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Gianni Cesareni
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2020 – today
- 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)
2010 – 2019
- 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) - [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) - 2017
- [c1]Alberto Calderone, Luana Licata, Elisa Micarelli, Livia Perfetto, Gianni Cesareni:
Revealing Disease Similarities by Text Mining. SWAT4LS 2017 - 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)
2000 – 2009
- 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)
1980 – 1989
- 1987
- [j1]Franco Felici
, Gianni Cesareni:
Structure of the Saccharomyces cerevisiae gene encoding tRNAIle (IAU). Nucleic Acids Res. 15(1): 364 (1987)
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