Elisa Cilia

Publications

Articles in scientific journals

• ELISA CILIA, STEFANO TESO, SERGIO AMMENDOLA, TOM LENAERTS, ANDREA PASSERINI
  Predicting virus mutations through statistical relational learning
  BMC Bioinformatics, 15:309, September 2014.
  [ Abstract | PDF | BibTeX ]
   
• ELISA CILIA, RITA PANCSA, PETER TOMPA, TOM LENAERTS, WIM VRANKEN
  The DynaMine webserver: predicting protein dynamics from sequence
  Nucleic Acid Research, April 2014.
  [ Abstract | html | PDF | citation ]
  

  DynaMine - sequence-based backbone dynamics predictor

   
• ELISA CILIA, RITA PANCSA, PETER TOMPA, TOM LENAERTS, WIM VRANKEN
  From protein sequence to dynamics and disorder with DynaMine
  Nature Communications, 4:2741, November 2013.
  [ Abstract | PDF | citation | Press Nature Structural Biology - Press ]
   
• ELISA CILIA, GEERTEN W. VUISTER, TOM LENAERTS
  Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e
  PLOS Computational Biology, 8(11), November 2012.
  [ Abstract | PDF | BibTeX ]
   
• MARCO FALDA, STEFANO TOPPO, ALESSANDRO PESCAROLO, ENRICO LAVEZZO, BARBARA DI CAMILLO, ANDREA FACCHINETTI, ELISA CILIA, RICCARDO VELASCO, PAOLO FONTANA
  Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
  BMC Bioinformatics, Volume 13, Supplement 4, S14, March 2012.
  [ Abstract | PDF | BibTeX ]
   
• ELISA CILIA, NIELS LANDWEHR, ANDREA PASSERINI
  Relational Feature Mining with Hierarchical Multitask kFOIL
  Fundamenta Informaticae, Special Issue on Machine Learning in Bioinformatics, Volume 113, Number 2, pp. 151-177, December 2011.
  [ Abstract | PDF | BibTeX ]
   
• ELISA CILIA, ANDREA PASSERINI
  Automatic prediction of catalytic residues by modeling residue structural neighborhood
  BMC Bioinformatics, Volume 11, Number 1, pp. 115, March 2010.
  [ Abstract | PDF | BibTeX ]
  
  

  CatANalyst - catalytic residue predictor

   
• ELISA CILIA, SERGIO AMMENDOLA
  Identification of the Amino Acid Residues Affecting the Catalytic Pocket of the Sulfolobus solfataricus Signature Amidase
  Protein & Peptide Letters, Volume 17, Number 2, pp. 146-150(5), February 2010.
  [ Abstract | PDF | BibTeX ]
   
• ELISA CILIA, ARMANDO FABBRI, MONICA URIANI, GIUSEPPE G. SCIALDONE, SERGIO AMMENDOLA
  The signature amidase from Sulfolobus solfataricus belongs to the CX3C subgroup of enzymes cleaving both amides and nitriles: Ser195 and Cys145 are predicted to be the active site nucleophiles
  FEBS Journal, Volume 272 , Issue 18, Pages 4716-4724, September 2005.
  [ Abstract | PDF | BibTeX ]
   

Conference proceedings

• ELISA CILIA, STEFANO TESO, SERGIO AMMENDOLA, TOM LENAERTS, ANDREA PASSERINI
  Predicting virus mutations through relational learning
  In Proceedings of the AIMM@ECCB2012 (Annotation, Interpretation and Management of Mutations Workshop 2012), Basel (Switzerland), September 9, 2012.
  [ Abstract | PDF | BibTeX ]
   
• ELISA CILIA, ANDREA PASSERINI
  Frankenstein Junior: a relational learning approach toward protein engineering
  In Proceedings of the AIMM@ECCB2010 (Annotation, Interpretation and Management of Mutations Workshop 2010), Ghent (Belgium), September 26, 2010.
  [ Abstract | PDF | BibTeX ]
   
