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<h4>Background</h4>Tuberculosis (TB) remains a global health threat, affecting over a million children under the age of 15 annually. Many children with TB do not receive treatment due to challenges in diagnosis.<h4>Methods</h4>We performed a multi-omics analysis …
Read PDFClinical proteomics has the potential to add a valuable data layer to genomic and histopathological analyses in precision oncology, but its application to limited clinical material remains challenging. Here, we demonstrate that state-of-the-art mass spectrometry-based …
Read PDFProteomics has become central to pharmacological research by providing quantitative readouts of protein abundance, post-translational modifications, interactions, and spatial context. However, proteomic datasets are high-dimensional, heterogeneous, and frequently affected by missingness, batch effects, and limited …
Read PDFThe blood plasma proteome is a rich reservoir of potential biomarkers, yet its analysis is hindered by a protein concentration dynamic range exceeding ten orders of magnitude. Traditional fractionation and enrichment methods often present limitations …
Read PDF<h4>Background</h4>Polygenic risk scores (PRS), metabolomics, and proteomics have each shown promise in improving type 2 diabetes risk prediction, but their combined utility beyond established clinical models remains unclear. We aimed to evaluate whether integrating multi-omics …
Read PDFMaintaining mitochondrial integrity and function is fundamental to cellular homeostasis. Cells rely on coordinated protein quality control (QC) systems-including intricate chaperone-protease networks, the ubiquitin-proteasome system, and cytosolic surveillance pathways-that together form a dynamic, cell-wide mitostasis …
Read PDF[This corrects the article DOI: 10.1371/journal.pone.0342705.].
Read PDF<h4>Background</h4>Heart failure (HF) is a complex syndrome with high mortality. Proteomics risk scores have shown promise in predicting mortality beyond guideline-recommended clinical tools. It is crucial to understand how risk scores generated by different methods …
Read PDFPathogenic variants in the OPN1LW/OPN1MW gene cluster are causal for a range of mild to severe visual impairments with color deficiencies. The widely utilized short-read next-generation sequencing (NGS) is inappropriate for the analysis of the …
Read PDF<h4>Objective</h4>The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia.<h4>Materials and methods</h4>Processes were established for registering and …
Read PDFAdvances in long-read DNA sequencing technologies have enabled researchers to obtain high-quality genomes and finely resolve structural variants (SVs) in many species, even from small laboratories. The hands-on protocol presented here will guide you through …
Read PDFA recent paper by Jiang et al. in BMC Bioinformatics presented guidelines on long-read sequencing settings for structural variation (SV) calling, and benchmarked the performance of various SV calling tools, including NanoVar. In their simulation-based …
Read PDFThe microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping …
Read PDF<b>Background:</b> Inter-individual differences in drug response based on genetic variations can lead to drug toxicity and treatment inefficacy. A large part of this variability is caused by genetic variants in pharmacogenes. Unfortunately, the Single Nucleotide …
Read PDFComplex congenital chromosome abnormalities are rare but often cause severe symptoms. However, the structures and biological impacts of such abnormalities have seldomly been analyzed at the molecular level. Previously, we reported a Japanese female patient …
Read PDF<h4>Importance</h4>The gut and salivary microbiomes have been widely reported to be significantly associated with a number of neurological disorders. The stability of the microbiome in the oral cavity makes it a potentially ideal sample that …
Read PDFStructural Variants (SVs) are a crucial type of genetic variant that can significantly impact phenotypes. Therefore, the identification of SVs is an essential part of modern genomic analysis. In this article, we present kled, an …
Read PDFDue to factors such as lower biosecurity, greater wildlife/farm animal interfaces, and environmental challenges, cattle in sub-Saharan Africa are exposed to more diverse and intensive bacterial, viral and protozoan pathogen challenges than cattle in Europe …
Read PDFLong-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational …
Read PDFStructural variation (SV) is an important form of genomic variation that influences gene function and expression by altering the structure of the genome. Although long-read data have been proven to better characterize SVs, SVs detected …
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