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Journal Articles
- 2023
[j31]Prisca Lo Surdo
, Marta Iannuccelli, Silvia Contino, Luisa Castagnoli, Luana Licata, Gianni Cesareni, Livia Perfetto:
SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update. Nucleic Acids Res. 51(D1): 631-637 (2023)- 2022
- [j30]Ilaria De Marinis, Prisca Lo Surdo, Gianni Cesareni, Livia Perfetto:
SIGNORApp: a Cytoscape 3 application to access SIGNOR data. Bioinform. 38(6): 1764-1766 (2022) - [j29]Noemi del-Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin W. Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Bálint Mészáros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret J. Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwínski, Sandra E. Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob:
The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Res. 50(D1): 648-653 (2022) - 2020
- [j28]Livia Perfetto, Chiara Pastrello, Noemi del-Toro, Margaret J. Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, Kalpana Panneerselvam, Simona Panni, N. Rahimzadeh, Sylvie Ricard-Blum, Lukasz Salwínski, Anjali Shrivastava, Gianni Cesareni, Matteo Pellegrini, Sandra E. Orchard, Igor Jurisica, Henning Hermjakob, Pablo Porras:
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. Database J. Biol. Databases Curation 2020 (2020) - [j27]Stefano Pirrò, Filomena Spada, Emanuela Gadaleta, Federica Ferrentino, Graeme J. Thorn, Gianni Cesareni, Claude Chelala:
HiPPO and PANDA: Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data. J. Comput. Biol. 27(8): 1283-1294 (2020) - [j26]Marta Iannuccelli, Elisa Micarelli, Prisca Lo Surdo, Alessandro Palma, Livia Perfetto, Ilaria Rozzo, Luisa Castagnoli, Luana Licata, Gianni Cesareni:
CancerGeneNet: linking driver genes to cancer hallmarks. Nucleic Acids Res. 48(Database-Issue): D416-D421 (2020) - [j25]Luana Licata, Prisca Lo Surdo, Marta Iannuccelli, Alessandro Palma, Elisa Micarelli, Livia Perfetto, Daniele Peluso, Alberto Calderone, Luisa Castagnoli, Gianni Cesareni:
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. Nucleic Acids Res. 48(Database-Issue): D504-D510 (2020) - 2019
- [j24]Livia Perfetto, Marcio Luis Acencio, Glyn Bradley, Gianni Cesareni, Noemi del-Toro, Dávid Fazekas, Henning Hermjakob, Tamás Korcsmáros, Martin Kuiper, Astrid Lægreid, Prisca Lo Surdo, Ruth C. Lovering, Sandra E. Orchard, Pablo Porras, Paul D. Thomas, Vasundra Touré, John Zobolas, Luana Licata:
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinform. 35(19): 3779-3785 (2019) - 2018
- [j23]Alberto Calderone, Gianni Cesareni:
SPV: a JavaScript Signaling Pathway Visualizer. Bioinform. 34(15): 2684-2686 (2018) - [j22]M. Sivade Dumousseau, Diego Alonso-López, Mais G. Ammari, Glyn Bradley, Nancy H. Campbell, Arnaud Céol, Gianni Cesareni, Colin W. Combe, Javier De Las Rivas, Noemi del-Toro, Joshua Heimbach, Henning Hermjakob, Igor Jurisica, Maximilian Koch, Luana Licata, Ruth C. Lovering, David J. Lynn, Birgit H. M. Meldal, Gos Micklem, Simona Panni, Pablo Porras, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwínski, Anjali Shrivastava, Julie M. Sullivan, Nicolas Thierry-Mieg, Yo Yehudi, Kim Van Roey, Sandra E. Orchard:
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinform. 19(1): 134:1-134:8 (2018) - [j21]Prisca Lo Surdo, Alberto Calderone, Marta Iannuccelli, Luana Licata, Daniele Peluso, Luisa Castagnoli, Gianni Cesareni, Livia Perfetto:
DISNOR: a disease network open resource. Nucleic Acids Res. 46(Database-Issue): D527-D534 (2018) - 2016
- [j20]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:
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(Database-Issue): 38-47 (2016) - [j19]Livia Perfetto, Leonardo Briganti, Alberto Calderone, Andrea Cerquone Perpetuini, Marta Iannuccelli, Francesca Langone, Luana Licata, Milica Marinkovic, Anna Mattioni, Theodora Pavlidou, Daniele Peluso, Lucia Lisa Petrilli, Stefano Pirrò, Daniela Posca, Elena Santonico, Alessandra Silvestri, Filomena Spada, Luisa Castagnoli, Gianni Cesareni:
SIGNOR: a database of causal relationships between biological entities. Nucleic Acids Res. 44(Database-Issue): 548-554 (2016) - 2015
- [j18]Eugenia Galeota, Caius Gavrila, Filippo Castiglione, Massimo Bernaschi, Gianni Cesareni:
The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells. BMC Syst. Biol. 9(S-3): S3 (2015) - [j17]Alberto Calderone, Luana Licata, Gianni Cesareni:
VirusMentha: a new resource for virus-host protein interactions. Nucleic Acids Res. 43(Database-Issue): 588-592 (2015) - 2014
