The core competences of BIOBIX (within the The Department of Mathematical Modelling, Statistics and Bioinformatics) are bioinformatics, data-integration and analysis, particularly in combination with high-throughput applications. Based on these competences, BIOBIX obtained ample expertise in epigenetic research, more specifically DNA-methylation and telomere length profiling, but also histone modification and non-coding RNA analyses. Within BIOBIX there is a general focus on systems biology and comparative genomics reflected in different supported technologies: next-generation sequencing, NMR-based metabonomics, MS-based proteomics, proteogenomics, transcriptomics, ribosome profiling, phylogenetic footprinting, heterogenous data-integration statistics, ncRNA detection and target prediction, selection of novel targets, etc.. These technologies are applied in many different disease areas, but with cancer and (cardiovascular) aging as two most important targets. Our lab has also extensive IT knowledge in setting up high performance computer environments and is one of the few European labs actively mirroring all available sequence data on dedicated hardware using in-house software.
BIOBIX is working in close collaboration with MDxHealth and can rely on a broad collaboration network, consisting of many of the world’s leading cancer research institutes, particularly in the epigenetics field (e.g. Stephen Baylin and James Herman, Johns Hopkins University, Baltimore). The aging oriented research particularly involves BIOBIX’s participation in the Asklepios study, a longitudinal population study, with more than 2500 volunteers included, focusing on the interplay between aging, cardiovascular haemodynamics and inflammation in (preclinical) cardiovascular disease. During the first round of the study, telomere lengths were assessed for (almost) all of the subjects. Currently, research is particularly focused on the identification of DNA-methylation markers for atherosclerosis in the complete peripheral blood leukocyte fraction. Isolation and analysis of the monocyte fraction for a portion of the population is possible during the second round of the study (starting during 2010), and would provide a clearly more functional overview, thereby exceeding the simple “biomarker” approach and providing actual targets for modification. For this purpose, BIOBIX clearly benefits from the collaboration with Prof. Dr. Wim Vanden Berghe, whose field of interest is in fact how personal epigenetic profiles can be altered, particularly through dietary (also supplementation) and lifestyle modification. Next to the aforementioned partnerships in the cancer and aging disease areas, BIOBIX also has collaborations running with Prof. Petra Van Damme (VIB, Dept. of Medical Protein Research) for MS-based (positional) proteomics and ribosome profiling studies and with pioneering researchers in the peptidomics and peptide tandem mass spectrometry area: Prof. Liliane Schoofs, Dr. Geert Baggerman and Prof. Walter Luyten.
BIOBIX is also involved in a research valorization platform, BIOMARKED (http://www.biomarked.net), on validation of biomarkers in aging and cancer (Industrial Research Fund IOF-UGent). Several new approaches are on the verge of clinical implementation. In Biomarked we focus on the most innovative technology platforms with the final purpose of generating a new and innovative platform for the identification and validation of novel and more accurate biomarkers for the prediction of both response to therapy and relapse. In 2008, BIOBIX, in collaboration with the Department for Medical Genetics (CMGG-UGent) and the Department of Pharmaceutics received Hercules funding to deploy a next generation sequencing and genome analysis facility, NXTGNT (http://www.nxtgnt.com). Meanwhile several epigenetics oriented applications have been successfully tested on different platforms, e.g. ampliconsequencing after bisulphite treatment, ChIP-sequencing of methylated DNA-fragments. In 2012, BIOBIX became a partner in the IAP project PLASTOSCINE, addressing the question how brain plasticity is regulated at the cellular level in songbirds. This project will lead to major advances in our understanding of molecular (genetic and epigenetic) mechanisms underlying brain plasticity as it occurs spontaneously during ontogeny or during the annual cycle under the influence of steroid and thyroid hormones. This knowledge is important for the understanding of brain functioning in general (control of behavior, learning, effects of hormones …) but it should also have an impact on the understanding of the mechanisms that could promote brain repair in pathological conditions such as brain trauma or neurodegenerative diseases.
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