Dr Gianluca Pollastri MSC PhD
Contact Details
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Biography:
| Since September 2003 I've been a College Lecturer (and Senior Lecturer since October 2008) in the School of Computer Science and Informatics at University College Dublin. Before then I was a working in Pierre Baldi's group at University of California, Irvine, where it was a little bit dryer than in Dublin, but Guinness tasted remarkably foul. I am the head of the AmMBio lab, which has employed up to two postdoctoral fellows and ten postgraduate students, funded through a number of grants from Science Foundation Ireland, the Health Research Board of Ireland, the Irish Research Council for Science, Engineering and Technology (IRCSET) and UC Dublin. |
Research Interests
There are two main related focuses to my research: one is the development of Machine Learning models for complex structured data; the other is the field of Bioinformatics, and Structural Genomics and Proteomics in particular. The two things are inextricably tied, since virtually all the applicative domains I tested my models on are in molecular biology. |
Book Chapters
| C. Mooney, N. Davey, A.J.M. Martin, I.Walsh, D.C.Shields, G.Pollastri; (2011) 'In Silico Protein Motif Discovery and Structural Analysis' In: In Silico Tools for Gene Discovery. -: Springer. [Details] |
C. Mooney, Y. Wang, G.Pollastri; (2011) 'De Novo Protein Subcellular Localization Prediction by N-to-1 Neural Networks' In: Computational Intelligence Methods for Bioinformatics and Biostatistics. -: Springer.  [Details] |
| A.J.M.Martin, C. Mooney, I.Walsh, G.Pollastri; (2010) 'Contact Map Prediction by Machine Learning' In: H.Rangwala and G.Karpys (eds). Protein Structure Prediction. Wiley's. [Details] |
| Ian Walsh, Alessandro Vullo, Gianluca Pollastri; (2009) 'Recursive Neural Networks for Undirected Graphs for Learning Molecular Endpoints' In: Pattern Recognition in Bioinformatics. Heidelberg: Springer. [DOI] [Details] |
| Bau, D. and Walsh, I. and Pollastri, G. and Vullo, A.; (2009) 'Fast Modeling of Protein Structures Through Multi-level Contact Maps' In: Alona S. Russe (eds). Computational Biology: New Research. Hauppauge, New York: Nova Publishers. [Details] |
| G.Pollastri, D.Bau, A.Vullo; (2007) 'Distill: a machine learning approach to ab initio protein structure prediction' In: S. Bandyopadhyay, U. Maulik and J. T. L. Wang (eds). Analysis of Biological Data: A Soft Computing Approach. London: World Scientific. [Details] |
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| P.Baldi, G.Pollastri, P.Frasconi, and A.Vullo; (2003) 'New Machine Learning Methods for the Prediction of Protein Topologies' In: P. Frasconi and R. Shamir (eds). Artificial Intelligence and Heuristic Methods in Bioinformatics. Amsterdam: IOS press. [Details] | |||||||||
| P.Baldi, G.Pollastri, C.A.F. Andersen, and S. Brunak; (2000) 'Protein β-Sheet Partner Prediction by Neural Networks' In: H. Malmgren, M. Borga and L. Niklasson (eds). Artificial Neural Networks in Medicine and Biology (proceedings of the ANNIMAB-1 Conference, Göteborg, Sweden). New York: Springer Verlag. [Details] |
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| P.Baldi, S.Brunak, P.Frasconi, and G.Pollastri; (2000) 'Bidirectional IOHMMs and recurrent neural networks for protein secondary structure prediction' In: Rita Casadio and Lanfranco Masotti Editors (eds). Protein Sequence Analysis in the Genomic Era. Bologna: CLUEB. [Details] | |||||||||
