This month’s Integrative Biology issue is a themed issue, focusing on integrative computational biology. The guest editor, Dr Jan Baumbach, shares his thoughts on the issue in the editorial, available here.
Two HOT articles feature in the issue; the first of these is a paper by Jennifer Hallinan and colleagues at the University of Newcastle, in which they analyse the changes in four online databases and evaluate how these changes affect the protein function prediction performance of probabilistic functional integrated networks in Saccharomyces cerevisiae. They found that whilst the predictions improved over time, the newer datasets on their own were not necessarily always better – selecting the correct combination of datasets was important.
Is newer better?—evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae
Katherine James, Anil Wipat and Jennifer Hallinan
The other HOT paper is an article from Josch Pauling, Richard Röttger and co-workers, in which they introduce a new integrated online database and analysis platform, EhecRegNet. Motivated by the epidemic outbreak of a multi-resistant Enterohemorrhagic Escherichia coli (EHEC) strain in Western Europe, the group used transcriptional regulatory interactions from E. coli K-12 (a harmless strain) to predict unknown gene regulatory interactions in 16 human pathogens, to potentially aid new treatments.
On the trail of EHEC/EAEC—unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler and Jan Baumbach
Other papers in the issue include a laboratory information management system for DNA barcoding workflows, a novel method for annotating protein function and drug repositioning through incomplete bi-cliques.
Read the rest of the issue here