Despite only becoming popular at the beginning of this decade, biomolecular networks are
now frameworks that facilitate many discoveries in molecular biology. The nodes of these …

The elucidation of gene regulatory networks is one of the major challenges of systems
biology. Measurements about genes that are exploited by network inference methods are …

To study basic principles of transcriptome organization in bacteria, we analyzed one of the
smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific …

The proteomes that make up the collection of proteins in contemporary organisms evolved
through recombination and duplication of a limited set of domains. These protein domains …

We have compared the transcriptomic profiles of microdissected live ovules at four
developmental stages between a diploid sexual and diploid apomictic Boechera. We …

Background The modulation of mRNA levels across tissues and time is key for the
establishment and operation of the developmental programs that transform the fertilized egg …

Background Time course data from microarrays and high-throughput sequencing
experiments require simple, computationally efficient and powerful statistical models to …

Gaining insights on gene regulation from large-scale functional data sets is a grand
challenge in systems biology. In this article, we develop and apply methods for …

Background Charting the interactions among genes and among their protein products is
essential for understanding biological systems. A flood of interaction data is emerging from …

Primordial organisms of the putative RNA world would have required polymerase ribozymes
able to replicate RNA. Known ribozymes with polymerase activity best approximating that …