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Bart Cuypers

  • Research interest:Dr. Bart Cuypers (Msc. 2013, PhD 2018) is FWO post-doc and a bioinformatics scientist who uses multi 'omic and machine learning methods to unravel the molecular biology and drug-resistance mechanisms of pathogens, as well as their host responses. Currently, his post-doctoral at the interface the Adrem Data Lab (University of Antwerp, Antwerp, Belgium).Bart Cuypers has a background in biology (BSc) and cell- and systems biology (MSc). During his PhD, he studied the functional impact and adaptive role of aneuploidy and gene copy number variation in the protozoan parasite Leishmania, a pathogen of which the molecular biology is still elusive. As such, he worked on the collection, analysis, integration and interpretation of (epi-) genomics, transcriptomics, proteomics and metabolomics data over a wide array of genetic backgrounds, life stages and resistance profiles. As such, he has both wet-lab and computational experience. His post-doc focussed on unravelling the (poorly characterised) post-transcriptional regulatory chain of Leishmania by integration of third generation sequencing data (PacBio) with ribosome profiling and proteomics. Bart Cuypers has obtained several competitive grants and fellowships. Firstly, he has started his career with an FWO Aspirant fellowship (2013) and later continued with and FWO post-doc fellowship (2018). To strengthen his post-doc project, he has obtained additional BOF funding (BOF KP, 2019) as well as an FWO credit for post-docs (2020) and a credit for a long research stay abroad at the Notredame Lab (7 months, 2019-2020). He is co-promotor the SB fellowship of Katlijn de Meulenaere (2019) that investigates Plasmodium vivax reticulocyte invasion pathways and ligand candidates using a multi-omic approach. Finally, he obtained an award from the UA research council for promising young researchers (2015). In total this accounts to more than 660 000 euro in acquired funding.As a bioinformatics enthusiast and strong supporter of interdisciplinary research Bart Cuypers has a leading role in the International Society for Computational Biology Student Council (Executive team, treasurer) a global network of more than 2000 master students, PhD students and young post-docs that are passionate about computational biology. He is one of the main organisers of the International Society for Computational Biology Student Council webinar programme (ISCB Academy). Further, Bart is involved in several research consortia, such as BIOMINA (Biomedical Informatics Research Network, Antwerp, steering committee member) and the Tuberculosis ‘Omics Research Consortium (TORCH). He also represents the Institute of Tropical Medicine (ITM) in the CalcUA Supercomputer User Board, is member of the academic council at ITM and Faculty of Science Faculty Board at UA.Keywords: Systems Biology, Multi 'omics, Data Mining, Molecular Biology, Molecular Parasitology.
  • Disciplines:Artificial intelligence, Other information and computing sciences, Scientific computing, Analysis of next-generation sequence data, Bioinformatics data integration and network biology, Bioinformatics of disease, Computational biomodelling and machine learning, Computational evolutionary biology, comparative genomics and population genomics, Computational transcriptomics and epigenomics, Development of bioinformatics software, tools and databases, Bioinformatics and computational biology not elsewhere classified, Infectious diseases, Parasitology, Posttranslational modifications, Transcription and translation, Epigenomics, Genomics, Metabolomics, Proteomics, Transcriptomics, Systems biology not elsewhere classified
  • Research techniques:From sample prep to data analysis for genomics, transcriptomics, proteomics, metabolomics, as well as integrated multi-omics solutions, particularly in the context of infectious diseases. Computationele immunologie (inc. epitope prioritisation) of infectious diseases.
  • Users of research expertise:Academic and industrial researchers interested in: (1) (integrated) multi-omics, genomics, transcriptomics, proteomics or metabolomics of infectious diseases, (2) the molecular interactions of pathogens with the human immune system.