12 full-time PhD positions in the MSCA Doctoral Network LongTREC

Date limit
11 instittutions across Europe

LongTREC is a Doctoral Network of the Marie Sklodowska-Curie action program (MSCA-DN) that will develop methods and tools for the analysis of transcriptomic data obtained with the most recent single-molecule, long-reads sequencing technologies.

The LongTREC MSCA-DN will train 12 Doctoral Candidates who will perform research in top European computational biology laboratories.

Scientific project

lrRNA-seq is an effervescent field, where new experimental protocols, biological applications and analysis solutions are constantly emerging in pace with the rapid improvements in third-generation sequencing technologies. lrRNA-seq has already displayed great potential, but much work is still needed. e lrRNA-seq technology can unravel novel biological insights which have been hidden until now due to technological limitations. Because of their potential for full-length transcript sequencing, lrRNAseq can improve genome annotation by providing an accurate representation of transcript start and end sites, as well as alternatively spliced sites and discover novel genes and transcripts. lrRNAseq is triggering a paradigm shift in transcriptome biology research by progressively moving away from a gene focus to embrace a transcript-centric view. A new generation of computational biologists is essential to consolidate current methods, develop new tools, envision new applications, and lead the unstoppable transition of transcriptome analysis to effectively become LRS-based. The LongTREC network will provide all the key expertise, training, skills, values and infrastructure to support the scientific excellence of our PhD candidates.

List of PhD projects (all project descriptions):

  •     PhD Project 1: Alternative splicing regulation at the single cell resolution: Protocols and computational developments for long read RNA-Seq in single cell.
  •     PhD Project 2: Develop an improved adaptive sampling method for Nanopore dRNA and cDNA sequencing.
  •     PhD Project 3: Algorithm development for splice alignment of long-read sequence data.       
  •     PhD Project 4: Long read RNA sequencing to annotate the genomes across the eukaryotic tree of life.
  •     PhD Project 5: Investigation of allele-specific expression in stress-challenged polyploid potato plants using long read transcriptomics.
  •     PhD Project 6: Long-read single-cell and spatial transcriptomics to explore the diversity of isoform expression.
  •     PhD Project 7: Interactome predictions from long-read transcriptome sequencing data.
  •     PhD Project 8: Exploring the transcriptional landscape of environmental samples using metatranscriptomics long reads.
  •     PhD Project 9: Analysis of tRNA dynamics using native RNA nanopore sequencing.
  •     PhD Project 10: Characterization of microRNA primary transcripts by Nanopore direct RNA sequencing.
  •     PhD Project 11: Long Reads multiomics methods to understand isoform regulatory biology.
  •     PhD Project 12: Development of a user-friendly software solutions of lrRNA-seq data analysis. From mapping to pathway analysis.

What we offer to Doctoral Candidates

  •     PhD position for 36 months in one of the European leading groups for lrRNA-seq technologies.
  •     Mobility: host institution and secondments in both public and industry partners.
  •     An intensive training programme in Science, Skills and Values.
  •     Interdisciplinary, international work environment with courses, workshops and lectures of leaders in the field of long-reads.
  •     MSCA-DN offers a highly competitive salary and additional benefits.

Eligibility criteria for applying to our opening positions

Mobility: Eligible candidates must not have resided for more than 12 months in the 3 years prior the start of this project (June-September 2023). Example: from June 2020 to June 2023 you cannot have lived more than 12 months in the country in which you want to apply for.

Master's degree: Eligible candidates must have a master’s degree relevant to the chosen position by September 2023 or an equivalent experience 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.

Research experience: Eligible candidates shall at the date of recruitment by the host institution not have been awarded a doctoral degree. Researchers who have defended their PhD project but haven't received their Doctoral award yet, are not eligible.

Application limit: Candidates can apply for a maximum of 3 PhD positions

Doctoral school: In all cases, employment will be conditioned to acceptance by the Doctoral school of the associated PhD awarding institution.


LongTREC website: https://longtrec.eu

Application website: https://career.longtrec.eu

EURAXESS job post: https://euraxess.ec.europa.eu/jobs/869584