• FRANCO MASCIA, ELISA CILIA, MAURO BRUNATO, ANDREA PASSERINI
  Predicting structural and functional sites in proteins by searching for maximum-weight cliques
  In Proceedings of the Twenty-Fourth AAAI Conference on Artificial Intelligence (AAAI-10), July 11-15, Atlanta, Georgia, USA.
  [ Abstract | PDF | BibTeX ]
   
• ELISA CILIA, NIELS LANDWEHR, ANDREA PASSERINI
  Mining Drug Resistance Relational Features with Hierarchical Multitask kFOIL
  In Proceedings of the Bio-Logical@AI*IA2009 Workshop (BIO-LOGICAL 2009), Reggio Emilia (Italy), December 12, 2009.
  [ PDF | BibTeX ]
   
• ELISA CILIA, ALESSANDRO MOSCHITTI
  Advanced Tree-Based kernels for Protein Classification
  In Proceeding of the 10th Congress of Italian Association for Artificial Intelligence (AI*IA 2007), Roma (RM), Italy, September 10-13, 2007.
  [ Abstract | PDF | BibTeX ]
   
• ELISA CILIA, ALESSANDRO MOSCHITTI, SERGIO AMMENDOLA, ROBERTO BASILI
  Structured Kernels for the Automatic Detection of Protein Active Sites
  In Proceedings of Mining and Learning with Graphs (MLG 2006) Workshop held in conjunction with ECML/PDKK Conference, Berlin, Germany, September 18-22, 2006.
  [ PDF | BibTeX ]
   

Technical reports

• S BECCARA, R ALFIERI, F ARTICO, G BILARDI, M BRAMBILLA, F BOSO, V M CAPPELLERI, A CESTARO, E CILIA, M CRISTOFORETTI, M DALLA BRIDA, M D'ANTONIO, F DI RENZO, C DESTRI, P FACCIOLI, C FANTOZZI, P FONTANA, G GARGANO, M GROSSI, A Y ILLARIONOV, R LEONARDI, W LEIDEMANN, G MARCHESINI, E MILANI, C MOSER, E ONOFRI, G ORLANDINI, F PEDERIVA, F PERUCH, E PESERICO, A PIETRACAPRINA, M PIVANTI, F POZZATI, G PUCCI, F RAPUANO, A RICHTER, M SEGA, S F SCHIFANO, M SCHIMD, M SCHWARZ, L SCORZATO, H SIMMA, T SKRBICA, E TAGLIAVINI, M TRAINI, R TRIPICCIONE, R VELASCO, P VERROCCHIO, F VERSACI, L YUAN, N ZAGO
  AuroraScience Project. Report on the First Phase
  ISBN: 978-88-907711-0-1, FBK Press, 2012.
   
• ELISA CILIA, ANDREA PASSERINI, MAURO BRUNATO
  Automatic Prediction of Functional Residues from Sequence and Structural Information
  Technical Report, DISI-08-036, Dipartimento di Ingegneria dell'Informazione, University of Trento, September 2008.
  [ Abstract | PDF | BibTeX ]
   

Other conference contributions

• WIM VRANKEN, TOM LENAERTS, ELISA CILIA
  Deriving networks of reciprocal amino acid influences on dynamics and secondary structure
  The BeNeLux Bioinformatics Conference (BBC) 2014, Luxembourg, 8-9 December 2014.
   
• ASHLEY CONARD, ELISA CILIA, TOM LENAERTS
  Determining the winning SH3 coalition: how cooperative game theory reveals the importance of domain residues in peptide binding
  The BeNeLux Bioinformatics Conference (BBC) 2014, Luxembourg, 8-9 December 2014.
   
• ANDREA GAZZO, DORIEN DANEELS, GUILLAME SMITS, SONIA VAN DOOREN, ELISA CILIA, TOM LENAERTS
  DIDA: a first database of digenic diseases
  The BeNeLux Bioinformatics Conference (BBC) 2014, Luxembourg, 8-9 December 2014.
   
