Research Project 12

Development of a user-friendly software solution of lrRNA-seq analysis. From mapping to pathway analysis

About the Project

BioBam Bioinformatics Solutions

Valencia, Spain

Fabian Jetzinger

Early Stage Researcher

Stefan Götz

Main Supervisor

Ana Conesa


Universitat de València

PhD enrolment

Research Objectives

lrRNA-seq data analysis is poorly accessible to users without bioinformatics expertise. OmicsBox is a user-friendly software with modules for RNA-seq and functional enrichment analysis. lrRNA-seq is not yet supported. Our objectives are:

  • Compare existing long reads analysis pipelines for mapping, quantification, and differential expression analysis in non-model species.
  • Develop novel pathway analysis method for isoform-resolved data.
  • Implement methods in OmicsBox user-friendly software.

Envisioned Secondments

  • UU-SciLifeLab (Adam Ameur). Learn library preparation methods and collaborate in Aim 1.
  • CNRS (Pascal Barbry): Compare OmicsBox methods to Barbry’s AI methods.

Early Stage Researcher

Fabian Jetzinger


I completed both my Bachelor’s and Master’s degrees at the University of Applied Sciences Upper Austria, Campus Hagenberg. I finished my Bachelor of Science in Medical and Bioinformatics, which is a degree program designed to educate software engineers who can efficiently communicate with biologists and medical professionals, in 2021. My Bachelor’s thesis focused on utilizing nonlinear dimension reduction to visualize medical time-series data. I completed my Master of Science in Data Science and Engineering in 2023, my Master’s thesis focusing on the use of large language models for named-entity recognition.

My primary motivation for applying to the LongTREC program was my desire to contribute to solving humanity’s problems with my work. I believe that I have had great luck in receiving this opportunity to learn and I aim to make the most of this unique chance to kickstart my career in academia. I am also excited about living in a foreign country, learning a new language and culture, and getting to know researchers from around the world.

About the Main Supervisor and Host Group

Stefan Götz

Biobam Bioinformatics,

BioBam is a leading bioinformatics solution provider which accelerate research in disciplines such as agricultural genomics, microbiology and environmental NGS studies, amongst others. BioBam is committed to the development of user-friendly software solutions for biological research. Our mission is to transform complex data analysis procedures into an attractive and interactive task. BioBam is devoted to close the gap between experimental work, bioinformatics analysis and applied research.