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Gianluca Pollastri - Publications

Affiliations: 
School of Computer Science and Informatics University College Dublin, Dublin, County Dublin, Ireland 
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Kaleel M, Ellinger L, Lalor C, Pollastri G, Mooney C. SCLpred-MEM: Subcellular localization prediction of membrane proteins by deep N-to-1 convolutional neural networks. Proteins. 89: 1233-1239. PMID 33983651 DOI: 10.1002/prot.26144  0.424
2020 Urban G, Torrisi M, Magnan CN, Pollastri G, Baldi P. Protein profiles: Biases and protocols. Computational and Structural Biotechnology Journal. 18: 2281-2289. PMID 32994887 DOI: 10.1016/J.Csbj.2020.08.015  0.526
2020 Torrisi M, Pollastri G, Le Q. Deep learning methods in protein structure prediction. Computational and Structural Biotechnology Journal. 18: 1301-1310. PMID 32612753 DOI: 10.1016/J.Csbj.2019.12.011  0.553
2020 O'Brien KT, Mooney C, Lopez C, Pollastri G, Shields DC. Prediction of polyproline II secondary structure propensity in proteins. Royal Society Open Science. 7: 191239. PMID 32218953 DOI: 10.1098/Rsos.191239  0.577
2020 Torrisi M, Pollastri G. Brewery: deep learning and deeper profiles for the prediction of 1D protein structure annotations. Bioinformatics. 36: 3897-3898. PMID 32207516 DOI: 10.1093/Bioinformatics/Btaa204  0.594
2020 Kaleel M, Zheng Y, Chen J, Feng X, Simpson JC, Pollastri G, Mooney C. SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks. Bioinformatics (Oxford, England). PMID 32142105 DOI: 10.1093/Bioinformatics/Btaa156  0.545
2019 Torrisi M, Kaleel M, Pollastri G. Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction. Scientific Reports. 9: 12374. PMID 31451723 DOI: 10.1038/S41598-019-48786-X  0.552
2019 Kaleel M, Torrisi M, Mooney C, Pollastri G. PaleAle 5.0: prediction of protein relative solvent accessibility by deep learning. Amino Acids. 51: 1289-1296. PMID 31388850 DOI: 10.1007/S00726-019-02767-6  0.636
2016 Walsh I, Pollastri G, Tosatto SCE. Correct machine learning on protein sequences: a peer-reviewing perspective Briefings in Bioinformatics. 17: 831-840. PMID 26411473 DOI: 10.1093/Bib/Bbv082  0.393
2015 Volpato V, Alshomrani B, Pollastri G. Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets. International Journal of Molecular Sciences. 16: 19868-85. PMID 26307973 DOI: 10.3390/ijms160819868  0.494
2015 Volpato V, Alshomrani B, Pollastri G. Accurate Ab initio and template-based prediction of short intrinsically-disordered regions by bidirectional recurrent neural networks trained on large-scale datasets International Journal of Molecular Sciences. 16: 19868-19885. DOI: 10.3390/Ijms160819868  0.559
2014 Mirabello C, Adelfio A, Pollastri G. Reconstructing protein structures by neural network pairwise interaction fields and iterative decoy set construction. Biomolecules. 4: 160-80. PMID 24970210 DOI: 10.3390/biom4010160  0.307
2014 Kukic P, Mirabello C, Tradigo G, Walsh I, Veltri P, Pollastri G. Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks. Bmc Bioinformatics. 15: 6. PMID 24410833 DOI: 10.1186/1471-2105-15-6  0.574
2013 Adelfio A, Volpato V, Pollastri G. SCLpredT: Ab initio and homology-based prediction of subcellular localization by N-to-1 neural networks. Springerplus. 2: 502. PMID 24133649 DOI: 10.1186/2193-1801-2-502  0.549
2013 Holton TA, Pollastri G, Shields DC, Mooney C. CPPpred: prediction of cell penetrating peptides. Bioinformatics (Oxford, England). 29: 3094-6. PMID 24064418 DOI: 10.1093/Bioinformatics/Btt518  0.415
2013 Khan W, Duffy F, Pollastri G, Shields DC, Mooney C. Predicting binding within disordered protein regions to structurally characterised peptide-binding domains. Plos One. 8: e72838. PMID 24019881 DOI: 10.1371/Journal.Pone.0072838  0.495
