List of works - Toby J. Gibson

A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins

scientific article

A careful disorderliness in the proteome: sites for interaction and targets for future therapies.

scientific article published on 20 February 2008

A community standard format for the representation of protein affinity reagents

scientific article

A comparative analysis to study editing of small noncoding BC200- and Alu transcripts in brain of prion-inoculated rhesus monkeys (M. Mulatta).

scientific article published in January 2012

A million peptide motifs for the molecular biologist

scientific article published on July 2014

A new method for isolating tyrosine kinase substrates used to identify Fish, an SH3 and PX domain-containing protein, and Src substrate ⬇️

scientific article published on August 3, 1998

A new protein linear motif benchmark for multiple sequence alignment software

scientific article

A regular pattern of two types of 100-residue motif in the sequence of titin

scientific journal article

A structure filter for the Eukaryotic Linear Motif Resource

scientific article

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

scientific article

An estimate of large-scale sequencing accuracy

scientific article published on July 2000

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

scientific journal article

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction

scientific article

Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei ⬇️

scientific article

Assignment of the 1H, 15N, and 13C resonances of the C-terminal domain of frataxin, the protein responsible for Friedreich ataxia

article

Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems

scientific article

Attributes of short linear motifs.

scientific article

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

scientific article

Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?

scientific article

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

scientific article

Capturing cooperative interactions with the PSI-MI format

scientific article (publication date: 2013)

Cell regulation: determined to signal discrete cooperation

scientific article

CiliaCarta: An integrated and validated compendium of ciliary genes

scientific article published on 16 May 2019

Clustal W and Clustal X version 2.0

scientific article (publication date: November 2007)

Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1.

scientific article

Degrons in cancer

scientific article published on 14 March 2017

Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60

scientific article

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation

scientific article published on 09 January 2008

Drift and conservation of differential exon usage across tissues in primate species

scientific article published on 03 September 2013

Dystrophin and utrophin: the missing links! ⬇️

scientific article published on August 1, 1995

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

scientific article

ELM--the database of eukaryotic linear motifs

scientific article

ELM: the status of the 2010 eukaryotic linear motif resource

scientific article

Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry

scientific article

EpiC: an open resource for exploring epitopes to aid antibody-based experiments

scientific article published on July 2010

Evidence for the concerted evolution between short linear protein motifs and their flanking regions

scientific article

Evidence in favour of ancient octaploidy in the vertebrate genome

scientific article

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

scientific article (publication date: 11 October 2011)

From sequence to structural analysis in protein phosphorylation motifs

scientific article published on January 2011

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries

scientific article

Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins

scientific article published on February 1998

Homology-based method for identification of protein repeats using statistical significance estimates

scientific article published in May 2000

How viruses hijack cell regulation

scientific article

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

scientific article

KH domains within the FMR1 sequence suggest that fragile X syndrome stems from a defect in RNA metabolism ⬇️

scientific article published on September 1, 1993

Linear motifs confer functional diversity onto splice variants

scientific article published on 25 May 2012

Linear motifs: lost in (pre)translation ⬇️

scientific article published on June 15, 2012

Malectin: A Novel Carbohydrate-binding Protein of the Endoplasmic Reticulum and a Candidate Player in the Early Steps of Protein N-Glycosylation

scientific article

Metabolic complexity in the RNA world and implications for the origin of protein synthesis ⬇️

scientific article published on January 1, 1990

Motif switches: decision-making in cell regulation

scientific article published on 03 April 2012

Multiple sequence alignment with the Clustal series of programs

scientific article

Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300.

scientific article published in April 2004

PH domain: the first anniversary

scientific article (publication date: September 1994)

Patterns and clusters within the PSM column in TiBS, 1992-2004.

scientific article published in December 2004

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

scientific article

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

scientific article published on 25 October 2007

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

scientific article

Phosphorylation of S776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors

scientific article

Possible editing of Alu transcripts in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD).

scientific article published in January 2011

Prion infected rhesus monkeys to study differential transcription of Alu DNA elements and editing of Alu transcripts in neuronal cells and blood cells

scientific article published on 2 March 2012

Protein disorder prediction: implications for structural proteomics

scientific article (publication date: November 2003)

Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?

scientific article published on October 2014

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

article

RACK1 research – ships passing in the night? ⬇️

scientific article published on 08 May 2012

Rop/Helix-loop-helix similarity ⬇️

scientific article published on January 1, 1991

RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein

scientific article published on 01 January 2001

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

scientific article

Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation.