- [j16]Sandra E. Orchard, Mais G. Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Eugenia Galeota, Ursula Hinz, Marta Iannuccelli, Sruthi Jagannathan, Rafael C. Jiménez, Jyoti Khadake, Astrid Lægreid, Luana Licata, Ruth C. Lovering, Birgit Meldal, Anna N. Melidoni, Mila Milagros, Daniele Peluso, Livia Perfetto, Pablo Porras, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Andre Stutz, Michael Tognolli, Kim Van Roey, Gianni Cesareni, Henning Hermjakob:
The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 42(Database-Issue): 358-363 (2014) - 2012
- [j15]Luana Licata, Leonardo Briganti, Daniele Peluso, Livia Perfetto, Marta Iannuccelli, Eugenia Galeota, Francesca Sacco, Anita Palma, Aurelio Nardozza, Elena Santonico, Luisa Castagnoli, Gianni Cesareni:
MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 40(Database-Issue): 857-861 (2012) - 2011
- [j14]Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis M. Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu:
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12(S-8): S3 (2011) - [j13]Cecilia N. Arighi, Phoebe M. Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle G. Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J. Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman, Cathy H. Wu:
BioCreative III interactive task: an overview. BMC Bioinform. 12(S-8): S4 (2011) - [j12]Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers:
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. BMC Bioinform. 12(S-8): S8 (2011) - 2010
- [j11]Damian Smedley, Paul N. Schofield, Chao-Kung Chen, Vassilis Aidinis, Crysanthi Ainali, Jonathan B. L. Bard, Rudi Balling, Ewan Birney, Andrew Blake, Erik Bongcam-Rudloff, Anthony J. Brookes, Gianni Cesareni, Christina Chandras, Janan T. Eppig, Paul Flicek, Georgios V. Gkoutos, Simon Greenaway, Michael Gruenberger, Jean-Karim Hériché, Andrew Lyall, Ann-Marie Mallon, Dawn Muddyman, Florian Reisinger, Martin Ringwald, Nadia A. Rosenthal, Klaus Schughart, Morris A. Swertz, Gudmundur A. Thorisson, Michael Zouberakis, John M. Hancock:
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database J. Biol. Databases Curation 2010 (2010) - [j10]Arnaud Céol, Andrew Chatr-aryamontri, Luana Licata, Daniele Peluso, Leonardo Briganti, Livia Perfetto, Luisa Castagnoli, Gianni Cesareni:
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res. 38(Database-Issue): 532-539 (2010) - [j9]Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia:
An Overview of BioCreative II.5. IEEE ACM Trans. Comput. Biol. Bioinform. 7(3): 385-399 (2010) - 2009
- [j8]Andrew Chatr-aryamontri, Arnaud Céol, Daniele Peluso, Aurelio Nardozza, Simona Panni, Francesca Sacco, Michele Tinti, Alex Smolyar, Luisa Castagnoli, Marc Vidal, Michael E. Cusick, Gianni Cesareni:
VirusMINT: a viral protein interaction database. Nucleic Acids Res. 37(Database-Issue): 669-673 (2009) - 2007
- [j7]Massimo Bernaschi, Filippo Castiglione, Alessandra Ferranti, Caius Gavrila, Michele Tinti, Gianni Cesareni:
ProtNet: a tool for stochastic simulations of protein interaction networks dynamics. BMC Bioinform. 8(S-1) (2007) - [j6]Arnaud Céol, Andrew Chatr-aryamontri, Elena Santonico, Roberto Sacco, Luisa Castagnoli, Gianni Cesareni:
DOMINO: a database of domain-peptide interactions. Nucleic Acids Res. 35(Database-Issue): 557-560 (2007) - [j5]Andrew Chatr-aryamontri, Arnaud Céol, Luisa Montecchi-Palazzi, Giuliano Nardelli, Maria Victoria Schneider, Luisa Castagnoli, Gianni Cesareni:
MINT: the Molecular INTeraction database. Nucleic Acids Res. 35(Database-Issue): 572-574 (2007) - 2005
- [j4]Maria Persico, Arnaud Céol, Caius Gavrila, Robert Hoffmann, Arnaldo Florio, Gianni Cesareni:
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinform. 6(S-4) (2005) - 2004
- [j3]Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra E. Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David James Sherman, Rolf Apweiler:
IntAct: an open source molecular interaction database. Nucleic Acids Res. 32(Database-Issue): 452-455 (2004) - 2003
- [j2]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 Res. 31(13): 3625-3630 (2003) - 1987
- [j1]Franco Felici, Gianni Cesareni:
Structure of the Saccharomyces cerevisiae gene encoding tRNAIle (IAU). Nucleic Acids Res. 15(1): 364 (1987)
Conference and Workshop Papers
- 2017
- [c1]Alberto Calderone, Luana Licata, Elisa Micarelli, Livia Perfetto, Gianni Cesareni:
Revealing Disease Similarities by Text Mining. SWAT4LS 2017
Informal and Other Publications
- 2018
- [i1]Alberto Calderone, Gianni Cesareni:
Analysis of Triplet Motifs in Biological Signed Oriented Graphs Suggests a Relationship Between Fine Topology and Function. CoRR abs/1803.06520 (2018)
Coauthor Index
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