Exploiting the past and the future in protein secondary structure prediction. - Pierre Baldi; Søren Brunak; Paolo Frasconi; Giovanni Soda; Gianluca Pollastri (Bioinform., 1999)

Protein β-Sheet Partner Prediction by Neural Networks. - Pierre Baldi; Gianluca Pollastri; Claus A. F. Andersen; Søren Brunak (ANNIMAB, 2000)

Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. - Pierre Baldi; Gianluca Pollastri; Claus A. F. Andersen; Søren Brunak (ISMB, 2000)

Improved prediction of the number of residue contacts in proteins by recurrent neural networks. - Gianluca Pollastri; Pierre Baldi; Piero Fariselli; Rita Casadio (ISMB (Supplement of Bioinformatics), 2001)

Bidirectional Dynamics for Protein Secondary Structure Prediction. - Pierre Baldi; Søren Brunak; Paolo Frasconi; Gianluca Pollastri; Giovanni Soda (Sequence Learning, 2001)

Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. - Gianluca Pollastri; Pierre Baldi (ISMB, 2002)

Prediction of Protein Topologies Using Generalized IOHMMS and RNNs. - Gianluca Pollastri; Pierre Baldi; Alessandro Vullo; Paolo Frasconi (NIPS, 2002)

A Machine-Learning Strategy for Protein Analysis. - Pierre Baldi; Gianluca Pollastri (IEEE Intell. Syst., 2002)

The Principled Design of Large-Scale Recursive Neural Network Architectures–DAG-RNNs and the Protein Structure Prediction Problem. - Pierre Baldi; Gianluca Pollastri (J. Mach. Learn. Res., 2003)

ICBS: a database of interactions between protein chains mediated by ?-sheet formation. - Yimeng Dou; Pierre-François Baisnée; Gianluca Pollastri; Yann Pécout; James Nowick; Pierre Baldi (Bioinform., 2004)

Combining protein secondary structure prediction models with ensemble methods of optimal complexity. - Yann Guermeur; Gianluca Pollastri; André Elisseeff; Dominique Zelus; Hélène Paugam-Moisy; Pierre Baldi (Neurocomputing, 2004)

Porter: a new, accurate server for protein secondary structure prediction. - Gianluca Pollastri; Aoife McLysaght (Bioinform., 2005)

Learning protein secondary structure from sequential and relational data. - Alessio Ceroni; Paolo Frasconi; Gianluca Pollastri (Neural Networks, 2005)

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. - Davide Baù; Alberto J. M. Martin; Catherine Mooney; Alessandro Vullo; Ian Walsh; Gianluca Pollastri (BMC Bioinform., 2006)

A two-stage approach for improved prediction of residue contact maps. - Alessandro Vullo; Ian Walsh; Gianluca Pollastri (BMC Bioinform., 2006)

Protein Structural Motif Prediction in Multidimensional ø-Psi Space Leads to Improved Secondary Structure Prediction. - Catherine Mooney; Alessandro Vullo; Gianluca Pollastri (J. Comput. Biol., 2006)

Modular DAG-RNN Architectures for Assembling Coarse Protein Structures. - Gianluca Pollastri; Alessandro Vullo; Paolo Frasconi; Pierre Baldi (J. Comput. Biol., 2006)

Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. - Alessandro Vullo; Oscar Bortolami; Gianluca Pollastri; Silvio C. E. Tosatto (Nucleic Acids Res., 2006)

Distill: A Machine Learning Approach to Ab Initio Protein Structure Prediction. - Gianluca Pollastri; Davide Baù; Alessandro Vullo (Analysis of Biological Data: A Soft Computing Approach, 2007)

Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. - Gianluca Pollastri; Alberto J. M. Martin; Catherine Mooney; Alessandro Vullo (BMC Bioinform., 2007)

On the Convergence of Protein Structure and Dynamics. Statistical Learning Studies of Pseudo Folding Pathways. - Alessandro Vullo; Andrea Passerini; Paolo Frasconi; Fabrizio Costa; Gianluca Pollastri (EvoBIO, 2008)

A neural network approach to ordinal regression. - Jianlin Cheng; Zheng Wang 025; Gianluca Pollastri (IJCNN, 2008)