• GURDEEP SINGH, ELISA CILIA, DANIELE RAIMONDI, WIM VRANKEN
  Effects of protein dynamics in predicting protein-protein interaction sites
  The BeNeLux Bioinformatics Conference (BBC) 2014, Luxembourg, 8-9 December 2014.
   
• ELISA CILIA, RITA PANCSA, PETER TOMPA, TOM LENAERTS, WIM VRANKEN
  Dynamine: a web-server for predicting protein dynamics from sequence
  The 13th European Conference on Computational Biology (ECCB) 2014, Strasbourg, France, 7-10 September 2014.
  [ Poster on F1000 ]
   
• ELISA CILIA, DANIELE RAIMONDI, TOM LENAERTS, WIM VRANKEN
  Applying dynamics-based interaction potentials in a residue network
  The 13th European Conference on Computational Biology (ECCB) 2014, Strasbourg, France, 7-10 September 2014.
   
• ELISA CILIA, RITA PANCSA, PETER TOMPA, TOM LENAERTS, WIM VRANKEN
  Dynamine: sequence-based protein backbone dynamics and disorder prediction
  The 11th Bioinformatics ITalian Society annual meeting (BITS) 2014, Rome, Italy, 26-28 February 2014.
   
• ELISA CILIA, RITA PANCSA, PETER TOMPA, TOM LENAERTS, WIM VRANKEN
  DynaMine: from protein sequence to dynamics and disorder
  The 8th BeNeLux Bioinformatics Conference (BBC) 2013, Brussels, Belgium, 9-10 December 2013.
   
• ASHLEY CONARD, ELISA CILIA, TOM LENAERTS
  Cooperative game theory and feature selection to describe dependencies between amino acid within the SH3 Fyn protein domain
  The Grace Hopper Celebration (GHC) of Women in Computing 2013, Minneapolis, United States, October 2-5, 2013.
   
• ELISA CILIA, GEERTEN W. VUISTER, TOM LENAERTS
  Accurate prediction of peptide-induced dynamical changes within the second PDZ domain of PTP1e
  Highlight presentation of the published paper at the ISMB/ECCB 2013, Berlin (Germany), July 20-23, 2013.
   
• ELISA CILIA, RITA PANCSA, PETER TOMPA, TOM LENAERTS, WIM VRANKEN
  Dynamine: sequence-based protein backbone dynamics and disorder prediction
  Poster at the ISMB/ECCB 2013 and 3D SIG, Berlin (Germany), July 18-23, 2013.
   
• ELISA CILIA, GEERTEN W. VUISTER, TOM LENAERTS
  Accurate prediction of peptide-induced dynamical changes within the second PDZ domain of PTP1e
  Abstract at the Benelux Bioinformatics Conference (BBC) 2012, Nijmegen (Netherlands), December 10-11, 2012.
   
• ELISA CILIA, TOM LENAERTS
  Betweenness measures on PDZ residue-contact networks are insufficient to predict their intra-domain communication.
  Poster at the Benelux Bioinformatics Conference (BBC) 2012, Nijmegen (Netherlands), December 10-11, 2012.
   
• ELISA CILIA, GEERTEN W. VUISTER, TOM LENAERTS
  Accurate prediction of peptide-induced dynamical changes within the second PDZ domain of PTP1e
  Abstract at the Netherlands Society on Biomolecular Modelling Fall Meeting 2012, Utrecht (Netherlands), November 26, 2012.
   
• ELISA CILIA, GEERTEN W. VUISTER, TOM LENAERTS
  Prediction of intra-protein communication pathways within the second PDZ domain of PTP1e
  Abstract and Poster at the International Conference on Bioinformatics and Computational Biology (BIOCOMP) 2012, Varna (Bulgaria), September 20-21, 2012.
   
• ELISA CILIA, GEERTEN W. VUISTER, TOM LENAERTS
  Accuracy of information flow predictions within the PTP1e PDZ2 domain
  Poster at the Benelux Bioinformatics Conference 2011, Luxembourg, December 12-13, 2011.
   
