SBL News

publications – Featured Publication

Virtual Reference Environments: a simple way to make research reproducible

'Reproducible research' has received increasing attention over the past few years as bioinformatics and computational biology methodologies become more complex. Although reproducible research is progressing in several valuable ways, we suggest that recent increases in internet bandwidth and disk space, along with the availability of open-source and free-software licences for tools, enable another simple step to make research reproducible. In this article, we urge the creation of minimal virtual reference environments implementing all the tools necessary to reproduce a result, as a standard part of publication. We address potential problems with this approach, and show an example environment from our own work. Read More ›

publications – Featured Publication

The flavoprotein FOXRED2 reductively activates nitro-chloromethylbenzindolines and other hypoxia-targeting prodrugs

Blog Hypoxia is a prevalent feature of solid malignancies that arises as a result of structural and functional irregularities in tumour microvasculature. In this work, we built correlation and partial correlation networks from microarray data to identify enzymes which convert hypoxia-activated prodrugs (HAPs) to their active form. Read More ›

publications – Featured Publication

Links between the Oncoprotein YB-1 and Small Non-Coding RNAs in Breast Cancer

Blog The nucleic acid-binding protein YB-1, a member of the cold-shock domain protein family, has been implicated in the progression of breast cancer and is associated with poor patient survival. YB-1 has sequence similarity to LIN28, another cold-shock protein family member, which has a role in the regulation of small noncoding RNAs (sncRNAs) including microRNAs (miRNAs). Therefore, to investigate whether there is an association between YB-1 and sncRNAs in breast cancer, we investigated whether sncRNAs were bound by YB-1 in two breast cancer cell lines (luminal A-like and basal cell-like), and whether the abundance of sncRNAs and mRNAs changed in response to experimental reduction of YB-1 expression. Read More ›

research – Research Areas

Reproducible research

Replication of results is a central tenet of science; the idea that a meaningful result should be able to be replicated, and that publication should describe it in enough detail for this to be possible, motivates a large part of the basic activity of science. Read More ›

research – Research Areas

Nanobiological modelling

Determining the interactions between a nanomaterial and a biological system is one of the most important problems in nanotechnology today, with significant implications for safety and drug design. Read More ›