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Transcriptome analysis identified a novel 3-LncRNA regulatory network of transthyretin attenuating glucose induced hRECs dysfunction in diabetic retinopathy
BackgroundDiabetic retinopathy (DR) is the leading cause of blindness in the working age population. Transthyretin (TTR) showed a significantly...
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CAMISIM: simulating metagenomes and microbial communities
BackgroundShotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying...
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Fecal, oral, blood and skin virome of laboratory rabbits
Here, we investigated the fecal, oral, blood, and skin virome of 10 laboratory rabbits using a viral metagenomic method. In the oral samples, we...
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An ex vivo tumor fragment platform to dissect response to PD-1 blockade in cancer
Inhibitors of the PD-1–PD-L1 axis have been approved as therapy for many human cancers. In spite of the evidence for their widespread clinical...
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Bioinformatics of nanopore sequencing
Nanopore sequencing is one of the most exciting new technologies that undergo dynamic development. With its development, a growing number of...
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Global transcriptome landscape of the rabbit protozoan parasite Eimeria stiedae
BackgroundCoccidiosis caused by Eimeria stiedae is a widespread and economically significant disease of rabbits. The lack of studies on the...
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HLA Ty** from RNA Sequencing and Applications to Cancer
The human leukocyte antigen (HLA) complex is necessary for antigen presentation and regulates both innate and adaptive immune responses. In the...
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Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students
BackgroundStudies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and...
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Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton
Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to...
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Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils
BackgroundMicrobial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria , one of the...
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The maize W22 genome provides a foundation for functional genomics and transposon biology
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have...
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Arthropod Genome Sequencing and Assembly Strategies
As in any endeavor, the strategy applied to a genome project can mean the difference between success and failure. This is especially important when...
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Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study
The Seven Bridges Cancer Genomics Cloud (CGC) is part of the National Cancer Institute Cloud Resource project, which was created to explore the...
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Durum wheat genome highlights past domestication signatures and future improvement targets
The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase...
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Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus
BackgroundIxodes ricinus is the most important vector of tick-borne diseases in Europe. A better knowledge of its genome and transcriptome is...
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Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans
BackgroundApicomplexans are the causative agents of major human diseases such as malaria and toxoplasmosis. A novel group of apicomplexans, recently...
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Accurate genoty** across variant classes and lengths using variant graphs
Genotype estimates from short-read sequencing data are typically based on the alignment of reads to a linear reference, but reads originating from...
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Long-read sequencing in deciphering human genetics to a greater depth
Through four decades’ development, DNA sequencing has inched into the era of single-molecule sequencing (SMS), or the third-generation sequencing...
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Ochratoxin A induces liver inflammation: involvement of intestinal microbiota
BackgroundOchratoxin A (OTA) is a widespread mycotoxin and induces liver inflammation to human and various species of animals. The intestinal...
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Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation....
