Purpose Of Review: Most primary immunodeficiencies (PIDs) have overlapping signs and symptoms - presenting a challenge for diagnosis. The information available from the Internet for over 200 PIDs is scattered between numerous services and databases. Patient information has been collected in different patient registries. Several software tools have been developed in order to build the databases, expert systems and other information systems useful in diagnosis or prediction.
Recent Findings: Previously released services have been significantly improved and some new bioinformatics tools have been developed to help in diagnosis, prediction, mutation analysis and classification of PIDs. Several national initiatives have been launched for centralized PID information services. The very latest additions are tools and approaches for PID candidate gene prioritization, systematic classification and a medical expert system to help in diagnosis.
Summary: Many bioinformatics tools for PIDs are already freely available over the Internet. We expect bioinformatics tools to further help healthcare professionals in diagnosis, analysis and prediction. Currently, most of the resources are stand-alone and thus their integration will be a challenge for the future. Another challenge is to develop terminologies, ontologies and standards to achieve semantic interoperability.
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http://dx.doi.org/10.1097/ACI.0b013e3283327dc1 | DOI Listing |
Epidemiol Psychiatr Sci
January 2025
Health Service and Population Research Department, Institute of Psychiatry, Psychology and Neuroscience, Center for Global Mental Health, King's College London, London, UK.
In low- and middle-income countries, fewer than 1 in 10 people with mental health conditions are estimated to be accurately diagnosed in primary care. This is despite more than 90 countries providing mental health training for primary healthcare workers in the past two decades. The lack of accurate diagnoses is a major bottleneck to reducing the global mental health treatment gap.
View Article and Find Full Text PDFBioinformatics
January 2025
School of Computer Science and engineering, Central South University, Changsha, 410083, China.
Motivation: T-cell receptors (TCRs) elicit and mediate the adaptive immune response by recognizing antigenic peptides, a process pivotal for cancer immunotherapy, vaccine design, and autoimmune disease management. Understanding the intricate binding patterns between TCRs and peptides is critical for advancing these clinical applications. While several computational tools have been developed, they neglect the directional semantics inherent in sequence data, which are essential for accurately characterizing TCR-peptide interactions.
View Article and Find Full Text PDFMol Cell Proteomics
January 2025
VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Department of Biology, University of Padova, Via U.Bassi 58/ B, 35131, Italy.
Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner.
View Article and Find Full Text PDFClin Microbiol Rev
January 2025
Department of Medicine, Division of Pulmonary/Allergy/Critical Care, The University of Alabama at Birmingham, Birmingham, Alabama, USA.
SUMMARY (the "pneumococcus") is a significant human pathogen. The key determinant of pneumococcal fitness and virulence is its ability to produce a protective polysaccharide (PS) capsule, and anti-capsule antibodies mediate serotype-specific opsonophagocytic killing of bacteria. Notably, immunization with pneumococcal conjugate vaccines (PCVs) has effectively reduced the burden of disease caused by serotypes included in vaccines but has also spurred a relative upsurge in the prevalence of non-vaccine serotypes.
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