scientific article

Solution structure of the DNA-binding domain of the yeast transcriptional activator protein GCN4

scientific article published on 01 October 1990

Solution structure of the basic region from the transcriptional activator GCN4

scientific article published on 01 February 1991

Structure of murine complement component C3. II. Nucleotide sequence of cloned complementary DNA coding for the alpha chain ⬇️

scientific article published on November 25, 1984

Systematic discovery of new recognition peptides mediating protein interaction networks

scientific article

The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor

scientific article

The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre

scientific journal article

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

scientific article published in December 1997

The eukaryotic linear motif resource ELM: 10 years and counting

scientific article (publication date: 2014)

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

scientific article published on 10 February 2012

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

scientific article published on 01 October 2001

The switches.ELM resource: a compendium of conditional regulatory interaction interfaces

scientific article published on 2 April 2013

The transience of transient overexpression

scientific article published on August 2013

Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD).

scientific article

Understanding eukaryotic linear motifs and their role in cell signaling and regulation.

scientific article

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

scientific article published on 25 May 2012

List of works by Toby J. Gibson

A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins

A careful disorderliness in the proteome: sites for interaction and targets for future therapies.

A community standard format for the representation of protein affinity reagents

A comparative analysis to study editing of small noncoding BC200- and Alu transcripts in brain of prion-inoculated rhesus monkeys (M. Mulatta).

A million peptide motifs for the molecular biologist

A new method for isolating tyrosine kinase substrates used to identify Fish, an SH3 and PX domain-containing protein, and Src substrate ⬇️

A new protein linear motif benchmark for multiple sequence alignment software

A regular pattern of two types of 100-residue motif in the sequence of titin

A structure filter for the Eukaryotic Linear Motif Resource

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

An estimate of large-scale sequencing accuracy

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction

Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei ⬇️

Assignment of the 1H, 15N, and 13C resonances of the C-terminal domain of frataxin, the protein responsible for Friedreich ataxia

Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems

Attributes of short linear motifs.

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

Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Capturing cooperative interactions with the PSI-MI format

Cell regulation: determined to signal discrete cooperation

CiliaCarta: An integrated and validated compendium of ciliary genes

Clustal W and Clustal X version 2.0

Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1.

Degrons in cancer

Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation

Drift and conservation of differential exon usage across tissues in primate species

Dystrophin and utrophin: the missing links! ⬇️

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

ELM--the database of eukaryotic linear motifs

ELM: the status of the 2010 eukaryotic linear motif resource

Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry

EpiC: an open resource for exploring epitopes to aid antibody-based experiments

Evidence for the concerted evolution between short linear protein motifs and their flanking regions

Evidence in favour of ancient octaploidy in the vertebrate genome

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

From sequence to structural analysis in protein phosphorylation motifs

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries

Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins

Homology-based method for identification of protein repeats using statistical significance estimates

How viruses hijack cell regulation

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

KH domains within the FMR1 sequence suggest that fragile X syndrome stems from a defect in RNA metabolism ⬇️

Linear motifs confer functional diversity onto splice variants

Linear motifs: lost in (pre)translation ⬇️

Malectin: A Novel Carbohydrate-binding Protein of the Endoplasmic Reticulum and a Candidate Player in the Early Steps of Protein N-Glycosylation

Metabolic complexity in the RNA world and implications for the origin of protein synthesis ⬇️

Motif switches: decision-making in cell regulation

Multiple sequence alignment with the Clustal series of programs

Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300.

PH domain: the first anniversary

Patterns and clusters within the PSM column in TiBS, 1992-2004.

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

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

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

Phosphorylation of S776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors

Possible editing of Alu transcripts in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD).

Prion infected rhesus monkeys to study differential transcription of Alu DNA elements and editing of Alu transcripts in neuronal cells and blood cells

Protein disorder prediction: implications for structural proteomics

Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

RACK1 research – ships passing in the night? ⬇️

Rop/Helix-loop-helix similarity ⬇️

RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation.

Solution structure of the DNA-binding domain of the yeast transcriptional activator protein GCN4

Solution structure of the basic region from the transcriptional activator GCN4

Structure of murine complement component C3. II. Nucleotide sequence of cloned complementary DNA coding for the alpha chain ⬇️

Systematic discovery of new recognition peptides mediating protein interaction networks

The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor

The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

The eukaryotic linear motif resource ELM: 10 years and counting

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

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

The switches.ELM resource: a compendium of conditional regulatory interaction interfaces