Toby J. Gibson - researchr alias

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Viewing Publication 1 - 32 from 32

2024

Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalentsAndrás Zeke, Toby J. Gibson, Laszlo Dobson. ploscb, 20(2), February 2024. [doi]

2023

Leishmania proteinsGábor E. Tusnády, András Zeke, Zsofia E. Kalman, Marie Fatoux-Ardore, Sylvie Ricard-Blum, Toby J. Gibson, Laszlo Dobson. biodb, 2023, 2023. [doi]

2022

PDBe-KB: collaboratively defining the biological context of structural dataMihaly 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 0001, 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. nar, 50(D1):534-542, 2022. [doi]

2020

The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classificationNicolas Palopoli, Javier Iserte, Lucía B. Chemes, Cristina Marino Buslje, Gustavo D. Parisi, Toby J. Gibson, Norman E. Davey. biodb, 2020, 2020. [doi]

PDBe-KB: a community-driven resource for structural and functional annotationsMihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath S. 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 0001, Henry J. Martell, Stuart 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 0001, 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. nar, 48(Database-Issue), 2020. [doi]

2018

2016

2014

2013

Capturing cooperative interactions with the PSI-MI formatKim Van Roey, Sandra E. Orchard, Samuel Kerrien, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob, Toby J. Gibson. biodb, 2013, 2013. [doi]

2012

iELM - a web server to explore short linear motif-mediated interactionsRobert J. Weatheritt, Peter Jehl, Holger Dinkel, Toby J. Gibson. nar, 40(Web-Server-Issue):364-369, 2012. [doi]

The identification of short linear motif-mediated interfaces within the human interactomeRobert J. Weatheritt, Katja Luck, E. Petsalaki, Norman E. Davey, Toby J. Gibson. bioinformatics, 28(7):976-982, 2012. [doi]

2011

Phospho.ELM: a database of phosphorylation sites - update 2011Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars J. Jensen, Toby J. Gibson, Francesca Diella. nar, 39(Database-Issue):261-267, 2011. [doi]

2010

2009

2008

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequencesClaudia Chica, Alberto Labarga, Cathryn M. Gould, Rodrigo Lopez, Toby J. Gibson. bmcbi, 9, 2008. [doi]

Phospho.ELM: a database of phosphorylation sites - update 2008Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, Toby J. Gibson. nar, 36(Database-Issue):240-244, 2008. [doi]

Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservationSushama Michael, Gilles Travé, Chenna Ramu, Claudia Chica, Toby J. Gibson. bioinformatics, 24(4):453-457, 2008. [doi]

A new protein linear motif benchmark for multiple sequence alignment softwareEmmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J. Gibson, Julie Dawn Thompson. bmcbi, 9, 2008. [doi]

2007

Clustal W and Clustal X version 2.0M. A. Larkin, Gordon Blackshields, N. 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. bioinformatics, 23(21):2947-2948, 2007. [doi]

2004

Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteinsFrancesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson. bmcbi, 5:79, 2004. [doi]

2003

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databasesKonstantinos Bimpikis, Aidan Budd, Rune Linding, Toby J. Gibson. nar, 31(13):3792-3794, 2003.

GlobPlot: exploring protein sequences for globularity and disorderRune Linding, Robert B. Russell, Victor Neduva, Toby J. Gibson. nar, 31(13):3701-3708, 2003.

Multiple sequence alignment with the Clustal series of programsChenna Ramu, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie Dawn Thompson. nar, 31(13):3497-3500, 2003.

2000

Object-oriented parsing of biological databases with PythonChenna Ramu, Christine Gemünd, Toby J. Gibson. bioinformatics, 16(7):628-638, 2000.

1994

Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicasesToby J. Gibson, Julie Dawn Thompson. nar, 22(13):2552-2556, 1994.

Improved sensitivity of profile searches through the use of sequence weights and gap excisionJulie Dawn Thompson, Desmond G. Higgins, Toby J. Gibson. bioinformatics, 10(1):19-29, 1994.

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2024

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2020

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2012

2011

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1994

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