Europe: 12 Phd Positions In The Msca Doctoral Network Longtrec (# Of Pos: 12)

Universities and Institutes of Slovenia
January 16, 2023
Offerd Salary:Negotiation
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Contract Type:Temporary
Working Time:Full time
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  • Organisation/Company: CSIC
  • Research Field: Computer science › Programming Technology › Biotechnology Technology › Computer technology
  • Researcher Profile: First Stage Researcher (R1)
  • Application Deadline: 16/01/2023 23:00 - Europe/Brussels
  • Location: Multiple locations, see work locations below.
  • Type Of Contract: Temporary
  • Job Status: Full-time
  • Hours Per Week: 37.5
  • Offer Starting Date: 01/06/2023
  • Eu Research Framework Programme: H2020 / Marie Skłodowska-Curie Actions
  • Marie Curie Grant Agreement Number: 101072892
  • The Long-reads TRanscriptome European Consortium (LongTREC): "The next generation transcriptome biology revealed by single molecule sequencing technologies" is a European Network funded by MSCA Doctoral Network that is recruiting 12 Doctoral candidates to undertake projects on long-reads transcriptome. Doctoral candidates will be located across the following institutions: Consejo Superior de Investigaciones Científicas (1 position), Stockholm Universitet (1 position), Istituto Italiano di Technologia (1 position), Centre Nationale de la Recherche Scientifique (1 position), Centre de Regulació Genòmica (2 positions), Max-Planck (1 position), Nacionalni Institut la Biologijo (1 position), Genoscope (1 position), Oxford Nanopore Technologies (1 position), Earlham Institute (1 position), Biobam Bioinformatics (1 position). Doctoral candidates hired to this network will be enrolled in local programs accessing seminars, training as well as local activities but also network activities and training.

    The offered positions are available for a duration of 36 months. The fellowships are funded as part of the Marie Skłodowska-Curie Actions (MSCA) Doctoral Network under the European Commission's Horizon program. MARIE CURIE GRANT AGREEMENT NUMBER: 101072892.

    See more info at: https: //

    We are now accepting applications from potential doctoral researchers. Applications are due by 16 January 2023. The PhD positions will begin between June and September 2023.

    About the LONGTREC network

    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 (DC) who will perform research in top European computational biology laboratories guided by current European leaders of the lrRNA-seq technologies, both at experimentation and computation. Each candidate will develop a specific project under the supervision of a Principal Investigator within the LongTREC network.

    All LongTREC DCs will enroll in local PhD programs from top-tier universities. Taking part in local programs will allow our DCs to be embedded in their respective graduate environments, gaining access to seminars, graduate retreats, training, and local scientific activities. Moreover, LongTREC DCs will be fully integrated in the research lab and R&D departments of their host institutions, participating in the day-to-day scientific life of their groups, which includes project discussions, journal clubs, interaction with visiting scientists, co-supervision of undergraduate or master's thesis, institutional seminars, etc. DCs will be encouraged to enroll in local/national/European Young Scientist Organizations to promote peer engagement, leadership, and networking skills. Moreover, LongTREC will structure doctoral training as an intersectoral endeavor by systematically involving the academic and private sector of the training of our DCs. Every DC will carry out at least two research-based, intersectoral and international secondments.

    The recruitment procedure will be through an international and open call in which future candidates who possess less than 4 years of research experience and are interested in the lrRNA-seq transcriptomics are welcome to apply.

    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:

  • 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.

  • All project descriptions can be viewed here.


    • 3-year full-time employment contract (salary depends on the country of the recruitment considering both the local and MSCA regulations for Early Stage Researchers and their family status at the time of the recruitment).

    • Enrolment in a PhD program.

    • Shared research and innovative multidisciplinary and multisectoral training by experts and experienced trainers from two sectors (academia and industry).

    • A structured training programme consisting of soft skill courses, targeted workshops, retreats, social events and networking.

    • Secondments at other institutions within the LONGTREC consortium.

    • Gaining experience abroad.

    • Opportunities for participation in national and international meetings.

    • Enlarged professional network and improved future scientific career perspective in academia and the private sector.

    For further information on the LONGTREC MSCA-DN and the application process, please visit https: //

    Eligibility criteria

    We welcome applications from PhD candidates from any country fulfilling the following criteria:

  • 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). This is applicable to all jobs except for the PhD position 2 in which the mobility criteria is not required.
  • 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 hold or be in the process of gaining a master's degree relevant for the chosen position (including biology, medicine, biochemistry, bioinformatics or a related discipline, depending on each PhD project) by June 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.
  • In all cases, employment will be conditioned to acceptance by the Doctoral school of the associated PhD awarding institution.
  • Successful candidates must have a high level of proficiency in written and spoken English, which will be assessed with the motivation letter and the interview, respectively.

    Selection process

    The application will be done through an online application platform to be found on the LONGTREC website: https: // and/or directly to our career site

    Applications must be in English. Each applicant may apply to a maximum of three individual research projects.

    Candidates must apply through our career site in which they will be able to upload the following documents (in pdf):

  • a CV (including publications, if any),
  • a motivation letter,
  • 2 reference letters (please, combine in 1 pdf both reference letters),
  • Copies of Bachelor's and Master's degree certificates. Candidates should include the transcripts in English of academic records for the studies that make them eligible for a doctoral program. If these studies have been completed by the deadline for applications, the total number of credits for the degree and the credits awarded must also appear.
  • Eligible applications will be ranked on the basis of CVs and merits by a selection committee: up to 30 points for the CV, up to 15 points for the motivation letter, and up to 5 points for the two reference letters.

    The 3 best candidates for each position will be invited to a recruitment workshop in February 2023 (date to be confirmed) where the final candidates will be selected.

    Applicants with a positive evaluation but not selected will be included on a reserve list to cover eventual future positions and might be contacted at a later stage.

    Additional comments


  • Application deadline: 16 January 2023
  • Announcement of preselection results and call for interviews: 1 February 2023
  • Recruitment workshop: Short-listed candidates will be interviewed at the end of February 2023 (date to be confirmed). To give same opportunities to all candidates, we anticipate that workshop and interviews will be run in a virtual format. Full details regarding the interview process will be sent to invited candidates during the arrangement of interviews.
  • Communication of the final results: 1 April 2023
  • Hiring process: between June and September 2023 (depending on end of Master's degree)
  • Enrolment on Doctoral school deadline: October 2023
  • Web site for additional job details

    https: //

    https: //

    Offer Requirements
  • ENGLISH: Excellent


    Eligible candidates must hold or be in the process of gaining a master's degree relevant to the chosen position (including biology, medicine, biochemistry, bioinformatics, or a related discipline, depending on each PhD project) by June 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.

    Specific Requirements

    Every project might require specific requirements or skills. To ensure candidates meet these criteria, we encourage to check our PhD positions for specific requirements on our career website.

    Contact Information
  • Organisation/Company: CSIC
  • Department: Genomics of Gene Expression
  • Organisation Type: Public Research Institution
  • Website: https: //
  • E-Mail:
  • Country: Spain
  • City: Paterna
  • State/Province: Valencia
  • Street: Agustin Catedratico Escardino
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