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...

Despite the importance of stony corals in many research fields related to global issues, such as marine ecology, climate change, paleoclimatogy, and metazoan evolution, very little is known about the evolutionary origin of coral skeleton formation. In order to investigate the evolution of coral biomineralization, we have identified skeletal organic matrix proteins (SOMPs) in the skeletal proteo...

Animals inhabiting cryptic environments are often subjected to morphological stasis due to the lack of obvious agents driving selection, and hence chemical cues may be important drivers of sexual selection and individual recognition. Here, we provide a comparative analysis of de novo-assembled transcriptomes in two Mediterranean earthworm species with the objective to detect pheromone proteins ...

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, ...