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Briefings in bioinformatics
Sep 22, 2023
Single-cell RNA-sequencing (scRNA-seq) allows for obtaining genomic and transcriptomic profiles of individual cells. That data make it possible to characterize tissues at the cell level. In this context, one of the main analyses exploiting scRNA-seq ...
Bioinformatics (Oxford, England)
Jul 1, 2023
MOTIVATION: The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and repr...
Mathematical biosciences and engineering : MBE
Mar 9, 2023
OBJECTIVE: Quantification of disease-disease association (DDA) enables the understanding of disease relationships for discovering disease progression and finding comorbidity. For effective DDA strength calculation, there is a need to address the main...
Bioinformatics (Oxford, England)
Mar 1, 2023
MOTIVATION: The rapid accumulation of high-throughput sequence data demands the development of effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotatio...
Bioinformatics (Oxford, England)
Jan 1, 2023
MOTIVATION: Ontologies contain formal and structured information about a domain and are widely used in bioinformatics for annotation and integration of data. Several methods use ontologies to provide background knowledge in machine learning tasks, wh...
Bioinformatics (Oxford, England)
Dec 13, 2022
MOTIVATION: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan bi...
Bioinformatics (Oxford, England)
Dec 13, 2022
MOTIVATION: Interactions between proteins help us understand how genes are functionally related and how they contribute to phenotypes. Experiments provide imperfect 'ground truth' information about a small subset of potential interactions in a specif...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: Experimental testing and manual curation are the most precise ways for assigning Gene Ontology (GO) terms describing protein functions. However, they are expensive, time-consuming and cannot cope with the exponential growth of data genera...
Bioinformatics (Oxford, England)
Jun 27, 2022
MOTIVATION: Protein design has become increasingly important for medical and biotechnological applications. Because of the complex mechanisms underlying protein formation, the creation of a novel protein requires tedious and time-consuming computatio...
Briefings in bioinformatics
May 13, 2022
Gene Ontology (GO) is widely used in the biological domain. It is the most comprehensive ontology providing formal representation of gene functions (GO concepts) and relations between them. However, unintentional quality defects (e.g. missing or erro...