PhD student - Signal processing and machine learning for high-throughput next-generation proteomics

About UGent

Ghent University is a major Belgian university, enjoying high rankings in international surveys (66 ac-cording to the Shanghai Academic Ranking of World Universities, 103 according to the Times Higher Education (THE) World Universities Ranking). The university employs more than 8,000 people and is actively involved in education and research, management and administration, as well as technical and social service provision on a daily basis. With 11 faculties and more than 80 departments offering state-of-the-art study programmes grounded in research in a wide range of academic fields, Ghent University offers several exciting and challenging career opportunities.

The research will be carried out within IDLab, which is also a core research group of imec, the world-leading research and innovation hub in nanoelectronics and digital technologies. IDLab performs fun-damental and applied research, among others, in the areas of machine learning and data mining with applications to healthcare, multimedia, etc. A consistent, underlying goal of the group is to leverage these technologies for the benefit of society.

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).

Who you are

• Applicants should hold (or shortly acquire) an academic Master’s degree (or equivalent), in any of the following branches of engineering: Electrical/Computer, Signal Processing, Communications, Artificial Intelligence, Biomedical.
• Fluency in high-level programming languages (e.g., Python) and expertise in statistical signal processing are essential. Experience with stochastic modelling (e.g., (hidden) Markov models, Gaussian mixture models, etc.) is desirable. Prior experience with GPU programming is a big plus.
• Prior knowledge of, or background in, proteomics is not a prerequisite, but is a plus.
• Candidates are expected to have excellent communication skills and proficiency in written and oral English.
• A problem-solving attitude, the ability to take initiative and work independently to deliver high-quality research is essential. We also expect the candidates to be capable of critical self-reflection, demonstrate an eagerness to learn, and be a team-player.

What we do for you

• A full-time PhD scholarship for 4 years (coupled to a yearly positive evaluation) at Ghent University.
• A pleasant work climate and collegial atmosphere in an international and interdisciplinary research team, with active support from experienced (international) researchers.
• An attractive remuneration along with several benefits, such as a wide range of training and education opportunities, 35 days of holiday leave (on an annual basis for a full-time job) supplemented by annual fixed bridge days, a bicycle allowance and eco vouchers.

Interested?

Please send your application package via email to nilesh.madhu@ugent.be before the application deadline of 29/08/2021, 23:59 CEST. 

Your application package must include the following documents:

• Your CV and a copy of your latest transcripts (preferably merged into one pdf file).
• A cover letter outlining the reasons for your application/motivation (in pdf format).
• A transcript of the required degree (if already in your possession). If your degree is in a language other than our national languages (Dutch, French or German) or English, please add a translation in either English, Dutch or German. 

Ghent University maintains an equal opportunities and diversity policy, everyone is encouraged to apply for this position.

For more information about this vacancy, please feel free to contact Prof. Dr.-Ing. Nilesh Madhu at the above email address.