We address the applicability of blind source separation (BSS) methods for the estimation of hidden influences in biological dynamic systems such as metabolic or gene regulatory net...
Background: Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index o...
Background: Many vital biological processes, including transcription and splicing, require a combination of short, degenerate sequence patterns, or motifs, adjacent to defined seq...
Micah Hamady, Erin Peden, Rob Knight, Ravinder Sin...
Background: A transcriptional regulatory module (TRM) is a set of genes that is regulated by a common set of transcription factors (TFs). By organizing the genome into TRMs, a liv...
Background: An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expres...