ArticleBMC bioinformatics2013
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA).
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- On the state of protein function prediction: a report on the fourth CAFA challenge.bioRxiv : the preprint server for biology · 2026Article
- Evaluating network-based algorithms for protein function prediction using plant protein-protein interaction networks.BMC plant biology · 2026Article
- Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).Journal of biomedical semantics · 2024Article
- Fine-tuning protein embeddings for functional similarity evaluation.Bioinformatics (Oxford, England) · 2024Article
- Article
- Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.PLoS computational biology · 2022Article
- Article
- TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.Genomics, proteomics & bioinformatics · 2022Article
- PANNZER-A practical tool for protein function prediction.Protein science : a publication of the Protein Society · 2022Article
- The language of proteins: NLP, machine learning & protein sequences.Computational and structural biotechnology journal · 2021Review
- SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction.Frontiers in bioengineering and biotechnology · 2020Article
- Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.PLoS computational biology · 2019Article
- Advances and Applications in the Quest for Orthologs.Molecular biology and evolution · 2019Article
- NetGO: improving large-scale protein function prediction with massive network information.Nucleic acids research · 2019Article
- MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.Journal of molecular biology · 2018Article
- Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions.Molecular & cellular proteomics : MCP · 2017Article
- EGAD: ultra-fast functional analysis of gene networks.Bioinformatics (Oxford, England) · 2017Article
- PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- Functional Annotations of Paralogs: A Blessing and a Curse.Life (Basel, Switzerland) · 2016Article
- An expanded evaluation of protein function prediction methods shows an improvement in accuracy.Genome biology · 2016Article
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2 authors.
Funding
Abstract
The assignment of gene function remains a difficult but important task in computational biology. The establishment of the first Critical Assessment of Functional Annotation (CAFA) was aimed at increasing progress in the field. We present an independent analysis of the results of CAFA, aimed at identifying challenges in assessment and at understanding trends in prediction performance. We found that well-accepted methods based on sequence similarity (i.e., BLAST) have a dominant effect. Many of the most informative predictions turned out to be either recovering existing knowledge about sequence similarity or were "post-dictions" already documented in the literature. These results indicate that deep challenges remain in even defining the task of function assignment, with a particular difficulty posed by the problem of defining function in a way that is not dependent on either flawed gold standards or the input data itself. In particular, we suggest that using the Gene Ontology (or other similar systematizations of function) as a gold standard is unlikely to be the way forward.
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Registered trials
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