Allegra Via

Maria Victoria Schneider, Peter Walter, Marie-Claude Blatter, James Watson, Michelle D. Brazas, Kristian Rother, Aidan Budd, Allegra Via, Celia W. G. van Gelder, Joachim Jacob, Pedro Fernandes, Tommi H. Nyrönen, Javier De Las Rivas, Thomas Blicher, Rafael C. Jimenez, Jane Loveland, Jennifer McDowall, Philip Jones, Brendan W. Vaughan, Rodrigo Lopez, Teresa K. Attwood, Catherine Brooksbank: Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. Briefings in Bioinformatics 13(3): 383-389 (2012)

Holger Dinkel, Sushama Michael, Robert J. Weatheritt, Norman E. Davey, Kim Van Roey, Brigitte Altenberg, Grischa Toedt, Bora Uyar, Markus Seiler, Aidan Budd, Lisa Jödicke, Marcel A. Dammert, Christian Schroeter, Maria Hammer, Tobias Schmidt, Peter Jehl, Caroline McGuigan, Magdalena Dymecka, Claudia Chica, Katja Luck, Allegra Via, Andrew Chatr-aryamontri, Niall Haslam, Gleb Grebnev, Richard J. Edwards, Michel O. Steinmetz, Heike Meiselbach, Francesca Diella, Toby J. Gibson: ELM - the database of eukaryotic linear motifs. Nucleic Acids Research 40(Database-Issue): 242-251 (2012)

Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars Juhl Jensen, Toby J. Gibson, Francesca Diella: Phospho.ELM: a database of phosphorylation sites - update 2011. Nucleic Acids Research 39(Database-Issue): 261-267 (2011)

Andreas Zanzoni, Daniel Carbajo, Francesca Diella, Pier Federico Gherardini, Anna Tramontano, Manuela Helmer-Citterich, Allegra Via: Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Research 39(Database-Issue): 268-271 (2011)

Allegra Via, Javier De Las Rivas, Teresa K. Attwood, David Landsman, Michelle D. Brazas, Jack A. M. Leunissen, Anna Tramontano, Maria Victoria Schneider: Ten Simple Rules for Developing a Short Bioinformatics Training Course. PLoS Computational Biology 7(10) (2011)

Maria Victoria Schneider, James Watson, Teresa K. Attwood, Kristian Rother, Aidan Budd, Jennifer McDowall, Allegra Via, Pedro Fernandes, Tommi H. Nyrönen, Thomas Blicher, Philip Jones, Marie-Claude Blatter, Javier De Las Rivas, David Phillip Judge, Wouter van der Gool, Catherine Brooksbank: Bioinformatics training: a review of challenges, actions and support requirements. Briefings in Bioinformatics 11(6): 544-551 (2010)

Cathryn M. Gould, Francesca Diella, Allegra Via, Pål Puntervoll, Christine Gemünd, Sophie Chabanis-Davidson, Sushama Michael, Ahmed Sayadi, Jan Christian Bryne, Claudia Chica, Markus Seiler, Norman E. Davey, Niall J. Haslam, Robert J. Weatheritt, Aidan Budd, Tim Hughes, Jakub Pas, Leszek Rychlewski, Gilles Travé, Rein Aasland, Manuela Helmer-Citterich, Rune Linding, Toby J. Gibson: ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Research 38(Database-Issue): 167-180 (2010)

Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich: A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics 10: 351 (2009)

Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich: FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics 9(S-2) (2008)

Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson: Phospho.ELM: a database of phosphorylation sites - update 2008. Nucleic Acids Research 36(Database-Issue): 240-244 (2008)

Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich: Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics 8(S-1) (2007)

Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich: False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinformatics 8 (2007)

Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich: Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Research 35(Database-Issue): 229-231 (2007)

Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich: 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Research 35(Web-Server-Issue): 416-419 (2007)

Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich: SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucleic Acids Research 35(Web-Server-Issue): 451-454 (2007)

Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich: A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinformatics 22(19): 2333-2339 (2006)

Allegra Via, Andreas Zanzoni, Manuela Helmer-Citterich: Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics 21(4): 551-553 (2005)

Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich: Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics 6(S-4) (2005)

Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich: A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinformatics 6(S-4) (2005)

Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich: pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Research 33(Web-Server-Issue): 133-137 (2005)

Allegra Via, Manuela Helmer-Citterich: A structural study for the optimisation of functional motifs encoded in protein sequences. BMC Bioinformatics 5: 50 (2004)

Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson: Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5: 79 (2004)

Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M. A. Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Stanislaw Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson: ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research 31(13): 3625-3630 (2003)