Welcome to Komorowski's BioInformatics Lab
The bioinformatics group research is a reflection of the field: on one hand we develop algorithms and build tools and software systems that enable answering complex questions in Life Sciences, on the other hand we try to come with answers to these questions. Our modus of work is distinguished by collaboration.
Our flagship is the Rosetta system that implements an environment for developing rough set classifiers from large and very large data collected in decision systems. In recent years we moved towards decision systems with thousands of features and extended our computational framework with Monte Carlo Feature Selection and Random Reducts. Rosetta can now be executed on multicore architecture. We take a step away from univariate and linear thinking and help answer questions which groups of features (variables) and in which combinations contribute most to the outcome (decision).
Data in the form of decision tables is omnipresent in Life Sciences. Examples of solved problems in different domains include but are not limited to:
- functional genomics - how to predict gene’s participation in a biological process from gene expression time profiles and how to assign function to new genes from such profiles; Genome Research and Bioinformatics
- proteomics - which positions of octamer polypeptides and for what values, ie. amino acids are decisive for cleavage or non-cleavage by HIV protease; Proteins
- chromatin - what is organization of nucleosomes in gene bodies; Genome Research
- medicine - which gene-gene pairs and with which environmental factors interact in allergy; PLoS One
- epigenetics - what are combinatorial associations of histone modifications to exon expression; PLoS One
Our present interest is in transcriptomics with a particular focus on the interplay of chromatin structure and DNA and their modifications. Of major interest are common mechanisms behind common disease such as diabetes type II, gliomas and cervix cancer. We also continue our work in proteomics and virology, and, it goes without saying, on the algorithms and tools.
Our main collaborators are:
- Professor Claes Wadelius, Department of Immunology, Genetics and Pathology, Uppsala University
- Professor Jacek Koronacki, Institute of Computer Science, Polish Academy of Sciences
- Professor Bozena Kaminska, The Nencki Institute of Experimental Biology, Polish Academy of Sciences.