Publications by authors named "S Shiu"

Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years.

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Article Synopsis
  • - Predicting how genetic and environmental factors influence traits (phenotypes) is a critical challenge in biology, with potential benefits like improved health, food security, and environmental care.
  • - The Genomes to Fields (G2F) initiative hosted a competition in 2022 and 2023, inviting global participants from various disciplines to develop models using a comprehensive dataset gathered over nine years, including genetic and environmental data.
  • - Winning methods combined machine learning with traditional breeding techniques, showcasing a variety of approaches such as quantitative genetics and deep learning, indicating that no single strategy was universally superior in predicting phenotypes in this context.
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Background: Intensive care unit acquired weakness (ICUAW) is a common neuromuscular complication of critical illness, impacting patients' recovery and long-term outcomes. However, limited evidence is available on pooled prevalence and risk factors of ICUAW specifically in the COVID-19-infected population.

Methods: We searched on PubMed, Embase, Cochrane Library, Web of Science, PEDro, and EBSCOhost/CINAHL up to January 31, 2024.

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The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits.

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