The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes
characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities …

Antisense transcription, which was initially considered by many as transcriptional noise, is
increasingly being recognized as an important regulator of gene expression. It is …

De novo assembly of RNA-seq data enables researchers to study transcriptomes without the
need for a genome sequence; this approach can be usefully applied, for instance, in …

Massively parallel sequencing of cDNA has enabled deep and efficient probing of
transcriptomes. Current approaches for transcript reconstruction from such data often rely on …

Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of
transcriptomes. Current approaches for transcript reconstruction from such data often rely on …

Transcription factors canonically bind nucleosome-free DNA, making the positioning of
nucleosomes within regulatory regions crucial to the regulation of gene expression. Using …

Background Genome annotation is of key importance in many research questions. The
identification of protein-coding genes is often based on transcriptome sequencing data, ab …

Data on absolute molecule numbers will empower the modeling, understanding, and
comparison of cellular functions and biological systems. We quantified transcriptomes and …

Motivation: As high-throughput transcriptome sequencing provides evidence for novel
transcripts in many species, there is a renewed need for accurate methods to classify small …

The fission yeast Schizosaccharomyces pombe is an important model organism for the study
of eukaryotic molecular and cellular biology. Studies of S. pombe, together with studies of its …