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PhD training opportunity: Development of individual-specific molecular networks

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  • Full or part time
    Prof K Van Steen
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

Describing a system implies describing its behaviour and important control mechanisms that regulate this behaviour. Crucial in this process are interactions, which mayoccur at different levels or scales, and thus network theory and networkvisualization are increasingly being used to understand biological mechanismsoperating in human systems. However, an individual, especially when in poor health, is likely to deviate from the “norm” in human systems. In this project,we wish to develop omics data integrative gene-based networks to enhance Precision Medicine. Such a network would enable the identification of gene modules that are subject-specific (in network nodes/edges) and comprise multi-layer cellular information. It goes beyond existing work in that genes or pathways are considered to be complex multi-omics systems, and that statistical significance is assessed for individual-specific gene or pathway profiles (in contrast to f.i. Menche et al. 2017 and Kuijjer et al. 2018). We aim to achieve our goal by building upon the aforementioned references and our work on gene representations using diffusion kernels and network theory (Fouladi et al.2018). Personalized gene omics-integrative signatures will primarily be derived by combining genome, transcriptome and epigenome data for complex diseases with an inflammatory component.
The project outcome will lead to an integrative workflow for patient-specific prognostic or predictive biomarker discovery. The opportunity to carry out secondments at Institut Pasteur (France – Prof Benno Schwikowski) and the Golden HelixFoundation (UK – Prof George Patrinos), will further foster assessing the general feasibility of the developed techniques towards clinical application, formulating preliminary guidelines regarding multi-target (rather thansingle-target) drug strategies, and making recommendations about drug efficacy study designs.

• We offer an interesting project in the field of human genetics in close collaboration with researchers in computational imaging and biology. You will be embedded in an interdisciplinary research group and you will be involved in international collaborations.
• Attractive 3-year full-time employment contract in accordance with the MSCA regulations for early stage researchers of the European Commission.
• Enrolment in a PhD program whereby PhD tuition fee is paid by project.
• Supervision by recognized experts and access to (beyond) state-of-the-art research and pilot-scale infrastructure.
• Training in complementary skills via participation at local and network-based events.
• Terms of appointment and payment according to the rules and regulations laid down by European Union’s Horizon 2020 Marie S. Curie Innovative Training Networks andregulations followed by the host institution.
• All beneficiaries will be full-time employed at their (host) institution. The researchers are expected to conduct secondments at other network partners andcountries, as planned by the main host.

The position remains open till May 17, 2020 or till the envisaged candidate has been identified (whatever comes first): apply via as soon as possible!
Only applications for which the following information has been uploaded will be considered:
Cover Letter, describing your motivation to apply, your research career goals, skills and experience.
Diploma and transcripts of records (BSc and MSc)
Full contact details of two reference persons
Documentation of English language qualifications
Other information for consideration (e.g., a list of publications if applicable)

Only applications in English are considered. The board of the network will evaluate all applications, and the top-ranked candidates will be invited for interviews. As we collect all applications from all different EU countries in 1 application tool, we request to use the TranSYS application tool:

For more information please contact Prof. dr. Kristel Van Steen, mail: [Email Address Removed] .

Funding Notes

part of a larger Innovative Training Network (ITN) EU funded project


• A strong background in network analysis, machine learning and statistics.
• Experience with multi-omics data, bioinformatics or computational biology, big data handling, is an advantage.
• Interested in collaborative, interdisciplinary and intensive research experience.
• A team player.
• Eager to go beyond scientific comfort zones
• Good skills in oral and written English.
TranSYS wishes to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. In total 15 early-stage researchers will be recruited that will work at the 13 beneficiaries all across Europe.
We expect that applicants hold a university degree that qualifies them for doctoral studies at their recruiting organization.
At the time of commencement, it is required that the candidate has not been awarded a doctorate degree and is within the first 4 years (full-time equivalent) of her/his research career. Furthermore, the candidate must not have resided or carried out her/his main activity (work, studies, etc.) in the host country for more than 12 months in the 3 years immediately prior to her/his recruitment. Short stays, such as holidays, are not taken into account. The candidate is required to spend part of his/her project period at other institutions in the TranSYS consortium on secondments.

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