UCL DEPARTMENT OF COMPUTER SCIENCE
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Papers on peer reviewed journals:

  • Jiang Y., Oron T.R. et al. 2016 An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 17(1):184 PubMed
  • Cozzetto D., Minneci F., Currant H. and Jones, D.T. 2016 FFPred 3: feature-based function prediction for all Gene Ontology domains. Sci Rep. 6:31865 PubMed
  • Jones, D.T. and Cozzetto, D. 2015 DISOPRED3: Precise disordered region predictions with annotated protein binding activity. Bioinformatics 31(6):857-63 PubMed
  • Lewis, T.E., Sillitoe, I. et al. 2015 Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res. 43:D382-6 PubMed
  • Nugent, T., Cozzetto, D. and Jones, D.T. 2014 Evaluation of predictions in the CASP10 model refinement category. Proteins 82(S2):98-111 PubMed
  • Minneci, F., Piovesan, D., Cozzetto, D. and Jones, D.T. 2013 FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences. PloS one 8 (5) PubMed
  • Cozzetto, D. and Jones, D.T. 2013 The contribution of intrinsic disorder prediction to the elucidation of protein function. Curr Opin Struct Biol. 23(3):467-72 PubMed
  • Cozzetto, D., Buchan, D.W.A., Bryson, K. and Jones, D.T. 2013 Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics 14 (Suppl 3): S1 PubMed
  • Radivojac, P., Clark, W.T. et al. 2013 A large-scale evaluation of computational protein function prediction. Nature methods 10(3):221-227 PubMed
  • Jones, D.T., Buchan, D.W.A., Cozzetto, D. and Pontil, M. 2012 PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28(2):184-190 PubMed
  • Cozzetto, D., Kryshtafovych, A. and Tramontano, A. 2009 Evaluation of CASP8 Model Quality Predictions. Proteins 77(S9):157-166 PubMed
  • Cozzetto, D., Kryshtafovych, A., Fidelis, K., Moult, J., Rost, B. and Tramontano, A. 2009 Evaluation of Template-Based Models in CASP8 with Standard Measures. Proteins 77(S9): 18-28 PubMed
  • Cozzetto, D. and Tramontano, A. 2008 Advances and pitfalls in potein structure prediction Curr Protein Pept Sci. 9: 567-577 PubMed
  • Cozzetto, D., Giorgetti, A., Raimondo, D. and Tramontano A. 2007 The Evaluation of Protein Structure Prediction Results. Mol Biotechnol. 413:43-57, PubMed
  • Cozzetto, D., Kryshtafovych, A., Ceriani, M. and Tramontano A. 2007 Assessment of predictions in the Model Quality Assessment category. Proteins 69(S8): 175-183 PubMed
  • Bryson, K., Cozzetto, D. and Jones D.T. 2007 Computer-assisted Protein Domain Boundary Prediction using the DomPred Server Curr Protein Pept Sci.8: 181-188 PubMed
  • Tress, M.L., Cozzetto, D., Tramontano, A. and Valencia, A. 2006 An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinformatics 7: 213 PubMed
  • Castrignano, T., De Meo, P.D., Cozzetto, D., Talamo, I.G. and Tramontano, A. 2006 The PMDB Protein Model Database. Nucleic Acids Res. 34: D306-D309 PubMed
  • Cozzetto, D., Di Matteo, A. and Tramontano, A. 2005 Ten years of predictions... and counting. FEBS J. 272: 861-862 PubMed
  • Cozzetto, D. and Tramontano, A. 2005 Relationship between multiple sequence alignments and quality of protein comparative models. Proteins 58: 151-157 PubMed

Proceedings:

  • Raimondo, D., Giorgetti, A., Cozzetto, D. and Tramontano, A. Quality and effectiveness of protein structure comparative models. Proceedings of the Second International Symposium on Mathematical and Computational Biology / Fifth Brazilian Symposium on Mathematical and Computational Biology.
  • Tramontano, A. and Cozzetto, D. 2004. The relationship between protein sequence, structure and function. Supramolecular Structure and Function, 8: Proceedings Of The 18th International Summer School Of Biophysics, Kluwer Plenum, New York.

Book chapters:

  • Tramontano, A. and Cozzetto, D. Evaluation of Protein Structure Prediction Methods: Issues and Strategies in Multiscale Approaches to Protein Modeling. Edited by Andrzej Kolinski; Springer New York
  • Tramontano, A., Cozzetto, D., Giorgetti, A. and Raimondo R. The assessment of methods for protein structure prediction in Protein structure prediction: methods and protocols. 2nd edition. Edited by Chris Bystroff and Mohammed Zaki; The Humana Press, Inc