Data Analysis

MBASED – allele-specific expression detection in cancer tissues and cell line

rna-seq

Allele-specific gene expression, ASE, is an important aspect of gene regulation. Scientists at Genentech Inc have developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation ...

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trieFinder – an efficient program for annotating digital gene expression (DGE) tags

rna-seq

Quantification of a transcriptional profile is a useful way to evaluate the activity of a cell at a given point in time. Although RNA-Seq has revolutionized transcriptional profiling, the costs of RNA-Seq are still significantly higher than microarrays, and often ...

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The statistical universe is a single patient – pathway analysis from “N-of-1” RNA-Seq data

rna-seq

The emergence of precision medicine allowed the incorporation of individual molecular data into patient care. Indeed, DNA sequencing predicts somatic mutations in individual patients. However, these genetic features overlook dynamic epigenetic and phenotypic response to therapy. Meanwhile, accurate personal transcriptome ...

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The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) – New database provides vast trove of genetic information on tiny single-celled organisms in the ocean

rna-seq

The ocean holds a bewildering array of microscopic life. Many of the smaller organisms are difficult to study or even to identify under a microscope. For this reason, scientists often look at the genes of these microbes to figure out ...

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BioVLAB-MMIA-NGS – MicroRNA-mRNA Integrated Analysis using High Throughput Sequencing Data

rna-seq

It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence specific manner and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA-mRNA analysis remains a ...

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Enabling large-scale next-generation sequence assembly with Blacklight

rna-seq

A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. These include genomic sequence assembly, very large metagenomic sequence assembly, ...

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An iteration normalization and test method for differential expression analysis of RNA-seq data

rna-seq

Next generation sequencing technologies are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key to analyzing massive and complex sequencing data. In order to derive gene expression measures and compare ...

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