| P.Baldi, S.Brunak, P.Frasconi, G.Pollastri, and G.Soda; (2000) 'Bidirectional Dynamics for Protein Secondary Structure Prediction' In: R. Sun and L. Giles (eds). Sequence Learning: Paradigms, Algorithms, and Applications. [Details] | |||||||||
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Peer Reviewed Journals
| C. Mooney, Y. Wang, G.Pollastri; (2011) 'SCLpred: Protein Subcellular Localization Prediction by N-to-1 Neural Networks'. Bioinformatics, . [DOI] [Details] |
| I. Walsh, A.J.Martin, T. Di Domenico, A. Vullo , G.Pollastri, S.Tosatto; (2011) 'CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs'. Nucleic Acids Research, 39 (W):190-186. [Details] |
| Alberto J.M.Martin, Claudio Mirabello, Gianluca Pollastri; (2011) 'Neural Network Pairwise Interaction Fields for Protein Model Quality Assessment and Ab Initio Protein Folding'. Current Protein and Peptide Science, 12 (6):549-562. [Details] |
| P.Kukic, D.Farrell, U.Bjarnadottir, C.Søndergaard, G.Pollastri, J.E.Nielsen; (2010) 'Improving the analysis of NMR spectra tracking pH-induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift'. Proteins, . [Details] |
| C.Søndergaard, A.Garrett, T.Carstensen, G.Pollastri, J.E.Nielsen; (2009) 'Structural artefacts in protein-ligand X-ray structures: implications for the development of docking scoring functions'. Journal of Medicinal Chemistry, . [Details] |
| Ian Walsh, Alberto JM Martin, Catherine Mooney, Enrico Rubagotti, Alessandro Vullo, Gianluca Pollastri; (2009) 'Ab initio and homology based prediction of protein domains by recursive neural networks'. BMC Bioinformatics, 10 . [Details] | |||||||||
| C.Mooney and G.Pollastri; (2009) 'Beyond the Twilight Zone: Automated prediction of structural properties of proteins by recursive neural networks and remote homology information'. Proteins, 77 (1):181-190. [Details] | |||||||||
| I.Walsh, D.Baú, A.J.M.Martin, C. Mooney, A.Vullo, G.Pollastri; (2009) 'Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks'. BMC Structural Biology, 9 . [Details] | |||||||||
| Q.Le, G.Pollastri, P.Koehl; (2009) 'Structural Alphabets for Protein Structure Classification: a Comparison Study'. Journal of Molecular Biology, 387 (2):431-450. [Details] | |||||||||
| Martin AJ, Bau D, Vullo A, Walsh I, Pollastri G; (2008) 'Long-range information and physicality constraints improve predicted protein contact maps'. Journal of bioinformatics and computational biology, 5 (NA):1001-1020. [Details] | |||||||||
| C.R.Søndergaard, J.P.McIntosh, G.Pollastri, J.E.Nielsen; (2008) 'Determination of electrostatic interaction energies and protonation state populations in enzyme active sites'. Journal of Molecular Biology, 376 (1):269-287. [Details] |
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| G.Pollastri, A. J. M. Martin, C. Mooney, A. Vullo; (2007) 'Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information'. BMC Bioinformatics, 8 . [Details] |
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| Bau D, Martin AJM, Mooney C, Vullo A, Walsh I, Pollastri G ; (2006) 'Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins'. BMC Bioinformatics, 7 . [DOI] [Details] |
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| Vullo, A; Walsh, I; Pollastri, G; ; (2006) 'A two-stage approach for improved prediction of residue contact maps'. BMC Bioinformatics, 7 (NA). [Details] | |||||||||
| Mooney, C; Vullo, A; Pollastri, G; ; (2006) 'Protein structural motif prediction in multidimensional phi-psi space leads to improved secondary structure prediction'. Journal of Computational Biology, 13 (8):1489-1502. [Details] | |||||||||
