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C4-like Sesuvium sesuvioides (Aizoaceae) exhibits CAM in cotyledons and putative C4-like + CAM metabolism in adult leaves as revealed by transcriptome analysis
BackgroundThe co-occurrence of C 4 and CAM photosynthesis in a single species seems to be unusual and rare. This is likely due to the difficulty in...
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Evaluation of heritability partitioning approaches in livestock populations
BackgroundHeritability partitioning approaches estimate the contribution of different functional classes, such as coding or regulatory variants, to...
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A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis
BackgroundThe holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value....
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Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
MotivationAlignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained...
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Unveiling the translational dynamics of lychee (Litchi chinesis Sonn.) in response to cold stress
Cold stress poses a significant threat to the quality and productivity of lychee ( Litchi chinensis Sonn . ). While previous research has extensively...
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A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes
BackgroundAlthough genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis...
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METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data
BackgroundWith the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error...
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Comprehensive analysis of the Xya riparia genome uncovers the dominance of DNA transposons, LTR/Gypsy elements, and their evolutionary dynamics
Transposable elements (TEs) are DNA sequences that can move or replicate within a genome, and their study has become increasingly important in...
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expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer
BackgroundHomologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy...
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Expression genome-wide association study identifies key regulatory variants enriched with metabolic and immune functions in four porcine tissues
BackgroundIntegration of high throughput DNA genoty** and RNA-sequencing data enables the discovery of genomic regions that regulate gene...
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A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
BackgroundThe growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical...
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OBSERVE: guidelines for the refinement of rodent cancer models
Existing guidelines on the preparation (Planning Research and Experimental Procedures on Animals: Recommendations for Excellence (PREPARE)) and...
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SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
BackgroundSimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well...
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Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish
BackgroundCis -regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in...
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Comparative proteomics in tall fescue to reveal underlying mechanisms for improving Photosystem II thermotolerance during heat stress memory
BackgroundThe escalating impacts of global warming intensify the detrimental effects of heat stress on crop growth and yield. Among the earliest and...
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Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert
Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental...
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Mendelian randomization analysis reveals higher whole body water mass may increase risk of bacterial infections
Background and purposeThe association of water loading with several infections remains unclear. Observational studies are hard to investigate...
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Association between OX40L polymorphism and type 2 diabetes mellitus in Iranians
IntroductionDiabetes mellitus (DM) is one of the leading causes of morbidity and mortality worldwide. It is a multifactorial disease that genetic and...
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Understanding the responses of tillering to 2,4-D isooctyl ester in Setaria viridis L.
BackgroundGreen foxtail [ Setaria viridis (L.)] is one of the most abundant and troublesome annual grass weeds in alfalfa fields in Northeast China....