In this issue of Neuron, report different patterns of 5-HT2C pre-mRNA editing in suicide victims, as compared to controls. Treatment of mice with fluoxetine alters the pattern of 5-HT2C transcript editing in the direction opposite that observed for suicide victims. The authors speculate on a possible serotonergic mechanism controlling 5-HT2C pre-mRNA editing.

The murine embryonic stem cell test (EST) is an alternative testing method designed to assess potential developmental toxicity of compounds. The implementation of transcriptomics in the EST has been shown to reduce the culture duration and improve endpoint evaluation and is expected to result in an enhanced predictability and definition of the applicability domain. We evaluated the identificati...

One of the greatest hindrances to a comprehensive understanding of microbial genomics, cell biology, ecology, and evolution is that most microbial life is not in culture. Solutions to this problem have mainly focused on whole-community surveys like metagenomics, but these analyses inevitably loose information and present particular challenges for eukaryotes, which are relatively rare and posses...

Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory ne...

Recently, we presented ContextMap (Bonfert et al., 2012), a novel approach to mapping RNA-seq reads based on the concept of a so-called read context. A context is defined as a set of reads all originating from the same stretch of the genome, indicating that they all correspond to transcripts of the same gene. The original implementation we presented was focused on refining initial mappings prov...

Every human being is different based on genetics, lifestyle, and environmental factors. Novel medical technologies have become more precise owing to molecular information, including genomics, transcriptomics, proteomics, metabolomics, etc. The “omics” technologies have opened up new horizons for healthcare systems, enabling them to prevent and/or diagnose diseases more precisel...

With the advent of Next-generation sequencing and bioinformatic tools, gene expression studies have changed dramatically. Whole transcriptome studies are providing valuable resources for generating molecular markers like microsatellites and single-nucleotide polymorphisms and candidate genes. Transcriptome sequencing or RNA-Seq becomes more relevant in cases where whole-genome sequencing is not...

This review examines the extent to which transcriptomic methods have lived up to their promise in the context of nutrition research, placing particular emphasis on examples from micronutrient research. A case is made that the high quality platform technologies now available, together with established standards and systems for data storage and exchange and powerful new methods of data analysis, ...