In the few years since its initial application, massively parallel cDNA sequencing, or RNA-
seq, has allowed many advances in the characterization and quantification of …

Periodontitis is a chronic inflammatory condition of the periodontium involving interactions
between bacterial products, numerous cell populations and inflammatory mediators. It is …

Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key
challenge in transcript quantification from RNA-Seq data is the handling of reads that map to …

Spinal muscular atrophy (SMA), which results from the loss of expression of the survival of
motor neuron-1 (SMN1) gene, represents the most common genetic cause of pediatric …

Motivation: High-throughput sequencing has made the analysis of new model organisms
more affordable. Although assembling a new genome can still be costly and difficult, it is …

Alternative splicing is widely recognized for its roles in regulating genes and creating gene
diversity. However, despite many efforts, the repertoire of gene splicing variation is still …

The accurate mapping of reads that span splice junctions is a critical component of all
analytic techniques that work with RNA-seq data. We introduce a second generation splice …

Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic beta cells are killed by
infiltrating immune cells and by cytokines released by these cells. Signaling events …

Background The MYB superfamily constitutes one of the most abundant groups of
transcription factors described in plants. Nevertheless, their functions appear to be highly …