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
Co-Supervisor
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
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
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.