| Vullo, A., Bortolami, O., Pollastri, G., Tosatto, S.; (2006) 'Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines'. NUCLEIC ACIDS RESEARCH, . [Details] | |||||||||
| Pollastri, G.,Vullo, A.,Frasconi, P.,Baldi, P.; (2006) 'Modular DAG-RNN Architectures for assembling coarse protein structures'. Journal of Computational Biology, 13 (3):631-650. [Details] | |||||||||
| Ceroni, A; Frasconi, P; Pollastri, G; ; (2005) 'Learning protein secondary structure from sequential and relational data'. Neural Networks, 18 (8):1029-1039. [Details] | |||||||||
| Pollastri, G.,McLysaght, A.; (2005) 'Porter: a new, accurate server for protein secondary structure prediction'. Bioinformatics, 21 (8):1719-1720. [Details] | |||||||||
| Y.Guermeur, G.Pollastri, A.Eliseeff, D.Zelus, H. Paugam-Moisy, P.Baldi; (2004) 'Combining Protein Secondary Structure Prediction Models With Ensemble Methods of Optimal Complexity'. Neurocomputing, 56C :305-327. [Details] | |||||||||
| Y.Dou, P. Baisnee, G. Pollastri, Y. Pecout, J. Nowick, and P. Baldi; (2004) 'ICBS: A Database of Protein-Protein Interactions Mediated by β-Sheet Formation'. Bioinformatics, in press . [Details] | |||||||||
| G.Pollastri, P.Baldi, A.Vullo, P.Frasconi; (2003) 'Prediction of Protein Topologies Using GIOHMMs and GRNNs'. Advances in Neural Information Processing Systems, 15 . [Details] | |||||||||
| P.Baldi and G.Pollastri; (2003) 'The Principled Design of Large-Scale Recursive Neural Network Architectures - DAG-RNNs and the Protein Structure Prediction Problem'. Journal of Machine Learning Research, 4 :575-602. [Details] | |||||||||
| P.F. Baisnee, G. Pollastri, P.F. Baldi, J.S. Nowick.; (2002) 'Identification of protein-protein interactions mediated by interchain beta-sheet formation'. Abstracts of Papers of the American Chemical Society, 224 . [Details] | |||||||||
| G.Pollastri, P.Baldi, P.Fariselli, R.Casadio; (2002) 'Prediction of Coordination Number and Relative Solvent Accessibility in Proteins'. Proteins, 47 :142-153. [Details] | |||||||||
| G.Pollastri, D.Przybylski, B.Rost, P.Baldi; (2002) 'Improving the Prediction of Protein Secondary Strucure in Three and Eight Classes Using Recurrent Neural Networks and Profiles'. Proteins, 47 :228-235. [Details] | |||||||||
| P.Baldi, G.Pollastri; (2002) 'Machine Learning Structural and Functional Proteomics'. IEEE Intelligent Sysyems, 17, 2 :28-35. [Details] | |||||||||
| G.Pollastri and P.Baldi; (2002) 'Prediction of Contact Maps by Recurrent Neural Network Architectures and Hidden Context Propagation from All Four Cardinal Corners'. Bioinformatics, 18 (Supplement 1):62-70. [Details] | |||||||||
| G.Pollastri, P.Baldi, P.Fariselli, R.Casadio; (2001) 'Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks'. Bioinformatics, 17 (Supplement 1):234-242. [Details] | |||||||||
| P.Baldi, S.Brunak, P.Frasconi, G.Soda., G.Pollastri; (1999) 'Exploiting the Past and the Future in Protein Secondary Structure Prediction'. Bioinformatics, 15 :937-946. [Details] | |||||||||
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Conference Publications
| G.Tradigo, P.Veltri, G.Pollastri; (2011) Machine Learning approaches for Contact Map prediction in the CASP9 experiment SEBD 2011 Maratea (Italy), , 26-JUN-11 - 29-JUN-11 [Details] |
| I.Walsh, A.Vullo, G.Pollastri; (2009) An adaptive model for learning molecular endpoints . In: M.Biehl, B.Hammer, S.Hochreiter, S.C. Kremer and T.Villmann eds. Similarity-based learning on structures , Dagstuhl Seminars series Dagstuhl, Germany, , 15-FEB-09 - 20-FEB-09 [Details] |
