BioComputing UP

Description

We develop both bioinformatics methods and databases, which are then applied to in silico analysis of complex biological systems (e.g. cancer, intrinsically disordered proteins), suggesting possible novel links in the cellular protein interaction network. The laboratory actively participates to international Critical Assessment of techniques for protein Structure Prediction (CASP), Critical Assessment of Genome Interpretation (CAGI) and Critical Assessment of Function Annotation (CAFA) experiments. The group leads and coordinates several international projects on intrinsically disordered proteins and related phenomena: NGP-net, IDPfun, DisProtCentral, Integration and standardization of intrinsically disordered protein data (ELIXIR Implementation Study).

5 recent publications

  • Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, Vranken WF, Tosatto SCE. MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins.
    Nucleic Acids Res. 2018 Jan 4;46(D1):D471-D476. doi: 10.1093/nar/gkx1071.
    PubMed PMID: 29136219; PubMed Central PMCID: PMC5753340.
  • Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids
    Res. 2017 Jan 4;45(D1):D219-D227. doi: 10.1093/nar/gkw1056. Epub 2016 Nov 28.
    Erratum in: Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. PubMed PMID:
    27899601; PubMed Central PMCID: PMC5210544.
  • Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi:10.1093/nar/gkw1107. Epub 2016 Nov 29. PubMed PMID: 27899635; PubMed Central PMCID: PMC5210578.
  • Necci M, Piovesan D, Dosztányi Z, Tompa P, Tosatto SCE. A comprehensive assessment of long intrinsic protein disorder from the DisProt database. Bioinformatics. 2018 Feb 1;34(3):445-452. doi: 10.1093/bioinformatics/btx590. PubMed PMID: 28968848. Minervini G, Lopreiato R, Bortolotto R, Falconieri A, Sartori G, Tosatto SCE. Novel interactions of the von Hippel-Lindau (pVHL) tumor suppressor with the CDKN1 family of cell cycle inhibitors. Sci Rep. 2017 Apr 20;7:46562. doi: 10.1038/srep46562. PubMed PMID: 28425505; PubMed Central PMCID: PMC5397843.

 

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