Open vacancy

Development of novel ONT algorithms and library preparation strategies to study the epitranscriptome in liquid biopsy

PhD project description

Screening liquid biopsy (LB) samples has been proposed as a promising approach to diagnose cancer in earlier stages, since it is a minimally invasive approach that can be applied to the whole population. The discovery of relatively stable, extracellular RNAs in blood plasma has generated much interest in their potential use as non-invasive biomarkers. Most efforts have so far focused on capturing the dysregulation in the abundance of specific RNA molecules. However, RNA modifications remain largely unexplored as potential biomarkers, despite their information-rich nature and their well-documented dysregulation in cancer samples. Here we propose to take advantage of native RNA nanopore sequencing, to quantify small RNA abundances and modifications from RNA molecules present in liquid biopsy samples.

The Doctoral candidate will develop novel bioinformatic algorithms and tools to capture RNA modification information from liquid biopsy samples, as well as alignment-free classification methods of nanopore current intensity signals. The candidate will also optimize library preparation for small RNA sequencing from circulating and exosomal RNA samples from plasma. Once these tools have been established, the PhD candidate will train novel machine learning algorithms to classify and stratify samples based on different characteristics (disease, exposure to stress, cancer, metastasis, etc).

Objectives

Expected Results

Optimise direct RNA nanopore sequencing library preparation for small RNA populations

A novel direct RNA nanopore sequencing library preparation method, optimised for small RNA populations, such as those present in liquid biopsies

Develop novel algorithms and AI-based techniques for the analysis of nanopore sequencing data, including the detection of RNA modifications and bulk nanopore data analyses

Novel and/or improved algorithms to identify RNA modifications are present in small RNAs

Apply existing algorithms and those developed in Objective 2 to study the dysregulation of RNA modifications in liquid biopsy samples sequenced using nanopore direct RNA sequencing.

Comprehensive and reliable wet lab + dry lab pipeline to study RNA populations present in liquid biopsy samples (including their modifications) using nanopore sequencing.

General information

  • Research field:
  • Researcher profile: First Stage Researcher, R1
  • Position: PhD Position
  • Funding Programme: Horizon Europe – MSCA
  • Application deadline: November 2025
  • Type of Contract: Work contract for 4 years.
  • Job Status: Full-time
  • Hours Per Week: 38,5h / week
  • Offer Starting Date: June – September 2026
  • Marie Curie Grant Agreement Number: 101226733

Eligibility requirements

  • Eligible candidates must not have resided or carried out their main activity (work, studies, etc.) in the country of their host institution for more than 12 months in the 3 years immediately prior to their recruitment by the host institution (i.e. the starting date indicated in the employment contract/equivalent direct contract).
  • Eligible candidates shall at the date of recruitment by the host institution (i.e. the starting date indicated in the employment contract/equivalent direct contract), be in the first 4 years (full-time equivalent research experience) of their research careers and not have been awarded a doctoral degree.
  • Eligible candidates must have a master’s degree relevant for the chosen position (including biology, medicine, biochemistry, bioinformatics, or a related discipline, depending on each PhD project), or must hold an official university qualification from a country of the European Higher Education Area with a minimum of 300 ECTs of official university studies.

Skills/Qualifications

  • Master Degree in life sciences, biomedical sciences, molecular biology, bioinformatics, or related fields.
  • Experience in at least one of the following areas: cell and/or molecular biology, biochemistry, biotechnology, bioinformatics.
  • Demonstrated interest in cancer research and RNA biology
  • Demonstrated academic excellence is a pre.
  • Practical experience in laboratory environment is a plus (optional for bioinformatics).
  • Basic knowledge of Microsoft office, statistics, graphical data presentation.
  • Excellent organisation and communication skills and a collaborative mindset
  • Willing to travel for short or longer periods.
  • Flexible and co-operative with a well-structured and autonomous working style.
  • Fluency in written and spoken English is a must.

Where to apply

Please submit your application form in the CRG PhD international Call 2026 webpage.

Contact

CRG Training & Academic office: training@crg.eu