RNA sequencing (RNA-Seq) uses the capabilities of high-throughput sequencing methods
to provide insight into the transcriptome of a cell. Compared to previous Sanger sequencing …

High throughput platforms available in clinical settings or in research laboratories, such as
magnetic resonance imaging, microarray, mass spectrometry and next-generation …

Through the widespread implementation of next-generation sequencing (NGS), analyses of
the whole genome (the entire DNA content) and the whole transcriptome (the genes being …

Abstract Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …

The European chestnut, an important forest species for the economy of Southern Europe,
covers an area of 2.53 million hectares, including 75,000 ha devoted to fruit production …

Deep sequencing has recently emerged as a powerful alternative to microarrays for the high-
throughput profiling of gene expression. In order to account for the discrete nature of RNA …

The Smith-Waterman (SW) algorithm is universally used for a database search owing to its
high sensitively. The widespread impact of the algorithm is reflected in over 8000 citations …

Background. A common research goal in transcriptome projects is to find genes that are
differentially expressed in different phenotype classes. Biologists might wish to validate such …

With the advent of next-generation sequencing (NGS), including whole genome sequencing
(WGS), RNA sequencing (RNA-seq), and chromatin immunoprecipitation followed by …

We review existing methods for the analysis of RNA-Seq data and place them in a common
framework of a sequence of tasks that are usually part of the process. We show that many …