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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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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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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....
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gcplyr: an R package for microbial growth curve data analysis
BackgroundCharacterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of...
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ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
BackgroundStructural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external...
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Integrated proteomic and metabolomic profiling reveals novel insights on the inflammation and immune response in HFpEF
BackgroundThe precise mechanisms leading to the development of heart failure with preserved ejection fraction (HFpEF) remain incompletely defined. In...
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Exploring the genetic basis of anthracnose resistance in Ethiopian sorghum through a genome-wide association study
BackgroundSorghum anthracnose is a major disease that hampers the productivity of the crop globally. The disease is caused by the hemibiotrophic...
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Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors
BackgroundThe piRNA pathway in animal gonads functions as an ‘RNA-based immune system’, serving to silence transposable elements and prevent...
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Identification, validation and candidate gene analysis of major QTL for Supernumerary spikelets in wheat
BackgroundThe number of spikelets per spike is a key trait that affects the yield of bread wheat ( Triticum aestivum L.). Identification of the QTL...
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Dietary restriction promote sperm remodeling in aged roosters based on transcriptome analysis
BackgroundThe breeder rooster has played a pivotal role in poultry production by providing high-quality semen. Typically, fertility peaks between 30...
