Publications

Journal papers:

  1. “Ontology-Based Prediction and Prioritization of Gene Functional Annotations written with Marco Masseroli (Dipartimento di Elettronica e Informazione, Politecnico di Milano), IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 13, Issue 2, pp. 248 – 260, IEEE, 2016.
  2. “Software Suite for Gene and Protein Annotation Prediction and Similarity Search” written with Marco Masseroli (Dipartimento di Elettronica e Informazione, Politecnico di Milano), IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 12, Issue 4, pp. 837 – 843, IEEE, 2015.
  3. Computational algorithms to predict Gene Ontology annotationswritten with Marco Masseroli and Pietro Pinoli (Dipartimento di Elettronica e Informazione, Politecnico di Milano), BMC Bioinformatics, Volume 6, Supplement 6, S4, 2015.

Book chapters:

  1. [NEW] “Validation Pipeline for Computational Prediction of Genomics Annotations”, written with Marco Masseroli (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer Science (LNCS), Vol. 9874, pp. 233-244, Springer. Extended version of the paper entitled “Validation procedures for predicted Gene Ontology annotations”Proceedings of CIBB 2015 – the Twelfth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Naples, Italy, 10 – 12 September 2015.
  2. “Extended Spearman and Kendall Coefficients for Gene Annotation List Correlation”, written with Eleonora Ciceri and Marco Masseroli (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer Science (LNCS), Vol. 8623, pp. 1-12, Springer. Extended version of the paper entitled Correlation of Gene Function Annotation Lists through Enhanced Spearman and Kendall Measures”Proceedings of CIBB 2014 – the Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Cambridge, Great Britain, 26 – 28 June 2014.
  3. “Weighting Scheme Methods for Enhanced Genomic Annotation Prediction” written with Marco Masseroli and Pietro Pinoli (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer Science (LNCS), Vol. 8452, pag. 76-89, Springer. Extended version of the scientific paper entitled “Enhanced Probabilistic Latent Semantic Analysis with Weighting Schemes to Predict Genomic Annotations”  and presented at  CIBB2013 – the 10th International Meeting On Computational Intelligence Methods For Bioinformatics And Biostatistics, Nice, Cote d’Azur, France 20 – 22 June 2013.
  4. “Genomic Annotation Prediction Based on Integrated Information” written with Marco Masseroli and Marco Tagliasacchi (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer Science (LNCS), Vol. 7548, Springer. Editors: Biganzoli, E.; Vellido, A.; Ambrogi, F.; Tagliaferri, R. Extended version of the scientific paper entitled “Biomolecular annotation prediction through information integration”  and presented at  CIBB2011 – 8th International Meeting On Computational Intelligence Methods For Bioinformatics And Biostatistics, 30 June, 1° July, 2 July 2011, Gargnano Sul Garda, Lombardia, Italy.

Conference proceedings:

  1. “Validation Procedures for Predicted Gene Ontology Annotations”  written mainly by me and co-authored by Marco Masseroli (Politecnico di Milano).  Proceedings of CIBB 2015 – the Twelfth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Naples, Italy, 10-12 September 2015. IN PRESS.
  2. “Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions”, written mainly by me and co-authored by Peter J. Sadowski and Pierre Baldi (Institute for Genomics and Bioinformatics, University of California Irvine), Proceedings of ACM BCB 2014, the 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, Newport Beach, California, USA, 20-23 September 2014.
  3. Correlation of Gene Function Annotation Lists through Enhanced Spearman and Kendall Measures”, written mainly by me and co-authored by Eleonora Ciceri and Marco Masseroli (Dipartimento di Elettronica, Informazione e Bioingegneria – DEIB, Politecnico di Milano), Proceedings of CIBB 2014 – the Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Cambridge, Great Britain, 26 – 28 June 2014.
  4. “Latent Dirichlet Allocation based on Gibbs Sampling for gene function prediction” written mainly by Pietro Pinoli and co-authored by me and Marco Masseroli (Dipartimento di Elettronica Informazione e Bioingegneria – DEIB, Politecnico di Milano), Proceedings of CIBCB 2014, the 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, Honolulu, Hawaii, USA, 21-24 May 2014.
  5. “A Discrete Optimization Approach for SVD Best Truncation Choice based on ROC Curves”, written mainly by me and co-authored by Marco Masseroli (Dipartimento di Elettronica, Informazione e Bioingegneria – DEIB, Politecnico di Milano), Proceedings of IEEE BIBE 2013 – the 13rd IEEE International Conference on Bioinformatics and Bioengineering, Chania, Crete, Greece, 10 – 13 November 2013.
  6. “Enhanced Probabilistic Latent Semantic Analysis with Weighting Schemes to Predict Genomic Annotations”, written mainly by Pietro Pinoli and co-authored by me and Marco Masseroli. (Dipartimento di Elettronica, Informazione e Bioingegneria – DEIB, Politecnico di Milano), Proceedings of IEEE BIBE 2013 – the 13rd IEEE International Conference on Bioinformatics and Bioengineering, Chania, Crete, Greece, 10 – 13 November 2013.
  7. “Improved Biomolecular Annotation Prediction through Weighting Scheme Methods” written with Pietro Pinoli and Marco Masseroli (Dipartimento di Elettronica, Informazione e Bioingegneria – DEIB, Politecnico di Milano), Proceedings of CIBB 2013, Tenth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Nice, Cote d’Azur, France 20 – 22 June 2013.
  8. “Probabilistic Latent Semantic Analysis for prediction of Gene Ontology annotations” written with Marco Masseroli and Pietro Pinoli (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), for the conference WCCI2012 – IEEE World Congress on Computational Intelligence, June 10-15, Brisbane, Queensland, Australia
  9. “Semantically Improved Genome-Wide Prediction of Gene Ontology Annotations” written with Marco Masseroli and Marco Tagliasacchi (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), for the conference ISDA2011, 11th International Conference on  Intelligent Systems Design and Applications (ISDA) November 22-24, 2011 – Córdoba, Spain, EU
  10.  Biomolecular annotation prediction through information integration written with Marco Masseroli and Marco Tagliasacchi (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), for the conference CIBB2011 – 8th International Meeting On Computational Intelligence Methods For Bioinformatics And Biostatistics, 30 June, 1° July, 2 July 2011, Gargnano Sul Garda, Lombardia, Italia.
    Paper awarded with the  International Neural Network Society Best Student Paper Award prize.
  11. “An intraday trading model based on Artificial Immune Systems”, written with Marina Resta (Dipartimento d’Economia e Metodi Quantitativi – DIEM, University of Genoa), for the conference WILF 2010 – Italian Workshop on Neural Networks, Vietri Sul Mare, Campania, Italy, 27-29 May 2010. Publised for IOSpress.

