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Identification of a Novel Candidate Gene for Chilling Tolerance in Pumpkin (Cucurbita moschata) Using Whole-Genome Resequencing
Chilling stress is one of the major abiotic constraints limiting cucurbit crop winter cultivation globally. Pumpkins ( Cucurbita moschata ) have been...
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Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid
Actinidia arguta , known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such as small and smooth-fruited,...
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Variant phasing and haplotypic expression from long-read sequencing in maize
Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic...
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NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule
Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory...
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Genome-wide analysis reveals the spatiotemporal expression patterns of SOS3 genes in the maize B73 genome in response to salt stress
BackgroundSalt damage is an important abiotic stress that affects the growth and yield of maize worldwide. As an important member of the salt overly...
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Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes
Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. Single-cell RNA sequencing (scRNA-seq)...
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Investigating the relationship between the VNTR variant of the interleukin-1 receptor antagonist gene and coronary in-stent restenosis
ObjectiveThis study aimed to examine the association between the interleukin-1 receptor antagonist gene (IL-1RN) and coronary in-stent restenosis...
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Pulmonary artery embolism: comprehensive transcriptomic analysis in understanding the pathogenic mechanisms of the disease
BackgroundPulmonary embolism (PE) is a severe disease that usually originates from deep vein thrombosis (DVT) of the lower extremities. This study...
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Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids
BackgroundRegulation of transcription by DNA methylation in 5’-CpG-3’ context is a widespread mechanism allowing differential expression of...
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Graph construction method impacts variation representation and analyses in a bovine super-pangenome
BackgroundSeveral models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant...
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Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements...
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Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs
BackgroundAllele-specific binding (ASB) events occur when transcription factors (TFs) bind more favorably to one of the two parental alleles at...
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Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome
Tea plants ( Camellia sinensis ) are commercially cultivated in >60 countries, and their fresh leaves are processed into tea, which is the most widely...
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Body mass index stratified meta-analysis of genome-wide association studies of polycystic ovary syndrome in women of European ancestry
BackgroundPolycystic ovary syndrome (PCOS) is a complex multifactorial disorder with a substantial genetic component. However, the clinical...
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Deep Learning-Enhanced MHC-II Presentation Prediction and Peptidome Deconvolution
Antigen-presenting cells can elicit a CD4 \(^+\)...
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XIST dampens X chromosome activity in a SPEN-dependent manner during early human development
XIST (X-inactive specific transcript) long noncoding RNA (lncRNA) is responsible for X chromosome inactivation (XCI) in placental mammals, yet it...
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Integration of transcriptomic and proteomic analyses reveals several levels of metabolic regulation in the excess starch and early senescent leaf mutant lses1 in rice
BackgroundThe normal metabolism of transitory starch in leaves plays an important role in ensuring photosynthesis, delaying senescence and...
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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this...
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Association between polymorphisms of TLR2-1-6 and bipolar disorder in a tunisian population
BackgroundBipolar disorder (BD) is a complex neuropsychiatric disease that has been strongly linked to immune dysregulation. In particular, an...
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Mechanisms of salinity tolerance and their possible application in the breeding of vegetables
BackgroundIn dry and semi-arid areas, salinity is the most serious hazard to agriculture, which can affect plant growth and development adversely....