2013 Lusci A, Pollastri G, Baldi P. Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules. Journal of Chemical Information and Modeling. 53: 1563-75. PMID 23795551 DOI: 10.1021/Ci400187Y  0.401
2013 Mirabello C, Pollastri G. Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility. Bioinformatics (Oxford, England). 29: 2056-8. PMID 23772049 DOI: 10.1093/Bioinformatics/Btt344  0.586
2013 Mooney C, Cessieux A, Shields DC, Pollastri G. SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor. Amino Acids. 45: 291-9. PMID 23568340 DOI: 10.1007/S00726-013-1491-3  0.513
2013 Mooney C, Haslam NJ, Holton TA, Pollastri G, Shields DC. PeptideLocator: prediction of bioactive peptides in protein sequences. Bioinformatics (Oxford, England). 29: 1120-6. PMID 23505299 DOI: 10.1093/Bioinformatics/Btt103  0.424
2013 Volpato V, Adelfio A, Pollastri G. Accurate prediction of protein enzymatic class by N-to-1 Neural Networks. Bmc Bioinformatics. 14: S11. PMID 23368876 DOI: 10.1186/1471-2105-14-S1-S11  0.504
2012 Mooney C, Haslam NJ, Pollastri G, Shields DC. Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity. Plos One. 7: e45012. PMID 23056189 DOI: 10.1371/Journal.Pone.0045012  0.328
2012 Mooney C, Pollastri G, Shields DC, Haslam NJ. Prediction of short linear protein binding regions. Journal of Molecular Biology. 415: 193-204. PMID 22079048 DOI: 10.1016/J.Jmb.2011.10.025  0.578
2011 Mooney C, Wang YH, Pollastri G. SCLpred: protein subcellular localization prediction by N-to-1 neural networks. Bioinformatics (Oxford, England). 27: 2812-9. PMID 21873639 DOI: 10.1093/Bioinformatics/Btr494  0.542
2011 Martin AJ, Mirabello C, Pollastri G. Neural network pairwise interaction fields for protein model quality assessment and ab initio protein folding. Current Protein & Peptide Science. 12: 549-62. PMID 21787307 DOI: 10.2174/138920311796957649  0.539
2011 Mooney C, Davey N, Martin AJ, Walsh I, Shields DC, Pollastri G. In silico protein motif discovery and structural analysis. Methods in Molecular Biology (Clifton, N.J.). 760: 341-53. PMID 21780007 DOI: 10.1007/978-1-61779-176-5_21  0.589
2011 Walsh I, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC. CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. Nucleic Acids Research. 39: W190-6. PMID 21646342 DOI: 10.1093/Nar/Gkr411  0.596
2009 Søndergaard CR, Garrett AE, Carstensen T, Pollastri G, Nielsen JE. Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions. Journal of Medicinal Chemistry. 52: 5673-84. PMID 19711919 DOI: 10.1021/Jm8016464  0.38
2009 Walsh I, Martin AJ, Mooney C, Rubagotti E, Vullo A, Pollastri G. Ab initio and homology based prediction of protein domains by recursive neural networks. Bmc Bioinformatics. 10: 195. PMID 19558651 DOI: 10.1186/1471-2105-10-195  0.542
2009 Mooney C, Pollastri G. Beyond the Twilight Zone: automated prediction of structural properties of proteins by recursive neural networks and remote homology information. Proteins. 77: 181-90. PMID 19422056 DOI: 10.1002/Prot.22429  0.584
2009 Walsh I, Baù D, Martin AJ, Mooney C, Vullo A, Pollastri G. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks. Bmc Structural Biology. 9: 5. PMID 19183478 DOI: 10.1186/1472-6807-9-5  0.542
2009 Le Q, Pollastri G, Koehl P. Structural alphabets for protein structure classification: a comparison study. Journal of Molecular Biology. 387: 431-50. PMID 19135454 DOI: 10.1016/J.Jmb.2008.12.044  0.513
2008 Martin AJ, Baù D, Vullo A, Walsh I, Pollastri G. Long-range information and physicality constraints improve predicted protein contact maps. Journal of Bioinformatics and Computational Biology. 6: 1001-20. PMID 18942163 DOI: 10.1142/S0219720008003783  0.456