Long-Range Information and Physicality Constraints Improve predicted protein Contact Maps. - Alberto J. M. Martin; Davide Baù; Alessandro Vullo; Ian Walsh; Gianluca Pollastri (J. Bioinform. Comput. Biol., 2008)

An adaptive model for learning molecular endpoints. - Ian Walsh; Alessandro Vullo; Gianluca Pollastri (Similarity-based learning on structures, 2009)

Neural Network Pairwise Interaction Fields for Protein Model Quality Assessment. - Alberto J. M. Martin; Alessandro Vullo; Gianluca Pollastri (LION, 2009)

Recursive Neural Networks for Undirected Graphs for Learning Molecular Endpoints. - Ian Walsh; Alessandro Vullo; Gianluca Pollastri (PRIB, 2009)

Ab initio and homology based prediction of protein domains by recursive neural networks. - Ian Walsh; Alberto J. M. Martin; Catherine Mooney; Enrico Rubagotti; Alessandro Vullo; Gianluca Pollastri (BMC Bioinform., 2009)

De Novo Protein Subcellular Localization Prediction by N-to-1 Neural Networks. - Catherine Mooney; Yong-Hong Wang; Gianluca Pollastri (CIBB, 2010)

Machine Learning Approaches for Contact Maps Prediction in CASP9 Experiment. - Giuseppe Tradigo; Pierangelo Veltri; Gianluca Pollastri (SEBD, 2011)

SCLpred: protein subcellular localization prediction by N-to-1 neural networks. - Catherine Mooney; Yong-Hong Wang; Gianluca Pollastri (Bioinform., 2011)

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. - Ian Walsh; Alberto J. M. Martin; Tomás Di Domenico; Alessandro Vullo; Gianluca Pollastri; Silvio C. E. Tosatto (Nucleic Acids Res., 2011)

CPPpred: prediction of cell penetrating peptides. - Thérèse A. Holton; Gianluca Pollastri; Denis C. Shields; Catherine Mooney (Bioinform., 2013)

Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility. - Claudio Mirabello; Gianluca Pollastri (Bioinform., 2013)

PeptideLocator: prediction of bioactive peptides in protein sequences. - Catherine Mooney; Niall J. Haslam; Thérèse A. Holton; Gianluca Pollastri; Denis C. Shields (Bioinform., 2013)

Accurate prediction of protein enzymatic class by N-to-1 Neural Networks. - Viola Volpato; Alessandro Adelfio; Gianluca Pollastri (BMC Bioinform., 2013)

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules. - Alessandro Lusci; Gianluca Pollastri; Pierre Baldi (J. Chem. Inf. Model., 2013)

Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks. - Predrag Kukic; Claudio Mirabello; Giuseppe Tradigo; Ian Walsh; Pierangelo Veltri; Gianluca Pollastri (BMC Bioinform., 2014)

G-quadruplex Structure Prediction and integration in the GenData2020 data model. - Giuseppe Tradigo; Francesca Cristiano; Stefano Alcaro; Sergio Greco; Gianluca Pollastri; Pierangelo Veltri; Mattia Prosperi (BCB, 2016)

Correct machine learning on protein sequences: a peer-reviewing perspective. - Ian Walsh; Gianluca Pollastri; Silvio C. E. Tosatto (Briefings Bioinform., 2016)

Algorithms for Structure Comparison and Analysis: Prediction of Tertiary Structures of Proteins. - Giuseppe Tradigo; Francesca Rondinelli; Gianluca Pollastri (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Algorithms for Structure Comparison and Analysis: Docking. - Giuseppe Tradigo; Francesca Rondinelli; Gianluca Pollastri (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks. - Manaz Kaleel; Yandan Zheng; Jialiang Chen; Xuanming Feng; Jeremy C. Simpson; Gianluca Pollastri; Catherine Mooney (Bioinform., 2020)

Brewery: deep learning and deeper profiles for the prediction of 1D protein structure annotations. - Mirko Torrisi; Gianluca Pollastri (Bioinform., 2020)

Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states. - Leandro Murgas; Gianluca Pollastri; Erick Riquelme; Mauricio Sáez; Alberto J. M. Martin (Briefings Bioinform., 2024)