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Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
Adeno-associated viruses 2 (AAV2) are minute viruses renowned for their capacity to infect human cells and akin organisms. They have recently emerged...
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Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2
BackgroundFungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with...
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Genome-wide identification and expression pattern analysis of MIKC-Type MADS-box genes in Chionanthus retusus, an androdioecy plant
BackgroundThe MADS-box gene family is widely distributed in the plant kingdom, and its members typically encoding transcription factors to regulate...
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Observing isolated synaptic vesicle association and fusion ex vivo
Here, we present a protocol for isolating functionally intact glutamatergic synaptic vesicles from whole-mouse brain tissue and using them in a...
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Exploring selection signatures in the divergence and evolution of lipid droplet (LD) associated genes in major oilseed crops
BackgroundOil bodies or lipid droplets (LDs) in the cytosol are the subcellular storage compartments of seeds and the sites of lipid metabolism...
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Identification and expression analysis of Sox family genes in echinoderms
The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous...
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Breed of origin analysis in genome-wide association studies: enhancing SNP-based insights into production traits in a commercial Brangus population
BackgroundCarcass weight (HCW) and marbling (MARB) are critical for meat quality and market value in beef cattle. In composite breeds like Brangus,...
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Integrated transcriptome and microRNA analysis reveals molecular responses to high-temperature stress in the liver of American shad (Alosa sapidissima)
BackgroundFish reproduction, development and growth are directly affected by temperature, investigating the regulatory mechanisms behind high...
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Unexpected regulatory functions of cyprinid Viperin on inflammation and metabolism
BackgroundViperin, also known as radical S-adenosyl-methionine domain containing protein 2 (RSAD2), is an interferon-inducible protein that is...
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Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS
BackgroundAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 300,000 people worldwide. It is characterized by the...
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Genome-wide association analysis identify candidate genes for feed efficiency and growth traits in Wenchang chickens
BackgroundWenchang chickens are one of the most popular local chicken breeds in the Chinese chicken industry. However, the low feed efficiency is the...
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Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Spatial epigenetic map** of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue...
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Genome-wide identification of the Q-type C2H2 zinc finger protein gene family and expression analysis under abiotic stress in lotus (Nelumbo nucifera G.)
BackgroundLotus ( Nelumbo nucifera G.) is an important aquatic plant with high ornamental, economic, cultural and ecological values, but abiotic...
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Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET)
Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target...
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The genomic landscape of Ménière's disease: a path to endolymphatic hydrops
BackgroundMénière's disease (MD) is a disorder of the inner ear that causes episodic bouts of severe dizziness, roaring tinnitus, and fluctuating...
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UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example
BackgroundAt a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of...
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Genes divided according to the relative position of the longest intron show increased representation in different KEGG pathways
Despite the fact that introns mean an energy and time burden for eukaryotic cells, they play an irreplaceable role in the diversification and...
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Genetic correlation between smoking behavior and gastroesophageal reflux disease: insights from integrative multi-omics data
BackgroundObservational studies have preliminarily revealed an association between smoking and gastroesophageal reflux disease (GERD). However,...
