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Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.
G3 (Bethesda)
January 2025
School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA.
The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection.
View Article and Find Full Text PDFA comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Brief Bioinform
November 2024
Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, 999077, China.
The complexity of T cell receptor (TCR) sequences, particularly within the complementarity-determining region 3 (CDR3), requires efficient embedding methods for applying machine learning to immunology. While various TCR CDR3 embedding strategies have been proposed, the absence of their systematic evaluations created perplexity in the community. Here, we extracted CDR3 embedding models from 19 existing methods and benchmarked these models with four curated datasets by accessing their impact on the performance of TCR downstream tasks, including TCR-epitope binding affinity prediction, epitope-specific TCR identification, TCR clustering, and visualization analysis.
View Article and Find Full Text PDFUsing Large Language Models to Detect and Understand Drug Discontinuation Events in Web-Based Forums: Development and Validation Study.
J Med Internet Res
January 2025
Department of Industrial and Systems Engineering, The University of Florida, GAINESVILLE, FL, United States.
Background: The implementation of large language models (LLMs), such as BART (Bidirectional and Auto-Regressive Transformers) and GPT-4, has revolutionized the extraction of insights from unstructured text. These advancements have expanded into health care, allowing analysis of social media for public health insights. However, the detection of drug discontinuation events (DDEs) remains underexplored.
View Article and Find Full Text PDFGenetic diversity and selection signatures in sheep breeds.
J Appl Genet
January 2025
Departamento de Ciências Exatas, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil.
Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100 kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.
View Article and Find Full Text PDFComparative study of Mg/Al-LDH and Mg/Fe-LDH on adsorption and loss control of 2,4-dichlorophenoxyacetic acid.
Adv Biotechnol (Singap)
January 2025
School of Agriculture and Biotechnology, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, People's Republic of China.
Low efficiency and high surface runoff of 2,4-dichlorophenoxyacetic acid (2,4-D) from agricultural field threaten crop yield severely. Layered double hydroxides (LDH) have shown promising adsorption properties for 2,4-D. However, the comparison of two environmentally friendly LDHs (i.
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