• ELISA CILIA, GEERTEN W. VUISTER, TOM LENAERTS
  Network flow analysis of allosteric couplings in the second PDZ domain of PTP-Bas and PTP-BL
  Poster at the Protein Modules and Networks in Health and Disease FEBS Workshop 2011, Seefeld (Austria), September 14-18, 2011.
   
• MARCO FALDA, STEFANO TOPPO, ALESSANDRO PESCAROLO, ENRICO LAVEZZO, BARBARA DI CAMILLO, ANDREA FACCHINETTI, ELISA CILIA, RICCARDO VELASCO, PAOLO FONTANA
  Argot2: a large-scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
  Poster at the Automated Function Prediction SIG 2011 - CAFA Challenge: Critical Assessment of Function Annotations, Vienna (Austria), July 15-16, 2011.
   
• MARCO FALDA, ALESSANDRO PESCAROLO, ENRICO LAVEZZO, BARBARA DI CAMILLO, ANDREA FACCHINETTI, ELISA CILIA, PAOLO FONTANA, STEFANO TOPPO
  Large-scale Function Prediction using Semantic Similarity of Weighted Gene Ontology Terms
  Abstract at the Eighth Annual Meeting of the Bioinformatics Italian Society (BITS 2011), Pisa (Italy), June 20-22, 2011.
  [ Abstract | PDF ]
   
• LUCA BIANCO, ELISA CILIA, MATTIA D'ANTONIO, ALESSANDRO CESTARO, A RICO, TIZIANA CASTRIGNANÒ, RICCARDO VELASCO, PAOLO FONTANA
  Improving the Malus x domestica genome assembly
  Poster at the Next Generation Sequencing Workshop, Bari (Italy), October 6-9, 2010.
   
• ELISA CILIA, ANDREA PASSERINI
  CatANalyst: a web server for predicting catalytic residues
  Poster presentation at the 9th European Conference on Computational Biology (ECCB 2010), Ghent (Belgium), September 26-29, 2010.
  [ Abstract | PDF ]

  CatANalyst - catalytic residue predictor

   
• ELISA CILIA, ANDREA PASSERINI, MAURO BRUNATO
  Automatic Prediction of Functional Residues from Sequence and Structural Information
  Abstract and presentation contribution at the 5th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2008), Vietri sul mare, Salerno (Italy) October 3-4, 2008.
   
• ELISA CILIA
  Graph isomorphism for Protein Active Site Detection
  Abstract and presentation contribution at the 22nd European Conference on Operational Research (EURO XXII), Prague, July 8-11, 2007.
   
• ELISA CILIA, MAURO BRUNATO
  Reactive Search: an Application to Protein Active Site Detection
  Abstract contribution at the Seventh Metaheuristics International Conference (MIC 2007), Montreal, Canada, June 25-29, 2007.
   
• ELISA CILIA
  Protein Active Site Detection using SVMs and Kernel Methods
  Abstract and presentation contribution at the Learning and Intelligent Optimization Workshop (LION 2007), Andalo (TN), Italy, February 12-17, 2007.
   

Theses

• ELISA CILIA
  

  Statistical and relational learning for understanding enzyme function

  Ph.D. Thesis, advisor Dr. Andrea Passerini, University of Trento, December 2010.
  [ Abstract / PDF | BibTeX ]
   
• ELISA CILIA
  Kernel arborei per la classificazione automatica di siti attivi in strutture proteiche
  Master Degree Thesis, supervisors Prof. Roberto Basili, Dr. Alessandro Moschitti and Dr. Sergio Ammendola, University of Rome "Tor Vergata", May 2006.
   
• ELISA CILIA
  ANALISI E SVILUPPO DI UN SENSORE SOFTWARE - SENSOR: un componente software non invasivo per l'acquisizione di dati di validazione per piattaforme HW/SW Real Time
  Degree Thesis, supervisors Prof. Giovanni Cantone, Dr. Ing. Guido Pennella, University of Rome "Tor Vergata", October 2003.