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PhD candidate 'Deep Learning for tissue-specific RNA splicing predictions'

The focus of this PhD project is to critically improve the prediction of the effect of genetic variants on the splicing of human mRNAs with deep learning …

19 dagen geleden

Arbeidsvoorwaarden

Standplaats:
Geert Grooteplein Zuid, Nijmegen, Gelderland
Dienstverband:
Tijdelijk contract / Tijdelijke opdracht
Uren per week:
36 - 36 uur
Salarisindicatie:
€ 2422 - € 3103 per maand
Opleidingsniveau:
WO

Functieomschrijving

The focus of this PhD project is to critically improve the prediction of the effect of genetic variants on the splicing of human mRNAs with deep learning algorithms, with the ultimate goal to improve the diagnosis of inherited retinal disorders. We assume that many pathogenic variants underlying these disorders are missed, because current splice prediction algorithms are not tailored towards retinal tissue and because splicing is known to be tissue-specific.

The candidate will develop a combination of in silico and in vitro approaches to better predict and evaluate the effects of genetic variants on retina-specific splicing and the resulting proteins. For this, (long read) RNA-sequencing and proteomics data will be analysed. The candidate will introduce tissue specificity into neural network-based splice prediction algorithms such as SpliceAI, which are currently largely agnostic to the tissue, and derive retina-specific splicing motifs. The main expected outcomes of this project are an increase in diagnostic yield of inherited retinal diseases, and a workflow and software for tissue- and transcript-aware prediction of genetic variants on splicing, which can be reused for other tissue-specific disorders.

Tasks and responsibilities

  • Analysis of omics data.
  • Development of a deep learning framework based on experimental confirmation of likely pathogenic variants and/or binding motifs for tissue-specific splice factors.
  • Writing of scientific articles resulting in a PhD thesis.
  • Oral presentations in internal and external meetings.

Functie-eisen

  • You hold a Master of Science degree in Bioinformatics, or in Computer Science with proven interest in molecular biology, or in one of the biomedical sciences with proven programming skills.
  • Experience in the development or application of deep learning algorithms is preferred.
  • You must demonstrate a strong dedication to research and be interested in resolving important biomedical research questions with novel computational approaches.
  • You work in a structured way, document your code and results and use version control systems (like Git).
  • You are flexible and communicative, know how to explain your research to peers within and outside your field, and enjoy working in a multidisciplinary team.

Conditions

Upon commencement of employment we require a certificate of conduct (Verklaring Omtrent het Gedrag, VOG) and there will be, depending on the type of job, a screening based on the provided cv. Radboud university medical center's HR Department will apply for this certificate on your behalf.

Read more about the Radboudumc employment conditions and what our International Office can do for you when moving to the Netherlands.

Additional information

In your application letter, clearly indicate how your expertise and experience fits with the proposed project. The application procedure will consist of a first round of interviews and a presentation of one your research projects in a second stage.

All additional information about the vacancy can be obtained from Prof. Peter-Bram 't Hoen, professor of Bioinformatics and Head of the Center for Molecular and Biomolecular Informatics via +31 (0) 24 361 97 63.

Please apply before November 21, 2019.
Recruitment agencies are asked not to respond to this job posting.

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