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RNA-Seq

Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES

Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES

... Forty-four out of 45 partially penetrant base changes identified in the JY RNA-seq data are G-to-A changes. Notably, three out of four of the fully penetrant base changes identified are also G to A. These, ...

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HLA typing from RNA-Seq sequence reads

HLA typing from RNA-Seq sequence reads

... Seq2HLA does not rely on a priori knowledge of population-specific HLA distributions. To demonstrate the applicability of the method to different ethnic groups, we applied seq2HLA to 77 lung RNA-Seq pro- ...

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SeqOthello: querying RNA seq experiments at scale

SeqOthello: querying RNA seq experiments at scale

... of RNA-seq datasets. As of December 2017, over 12 petabytes of RNA-seq data were deposited in the Sequence Read Arch- ive (SRA) ...large-scale RNA-seq ...

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A survey of statistical software for analysing RNA-seq data

A survey of statistical software for analysing RNA-seq data

... DEGseq is another R package specifically designed to identify DE from RNA-seq data. 9 The package includes two novel methods, the MA plot-based method (where M is the log ratio of the counts between two ...

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Finding differential splice junctions in RNA-Seq data as transcriptional biomarkers for prostate cancer

Finding differential splice junctions in RNA-Seq data as transcriptional biomarkers for prostate cancer

... Lou et al. [35] proposed an approach based on maximum likelihood estimation, which relies on geometric-tail distribution of intron lengths for aligning of paired-end RNA-Seq reads. The authors used a ...

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Dual RNA seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host Pathogen Cross Talk

Dual RNA seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host Pathogen Cross Talk

... our RNA-seq data, many host ECM moieties, including genes encod- ing fibrillin 2 (FBN2), hemicentin 1 (HMCN1), laminin ␤3 (LAMB3), collagen type VII (COL7A1), cartilage intermediate layer protein (CILP), ...

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RNA-Seq Analysis in Fruit Science: A Review

RNA-Seq Analysis in Fruit Science: A Review

... principle, RNA-Seq allows analysis of all expressed transcripts, with three key goals: (i) annotating the structures of all transcribed genes including their 5′ and 3′ ends and all splice junctions [18, ...

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RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib.

RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib.

... of RNA-Seq to xenograft profiling and its potential in differentiating the tumour and host components on a single ...that RNA- Seq is highly comparable to a gold standard approach such as RT- ...

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A benchmark for RNA seq quantification pipelines

A benchmark for RNA seq quantification pipelines

... Although the results for genes are comparable to those seen for microarrays (see Fig. 4 in [8]), we note that the results for transcripts are not impressive in general. For example, to recover half of the real ...

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Methods For Robust Quantification Of Rna Alternative Splicing In Heterogeneous Rna-Seq Datasets

Methods For Robust Quantification Of Rna Alternative Splicing In Heterogeneous Rna-Seq Datasets

... from RNA-seq in a manner similar to traditional Ψ ...supplied RNA-seq alignments, adding new splice junctions and LSVs where there are enough reads to support ...

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The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments

The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments

... The RNA-seq data from the 50 cows analyzed in this study yielded 3,628,035 unique variants for the per-sam- ple method and 3,196,373 for the joint genotyping method, while 2,771,566 variants were detected ...

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Human splicing diversity and the extent of unannotated splice junctions across human RNA seq samples on the Sequence Read Archive

Human splicing diversity and the extent of unannotated splice junctions across human RNA seq samples on the Sequence Read Archive

... because of hg19’s continued prevalence, including use by the GEUVADIS consortium [37] in its study of 462 lym- phoblastoid cell line (LCL) samples as well as the GTEx consortium [38] in its ongoing large-scale study of ...

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Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data

Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data

... The goal of this thesis research was to develop software to be used with RNA-Seq data for transcriptome quantification that was capable of handling multireads and quantifying isoforms on a more global ...

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A framework for the RNA-Seq based classification and prediction of disease

A framework for the RNA-Seq based classification and prediction of disease

... years, RNA sequence (RNA-Seq) data are widely used for the transcriptomic ...Hence, RNA- Seq based classification of disease is in its ...on RNA-Seq ...process ...

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A survey of best practices for RNA seq data analysis

A survey of best practices for RNA seq data analysis

... which RNA-seq can be ...mapping RNA-seq reads onto the ...their RNA-seq analysis on the existing annotated reference transcrip- tome alone, or might try to identify new ...

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SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data

SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data

... SCRABBLE addresses several deficiencies of existing methods. First, several methods impute dropout events by using cell-cell distance, as quantified by either Euclidean distance or kernel distance. Such distance measures ...

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RNA-Seq-based transcriptome and the reproduction-related genes for the aphid Schlechtendalia chinensis (Hemiptera, Aphididae).

RNA-Seq-based transcriptome and the reproduction-related genes for the aphid Schlechtendalia chinensis (Hemiptera, Aphididae).

... as well as the sex differentiation genes ovo, yp1, yp3, and esg were differentially expressed. Using RNA-Seq technology we are able to observe differential expression of some genes, but we can gain no ...

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Challenges Analyzing RNA Seq Gene Expression Data

Challenges Analyzing RNA Seq Gene Expression Data

... More realistic models than RPKM addressed the case for multiple isoforms [9] proposing a Poisson distribu- tion for counts and create a continuous variable during the mapping process. The major assumption was that the ...

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Methods, challenges and potentials of single cell RNA seq

Methods, challenges and potentials of single cell RNA seq

... It is difficult to directly compare the technical performance of the existing scRNA-seq schemes based on their original descriptions, aside from the obvious differences such as strand specificity or transcript ...

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RNA seq based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis

RNA seq based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis

... Furthermore, RNA-Seq analysis demonstrates that in RSV-infected rice plants, down- regulation of chloroplast genes is associated with disease symptom development [18, 19] and host defense path- ways are ...

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