BMC bioinformatics

MotivationLong non-coding RNAs (lncRNAs) are a class of molecules involved in important biological processes. Extensive efforts have been provided to get deeper understanding of disease mechanisms at the lncRNA level, guiding towards the de…

BackgroundSingle-cell RNA sequencing (scRNA-seq) is a powerful tool for investigating cell abundance changes during tissue regeneration and remodeling processes. Differential cell abundance supports the initial clustering of all cells; then…

BackgroundPartitioning around medoids (PAM) is one of the most widely used and successful clustering method in many fields. One of its key advantages is that it only requires a distance or a dissimilarity between the individuals, and the fa…

BackgroundSelecting and prioritizing candidate disease genes is necessary before conducting laboratory studies as identifying disease genes from a large number of candidate genes using laboratory methods, is a very costly and time-consuming…

BackgroundDrug repositioning, meanings finding new uses for existing drugs, which can accelerate the processing of new drugs research and development. Various computational methods have been presented to predict novel drug-disease associati…

BackgroundDrug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost efficiency, drug reposit…

BackgroundPathway enrichment analysis (PEA) is a well-established methodology for interpreting a list of genes and proteins of interest related to a condition under investigation. This paper aims to extend our previous work in which we intr…

BackgroundThe study of functional associations between ncRNAs and human diseases is a pivotal task of modern research to develop new and more effective therapeutic approaches. Nevertheless, it is not a trivial task since it involves entitie…

BackgroundPredicting drug-disease interactions (DDIs) is time-consuming and expensive. Improving the accuracy of prediction results is necessary, and it is crucial to develop a novel computing technology to predict new DDIs. The existing me…

BackgroundClinical trial registries may allow for producing a global mapping of health research. However, health conditions are not described with standardized taxonomies in registries. Previous work analyzed clinical trial registries to im…

BackgroundData from biomedical domains often have an inherit hierarchical structure. As this structure is usually implicit, its existence can be overlooked by practitioners interested in constructing and evaluating predictive models from su…

BackgroundClinical data, such as patient history, laboratory analysis, ultrasound parameters-which are the basis of day-to-day clinical decision support-are often used to guide the clinical management of cancer in the presence of microarray…

BackgroundTumor cells are considered to have an aberrant cell state, and some evidence indicates different development states appearing in the tumorigenesis. Embryonic development and stem cell differentiation are ordered processes in which…

BackgroundEach organ has a specific function in the body. "Organ-specificity" refers to differential expressions of the same gene across different organs. An organ-specific gene/protein is defined as a gene/protein whose expression is signi…

BackgroundText mining has become a useful tool for biologists trying to understand the genetics of diseases. In particular, it can help identify the most interesting candidate genes for a disease for further experimental analysis. Many text…

BackgroundThis paper introduces the notion of optimizing different norms in the dual problem of support vector machines with multiple kernels. The selection of norms yields different extensions of multiple kernel learning (MKL) such as L(in…

BackgroundSeveral different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and inter-platform consistency of these platforms. Both high and low…