Jörg Fallmann

Universität Leipzig · Härtelstraße 16-18, 04107 Leipzig · 16667 · fall[at]bioinf.uni-leipzig.de

After my Masters in Molecular Biology at the University of Vienna, I finished my PhD at the Bioinformatics and Computational Biology/Theoretical Biochemistry research group of Ivo L. Hofacker in Vienna.
Currently, I am a PostDoctoral researcher with Peter F. Stadler at the Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics of the University of Leipzig.
Im interested in the processes and mechanisms behind the regulation of gene expression, especially on the level of RNA, RNA secondary structure and the plethora of interactions shaping this level. The recent advent of personalized medicine as a field involving huge amounts of data, particularly from high-throughput sequencing, opens new paths for investigations into the roles of RNA regulatory factors as disease initiators and progressors. My interest in non-coding RNAs as such regulators extends from Alzheimer's disease to cancer drivers and biomarker identification.



RNA-protein and RNA-RNA interactions

Gene expression is a very fluid process, enabling organisms to develop and adapt their cells to their environment and needs as necessary. A cruicial part of this process is tight regulation and the RNA interactome is a key layer of the latter. My studies of molecular biology has brought me to this field quite a while ago and what can I say, I'm still fascinated. Even more so, thanks to all the new discoveries enabled by next generation sequencing and the huge amount of insights we can gain from sequencing data. In this context I'm working with all sorts of NGS data, focusing on RIP and CLIP experiments and their integration with data from RNA-Seq and derivatives as well as RNA structure. During my research I was often struck by the feeling that there are two competing worlds, RNA research on the one and protein research on the other hand. Bringing those two worlds together is one of the remaining challenges in my field of research and one of my key interests, the same is true for bridging the gap between molecular biology and bioinformatics.

RNA secondary structure

In contrast to proteins, where the global formation of complex tertiary and quarternary structures is enforced by the hydrophobic effect, and secondary structure is limited to α helices and β sheets. In the world of RNA, folding is a hierarchical process, where base pairs and thus helices, are rapidly formed, while the spatial arrangement of complex tertiary structures usually is a slow process. Secondary structure forms a conceptually important intermediate level of description and explains the dominating part of the free energy of structure formation for RNA. Computation of RNA secondary structure is part of bioinformatical analyses for many years now, with many useful applications available. I'm using the constraint folding framework of the ViennaRNA package to investigate the role of RNA secondary structure as a mediator for cooperative and competitive effects of RNA-protein and RNA-RNA interactions.

RNA turnover

Cis-acting RNA regulatory elements

Kind of in between my other two main research interests is the identification and annotation of regulatory elements on RNA level. With AREsite2 and its predecessor ARESite I'm involved in the annotation of AU-/GU- and U-rich elemens in human and model organisms. This elements are preferred targets of many RNA binding proteins and my mission is to investigate the mechanics that make some of the elements preferred binding sites while other, very similar elements, remain unbound and how that correlates with the cell state and RNA decay mechanisms.

Non-coding RNAs as regulators

RNA as regulatory element

Non-coding RNAs are long known as regulators of transcription and translation. Especially micro-RNAs have gained a lot of attention, being a very versatile and ubiquitary species of RNA which can interact with many other RNAs, DNA or proteins and regulate their fate. I'm developing algorithms to annotate miRNAs in new genome assemblied, as well as fixing existing annotations based on sequence conservation and structure level. Long non-coding RNAs on the other hand are, although recognized as important regulators, not well understood. We still lack a comprehensive annotation of their genomic loci, as well as their role in gene expression regulation. The same is true for circular RNAs, which are potential regulators of many cellular processes and described as cancer progressors. I'm investigating the role of ncRNAs in various diseases, their effect on splicing and their potential as biomarkers.

Teaching and Training

I'm part of a team teaching RNA regulation and the practical course for bioinformatics of RNA and protein structures

As a member of the german platform for bioinformatics de.NBI I'm training people in how to use Galaxy to analyze their data and bioinformaticians how to integrate their tools into this and the bioconda framework.

I'm also involved in teaching algorithms and data structures at the university of Leipzig from 2016 on.

During my time as a student in Vienna I was tutor in various laboratory courses and lectures and courses for bioinformatics



Programming Languages & Tools
Other projects I'm currently involved in


Spare time is rare time and I tend to either use it to get some workout done or waste it with my wife and friends playing online or binge watching the rain away.


Or download my CV here