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BetaAlign: a deep learning approach for multiple sequence alignment.
Bioinformatics
December 2024
The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Article Synopsis
- The study explores a novel method for multiple sequence alignments in bioinformatics using natural language processing (NLP) techniques.
- Researchers developed BetaAlign, a deep learning aligner that outperforms traditional alignment algorithms and offers highly accurate results by leveraging transformer models.
- The findings highlight the potential of AI-based approaches to improve alignment tasks and advance phylogenomics, with training data and tools made available through Hugging Face.
Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings.
Infect Genet Evol
November 2024
University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Département de Biologie médicale, Centre Hospitalier Universitaire Gabriel Toure, Bamako, Mali.
SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa.
View Article and Find Full Text PDFThe Changes of Microbial Diversity and Isolation of Microorganism in Soil for Alleviating the Production Decreasing After Continuous Cultivation of Ganoderma lucidum.
Curr Microbiol
August 2024
National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, 1000 Jinqi Road, Shanghai, 201403, China.
Ganoderma lucidum is a medicinal mushroom usually cultivated in logs and covered with soil. Its production decreases after continuous cultivation. Changes of microbial diversity in soil are suggested to be one of the reasons.
View Article and Find Full Text PDFPappus phenotypes and flight performance across evolutionary history in the daisy family.
Ann Bot
November 2024
Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, 5000, Argentina.
Background And Aims: Diversity in pappus shapes and size in Asteraceae suggests an adaptive response to dispersion challenges adjusting diaspores to optimal phenotypic configurations. Here, by analysing the relationship among pappus-cypsela size relationships, flight performance and pappus types in an evolutionary context, we evaluate the role of natural selection acting on the evolution of diaspore configuration at a macro-ecological scale in the daisy family.
Methods: To link pappus-cypsela size relationships with flight performance we collected published data on these traits from 82 species.
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes.
Nat Microbiol
July 2024
Department of Biology, University of Oxford, Oxford, UK.
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state.
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