Stefan Hammer

Universität Leipzig Härtelstraße 16-18, 04107 Leipzig, Germany stefan.hammer@uni-leipzig.de GPG

Currently, I am a PostDoc researcher in the group of Peter Stadler at University Leipzig. I received my PhD in molecular biology at the Bioinformatics and Computational Biology/Theoretical Biochemistry research group in Vienna after studying Genetics and Microbiology at the University of Vienna.
My main research interest lies in designing functional RNA molecules for synthetic biology applications. Therefore, I focus on connecting bioinformatics and wet-lab such that the whole design approach from predictive model generation, computational design to experimental verification and characterization of the obtained candidates can be advanced.


Research

Multiple target sequence design

RNAblueprint Logo Finding RNA sequences that fulfill a desired function in the cellular context is a complex task that can be computationally solved by combining multiple methods.
Due to the properties of the solution landscape, it is crucial to sample RNA sequences given various necessary constraints, e.g., the secondary target structures. We developed RNAblueprint, a C++ library which implements a graph coloring approach to uniformly sample sequences compatible to structural and sequence constraints from the typically huge solution space. The successor, RNARedPrint, solves the same task in a more general fashion by applying dynamic programming over a tree decomposition to achieve Boltzmann weighted sampling of desired sequence candidates.

More information and source code:
https://github.com/yannponty/RNARedPrint
https://viennarna.github.io/RNAblueprint/

Thermodynamic models as RNA design objectives

Typically, the various RNA desig goals are specified by formulating an objective function, which is used for solving an optimization problem. Using structure prediction and thermodynamic models, we developed multiple objective functions in order to obtain RNA devices with specific functionality. These objectives are implemented in the python module RNAsketch, which also provides precoded optimization methods, as well as code to glue RNAblueprint, RNARedPrint, and structure prediction packages together.

More information and source code:
https://github.com/ViennaRNA/
https://viennarna.github.io/RNAsketch/

ODE system to model cellular interfacing

An artificial RNA molecule needs to interact with the cellular environment in order to be produced and to be able to fulfill its desired tasks. Therefore, we built an ODE system describing designed or natural riboswitches in the context of transcription and translation as part of the Ribonets Project.
The system created by the Keasling lab was minimized and adapted to model RNA devices such as translational and transcriptional ON or OFF switches.
To share these models we chose to use the Systems Biology Markup Language (SBML).

More information and details:
https://github.com/ribonets/rnadev-models

RNA Secondary Structure Visualization

Forna Logo Peter and I developed forna, a RNA secondary structure visualization tool using a force directed graph layout. This tool is capable of not only drawing nice layouts for huge structures, but also of projecting pseudoknots and secondary structures of PDB files including protein interactions.

Get it here:
http://rna.tbi.univie.ac.at/forna/
https://chrome.google.com/webstore/detail/forna/...

More information and source code:
https://github.com/ViennaRNA/forna
https://github.com/ViennaRNA/fornac

RNAdevices database collects artificial RNAs

I set up a database which collects artificial RNAs, their implemented regulatory mechanism and conducted experimental validation experiments. This database facilitates data-collection from literature and helps to organize previous RNA design attempts. It is built using MySQL and Xataface, thus human as well as machine readable input and output is possible. This project was part of the Ribonets Project.

Bioconda packaging

Bioconda Logo To provide a better user experience for bioinformatic tools, I started to construct and maintain various Bioconda packages.
Bioconda is a channel for the conda package manager specializing in bioinformatics software. It provides packaging recipes and a build system to create a repository countless software packages used for biological purposes.


Publications

Download the BibTeX file.

Education

University of Vienna

PhD Studies

Theoretical Biochemistry Group, Bioinformatics and Computational Biology

Thesis title: Design of context-sensitive, multi-stable RNA molecules
Supervisor: Ivo L. Hofacker
Graduated with highest honors on April 26th, 2018

September 2012 - April 2018

University of Vienna

Diploma's Studies

Genetics and Microbiology, specialization in Bioinformatics, Developmental Biology and Immunology

Thesis title: Target tissues of melatonin and PDF in Platynereis
Supervisor: Florian Raible
Graduated with hightest honors on June 5th, 2012

October 2006 - June 2012

Skills

Scientific

  • RNA structure prediction and thermodynamics
  • Algorithm design and data structures
  • Stochastic optimization techniques
  • Experimental data analysis and visualization
  • Gene regulation mechanisms
  • Predictive modeling of riboswitches and regulatory RNAs
  • Genome wide analyses