Our research interests cover the methodological advances in data science and their application to topical biomedical challenges, with the focus on advancing transcriptomics and metagenomics on the road to precision medicine. We are also active in the MetaSUB International Consortium where we do focus on establishing environmental metagenomics assays in healthcare as well as on enabling the use of environmental microbiome analysis for forensic purposes.
We are interested in pushing the state of the art in functional genomics, aiming to elucidate the role of the thousands of genes and gene products that are still not exhaustively characterized. A key source of information about the function of a gene is when, where, and how strongly it is being expressed. The most common studies are actually looking for differential expression: differences in expression between different samples or states. This is fortunate, as some of our recent work has shown that such comparative studies are much more robust to technical platform effects. Quantitative measurements are of course directly subject to bias and noise. When novel technologies emerge, the characterization of their measurement bias and noise, as well as the subsequent reduction of the effects of these becomes a critical prerequisite to meaningful reproducible results. With our collaborators we have made key contributions to the first systematic study of the power and limitations of RNA-seq within the US FDA MAQC-III/SEQC consortium. We continue this work, among others, in follow up SEQC2 project.
Another area of our interest is to study the microbial ecosystems of built-up environments in order to build a molecular portrait of cities. To achieve this ambitious goal we collaborate with groups from all over the world within the MetaSUB International Consortium.