2007 Pollastri G, Martin AJ, Mooney C, Vullo A. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. Bmc Bioinformatics. 8: 201. PMID 17570843 DOI: 10.1186/1471-2105-8-201  0.561
2006 Mooney C, Vullo A, Pollastri G. Protein structural motif prediction in multidimensional phi-psi space leads to improved secondary structure prediction. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1489-502. PMID 17061924 DOI: 10.1089/Cmb.2006.13.1489  0.59
2006 Baú D, Martin AJ, Mooney C, Vullo A, Walsh I, Pollastri G. Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. Bmc Bioinformatics. 7: 402. PMID 16953874 DOI: 10.1186/1471-2105-7-402  0.603
2006 Vullo A, Bortolami O, Pollastri G, Tosatto SC. Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Research. 34: W164-8. PMID 16844983 DOI: 10.1093/Nar/Gkl166  0.522
2006 Pollastri G, Vullo A, Frasconi P, Baldi P. Modular DAG-RNN architectures for assembling coarse protein structures. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 631-50. PMID 16706716 DOI: 10.1089/Cmb.2006.13.631  0.572
2006 Vullo A, Walsh I, Pollastri G. A two-stage approach for improved prediction of residue contact maps. Bmc Bioinformatics. 7: 180. PMID 16573808 DOI: 10.1186/1471-2105-7-180  0.43
2005 Ceroni A, Frasconi P, Pollastri G. Learning protein secondary structure from sequential and relational data. Neural Networks : the Official Journal of the International Neural Network Society. 18: 1029-39. PMID 16182513 DOI: 10.1016/J.Neunet.2005.07.001  0.491
2005 Pollastri G, McLysaght A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics (Oxford, England). 21: 1719-20. PMID 15585524 DOI: 10.1093/Bioinformatics/Bti203  0.562
2004 Dou Y, Baisnée PF, Pollastri G, Pécout Y, Nowick J, Baldi P. ICBS: a database of interactions between protein chains mediated by beta-sheet formation. Bioinformatics (Oxford, England). 20: 2767-77. PMID 15166020 DOI: 10.1093/Bioinformatics/Bth326  0.319
2004 Baldi P, Pollastri G. 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. DOI: 10.1162/153244304773936054  0.483
2004 Guermeur Y, Pollastri G, Elisseeff A, Zelus D, Paugam-Moisy H, Baldi P. Combining protein secondary structure prediction models with ensemble methods of optimal complexity Neurocomputing. 56: 305-327. DOI: 10.1016/J.Neucom.2003.10.004  0.515
2002 Pollastri G, Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics (Oxford, England). 18: S62-70. PMID 12169532 DOI: 10.1093/BIOINFORMATICS/18.SUPPL_1.S62  0.458
2002 Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins. 47: 228-35. PMID 11933069 DOI: 10.1002/Prot.10082  0.544
2002 Pollastri G, Baldi P, Fariselli P, Casadio R. Prediction of coordination number and relative solvent accessibility in proteins. Proteins. 47: 142-53. PMID 11933061 DOI: 10.1002/Prot.10069  0.551
2002 Baldi P, Pollastri G. A machine learning strategy for protein analysis Ieee Intelligent Systems and Their Applications. 17: 28-35. DOI: 10.1109/5254.999217  0.467
2001 Pollastri G, Baldi P, Fariselli P, Casadio R. Improved prediction of the number of residue contacts in proteins by recurrent neural networks. Bioinformatics (Oxford, England). 17: S234-42. PMID 11473014 DOI: 10.1093/Bioinformatics/17.Suppl_1.S234  0.533
2000 Baldi P, Pollastri G, Andersen CA, Brunak S. Matching protein beta-sheet partners by feedforward and recurrent neural networks. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 25-36. PMID 10977063  0.373
1999 Baldi P, Brunak S, Frasconi P, Soda G, Pollastri G. Exploiting the past and the future in protein secondary structure prediction. Bioinformatics (Oxford, England). 15: 937-46. PMID 10743560  0.507
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