In Genome Biology this week, scientists led by those at EMBL in Heidelberg used what they call a "trans-regulation screen" to study the regulation of Ath5, the central node in the gene regulatory network controlling retinal ganglion cell differentiation in vertebrates. They were able to identify potential Ath5 regulators that they then validated in vivo by functional assays in medakafish embryos.
A mini-review written in part by Stanford University's Russ Altman takes a look at how systems biology tools can be used to improve drug design and development. "Traditional drug design has relied heavily on the one drug-one target paradigm, but this may overlook system-wide effects that cause the drug to be unsuccessful," they write. Using systems biology tools in conjunction with chemical biology approaches allows drug makers the ability to use genomic data, structural analysis, high-throughput chemical screens, and other information to improve the process of predicting ligand binding and protein-protein interactions, which can unexpectedly lead to a drug being ineffective or toxic.
Bioinformaticist Charles DeLisi at Boston University led work that developed an "evidence-weighted functional-linkage network comprising 21,657 human genes" in order to find linked disease genes. They used the network to examine candidate genes for 110 diseases and were able to show previously unseen associations between diseases with different phenotpyes, such as hypercholesterolemia and Alzheimer's disease, says the abstract.
Researchers from the Broad Institute and Sweden's Uppsala University describe a new assembly algorithm that improves de novo genome assembly by using related species. In this article, they show that assisted assembly can significantly improve low-coverage mammalian assemblies and that "it can be successfully applied to genomes with locally low coverage caused by cloning bias, such as P. falciparum HB3."