What you will do
The PhD research proposal concerns the application of signal processing and machine learning for high-throughput next-generation proteomics, i.e., the large-scale study of all proteins expressed by a cell, tissue, or organism at a certain time. Presently, proteomics techniques are carried out in specialised institutes and on dedicated equipment (e.g., mass spectrometers) run by highly trained personnel. This results in queuing and run‐times in the order of days, thereby limiting its application to research pur-poses. Exploiting silicon CMOS‐based nanotechnology may help us realise proteomics-on-chip, thereby unleashing the full potential of high-throughput proteomics in clinical diagnostics. Solid state na-nopore sensor technology has the potential to read a single protein’s identity. The goal of the research would be the development of appropriate signal processing algorithms to identify proteins as they translocate through the nanopore, based on the electrical signals generated by a labelled subset of amino acids as the protein moves through the nanopore. This can be accomplished by e.g., deconvolu-tion or matched filtering followed by applying principles from detection and estimation theory. The next step would be the development of machine learning algorithms that map the detected sequence of amino acids to the underlying protein.
Proteomics making use of electrical nanopore sensing is currently a greenfield domain, with no proof-of‐concept demonstrations as yet. Thus, the research conducted in the scope of this project has a high impact potential.
The work will be carried out (in close collaboration with imec) at the Internet and Data Sciences Lab (IDLab), within the Faculty of Engineering and Architecture of Ghent University, Belgium. We offer can-didates the possibility to carry out challenging, high-impact research within a relaxed, supportive, in-ternational and interdisciplinary setting.
The work will be supervised by Prof. Dr.-Ing. Nilesh Madhu and Prof. dr. ir. Jan Fostier (IDLab) and dr. ir. Koen Martens (imec).
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