Related papers: YeastMed: an XML-Based System for Biological Data …
Brain Imaging Data Structure (BIDS) allows the user to organise brain imaging data into a clear and easy standard directory structure. BIDS is widely supported by the scientific community and is considered a powerful standard for…
Biomedical queries often rely on a deep understanding of specialized knowledge such as gene regulatory mechanisms and pathological processes of diseases. They require detailed analysis of complex physiological processes and effective…
The MammoGrid project aims to prove that Grid infrastructures can be used for collaborative clinical analysis of database-resident but geographically distributed medical images. This requires: a) the provision of a clinician-facing…
Recent advances in high-throughput sequencing technologies have enabled the extraction of multiple features that depict patient samples at diverse and complementary molecular levels. The generation of such data has led to new challenges in…
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes…
Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical…
Biomedical research yields a wealth of information, much of which is only accessible through the literature. Consequently, literature search is an essential tool for building on prior knowledge in clinical and biomedical research. Although…
This paper argues that there are three fundamental challenges that need to be overcome in order to foster the adoption of big data technologies in non-computer science related disciplines: addressing issues of accessibility of such…
The reuse of research software is central to research efficiency and academic exchange. The application of software enables researchers with varied backgrounds to reproduce, validate, and expand upon study findings. Furthermore, the…
Evidence-based health care (EBHC) is an important practice of medicine which attempts to provide systematic scientific evidence to answer clinical questions. In this context, Epistemonikos (www.epistemonikos.org) is one of the first and…
In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the…
Aims: Our Gulf War Illness (GWI) study conducts combinatorial screening of many interactive neural and humoral biomarkers in order to establish predictive, diagnostic, and therapeutic targets. We encounter obstacles at every stage of the…
Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Nowadays, with the increasing number of integrated data sources, there is a real trend to personalize mediation systems to improve user satisfaction. To make these systems user sensitive, we propose a personalization platform called 2P-Med.…
Microbiome research has immense potential for unlocking insights into human health and disease. A common goal in human microbiome research is identifying subgroups of individuals with similar microbial composition that may be linked to…
Routine clinical visits of a patient produce not only image data, but also non-image data containing clinical information regarding the patient, i.e., medical data is multi-modal in nature. Such heterogeneous modalities offer different and…
Diabetes devices, including Continuous Glucose Monitoring (CGM), Smart Insulin Pens, and Automated Insulin Delivery systems, generate rich time-series data widely used in research and machine learning. However, inconsistent data formats…
Computer-Aided Diagnosis has shown stellar performance in providing accurate medical diagnoses across multiple testing modalities (medical images, electrophysiological signals, etc.). While this field has typically focused on fully…
The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the…