Doctoral student – Lab for Computational Biology, Integromics and Gene Regulation (CBIGR) - Department of Biomedical Molecular Biology, Faculty of Sciences & Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, UGent
Principal investigator: prof. Vanessa Vermeirssen (PhD)
Recent studies have shown the interplay between transcription and metabolism, and hence the environment, in complex diseases such as cancer and neuro-inflammatory disorders. The accumulation of multi-omics data allows to investigate this crosstalk across multiple regulatory layers in the cell. The identification of regulatory metabolites and regulatory factors might open new avenues for biomarkers and therapeutics in precision medicine. Also epigenetic information e.g. open chromatin measured with ATAC-seq or methylation patterns provide additional insights and integration with expression data have shown to boost the precision of regulatory network inference. However, multi-omics data integration is still challenging, and available methods have not been comprehensively evaluated so far.
Our goal is to conduct a benchmarking of methods for multi-omics data integration that will provide context-specific guidelines for best practices in the field and allow to discover individual strength, weaknesses and potential synergies of multi-omics network inference methods. Based on our comparison, using an ensemble or composite approach or an optimization of an existing method, we aim to develop an improved methodology for multi-omics data integration in the context of regulatory networks to provide biomarker signatures and in-depth mechanistic understanding of complex diseases.
Finally, we will apply our methodology to data of neuro-inflammatory disorders and cancer to identify regulatory factors and their molecular interactions. An increased understanding of the interplay between transcriptome, epigenome and metabolome at a systems level will lead to opportunities for diagnostics, prognostics, therapeutics and prevention in these complex diseases.
- From 2012-2016, I studied Biotechnology and Bioinformatics at the University of Applied Sciences Emden/Leer (Germany) and obtained a Bachelor of Science degree. I wrote my Bachelor thesis at the Helmholtz-Centre for Infection Research (HZI) about the evolution and adaption of Influenza A viruses due to positive selection.
- From 2016 to 2018, I further worked for the HZI as scientific assistant and software developer during the time of my master studies.
- From 2016 to 2019 I studied Bioinformatics and Genome Research at Bielefeld University (Germany) and obtained a Master of Science. My thesis was focused on functional characterization of genomic variations in Vitis Vinifera.
- From 2019 to 2020 I worked for the biotechnology R & D Hub of Evonik Industries in Halle (Westfalen, Germany) i.a. to investigate the influence of probiotics on animal nutrition and to perform and automatize bioinformatic analyses.
- From 2020 on I work as doctoral student at Ghent University (Belgium) to elucidate cause and mechanisms of complex diseases such as cancer using multi-omics data integration. I am funded by a scholarship ‘special research fund’ (BOF) of Ghent University.