Stefan Hammer

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

After studying Genetics and Microbiology at the University of Vienna, I did a PhD at the Bioinformatics and Computational Biology/Theoretical Biochemistry research group in Vienna.
Currently, I am working as a PostDoc researcher at the Bioinformatics Group, Institut of Computer Science, Leipzig University.
My main research interest lies in RNA design and synthetic biology. Thus, I created tools able to design context-sensitive riboswitches with advanced prescribed properties and functions, and used it to create multipe RNA devices.

Research

Multiple target sequence design

Picture We developed RNAblueprint, a C++ library implementing a graph coloring approach to uniformly sample sequences compatible to structural and sequence constraints from the typically huge solution space. Fair sampling from the solution space makes optimization runs much more performant and raises the probability to find better solutions. Scripting interfaces allow to easily adapt existing code to new scenarios which makes the whole design process very universal and flexible. A python module RNAsketch provides code for glueing together RNAblueprint and structure prediction packages and to provide precoded optimization methods.

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

ODE system to model RNA devices

As part of the Ribonets Project we built an ODE system describing designed or natural riboswitches in the context of transcription and translation.
The system created by the Keasling lab was therefore 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

forna - RNA Secondary Structure Visualization

Picture 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/...

Vienna RNA Packaging

For a better user experience, I started to maintain Debian and Ubuntu packages for our Vienna RNA Package. Furthermore, there exists a Launchpad PPA for our Ubuntu-users.
The packages can be downloaded here, while the ppa is hosted at https://launchpad.net/~j-4/+archive/vienna-rna/.
If you are interested in some statistics about the ppa, check out the ppastats.

Publications

Download the bibtex file.

Education

University of Vienna

PhD Studies
Theoretical Biochemistry Group, Bioinformatics and Computational Biology

Graduated with 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

Graduated with honors on June 5th, 2012

October 2006 - June 2012

Skills

Scientific

  • RNA structure prediction and thermodynamics
  • Stochastic optmization techniques
  • Algorithm and data structure design
  • Gene regulation mechanisms
  • Riboswitches and regulatory RNAs
  • Genome wide analyses

Programming Languages, Tools & Platforms