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Marie-Sklodowska Curie PROTrEIN-ITN Early Stage Researcher (PhD student) position: Development of a complete data processing workflow for protein-protein and RNA-protein cross-linking (THERMO FISHER, Bremen, Germany)


   Gene Regulation, Stem Cells and Cancer

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  Dr Bernard Delanghe, Dr Mathias Wilhelm  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

Barcelona Spain Bioinformatics Data Analysis Computer Science 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 inter-sectoral and interdisciplinary set of skills to tackle the main challenges in the field and improve their future employability.

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Subproject 14: (Host: THERMO FISHER, Bremen, Germany)

Title:  Development of a complete data processing workflow for protein-protein and RNA-protein cross-linking

Objectives: The goals are i) implementation of algorithms for classification and identification of cross-linked peptides and ii) implementation of visualization of spectra of cross-linked peptides and proteins.

Methodology: Using the existing software development kit for Proteome Discoverer the ESR will implement a complete data processing workflow for protein-protein and RNA-protein crosslinking interactions including algorithms for classification and identification of cross-linked peptides and development of algorithms for calculating FDR, PEPs, and q-values and the implementation of visualization of spectra of cross-linked peptides and proteins.

Required skills:

Programming Skills

Strong command of English

Expected Results: A complete workflow for identifying and quantifying protein-protein and RNA-protein interactions within the Proteome Discoverer workflow.

Planned Secondments: 

Host: VIB (Belgium), Duration: 1 Month; When: Year 2; Goal: Learn algorithms FDR calculation.

Host: TUM (Germany), Duration: 3 Months; When: Year 2; Goal: Learn algorithms for rescoring peptide identifications.

Host: EKUT (Germany), Duration: 1 Month; When: Year 1; Goal: Learn algorithms for cross-linked peptides.

Enrolment in doctoral programs: Ph.D. in Bioinformatics from the Faculty of Medicine at TUM

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: 28 May 2021

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About Thermo Fisher Scientific:

Thermo Fisher Scientific is the world leader in serving science, with revenues of more than $20 billion and approximately 70,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner, and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics, deliver medicines to market, and increase laboratory productivity. Thermo Fisher Scientific (Bremen) GmbH is the centre of excellence in mass spectrometry R&D and manufacture. They offer a complete range of high-end analytical instruments and software services that support scientists/researchers within proteomics, clinical research, forensic toxicology, pharmaceutical, biotech, food safety, and environmental market segments.


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: http://protrein.eu/wp-content/uploads/2020/12/Protrein_ITN_Eligibility_Criteria.pdf