Review Publications

Finding RNA Thermometers with Next-Gen Sequencing

Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. Among the many ways to register temperature changes, bacteria often use temperature-modulated structures in the untranslated region of mRNAs. In this article, the authors ...

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RNA-seq Data – Challenges in and Recommendations for Experimental Design and Analysis

rna-seq

RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality ...

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Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

rna-seq

RNA sequencing (RNA-Seq) and mass spectrometry-based shotgun proteomics are powerful high-throughput technologies for identifying and quantifying RNA transcripts and proteins respectively. With the increasing affordability of these technologies, many projects have started to apply both to the same samples to ...

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Challenges and strategies for RNA-Seq data analysis

rna-seq

RNA-seq is a methodology for RNA profiling based on next-generation sequencing that enables to measure and compare gene expression patterns at unprecedented resolution. Although the appealing features of this technique have promoted its application to a wide panel of transcriptomics ...

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RNA sequencing – current and prospective uses in metabolic research

rna-seq

Previous global RNA analysis was restricted to known transcripts in species with a defined transcriptome. Next generation sequencing has transformed transcriptomics by making it possible to analyse expressed genes with an exon level resolution from any tissue in any species ...

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Bringing RNA-Seq closer to the clinic

rna-seq

Several multicenter benchmark data sets represent valuable steps toward using RNA-seq as a diagnostic tool with clinical utility. RNAs are excellent candidates for monitoring and diagnosing disease. In recent years, high-throughput RNA sequencing (RNA-seq) has opened new possibilities for determining ...

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Application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes

rna-seq

Researchers at the Academy of Sciences of the Czech Republic propose ways to improve read mapping accuracy and sensitivity such as modifying a reference genome at RNA editing sites, using splicing- and ambiguity-competent aligners, and masking chloroplast- or nucleus-derived sequences. ...

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International Review of Neurobiology – The Brain Transcriptome

rna-seq

The Brain Transcriptome International Review of Neurobiology – Volume 116, Pages 2-352 (2014) Chapter One – Introduction to Sequencing the Brain Transcriptome Pages 1-19 Robert Hitzemann, Priscila Darakjian, Nikki Walter, Ovidiu Dan Iancu, Robert Searles, Shannon McWeeney Chapter Two – ...

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Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits

rna-seq

The nomination of candidate genes underlying complex traits is often focused on genetic variations that alter mRNA abundance or result in non-conservative changes in amino acids. Although inconspicuous in complex trait analysis, genetic variants that affect splicing or RNA editing ...

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Introduction to RNA-Seq and its Applications to Drug Discovery and Development

rna-seq

The research and development (R&D) process in modern drug discovery and development is a challenging task. One of the reasons is because the biological system is complex. There are 20,000–25,000 genes in the human genome. Using traditional test methods such ...

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