Manuela Helmer-Citterich

Marco Pietrosanto, Marta Adinolfi, Riccardo Casula, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich:
BEAM web server: a tool for structural RNA motif discovery. Bioinformatics 34(6): 1058-1060 (2018)

Fabrizio Ferrè, Alessio Colantoni, Manuela Helmer-Citterich:
Revealing protein-lncRNA interaction. Briefings in Bioinformatics 17(1): 106-116 (2016)

Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak:
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research 44(Database-Issue): 38-47 (2016)

Angelo M. Facchiano, Claudia Angelini, Roberta Bosotti, Alessandro Guffanti, Anna Marabotti, Roberto Marangoni, Stefano Pascarella, Paolo Romano, Andreas Zanzoni, Manuela Helmer-Citterich:
Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 16(S-9): S1 (2015)

Eugenio Mattei, Marco Pietrosanto, Fabrizio Ferrè, Manuela Helmer-Citterich:
Web-Beagle: a web server for the alignment of RNA secondary structures. Nucleic Acids Research 43(Webserver-Issue): W493-W497 (2015)

Valerio Bianchi, Alessio Colantoni, Alberto Calderone, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich:
DBATE: database of alternative transcripts expression. Database 2013 (2013)

Carmela Gissi, Paolo Romano, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Angelo M. Facchiano, Manuela Helmer-Citterich:
Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 14(S-7): S1 (2013)

Luca Parca, Fabrizio Ferrè, Gabriele Ausiello, Manuela Helmer-Citterich:
Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. Nucleic Acids Research 41(Webserver-Issue): 281-285 (2013)

Valerio Bianchi, Iolanda Mangone, Fabrizio Ferrè, Manuela Helmer-Citterich, Gabriele Ausiello:
webPDBinder: a server for the identification of ligand binding sites on protein structures. Nucleic Acids Research 41(Webserver-Issue): 308-313 (2013)

Paolo Romano, Manuela Helmer-Citterich:
Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 13(S-4): I1 (2012)

Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich, Gabriele Ausiello:
Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics 13(S-4): S17 (2012)

Fabio Fioravanti, Manuela Helmer-Citterich, Enrico Nardelli:
Modeling gene regulatory network motifs using statecharts. BMC Bioinformatics 13(S-4): S20 (2012)

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)

Luca Parca, Iolanda Mangone, Pier Federico Gherardini, Gabriele Ausiello, Manuela Helmer-Citterich:
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Research 39(Web-Server-Issue): 278-282 (2011)

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)

Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani, Manuela Helmer-Citterich:
Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics 10 (2009)

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)

Graziano Pesole, Manuela Helmer-Citterich:
Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 9(S-2) (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)

Rita Casadio, Manuela Helmer-Citterich, Graziano Pesole:
Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics. 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)

Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich:
Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics 6: 194 (2005)

Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone:
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. 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)

Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich:
SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Research 32(Database-Issue): 240-244 (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)

Barbara Brannetti, Manuela Helmer-Citterich:
iSPOT: a web tool to infer the interaction specificity of families of protein modules. Nucleic Acids Research 31(13): 3709-3711 (2003)