SBL Archive

News Archive

Here's the archive of all SBL news articles.

Guide to Reference Environments
Featured Publication › Human skin as a model for signalling during cellular differentiation
A central research theme within the Systems Biology Laboratory is investigating how cells use molecular mechanisms to control tissue function. Read More ›

Featured Publication › Modelling the conditional regulatory activity of methylated and bivalent promoters
This project builds upon our previous work modelling gene expression from epigenetic data to model 'conditional' regulatory activity; we also provide the first genome-wide integration of DNA methylation bisulfite-sequencing data within such a model to substantially improve prediction accuracy and the reliability of downstream biological inference. Read More ›

Featured Publication › Predictive modelling of gene expression from transcriptional regulatory elements
Predictive modelling is a powerful in silico framework for exploring the regulatory interactions between the epigenetic and transcriptomic layers. Unlike network-based analyses that model genes as variables in an underdetermined system, these models treat genes as observations to allow statistically-significant insights to be gained regarding the complementary roles of histone modifications, transcription factors, DNA methylation and other key regulators. This study provides the first critical review of several epigenetic feature extraction and predictive modelling techniques across multiple cell lines and organisms. Read More ›

Featured Publication › Predicting expression: the complementary power of histone modification and transcription factor binding data
Statistical redundancy between epigenetic features is a critical issue in predictive gene expression modelling. Redundancy between histone modification and transcription factor binding data prevents their effective integration within a single model, reducing prediction accuracy and reliability of downstream biological inference. This study provides a detailed analysis of the biological phenomena underlying redundancy both within and between these epigenetic regulators, providing new insights into spatiotemporal gene regulation and laying the foundation for improved modelling frameworks. Read More ›

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 ›

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

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

Research Areas › Computational Cell Biology
Cellular function is determined by a complex network of interacting biological processes occurring within and between cells. Read More ›

Research Areas › Cellular Networks
Despite major advances, our understanding of the molecular networks that control cell function, and the way in which dysregulation of these networks promotes disease, remains far from complete. Read More ›

People › Students
People › Staff
Systems Biology Lab staff come from a variety of different backgrounds and specialise in many different research areas. Read More ›

People › Edmund Crampin
Professor Edmund Crampin is the Rowden White Chair of Systems and Computational Biology at the University of Melbourne. Edmund directs the Systems Biology Lab at the Melbourne School of Engineering, and is Adjunct Professor in the Faculties of Science (Mathematics & Statistics) and Medicine, Dentistry and Health Sciences (School of Medicine). Read More ›