| A.J.M.Martin, A.Vullo, G.Pollastri; (2009) Neural Network Pairwise Interaction Fields for protein model quality assessment LION3 Trento, Italy, , 14-JAN-09 - 18-JAN-09 [Details] |
| J.Cheng, G.Pollastri; (2008) A Neural Network Approach to Ordinal Regression IJCNN 2008 Hong Kong, , 01-JUN-08 - 06-JUN-08 [Details] |
| A. Vullo, A. Passerini, P. Frasconi, F. Costa, G. Pollastri; (2008) On the Convergence of Protein Structure and Dynamics. Statistical Learning Studies of Pseudo Folding Pathways EVOBIO 2008 [Details] |
| C.Søndergaard, L.P.McIntosh, G.Pollastri, J.E.Nielsen; (2007) Determination of electrostatic interaction energies and protonation state populations in enzyme active sites by global fits of NMR titration data and pH-activity profiles 21st Annual Symposium of The Protein Society Boston, [Details] | |||||||||
| P.F. Baisnee, G. Pollastri, P.F. Baldi, J.S. Nowick; (2002) Identification of protein-protein interactions mediated by interchain beta-sheet formation 224th National Meeting of the American Chemical Society Boston, [Details] | |||||||||
| P.Baldi, S.Brunak, P.Frasconi, G.Pollastri, and G.Soda; (1999) Bidirectional Dynamics for Protein Secondary Structure Prediction International Joint Conference on Artificial Intelligence (IJCAI99) Stockholm, [Details] | |||||||||
| P.Baldi, G.Pollastri, C.A.F. Andersen, and S. Brunak.; (2000) Matching Protein beta-Sheet Partners by Feedforward and Recurrent Neural Networks Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology, (ISMB00), La Jolla, CA, AAAI Press, 2000 La Jolla, CA, [Details] | |||||||||
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Reports
| C. Mooney, A. Vullo, G. Pollastri ; (2006) Protein Backbone Angle Prediction in Multidimensional phi-psi Space UCD CSI Technical Report 2006-1. Reports [Details] |
Technical Publication
| P. Baisnee, G. Pollastri, Y. Pecout, P. Baldi; (2003) ICBS: A Database of Protein-Protein Interactions Mediated by β-Sheet Formation. Technical Publication [Details] |
Articles
| G.Pollastri; (1999) Modelli Connessionistici non causali per l'analisi di sequenze e loro impiego nella classificazione delle proteine. Articles [Details] |
| G.Pollastri; (1997) Risoluzione dei giochi dell'8 e del 15 con algoritmo IDA* e funzione euristica calcolata mediante MLP. Articles [Details] |
Education
| Year 1999 Institution: University of Florence Qualification: MSc Subject: |
| Year 2003 Institution: Uni of California, Irvine, CA Qualification: PhD Subject: |
Teaching Interests
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Recent Postgraduates
| Davide Baú (Ph.D. 2008) Catherine Mooney (Ph.D. 2008) Ian Walsh (Ph.D. 2008) Chresten Søndergaard (Ph.D. 2009) Alberto J.Martin-Martin (Ph.D. 2009)
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Current Postgraduate Students
| Predrag Kukic, Doctor of Philosophy (PhD) - Thesis Supervisor |
| Alessandro Lusci, Doctor of Philosophy (PhD) - Thesis Supervisor |
| Claudio Mirabello, Doctor of Philosophy (PhD) - Thesis Supervisor |
| Alessandro Adelfio, Doctor of Philosophy (PhD) - Thesis Supervisor |
| Viola Volpato, Doctor of Philosophy (PhD) - Thesis Supervisor |
Modules Taught
| 201000 COMP10010 Computer Science: Introduction to Programming I |
| 201000 COMP10140 Computer Science: Programming for Radiography I |
| 200900 COMP20120 Computer Science: Introduction to Bioinformatics |
| 200900 COMP30230 Computer Science: Connectionist Computing |
| 200900 COMP40400 Computer Science: Bioinformatics |