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SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.
Brief 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 PDFUpdate on the evolving landscape of pneumococcal capsule types: new discoveries and way forward.
Clin 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.
View Article and Find Full Text PDFAugmenting Circadian Biology Research With Data Science.
J Biol Rhythms
January 2025
Shiu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California.
The nature of biological research is changing, driven by the emergence of big data, and new computational models to parse out the information therein. Traditional methods remain the core of biological research but are increasingly either augmented or sometimes replaced by emerging data science tools. This presents a profound opportunity for those circadian researchers interested in incorporating big data and related analyses into their plans.
View Article and Find Full Text PDFInnovative epitopes in Protein-A an immuno-informatics approach to combat MDR-MRSA infections.
Front Cell Infect Microbiol
January 2025
Department of Haematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China.
Background: Methicillin-resistant (MRSA) poses a significant challenge in clinical environments due to its resistance to standard antibiotics. Protein A (SpA), a crucial virulence factor of MRSA, undermines host immune responses, making it an attractive target for vaccine development. This study aimed to identify potential epitopes within SpA that could elicit robust immune responses, ultimately contributing to the combat against multidrug-resistant (MDR) MRSA.
View Article and Find Full Text PDFhsa-miR-548d-3p: a potential microRNA to target nucleocapsid and/or capsid genes in multiple members of the Flaviviridae family.
Front Bioinform
January 2025
Hakim's Lab, Department of Biology, School of STEM, Diné College, Tuba City, AZ, United States.
Introduction: Flaviviridae comprise a group of enveloped, positive-stranded RNA viruses that are mainly transmitted through either mosquitoes or tick bites and/or contaminated blood, blood products, or other body secretions. These viruses cause diseases ranging from mild to severe and are considered important human pathogens. MicroRNAs (miRNAs) are non-coding molecules involved in growth, development, cell proliferation, protein synthesis, apoptosis, and pathogenesis.
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