Direct RNA sequencing
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Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus.
18p vibransone 28-03-2024 4 1 Download
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Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consistency and temporal responses of the gut microbiome to glycans is critical for rationally developing and deploying these compounds as therapeutics.
16p vibransone 28-03-2024 6 2 Download
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Preclinical studies require models that recapitulate the cellular diversity of human tumors and provide insight into the drug sensitivities of specific cellular populations. The ideal platform would enable rapid screening of cell type-specific drug sensitivities directly in patient tumor tissue and reveal strategies to overcome intratumoral heterogeneity.
15p vibransone 28-03-2024 3 2 Download
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Although immune checkpoint inhibitor (ICI) is regarded as a breakthrough in cancer therapy, only a limited fraction of patients benefit from it. Cancer stemness can be the potential culprit in ICI resistance, but direct clinical evidence is lacking.
18p viellison 28-03-2024 5 1 Download
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Variation in cell composition can dramatically impact analyses in bulk tissue samples. A commonly employed approach to mitigate this issue is to adjust statistical models using estimates of cell abundance derived directly from omics data.
14p vicwell 29-02-2024 3 1 Download
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Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and growth rate upstream of highly multiplexed single-cell profiling such as single-cell RNA sequencing.
13p vigalileogalilei 27-02-2022 21 2 Download
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We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with differential abundance directly from the raw data files.
15p vialfrednobel 29-01-2022 13 0 Download
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Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different computational approaches for analysis.
21p vialfrednobel 29-01-2022 15 0 Download
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Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2.
12p viarchimedes 26-01-2022 11 0 Download
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Models developed using Nanopore direct RNA sequencing data from in vitro synthetic RNA with all adenosine replaced by N6 -methyladenosine (m6 A) are likely distorted due to superimposed signals from saturated m6 A residues.
23p viarchimedes 26-01-2022 13 0 Download
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There are no comprehensive methods to identify N6 -methyladenosine (m6 A) at single-base resolution for every single transcript, which is necessary for the estimation of m6 A abundance.
17p viarchimedes 26-01-2022 15 0 Download
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Enhancers are distal cis-regulatory elements that control gene expression. Despite an increasing appreciation of the importance of enhancers in cellular function and disease, our knowledge of enhancer-regulated transcription is very limited.
18p vitzuyu2711 29-09-2021 11 1 Download
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Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and accelerating devastation due to bleaching.
15p vigiselle2711 30-08-2021 2 1 Download
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Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming.
10p viansan2711 30-07-2021 6 2 Download
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Zebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types such as the oocyte.
15p vijeeni2711 24-07-2021 10 0 Download
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Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Limited knowledge of prestin is from experiments using site-directed mutagenesis or domainswapping techniques after the amino acid residues were identified by comparing the sequence of prestin to those of its paralogs and orthologs.
11p vijeeni2711 24-07-2021 11 0 Download
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Statins are widely prescribed to lower plasma low-density lipoprotein cholesterol levels. Though statins reduce cardiovascular disease risk overall, statin efficacy varies, and some people experience adverse side effects while on statin treatment. Statins also have pleiotropic effects not directly related to their cholesterollowering properties, but the mechanisms are not well understood.
18p vijeeni2711 30-06-2021 19 1 Download
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The function of an RNA in cellular processes is directly related to its structure. The free energy of RNA structure in another important key to its function as only some structures with a specific level of free energy can take part in cellular reactions.
11p vikentucky2711 26-11-2020 14 1 Download
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RNA sequencing (RNA-Seq) allows an unbiased survey of the entire transcriptome in a high-throughput manner. A major application of RNA-Seq is to detect differential isoform expression across experimental conditions, which is of great biological interest due to its direct relevance to protein function and disease pathogenesis.
12p vikentucky2711 24-11-2020 12 0 Download
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Exon recognition and splicing precisely and efficiently by spliceosome is the key to generate mature mRNAs. About one third or a half of disease-related mutations affect RNA splicing. Software PVAAS has been developed to identify variants associated with aberrant splicing by directly using RNA-seq data.
7p viflorida2711 30-10-2020 7 1 Download