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Sherlock-Genome: an R Shiny application for genomic analysis and visualization.
BMC Genomics
January 2025
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
Motivation: Next-generation sequencing technologies, such as whole genome sequencing (WGS), have become prominent in cancer genomics. However, managing, visualizing, and integratively analyzing WGS results across various bioinformatic pipelines remains challenging, particularly for non-bioinformaticians, hindering the usability of WGS data for biological discovery.
Results: We developed Sherlock-Genome, an R Shiny app for data harmonization, visualization, and integrative analysis of WGS-based cancer genomics studies.
Well-designed effective interventions promoting sustainable diets are urgently needed to benefit both human and planetary health. This study evaluated the feasibility, acceptability, and potential impact of a pilot blended digital intervention aimed at promoting sustainable diets. We conducted a series of ABA n-of-1 trials with baseline, intervention, and follow-up phases over the course of a year, involving twelve participants.
View Article and Find Full Text PDFDeveloping a Research Center for Artificial Intelligence in Medicine.
Mayo Clin Proc Digit Health
December 2024
Department Radiology, Stanford University, Stanford, CA.
Artificial intelligence (AI) and machine learning (ML) are driving innovation in biosciences and are already affecting key elements of medical scholarship and clinical care. Many schools of medicine are capitalizing on the promise of these new technologies by establishing academic units to catalyze and grow research and innovation in AI/ML. At Stanford University, we have developed a successful model for an AI/ML research center with support from academic leaders, clinical departments, extramural grants, and industry partners.
View Article and Find Full Text PDFGalaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq.
Gigascience
January 2025
School of Life, Health & Chemical Sciences, The Open University, Milton Keynes, Buckinghamshire, MK7 6AA, UK.
Background: Bioinformatics is fundamental to biomedical sciences, but its mastery presents a steep learning curve for bench biologists and clinicians. Learning to code while analyzing data is difficult. The curve may be flattened by separating these two aspects and providing intermediate steps for budding bioinformaticians.
View Article and Find Full Text PDFAn ecosystem for producing and sharing metadata within the web of FAIR Data.
Gigascience
January 2025
INRAE, Université de Bordeaux, F-33610 Cestas, France.
Background: Descriptive metadata are vital for reporting, discovering, leveraging, and mobilizing research datasets. However, resolving metadata issues as part of a data management plan can be complex for data producers. To organize and document data, various descriptive metadata must be created.
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