Toby J. Gibson

32 papers Journal 30Unranked 2
YearRankTypeTitle / Venue / Authors
2024 J jnl
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents.
PLoS Comput. Biol.
András Zeke, Toby J. Gibson, Laszlo Dobson
2023 J jnl
LeishMANIAdb: a comparative resource for
Database J. Biol. Databases Curation
Gábor E. Tusnády, András Zeke, Zsofia E. Kalman, Marie Fatoux-Ardore, Sylvie Ricard-Blum, Toby J. Gibson, Laszlo Dobson
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
2022 J jnl
The Eukaryotic Linear Motif resource: 2022 release.
Nucleic Acids Res.
Manjeet Kumar, Sushama Michael, Jesús Alvarado Valverde, Bálint Mészáros, Hugo Sámano-Sánchez, András Zeke, Laszlo Dobson, Tamas Lazar, Mihkel Örd, Anurag Nagpal, Nazanin Farahi, Melanie Käser, Ramya Kraleti, Norman E. Davey, Rita Pancsa, Lucía B. Chemes, Toby J. Gibson
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
2020 J jnl
The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification.
Database J. Biol. Databases Curation
Nicolas Palopoli, Javier Iserte, Lucía B. Chemes, Cristina Marino Buslje, Gustavo D. Parisi, Toby J. Gibson, Norman E. Davey
2018 J jnl
The eukaryotic linear motif resource - 2018 update.
Nucleic Acids Res.
Marc Gouw, Sushama Michael, Hugo Sámano-Sánchez, Manjeet Kumar, András Zeke, Benjamin Lang, Benoit Bely, Lucía B. Chemes, Norman E. Davey, Ziqi Deng, Francesca Diella, Clara-Marie Gürth, Ann-Kathrin Huber, Stefan Kleinsorg, Lara S. Schlegel, Nicolas Palopoli, Kim Van Roey, Brigitte Altenberg, Attila Reményi, Holger Dinkel, Toby J. Gibson
2016 J jnl
ELM 2016 - data update and new functionality of the eukaryotic linear motif resource.
Nucleic Acids Res.
Holger Dinkel, Kim Van Roey, Sushama Michael, Manjeet Kumar, Bora Uyar, Brigitte Altenberg, Vladislava Milchevskaya, Melanie Schneider, Helen Kühn, Annika Behrendt, Sophie Luise Dahl, Victoria Damerell, Sandra Diebel, Sara Kalman, Steffen Klein, Arne C. Knudsen, Christina Mäder, Sabina Merrill, Angelina Staudt, Vera Thiel, Lukas Welti, Norman E. Davey, Francesca Diella, Toby J. Gibson
2014 — conf
The Roles of Short Linear Motifs in Human Diseases.
IWBBIO
Bora Uyar, Toby J. Gibson
2014 J jnl
The eukaryotic linear motif resource ELM: 10 years and counting.
Nucleic Acids Res.
Holger Dinkel, Kim Van Roey, Sushama Michael, Norman E. Davey, Robert J. Weatheritt, Diana Born, Tobias Speck, Daniel Krüger, Gleb Grebnev, Marta Kuban, Marta Strumillo, Bora Uyar, Aidan Budd, Brigitte Altenberg, Markus Seiler, Lucía B. Chemes, Juliana Glavina, Ignacio E. Sánchez, Francesca Diella, Toby J. Gibson
2013 J jnl
Capturing cooperative interactions with the PSI-MI format.
Database J. Biol. Databases Curation
Kim Van Roey, Sandra E. Orchard, Samuel Kerrien, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob, Toby J. Gibson
2012 J jnl
ELM - the database of eukaryotic linear motifs.
Nucleic Acids Res.
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 J. Haslam, Gleb Grebnev, Richard J. Edwards, Michel O. Steinmetz, Heike Meiselbach, Francesca Diella, Toby J. Gibson
2012 J jnl
The identification of short linear motif-mediated interfaces within the human interactome.
Bioinform.
Robert J. Weatheritt, Katja Luck, Evangelia Petsalaki, Norman E. Davey, Toby J. Gibson
2012 J jnl
iELM - a web server to explore short linear motif-mediated interactions.
Nucleic Acids Res.
Robert J. Weatheritt, Peter Jehl, Holger Dinkel, Toby J. Gibson
2011 J jnl
Phospho.ELM: a database of phosphorylation sites - update 2011.
Nucleic Acids Res.
Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars Juhl Jensen, Toby J. Gibson, Francesca Diella
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 — conf
EpiC: A Resource for Integrating Information and Analyses to Enable Selection of Epitopes for Antibody Based Experiments.
DILS
Niall J. Haslam, Toby J. Gibson
2009 J jnl
KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors.
Bioinform.
Francesca Diella, Sophie Chabanis-Davidson, Katja Luck, Claudia Chica, Chenna Ramu, Claus Nerlov, Toby J. Gibson
2008 J jnl
A new protein linear motif benchmark for multiple sequence alignment software.
BMC Bioinform.
Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J. Gibson, Julie Dawn Thompson
2008 J jnl
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
BMC Bioinform.
Claudia Chica, Alberto Labarga, Cathryn M. Gould, Rodrigo Lopez, Toby J. Gibson
2008 J jnl
Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation.
Bioinform.
Sushama Michael, Gilles Travé, Chenna Ramu, Claudia Chica, Toby J. Gibson
2008 J jnl
Phospho.ELM: a database of phosphorylation sites - update 2008.
Nucleic Acids Res.
Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson
2007 J jnl
Clustal W and Clustal X version 2.0.
Bioinform.
Mark A. Larkin, Gordon Blackshields, Nigel P. Brown, R. Chenna, Paul A. McGettigan, Hamish McWilliam, Franck Valentin, Iain M. Wallace, Andreas Wilm, Rodrigo Lopez, Julie Dawn Thompson, Toby J. Gibson, Desmond G. Higgins
2004 J jnl
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins.
BMC Bioinform.
Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson
2003 J jnl
BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.
Nucleic Acids Res.
Konstantinos Bimpikis, Aidan Budd, Rune Linding, Toby J. Gibson
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
GlobPlot: exploring protein sequences for globularity and disorder.
Nucleic Acids Res.
Rune Linding, Robert B. Russell, Victor Neduva, Toby J. Gibson
2003 J jnl
Multiple sequence alignment with the Clustal series of programs.
Nucleic Acids Res.
Chenna Ramu, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie Dawn Thompson
2000 J jnl
Object-oriented parsing of biological databases with Python.
Bioinform.
Chenna Ramu, Christine Gemünd, Toby J. Gibson
1994 J jnl
Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases.
Nucleic Acids Res.
Toby J. Gibson, Julie Dawn Thompson
1994 J jnl
Improved sensitivity of profile searches through the use of sequence weights and gap excision.
Comput. Appl. Biosci.
Julie Dawn Thompson, Desmond G. Higgins, Toby J. Gibson