The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.
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http://dx.doi.org/10.1371/journal.pcbi.1005419 | DOI Listing |
Ann Surg Oncol
January 2025
Department of Surgery and Cancer, Imperial College London, London, UK.
Background: Early diagnosis of metastases is crucial but routine staging with contrast-enhanced multidetector computed tomography (ceMDCT) is suboptimal. A total of 20% will have indeterminate or too small to characterize (TSTC) liver lesions on CT, requiring formal characterization by magnetic resonance imaging (MRI). This UK cross-sectional study reports our experience undertaking routine abbreviated liver MRI (MRI).
View Article and Find Full Text PDFMol Carcinog
January 2025
Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.
The standard therapy for locally unresectable advanced non-small cell lung cancer (NSCLC) is comprised of chemoradiotherapy (CRT) before immunotherapy (IO) consolidation. However, how to predict treatment outcomes and recognize patients that will benefit from IO remain unclear. This study aimed to identify prognostic biomarkers by integrating computed tomography (CT)-based radiomics and genomics.
View Article and Find Full Text PDFBrief Bioinform
November 2024
School of Electrical and Information Engineering, Zhengzhou University, No. 100, Science Avenue, Hightech District, Zhengzhou City 450001, Henan Province, China.
Structural network control principles provided novel and efficient clues for the optimization of personalized drug targets (PDTs) related to state transitions of individual patients. However, most existing methods focus on one subnetwork or module as drug targets through the identification of the minimal set of driver nodes and ignore the state transition capabilities of other modules with different configurations of drug targets [i.e.
View Article and Find Full Text PDFArch Insect Biochem Physiol
January 2025
Division of Genomic Resources, ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, India.
RNA interference (RNAi) technology is widely used in gene functional studies and has been shown to be a promising next generation alternative for insect pest management. To understand the efficiency of RNAi machinery in Leucinodes orbonalis (L. orbonalis) Guenee, a destructive pest of eggplant, core RNAi pathway genes Argonaute-2, Dicer-2, Loquacious, and Sid-1 were mined from the transcriptome and characterized.
View Article and Find Full Text PDFFront Immunol
January 2025
Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Background: The Aryl Hydrocarbon Receptor (AhR) pathway significantly influences immune cell regulation, impacting the effectiveness of immunotherapy and patient outcomes in melanoma. However, the specific downstream targets and mechanisms by which AhR influences melanoma remain insufficiently understood.
Methods: Melanoma samples from The Cancer Genome Atlas (TCGA) and normal skin tissues from the Genotype-Tissue Expression (GTEx) database were analyzed to identify differentially expressed genes, which were intersected with a curated list of AhR-related pathway genes.
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