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Marie-Sklodowska Curie PROTrEIN-ITN Early Stage Researcher (PhD student) position: Strategies for molecular diagnosis of Rare Disease patients through integrated analysis of proteomics, metabolomics, genomics and phenomics data (CNAG-CRG, Barcelona, Spain)


Gene Regulation, Stem Cells and Cancer

Dr Sergi Beltran , Dr Jürgen Cox Saturday, January 30, 2021 Competition Funded PhD Project (Students Worldwide)
Barcelona Spain Artificial Intelligence Bioinformatics Data Analysis Machine Learning Networks Other Software Engineering

About the Project

PROTrEIN (www.protrein.eu) is a European Innovative Training Network composed of 11 beneficiaries, and 6 partner organizations, from the academic and non-academic sectors (including two SMEs and two large companies).

The network’s mission is to train a new generation of computational proteomics researchers by providing them an intersectoral and interdisciplinary set of skills to tackle the main challenges in the field and improve their future employability.

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Subproject 2: (Host: National Centre for Genomic Analysis CNAG-CRG, Barcelona, Spain)

Title: Strategies for molecular diagnosis of Rare Disease patients through integrated analysis of proteomics, metabolomics, genomics and phenomics data.

Objectives: Development and implementation of strategies for the integration of proteomics/metabolomics, genomics and phenomics data from Rare Disease patients, and diagnosis of Rare Disease patients through integrated analysis of multi-omics data.

Methodology: The student will join the Solve-RD Data Analysis Task Force, co-led by S. Beltran and A. Hoischen (Radboud University Medical Center, Nijmegen, NL), and will evaluate existing methods and strategies on the Solve-RD data. The student will design and develop a multi-omics workflow applicable to several diseases and the analysis of the metabolomics and proteomics data will be carried out in collaboration with J. Cox (MPI). Finally, the student will collaborate with the RD-Connect GPAP software developers to integrate the approach in the GPAP, including the development of a module to visualize the multi-omics data with metadata, and network information (Reactome and Wiki Pathways).

Required Skills: Good understanding of genetics and genomics, Computer programming basics, Strong command of English

Desirable Skills: Advanced computer programming, Experience with human genomics data analysis, Understanding of metabolomics, Training in bioinformatics, Knowledge of databases

Expected Results: We expect to obtain strategies evaluated, developed, and implemented for the integration of proteomics/metabolomics, genomics and phenomics data from Rare Disease patients, and the identification of pathogenic genes or molecules proposed for undiagnosed Rare Disease patients through the application of the implemented strategies.

Planned Secondments:

Host: MPIB (Germany), Duration: 1 Month; When: Year 2, Goal: Proteomics data analysis workflows.

Host: NOVO NORDISK (Denmark), Duration: 1 Month; When: Year 3, Goal: Multi-omics databases in rare-diseases.

Enrolment in doctoral programs: Ph.D. in Bioinformatics from Universitat de Barcelona (UB).

Application Procedure: 

An application is solely possible via the PROTrEIN application form: http://protrein.eu/call-for-applicants/

Applications must be in English. Applicants may indicate 3 ESR Projects which they would like to work on, ranking them in order to preference. Uploading reference letters is not mandatory, but applicants should be aware that referees will be automatically contacted after submission and receive a questionnaire. Candidates must provide all information before the deadline. Candidates should ensure that referees answer the questionnaire.

Application deadline: 31 January 2021

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About the CNAG-CRG

Created in 2009, the CNAG-CRG carries out projects in DNA sequencing and analysis in collaboration with researchers from Catalonia, Spain, and the international research community to ensure our country’s competitiveness in the strategic area of genomics.

After starting operations in March 2010, CNAG-CRG has positioned itself as one of the largest European centres concerning sequencing capacity. The highly qualified staff, combined with outstanding computing infrastructure, makes CNAG-CRG a centre of excellence in data analysis. It takes part in genome sequencing and analysis projects in areas as diverse as cancer genetics, rare disorders, host-pathogen interactions, the preservation of endangered species, evolutionary studies and the improvement of species of agricultural interest.

The CNAG-CRG is a non-profit organisation funded by the Spanish Ministry of Economy, Industry and Competitiveness and the Catalan Government through the Economy and Knowledge Department and the Health Department.


Funding Notes

DURATION
The position is fully funded for 36 months by the European Commission under the H2020 Marie Curie Innovative Training Network Programme.
SALARY
Marie Curie ITNs provide a highly competitive salary to the ESR, including a competitive monthly living and mobility allowance and (if eligible) a monthly family allowance.
ELIGIBILITY CRITERIA
The eligibility criteria dictated by the European Commission under the H2020 Marie Curie Innovative Training Network Programme must be fulfilled.
See: View Website

References

1. Matalonga, L., Laurie, S., Papakonstantinou, A., Piscia, D., Mereu, E., Bullich, G., Thompson, R., Horvath, R., Pérez-Jurado, L., Riess, O., Gut, I., van Ommen, G.-J., Lochmüller, H., Beltran, S., Renieri, A., Dursun, A., Matilla-Duenas, A., Cormand, B., Rivolta, C., … Sabater, M. (2020). Improved Diagnosis of Rare Disease Patients through Systematic Detection of Runs of Homozygosity. The Journal of Molecular Diagnostics, 22(9), 1205–1215. https://doi.org/10.1016/j.jmoldx.2020.06.008
2. Tort, F., Ugarteburu, O., Texidó, L., Gea‐Sorlí, S., García‐Villoria, J., Ferrer‐Cortès, X., Arias, Á., Matalonga, L., Gort, L., Ferrer, I., Guitart‐Mampel, M., Garrabou, G., Vaz, F. M., Pristoupilova, A., Rodríguez, M. I. E., Beltran, S., Cardellach, F., Wanders, R. J. A., Fillat, C., … Ribes, A. (2019). Mutations in TIMM50 cause severe mitochondrial dysfunction by targeting key aspects of mitochondrial physiology. Human Mutation, 40(10), 1700–1712. https://doi.org/10.1002/humu.23779
3. Graham, E., Lee, J., Price, M., Tarailo-Graovac, M., Matthews, A., Engelke, U., Tang, J., Kluijtmans, L. A. J., Wevers, R. A., Wasserman, W. W., van Karnebeek, C. D. M., & Mostafavi, S. (2018). Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review. Journal of Inherited Metabolic Disease, 41(3), 435–445. https://doi.org/10.1007/s10545-018-0139-6

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