E. Hassanien, T. Helmy, Eds. Hershey, PA: IGI Global, 2010
Conferences
2017
ISMB 2017, Prague (Czech Republic), July 21-25 (oral presentation & poster)
BITS Bioinformatics Italian Society Annual Meeting, Cagliari (Italy), July 5-7 (oral presentation & poster)
ELIXIR all-hands meeting, Rome (Italy), March 21-23
2016
ELIXIR Hackaton at NETTAB 2016, Rome (Italy), October 24
Function-SIG at ISMB 2016, Orlando (Florida), July 9 (oral presentation & poster)
Elixir all-hands meeting, Barcelona (Spain), March 8-9
2015
ECM29, Rovinj (Croatia), August 23-25 (oral presentation)
BITS 2015, Milan (Italy), June 3-5 (poster)
2014
Automated Function Prediction SIG at the 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston (USA), July 11-12 (poster, hon. mention)
5th International Conference on Bioinformatics Models, Methods and Algorithms, Eseo (France), March 3-6 (program committee)
2013
Variathon Workshop 2013. Udine, May 21. (slideshow draft)
International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2013). Granada (Spain), March 18-20. (slideshow draft)
4th International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona (Spain), February 11-14. (poster)
PhD dissertation
Graph algorithms for bioinformatics DOI 10.6092/unibo/amsdottorato/6914