Manuela Helmer-Citterich

40 papers Journal 40
YearRankTypeTitle / Venue / Authors
2022 J jnl
PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Res.
Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2021 J jnl
BRIO: a web server for RNA sequence and structure motif scan.
Nucleic Acids Res.
Andrea Guarracino, Gerardo Pepe, Francesco Ballesio, Marta Adinolfi, Marco Pietrosanto, Elisa Sangiovanni, Ilio Vitale, Gabriele Ausiello, Manuela Helmer-Citterich
2020 J jnl
PDBe-KB: a community-driven resource for structural and functional annotations.
Nucleic Acids Res.
Mihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath Nair, Aleksandras Gutmanas, David R. Armstrong, Lukás Pravda, Bissan Al-Lazikani, Stephen Anyango, Geoffrey J. Barton, Karel Berka, Tom L. Blundell, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2019 J jnl
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes.
Bioinform.
Luca Parca, Bruno Ariano, Andrea Cabibbo, Marco Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich
2018 J jnl
BEAM web server: a tool for structural RNA motif discovery.
Bioinform.
Marco Pietrosanto, Marta Adinolfi, Riccardo Casula, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich
2016 J jnl
Revealing protein-lncRNA interaction.
Briefings Bioinform.
Fabrizio Ferrè, Alessio Colantoni, Manuela Helmer-Citterich
2016 J jnl
Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res.
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. Jiménez, 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
2015 J jnl
Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics.
BMC Bioinform.
Angelo M. Facchiano, Claudia Angelini, Roberta Bosotti, Alessandro Guffanti, Anna Marabotti, Roberto Marangoni, Stefano Pascarella, Paolo Romano, Andreas Zanzoni, Manuela Helmer-Citterich
2015 J jnl
Web-Beagle: a web server for the alignment of RNA secondary structures.
Nucleic Acids Res.
Eugenio Mattei, Marco Pietrosanto, Fabrizio Ferrè, Manuela Helmer-Citterich
2013 J jnl
Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics.
BMC Bioinform.
Carmela Gissi, Paolo Romano, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Angelo M. Facchiano, Manuela Helmer-Citterich
2013 J jnl
DBATE: database of alternative transcripts expression.
Database J. Biol. Databases Curation
Valerio Bianchi, Alessio Colantoni, Alberto Calderone, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich
2013 J jnl
Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.
Nucleic Acids Res.
Luca Parca, Fabrizio Ferrè, Gabriele Ausiello, Manuela Helmer-Citterich
2013 J jnl
webPDBinder: a server for the identification of ligand binding sites on protein structures.
Nucleic Acids Res.
Valerio Bianchi, Iolanda Mangone, Fabrizio Ferrè, Manuela Helmer-Citterich, Gabriele Ausiello
2012 J jnl
Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics.
BMC Bioinform.
Paolo Romano, Manuela Helmer-Citterich
2012 J jnl
Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.
BMC Bioinform.
Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich, Gabriele Ausiello
2012 J jnl
Modeling gene regulatory network motifs using statecharts.
BMC Bioinform.
Fabio Fioravanti, Manuela Helmer-Citterich, Enrico Nardelli
2011 J jnl
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.
Nucleic Acids Res.
Luca Parca, Iolanda Mangone, Pier Federico Gherardini, Gabriele Ausiello, Manuela Helmer-Citterich
2011 J jnl
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.
Nucleic Acids Res.
Andreas Zanzoni, Daniel Carbajo, Francesca Diella, Pier Federico Gherardini, Anna Tramontano, Manuela Helmer-Citterich, Allegra Via
2010 J jnl
ELM: the status of the 2010 eukaryotic linear motif resource.
Nucleic Acids Res.
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
2009 J jnl
A structure filter for the Eukaryotic Linear Motif Resource.
BMC Bioinform.
Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich
2009 J jnl
Structural motifs recurring in different folds recognize the same ligand fragments.
BMC Bioinform.
Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani, Manuela Helmer-Citterich
2008 J jnl
Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics.
BMC Bioinform.
Graziano Pesole, Manuela Helmer-Citterich
2008 J jnl
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.
BMC Bioinform.
Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich
2007 J jnl
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.
Nucleic Acids Res.
Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich
2007 J jnl
Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics.
BMC Bioinform.
Rita Casadio, Manuela Helmer-Citterich, Graziano Pesole
2007 J jnl
False occurrences of functional motifs in protein sequences highlight evolutionary constraints.
BMC Bioinform.
Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich
2007 J jnl
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites.
BMC Bioinform.
Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich
2007 J jnl
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.
Nucleic Acids Res.
Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich
2007 J jnl
SH3-Hunter: discovery of SH3 domain interaction sites in proteins.
Nucleic Acids Res.
Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
2006 J jnl
A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity.
Bioinform.
Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
2005 J jnl
A neural strategy for the inference of SH3 domain-peptide interaction specificity.
BMC Bioinform.
Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
2005 J jnl
Functional annotation by identification of local surface similarities: a novel tool for structural genomics.
BMC Bioinform.
Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich
2005 J jnl
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society.
BMC Bioinform.
Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone
2005 J jnl
Query3d: a new method for high-throughput analysis of functional residues in protein structures.
BMC Bioinform.
Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich
2005 J jnl
Seq2Struct: a resource for establishing sequence-structure links.
Bioinform.
Allegra Via, Andreas Zanzoni, Manuela Helmer-Citterich
2005 J jnl
pdbFun: mass selection and fast comparison of annotated PDB residues.
Nucleic Acids Res.
Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich
2004 J jnl
A structural study for the optimisation of functional motifs encoded in protein sequences.
BMC Bioinform.
Allegra Via, Manuela Helmer-Citterich
2004 J jnl
SURFACE: a database of protein surface regions for functional annotation.
Nucleic Acids Res.
Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich
2003 J jnl
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Nucleic Acids Res.
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
2003 J jnl
iSPOT: a web tool to infer the interaction specificity of families of protein modules.
Nucleic Acids Res.
Barbara Brannetti, Manuela Helmer-Citterich