The group’s first preprint is now available on bioRxiv: Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. This project is what Nathan was working on through much of his time in the group, and has been continuing to finish and write up from Singapore. As a group, we’ve […]
TFBSTools (an R/bioconductor package for transcription factor binding site analysis) has been published in Bioinformatics. As a successor of our famous TFBS perl module, TFBSTools highly expands the functionality to provide efficient genome-wide analysis of TFBSs, while retaining equivalent class structure where possible. Some highlights include TFBS detection, de novo discovery, pairwise phylogenetic footprinting and matrix profile retrieval from […]
The paper associated with our GenomicInteractions R package is now out! You can read it here on the BMC Genomics website. The GenomicInteractions package came about because several members of the group (me, Nathan, Malcolm and Anja) were working with genomic interaction data, and realised that there were few tools designed to handle this kind […]
All forms of life undergo a process known as transcription, which sees genetic information transferred from DNA to RNA, marking the beginning of gene expression. The ‘on-switch’ or core promoter is a nearby stretch of DNA that signals all the necessary units needed to initiate transcription to come together. Now, in a collaborative discovery that […]
A perspective written by members of the group on the evolutionary dynamics and features of Conserved Noncoding Elements (CNEs) and the current hypotheses regarding the reason for their high levels of conservation has just being published in Phil. Trans. R. Soc. B.