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Marie-Sklodowska Curie PROTrEIN-ITN Early Stage Researcher (PhD student) position: Development of computational approaches for high precision and accuracy protein quantification (CRG, Barcelona, Spain)


Gene Regulation, Stem Cells and Cancer

Dr Eduard Sabidó , Dr Mathias Wilhelm Thursday, April 29, 2021 Competition Funded PhD Project (Students Worldwide)
Barcelona Spain Artificial Intelligence Bioinformatics Data Analysis Data Science Machine Learning Networks Biological Sciences

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 1 (Host: Centre for Genomic Regulation - CRG, Barcelona)

Title: Development of computational approaches for high precision and accuracy protein quantification

Objectives: Development of a machine learning tool to extract peptide stability patterns and predict peptide stability for new sequences, and of methods to explore the relationship between quantitative peptides and their sequence, post-translational modifications, polymorphisms, and point mutations.

Methodology: To predict peptide stability we will use the stability data of over 150,000 unique tryptic peptides from the human proteome through an active collaboration with M. Wilhelm (P6, TUM). Peptides will be analyzed by mass spectrometry for 3-4 weeks and several semi-supervised classification algorithms will be evaluated to build a classification model of peptide stability. Moreover, the models will be used to predict peptide stability for new sequences, and the knowledge generated will be integrated back to ProteomeTools and ProteomicsDB. Finally, we will explore the relationship between quantitative peptides and their sequence, post-translational modifications, polymorphisms and point mutations to identify properties and sequence variants that exhibit a significant relation with the quantitative behavior of peptides.

Required skills: Programming skills. Knowledge of machine learning algorithms, bioinformatics, and molecular biology.

Expected Results: A machine learning model to classify stable from non-stable peptides and predict the stability of new peptide sequences, and a map of the quantitative peptides concerning the known sites of peptide modifications, polymorphisms and point mutations.

Planned Secondments:

TUM (Germany), Duration: 3 Months; When: Year 2, Goal: Integration of results within ProteomicsDB.

EMBO (Germany), Duration: 2 Weeks; When: Year 3, Goal: Scientific writing and editing.

ANAXOMICS (Barcelona), Duration: 1 Month; When: Year 3, Goal: Network analysis.

Enrolment in doctoral programs: PhD in Bioinformatics from Universitat Pompeu Fabra.

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: 30 April 2021

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The CRG (www.crg.eu) is a first-class multidisciplinary and international research centre. It is ranked as 2nd in Spain SCImago Institutions Rankings for its research, innovation, and societal influence in the health field. CRG is also one of only 9 life-science research centres in Spain awarded a highly-competitive ‘Severo Ochoa’ grant of excellence (2017-2021). Organized in 4 research programmes (31 group leaders, of which half hold an ERC grant): (i) Systems Biology, (ii) Bioinformatics and Genomics, (iii) Gene Regulation, Stem Cells and Cancer and (iv) Cell and Developmental Biology. More than 60% of the research staff is non-Spanish (with 39 nationalities represented).

The CRG has an international Ph.D. programme and a Postdoc fellowship (co-funded by the EC). In 2013, the CRG was awarded the HR Excellence logo by the EC to recognize the institute´s commitment to improving human resources policies for researchers. CRG has been growing its expertise in ITN since previous funding programmes. In H2020 it has been involved in 8 ETN projects, coordinating 4 of them (OPATHY, DivIDE, ChromDesign, PROTrEIN).


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. Chiva, C., Pastor, O., Trilla-Fuertes, L., Gámez-Pozo, A., Fresno Vara, J. Á., & Sabidó, E. (2019). Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice. Analytical Chemistry, 91(8), 4934–4938. https://doi.org/10.1021/acs.analchem.8b05802
2. Borràs, E., & Sabidó, E. (2018). DIA+: A Data-Independent Acquisition Method Combining Multiple Precursor Charges to Improve Peptide Signal. Analytical Chemistry, 90(21), 12339–12341. https://doi.org/10.1021/acs.analchem.8b03418
3. Chiva, C., & Sabidó, E. (2017). Peptide Selection for Targeted Protein Quantitation. Journal of Proteome Research, 16(3), 1376–1380. https://doi.org/10.1021/acs.jproteome.6b00115

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