List of works - Julian Gough

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

scientific article published in December 2016

A comparison of profile hidden Markov model procedures for remote homology detection

scientific article

A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins

scientific article

A disease-drug-phenotype matrix inferred by walking on a functional domain network

scientific article

A domain-centric solution to functional genomics via dcGO Predictor

scientific article

A large-scale evaluation of computational protein function prediction

scientific article

A managerial model of investment: overlooked alternatives

A phylogenomic profile of globins

scientific article

A predictive computational framework for direct reprogramming between human cell types

scientific article

A promoter-level mammalian expression atlas

scientific article

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An atlas of human long non-coding RNAs with accurate 5' ends.

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

scientific article published on 11 January 2015

Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution

scientific article

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

scientific article published on 03 September 2019

Classification of intrinsically disordered regions and proteins

scientific article

Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins

scientific article published on September 2008

Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae

scientific article (publication date: June 2002)

Computational methods for direct cell conversion

scientific article

Convergent evolution of domain architectures (is rare).

scientific article published on 7 December 2004

DGEclust: differential expression analysis of clustered count data ⬇️

scientific article

DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

scientific article

Development and evaluation of an automated annotation pipeline and cDNA annotation system

scientific article

Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?

scientific article

Distinguishing protein-coding from non-coding RNAs through support vector machines

scientific article

D²P²: database of disordered protein predictions

scientific article

Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture

scientific article published on 17 June 2011

Evolution of the Calcium-Based Intracellular Signaling System

scientific article published on 29 June 2016

Evolution of the protein repertoire

scientific article

Evolutionarily consistent families in SCOP: sequence, structure and function

scientific article

Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5.

scientific article

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

scientific article published on 15 May 2015

Functional map and domain structure of MET, the product of the c- met protooncogene and receptor for hepatocyte growth factor/scatter factor ⬇️

scientific article published on October 3, 2003

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

scientific article

Genome3D: exploiting structure to help users understand their sequences

scientific article

Genomic and structural aspects of protein evolution

scientific article

Genomic scale sub-family assignment of protein domains

scientific article

Hologenome analysis of two marine sponges with different microbiomes

scientific article

Improving protein secondary structure prediction using a simple k-mer model

scientific article

InterPro in 2011: new developments in the family and domain prediction database

scientific article

InterPro in 2011: new developments in the family and domain prediction database

scientific article published on 19 May 2012

InterPro in 2017-beyond protein family and domain annotations

scientific article

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

article by Alex Mitchell et al published 6 November 2018 in Nucleic Acids Research

InterPro, progress and status in 2005

scientific article

InterPro: the integrative protein signature database

scientific article

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

scientific article published on 23 May 2017

Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer

scientific article published on August 2016

Mouse proteome analysis

scientific article

New developments in the InterPro database

scientific article

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.

scientific article

Predicting the functional consequences of cancer-associated amino acid substitutions

scientific article

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models

scientific article published on 2 November 2012

Proteins with class alpha/beta fold have high-level participation in fusion events

scientific article published on 01 July 2002

Ranking non-synonymous single nucleotide polymorphisms based on disease concepts

scientific article

SUPERFAMILY 1.75 including a domain-centric gene ontology method

scientific article

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny

scientific article

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments

scientific article (publication date: 2002)

Sequences and topology: disorder, modularity, and post/pre translation modification

scientific article published on 28 May 2013

Structured and disordered facets of the GPCR fold

scientific article published on August 2014

Supra-domains: evolutionary units larger than single protein domains

scientific article

The InterPro protein families database: the classification resource after 15 years

scientific article

The SUPERFAMILY 1.75 database in 2014: a doubling of data

scientific article

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.

scientific article published in January 2019

The SUPERFAMILY database in 2004: additions and improvements

scientific article

The SUPERFAMILY database in 2007: families and functions

scientific article

The SUPERFAMILY database in structural genomics

scientific article

The `dnet’ approach promotes emerging research on cancer patient survival

scientific article (publication date: 2014)

The evolution and structure prediction of coiled coils across all genomes

scientific article published on 9 September 2010

The evolution of human cells in terms of protein innovation

scientific article

The evolutionary dynamics of protein networks.

scientific article published on 11 October 2010

The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins

scientific article published in June 2004

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life

scientific article

Three reasons protein disorder analysis makes more sense in the light of collagen.

scientific article

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs

scientific article

TreeVector: scalable, interactive, phylogenetic trees for the web

scientific article published in 2010

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

scientific article published on 27 October 2016

supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map.

scientific article

List of works by Julian Gough

A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity

A comparison of profile hidden Markov model procedures for remote homology detection

A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins

A disease-drug-phenotype matrix inferred by walking on a functional domain network

A domain-centric solution to functional genomics via dcGO Predictor

A large-scale evaluation of computational protein function prediction

A managerial model of investment: overlooked alternatives

A phylogenomic profile of globins

A predictive computational framework for direct reprogramming between human cell types

A promoter-level mammalian expression atlas

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

An atlas of human long non-coding RNAs with accurate 5' ends.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

Classification of intrinsically disordered regions and proteins

Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins

Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae

Computational methods for direct cell conversion

Convergent evolution of domain architectures (is rare).

DGEclust: differential expression analysis of clustered count data ⬇️

DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

Development and evaluation of an automated annotation pipeline and cDNA annotation system

Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?

Distinguishing protein-coding from non-coding RNAs through support vector machines

D²P²: database of disordered protein predictions

Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture

Evolution of the Calcium-Based Intracellular Signaling System

Evolution of the protein repertoire

Evolutionarily consistent families in SCOP: sequence, structure and function

Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5.

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

Functional map and domain structure of MET, the product of the c- met protooncogene and receptor for hepatocyte growth factor/scatter factor ⬇️

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

Genome3D: exploiting structure to help users understand their sequences

Genomic and structural aspects of protein evolution

Genomic scale sub-family assignment of protein domains

Hologenome analysis of two marine sponges with different microbiomes

Improving protein secondary structure prediction using a simple k-mer model

InterPro in 2011: new developments in the family and domain prediction database

InterPro in 2011: new developments in the family and domain prediction database

InterPro in 2017-beyond protein family and domain annotations

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

InterPro, progress and status in 2005

InterPro: the integrative protein signature database

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer

Mouse proteome analysis

New developments in the InterPro database

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.

Predicting the functional consequences of cancer-associated amino acid substitutions

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models

Proteins with class alpha/beta fold have high-level participation in fusion events

Ranking non-synonymous single nucleotide polymorphisms based on disease concepts

SUPERFAMILY 1.75 including a domain-centric gene ontology method

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments

Sequences and topology: disorder, modularity, and post/pre translation modification

Structured and disordered facets of the GPCR fold

Supra-domains: evolutionary units larger than single protein domains

The InterPro protein families database: the classification resource after 15 years

The SUPERFAMILY 1.75 database in 2014: a doubling of data

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.

The SUPERFAMILY database in 2004: additions and improvements

The SUPERFAMILY database in 2007: families and functions

The SUPERFAMILY database in structural genomics

The `dnet’ approach promotes emerging research on cancer patient survival

The evolution and structure prediction of coiled coils across all genomes

The evolution of human cells in terms of protein innovation

The evolutionary dynamics of protein networks.

The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life

Three reasons protein disorder analysis makes more sense in the light of collagen.

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs

TreeVector: scalable, interactive, phylogenetic trees for the web

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals