Welcome to the Bioinformatics Research Group
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.
ProjectsWe are involved in number of national and international projects and consortia, including SEQC2 (Sequencing Quality Control phase 2), MetaSUB (Metagenomics & Metadesign of Subway & Urban Biomes), and MAQC Society (Massive Analysis and Quality Control). We are also involved in organisation of CAMDA conference (Critical Assessment of Massive Data Analysis).
- Łabaj, PP and Kreil, DP. Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls. Biology Direct, 2016; 11:66
- MetaSUB Consortium [Łabaj, PP]. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome, 2016; 4:24
- Su, Z*; Łabaj, PP*; Li, S*; et al. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology, 2014; 32:903-914
- Li, S*; Łabaj, PP*; Zumbo, P* et al. Detecting and correcting systematic variation in large-scale RNA sequencing data. Nature Biotechnology, 2014; 32, 888-895
- Łabaj, PP; Leparc, GG; Linggi, BE; Markillie, LM; Wiley, HS; Kreil, DP. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics, 2011; Vol. 27; i383-i391
- Łabaj, PP; Leparc, GG; Bardet, AF; Kreil, G; Kreil, DP. Single amino acid repeats in signal peptides. FEBS Journal. 2010; Vol. 277; 3147-3157