Toby J. Gibson

According to our database, Toby J. Gibson authored at least 32 papers between 1994 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents.

András Zeke, Toby J. Gibson, Laszlo Dobson

PLoS Comput. Biol., February, 2024

2023

LeishMANIAdb: a comparative resource for <i>Leishmania</i> proteins.

Gábor E. Tusnády, András Zeke, Zsofia E. Kalman, Marie Fatoux-Ardore, Sylvie Ricard-Blum, Toby J. Gibson, Laszlo Dobson

Database J. Biol. Databases Curation, 2023

2022

PDBe-KB: collaboratively defining the biological context of structural data.

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

Nucleic Acids Res., 2022

The Eukaryotic Linear Motif resource: 2022 release.

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

Nucleic Acids Res., 2022

2020

PDBe-KB: a community-driven resource for structural and functional annotations.

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

Nucleic Acids Res., 2020

The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification.

Nicolas Palopoli, Javier Iserte, Lucía B. Chemes, Cristina Marino Buslje, Gustavo D. Parisi, Toby J. Gibson, Norman E. Davey

Database J. Biol. Databases Curation, 2020

2018

The eukaryotic linear motif resource - 2018 update.

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

Nucleic Acids Res., 2018

2016

ELM 2016 - data update and new functionality of the eukaryotic linear motif resource.

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

Nucleic Acids Res., 2016

2014

The eukaryotic linear motif resource ELM: 10 years and counting.

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

Nucleic Acids Res., 2014

The Roles of Short Linear Motifs in Human Diseases.

Bora Uyar, Toby J. Gibson

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

2013

Capturing cooperative interactions with the PSI-MI format.

Kim Van Roey, Sandra E. Orchard, Samuel Kerrien, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob, Toby J. Gibson

Database J. Biol. Databases Curation, 2013

2012

iELM - a web server to explore short linear motif-mediated interactions.

Robert J. Weatheritt, Peter Jehl, Holger Dinkel, Toby J. Gibson

Nucleic Acids Res., 2012

ELM - the database of eukaryotic linear motifs.

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

Nucleic Acids Res., 2012

The identification of short linear motif-mediated interfaces within the human interactome.

Robert J. Weatheritt, Katja Luck, Evangelia Petsalaki, Norman E. Davey, Toby J. Gibson

Bioinform., 2012

2011

Phospho.ELM: a database of phosphorylation sites - update 2011.

Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars Juhl Jensen, Toby J. Gibson, Francesca Diella

Nucleic Acids Res., 2011

2010

ELM: the status of the 2010 eukaryotic linear motif resource.

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

Nucleic Acids Res., 2010

2009

A structure filter for the Eukaryotic Linear Motif Resource.

Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich

BMC Bioinform., 2009

KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors.

Francesca Diella, Sophie Chabanis-Davidson, Katja Luck, Claudia Chica, Chenna Ramu, Claus Nerlov, Toby J. Gibson

Bioinform., 2009

EpiC: A Resource for Integrating Information and Analyses to Enable Selection of Epitopes for Antibody Based Experiments.

Niall J. Haslam, Toby J. Gibson

Proceedings of the Data Integration in the Life Sciences, 6th International Workshop, 2009

2008

Phospho.ELM: a database of phosphorylation sites - update 2008.

Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson

Nucleic Acids Res., 2008

A new protein linear motif benchmark for multiple sequence alignment software.

Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J. Gibson, Julie Dawn Thompson

BMC Bioinform., 2008

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.

Claudia Chica, Alberto Labarga, Cathryn M. Gould, Rodrigo Lopez, Toby J. Gibson

BMC Bioinform., 2008

Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation.

Sushama Michael, Gilles Travé, Chenna Ramu, Claudia Chica, Toby J. Gibson

Bioinform., 2008

2007

Clustal W and Clustal X version 2.0.

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

Bioinform., 2007

2004

Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins.

Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson

BMC Bioinform., 2004

2003

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.

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

Nucleic Acids Res., 2003

GlobPlot: exploring protein sequences for globularity and disorder.

Rune Linding, Robert B. Russell, Victor Neduva, Toby J. Gibson

Nucleic Acids Res., 2003

Multiple sequence alignment with the Clustal series of programs.

Chenna Ramu, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie Dawn Thompson

Nucleic Acids Res., 2003

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.

Konstantinos Bimpikis, Aidan Budd, Rune Linding, Toby J. Gibson

Nucleic Acids Res., 2003

2000

Object-oriented parsing of biological databases with Python.

Chenna Ramu, Christine Gemünd, Toby J. Gibson

Bioinform., 2000

1994

Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases.

Toby J. Gibson, Julie Dawn Thompson

Nucleic Acids Res., 1994

Improved sensitivity of profile searches through the use of sequence weights and gap excision.

Julie Dawn Thompson, Desmond G. Higgins, Toby J. Gibson

Comput. Appl. Biosci., 1994