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)

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)

Object-oriented parsing of biological databases with Python. - Chenna Ramu; Christine Gemünd; Toby J. Gibson (Bioinform., 2000)

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)

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)

GlobPlot: exploring protein sequences for globularity and disorder. - Rune Linding; Robert B. Russell; Victor Neduva; Toby J. Gibson (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2003)

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)

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; et al. (Bioinform., 2007)

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)

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)

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)

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)

EpiC: A Resource for Integrating Information and Analyses to Enable Selection of Epitopes for Antibody Based Experiments. - Niall J. Haslam; Toby J. Gibson (DILS, 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)

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)

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; et al. (Nucleic Acids Res., 2010)

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)

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)

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; et al. (Nucleic Acids Res., 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)

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)

The Roles of Short Linear Motifs in Human Diseases. - Bora Uyar; Toby J. Gibson (IWBBIO, 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; et al. (Nucleic Acids Res., 2014)

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; et al. (Nucleic Acids Res., 2016)

The eukaryotic linear motif resource - 2018 update. - Marc Gouw; Sushama Michael; Hugo Sámano-Sánchez; Manjeet Kumar; András Zeke; Benjamin Lang 001; Benoit Bely; Lucía B. Chemes; Norman E. Davey; Ziqi Deng; Francesca Diella; Clara-Marie Gürth; et al. (Nucleic Acids Res., 2018)

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)

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; et al. (Nucleic Acids Res., 2020)

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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2022)

LeishMANIAdb: a comparative resource for Leishmania 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)

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., 2024)