Clinical Bioinformatics

Jan 10, 2025 | bmcgenomics.biomedcentral.com | Clinical Bioinformatics

We have integrated a diverse collection of four previously published AMR gene prediction workflows into Galaxy for comparative benchmarking via the BenchAMRking platform (Fig. 1; Tables 1 and 2). The platform can be found at https://erasmusmc-bioinformatics.github.io/benchAMRking/, including brief instructions on its use. The output of the BenchAMRking platform may be visualised using the R-based Confusion Matrix and Heatmap scripts available from the BenchAMRking website.

Jan 11, 2024 | academic.oup.com | Clinical Bioinformatics

The NanoString™ nCounter® technology platform is a widely used targeted quantification platform for the analysis of gene expression of up to ∼ 800 genes. Whereas the software tools by the manufacturer can perform the analysis in an interactive and GUI driven approach, there is no portable and user-friendly workflow available that can be used to perform reproducible analysis of multiple samples simultaneously in a scalable fashion on different computing infrastructures.

Nov 6, 2023 | academic.oup.com | Clinical Bioinformatics

With demographic changes leading to a growing elderly population in Western societies, neurodegenerative diseases have received increased attention due to their direct association with aging processes, often becoming more severe in advanced age. The progression of these diseases has been linked to various genetic origins, single-nucleotide polymorphisms (SNPs), and perturbed cell-type populations (1,2).

Oct 27, 2023 | frontiersin.org | Clinical Bioinformatics |Ryan Baxter |Bernadete L Liphaus |Elena W. Y

1 IntroductionSystemic lupus erythematosus (SLE) is a systemic multi-organ autoimmune disease with heterogeneous clinical presentation and an unpredictable waxing/waning disease course. Both features pose significant management challenges, as current diagnostic measures are insufficient to predict; i) severity of current/future organ involvement, ii) disease flare, and iii) response to specific immunomodulatory therapy.

Sep 8, 2023 | frontiersin.org | Clinical Bioinformatics |Bioinformatics Unit |Van Helden |Aix-Marseille Univ

Introduction High-throughput Sequencing (HTS) has made a huge impact in medicine, and pushed us into the era of personalized and genomic medicine. Microbiology is one of the fields where an unprecedented revolution has taken place, as HTS allows genomic characterization of pathogens of interest at clinical and public health levels, which eases their surveillance and outbreak control, making the concept of One Health (1, 2) a reality.