T
Toby J. Gibson
Researcher at European Bioinformatics Institute
Publications - 176
Citations - 177834
Toby J. Gibson is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Short linear motif & Eukaryotic Linear Motif resource. The author has an hindex of 78, co-authored 171 publications receiving 167371 citations. Previous affiliations of Toby J. Gibson include University of Rome Tor Vergata & University College Dublin.
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Journal ArticleDOI
Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins
Francesca Diella,Scott Cameron,Christine Gemünd,Rune Linding,Allegra Via,Bernhard Kuster,Thomas Sicheritz-Pontén,Nikolaj Blom,Toby J. Gibson +8 more
TL;DR: This work states that Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylated reactions.
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Understanding eukaryotic linear motifs and their role in cell signaling and regulation.
Francesca Diella,Niall J. Haslam,Claudia Chica,Aidan Budd,Sushama Michael,Nigel P. Brown,Gilles Travé,Toby J. Gibson +7 more
TL;DR: The current state of linear motif biology is summarized, which uses low affinity interactions to create cooperative, combinatorial and highly dynamic regulatory protein complexes, which suggest that models for cell regulatory networks in systems biology should neither be overly dependent on stochastic nor on smooth deterministic approximations.
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PH domain: the first anniversary.
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Improved sensitivity of profile searches through the use of sequence weights and gap excision
TL;DR: The performance of the database searches is enhanced by using a sequence weighting scheme which assigns higher weights to more distantly related sequences based on branch lengths derived from phylogenetic trees and the BLOSUM62 residue comparison matrix.
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Systematic discovery of new recognition peptides mediating protein interaction networks.
Victor Neduva,Rune Linding,Isabelle Su-Angrand,Alexander Stark,Federico De Masi,Toby J. Gibson,Joe Lewis,Luis Serrano,Robert B. Russell +8 more
TL;DR: The approach based on motif over-representation in non-homologous sequences, rediscovers known motifs and predicts dozens of others that will give molecular insight into protein networks and greatly illuminate cellular processes.