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List of works by Darren A. Natale

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

scientific article

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

scientific article published on 21 October 2022

A domain ontology for the Non-Coding RNA field

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions

article

Annotation of biologically relevant ligands in UniProtKB using ChEBI

scientific article published on 9 December 2022

BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks

scientific article published on 18 May 2020

COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases

scientific article published on 10 September 2020

COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model

scientific article published on 27 April 2021

Community annotation in biology

scientific article (publication date: 18 February 2010)

Computational clustering for viral reference proteomes.

scientific article published on 26 February 2016

Computational identification of strain-, species- and genus-specific proteins

scientific article

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes

scientific article

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework

scientific article published on 18 June 2015

Framework for a protein ontology

scientific article

Framework for a protein ontology

GlyGen data model and processing workflow

scientific article published on 23 April 2020

GlyGen: Computational and Informatics Resources for Glycoscience

scientific article published on 01 January 2020

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources.

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: the integrative protein signature database

scientific article

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis

scientific article

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

scientific article published on 13 October 2021

OMIT: dynamic, semi-automated ontology development for the microRNA domain

scientific article

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data

scientific article

PIRSF: family classification system at the Protein Information Resource

scientific article

PIRSitePredict for protein functional site prediction using position-specific rules

Perspectives on tracking data reuse across biodata resources

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

scientific article

Protein Ontology: a controlled structured network of protein entities

scientific article

Protein ontology on the semantic web for knowledge discovery

scientific article published on 12 October 2020

Protein-centric data integration for functional analysis of comparative proteomics data

scientific article

Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes

scientific article

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

scientific article (publication date: 2012)

Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

scientific article

Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology

scientific article published on August 2016

Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase

scientific article

TGF-beta signaling proteins and the Protein Ontology

scientific article

The COG database: an updated version includes eukaryotes

scientific article

The InterPro protein families and domains database: 20 years on

scientific article published on 06 November 2020

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

scientific article

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

scientific article

The Protein Ontology: a structured representation of protein forms and complexes

scientific article

The Universal Protein Resource (UniProt)

scientific article

The Universal Protein Resource (UniProt): an expanding universe of protein information

scientific article

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

scientific article

The development of non-coding RNA ontology

scientific article published on January 2016

The representation of protein complexes in the Protein Ontology (PRO).

scientific article

Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

scientific article

Tutorial on Protein Ontology Resources

scientific article published on January 2017

UniProt: the Universal Protein Knowledgebase in 2023

scientific article published on 21 November 2022

UniProt: the Universal Protein knowledgebase

scientific article from 2004

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

scientific article published on 12 May 2020

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

scientific article published in December 2020

Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint

scientific article published on 26 April 2013

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