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The annotation of genomic information is a major challenge in biology and bioinformatics. Existing databases of known gene functions are incomplete and prone to errors, and the bimolecular experiments needed to improve these databases are slow and costly. While computational methods are not a substitute for experimental verification, they can help in two(More)
Consistency and completeness of biomolecular annotations is a keypoint of correct interpretation of biological experiments. Yet, the associations between genes (or proteins) and features correctly annotated are just some of all the existing ones. As time goes by, they increase in number and become more useful, but they remain incomplete and some of them(More)
— Truncated Singular Value Decomposition (SVD) has always been a key algorithm in modern machine learning. Scientists and researchers use this applied mathematics method in many fields. Despite a long history and prevalence, the issue of how to choose the best truncation level still remains an open challenge. In this paper, we describe a new algorithm, akin(More)
Genomic annotations describing structural and functional features of genes and gene products through controlled terminologies and ontologies are extremely valuable, especially for computational analyses aimed at inferring new biomedical knowledge, which rely on available annotations. Yet, they are incomplete, especially for recently studied genomes, and(More)
Biomolecular annotation databases are very important in modern biomedical and genetic research. Correct interpretation of biological experiments depends on consistency and completeness of such databases. To improve their quality and coverage, computational methods that are able to supply a ranked list of predicted gene or gene products annotations are(More)
Gene function annotations are key elements in biology and bioinformatics. A typical annotation is the association between a gene and a feature term that describes a functional feature of the gene by using a controlled vocabulary term (e.g. a Gene Ontology (GO) feature term). Unfortunately, available annotations contain errors and biologically validated ones(More)
In the recent years, an increasingly large amount of biomedical and biomolec-ular information and data has become available to researchers, allowing to the scientific community to infer new knowledge and reach new objectives. As these information increase , so does the difficulty in managing it efficiently. In this paper, we present a short overview of our(More)
Genes and their protein products are essential molecular units of a living organism. The knowledge of their functions is key for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. The association of a gene or protein with its functions, described by controlled terms of(More)