Technical reports:

  1. Technical report: “Integration of Bioinformatics Web Services through the Search Computing Technology” TR-2012/02. Final doctoral minor research project report, Dipartimento di Elettronica e Informazione, Politecnico di Milano, 14th November 2013.
  2. Technical report: Support Vector Machines in Bioinformatics: a Survey” TR-2012/01 written with Alessandro Lazaric (INRIA, Lille, France, EU), and published online on October 2012.

Posters at international conferences:

  1. “Integration of a gene similarity service for explorative search computing”, written with Marco Masseroli,  fort the conference  Bits2013 – the 10th Annual Meeting of the Bioinformatics Italian Society, Udine, Italy, 2013.
  2. “Genome-Wide Annotation Prediction with SVD Truncation based on ROC Analysis“, written with Marco Masseroli, for the conferences ECCB12  – 11th European Conference on Computational Biology, September 9th-12th 2012, and ESCS – 2nd International Society for Computational Biology European Student Council Symposium, September 8th 2012, Basel, Basel-Stadt, Switzerland. The paper will be presented with a poster at ECC12 conference, and has been selected in the top 8 papers, out of 50 papers, at ESCS for oral presentation.
  3. “Truncated SVD best rank choice through ROC curves for genomic annotation prediction”, written with Marco Masseroli (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), for the conference Bits 2012 – 9th Annual Meeting of the Italian Bioinformatics Society
  4. Improved Singular Value Decomposition methods for Biomolecular Annotation Prediction“, scritto con Marco Masseroli e Marco Tagliasacchi (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), for the conference Bits 2011 – 8th Annual Meeting of the Bioinformatics Italian Society, organized by the Bioinformatics Italian Society, 20-21-22 June 2011, at Area della Ricerca of Cnr, Pisa, Tuscany, Italy.
  5. “Prediction of Gene Ontology Annotations using improved Single Value Decomposition methods”, scritto con Marco Masseroli e Marco Tagliasacchi (Dipartimento di Elettronica e Informazione – DEI, Politecnico di Milano), for the conference BioMed@PoliMi Ventennale del Dipartimento di Bioingegneria del Politecnico di Milano, at the Rectorate of Politecnico di Milano, Milan, Lumbardy, 30th november 2010. Published on Polipress.

Theses:

  1. Doctoral thesis; “Computational prediction of gene functions through machine learning methods and multiple validation procedure” (pdf file here). Doctoral Programme in Computer Engineering, 26th Cycle, Politecnico di Milano, March 2014.
  2. Tesi di laurea specialistica: “Elaborazione di dati bioinformatici attraverso l’uso di Particle Swarm Optimization” (sommario .pdf) Relatori: Francesco Masulli, Dipartimento d’Informatica, Universita’ di Genova, e Giuseppe Russo, Temple University, Filadelfia, Usa. Luglio 2010.
  3. Tesi di laurea triennale: “Middleware per la bioinformatica: implementazione dell’Algoritmo dei Distanti per il clustering dei dati nell’ambiente OpenAdap.net” (.pdf) Relatori: Francesco Masulli e Stefano Rovetta, Dipartimento d’Informatica, Universita’ di Genova;  Javier Iglesias, Universite’ de Lausanne; Alessandro Villa, Universite’ de Grenoble. Luglio 2007.

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