Gianluca Pollastri
Socio Ordinario
Professore associato
University College Dublin
Contact Information
website
RESEARCH AREA
algorithms,biological data modelling,structure analysis,structural genomics,machine learning
RESEARCH ACTIVITY
protein structure prediction, prediction of properties of small molecules, machine learning
SELECTED PUBLICATIONS
C. Mooney, G.Pollastri "Beyond the Twilight Zone: Automated prediction of structural properties of proteins by recursive neural networks and remote homology information" Proteins, in press.
I.Walsh, D.Baú, A.J.M.Martin, C. Mooney, A.Vullo, G.Pollastri "Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks" BMC Structural Biology, 9:5, 2009.
Q.Le, G.Pollastri, P.Koehl. "Structural Alphabets for Protein Structure Classification: a Comparison Study" Journal of Molecular Biology, in press.
G.Pollastri*, A. J. M. Martin, C. Mooney, A. Vullo. "Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information" BMC Bioinformatics, 8:201, 2007.
A. Vullo, O. Bortolami, G. Pollastri*, S. Tosatto. "Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines" Nucleic Acids Research, 34:W164-W168, 2006.
A. Vullo, I. Walsh, G. Pollastri*. "A two-stage approach for improved prediction of residue contact maps" BMC Bioinformatics, 7:180, 2006.
G. Pollastri*, A. McLysaght. "Porter: a new, accurate server for protein secondary structure prediction" Bioinformatics, 21(8):1719-20, 2005.
P. Baldi, G. Pollastri. "The Principled Design of Large-Scale Recursive Neural Network Architectures -- DAG-RNNs and the Protein Structure Prediction Problem", Journal of Machine Learning Research 4(Sep):575-602, 2003.
G.Pollastri, P.Baldi. "Prediction of Contact Maps by Recurrent Neural Network Architectures and Hidden Context Propagation from All Four Cardinal Corners", Bioinformatics, 18 Suppl 1, S62-S70, 2002.
G.Pollastri, P.Baldi, P.Fariselli, R.Casadio. "Prediction of Coordination Number and Relative Solvent Accessibility in Proteins", Proteins, 47, 142-153, 2002.
G.Pollastri, D.Przybylski, B.Rost, P.Baldi. "Improving the Prediction of Protein Secondary Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles", Proteins, 47, 228-235, 2002.
G.Pollastri, P.Baldi, P.Fariselli, R.Casadio. "Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks", Bioinformatics, 17 Suppl 1, S234-S242, 2001.
P.Baldi, S.Brunak, P.Frasconi, G.Soda and G.Pollastri. "Exploiting the Past and the Future in Protein Secondary Structure Prediction", Bioinformatics, 15, 937-946, 1999.
I.Walsh, D.Baú, A.J.M.Martin, C. Mooney, A.Vullo, G.Pollastri "Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks" BMC Structural Biology, 9:5, 2009.
Q.Le, G.Pollastri, P.Koehl. "Structural Alphabets for Protein Structure Classification: a Comparison Study" Journal of Molecular Biology, in press.
G.Pollastri*, A. J. M. Martin, C. Mooney, A. Vullo. "Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information" BMC Bioinformatics, 8:201, 2007.
A. Vullo, O. Bortolami, G. Pollastri*, S. Tosatto. "Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines" Nucleic Acids Research, 34:W164-W168, 2006.
A. Vullo, I. Walsh, G. Pollastri*. "A two-stage approach for improved prediction of residue contact maps" BMC Bioinformatics, 7:180, 2006.
G. Pollastri*, A. McLysaght. "Porter: a new, accurate server for protein secondary structure prediction" Bioinformatics, 21(8):1719-20, 2005.
P. Baldi, G. Pollastri. "The Principled Design of Large-Scale Recursive Neural Network Architectures -- DAG-RNNs and the Protein Structure Prediction Problem", Journal of Machine Learning Research 4(Sep):575-602, 2003.
G.Pollastri, P.Baldi. "Prediction of Contact Maps by Recurrent Neural Network Architectures and Hidden Context Propagation from All Four Cardinal Corners", Bioinformatics, 18 Suppl 1, S62-S70, 2002.
G.Pollastri, P.Baldi, P.Fariselli, R.Casadio. "Prediction of Coordination Number and Relative Solvent Accessibility in Proteins", Proteins, 47, 142-153, 2002.
G.Pollastri, D.Przybylski, B.Rost, P.Baldi. "Improving the Prediction of Protein Secondary Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles", Proteins, 47, 228-235, 2002.
G.Pollastri, P.Baldi, P.Fariselli, R.Casadio. "Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks", Bioinformatics, 17 Suppl 1, S234-S242, 2001.
P.Baldi, S.Brunak, P.Frasconi, G.Soda and G.Pollastri. "Exploiting the Past and the Future in Protein Secondary Structure Prediction", Bioinformatics, 15, 937-946, 1999.
OTHER MEMBERSHIPS
International Society for Computational Biology
EDITORIAL BOARDS
OJAI
MAIN TEACHINGS
Connectionist Computing, Bioinformatics, Introduction to Bioinformatics at University College Dublin
