Large-scale ontologies like the Gene Ontology (GO) provide essential background knowledge for understanding protein activity. We develop the DeepGO family of systems, which utilize formalized axioms to constrain deep learning models for protein function prediction. These systems are used to derive functional insights from sequence and interaction data.
- Section
- Applications
- Keywords
- Gene Ontology, GO, DeepGO, DeepGOPlus, DeepGO-SE, DeepGOZero, protein function, semantic entailment, metagenomics function
Connections
related papers borg:linkedPaper
- Predicting protein functions using positive-unlabeled ranking with ontology-based priors
- DeepGOPlus: improved protein function prediction from sequence
- Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
- DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
- DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
- DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
- DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
- LLM Agent Based Protein Function Prediction
- Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
- Exploring Gene Ontology Annotations with OWL
- Computational prediction of protein functional annotations
- Annotating genomes with DeepGO protein function prediction tools
related projects borg:linkedProject
related people borg:linkedPerson
related courses borg:linkedCourse
Referenced by
research topics borg:topic
- Enabling desert revegetation by AI-tailored soil microbiome fortification
- Evolutionary potential of corals to adapt to climate warming
- Computational methods for functional metagenomics: from protein functions to multi-scale interactions
- Robert Hoehndorf
- Imane Boudellioua
- Maxat Kulmanov
- Rund Tawfiq
- Yang Liu
- Daulet Toibazar
- Amal Alhelal
- Md Nurul Muttakin
- Shahad Qatan
- Kexin Niu
- Zhenwei Tang
- Asaad Mohammedsaleh
- Heribert Hirt
- Gabriel Wittum
- Arne Nägel
- Manuel Aranda
- Takashi Gojobori
- DeepGOPlus: improved protein function prediction from sequence
- Predicting protein functions using positive-unlabeled ranking with ontology-based priors
- Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
- DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
- DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
- DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
- DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
- LLM Agent Based Protein Function Prediction
- Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
- Exploring Gene Ontology Annotations with OWL
- Computational prediction of protein functional annotations
- Annotating genomes with DeepGO protein function prediction tools
- Application of AI in Bioinformatics
- Algorithms in Bioinformatics
- Algorithms in Bioinformatics
- Algorithms in Bioinformatics
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