Home | Research | HowTos Martin Raden, nee Mann

Bioinformatics Group
Institute for Computer Science
Albert-Ludwigs-University of Freiburg
Georges-Koehler-Allee 106
D-79110, Freiburg, Germany

Phone: +49 (0)761 203-8254
Fax: +49 (0)761 203-7462
Room: 106-02-012

https://orcid.org/0000-0002-7926-5911

About me ...

Research and Interests

• method development and implementation
• energy landscapes of biopolymer models
• simplified RNA models
• computational chemistry
• constraint programming
• object oriented programming

Software and Information



• IntaRNA is one of the leading RNA-RNA interaction prediction tools and continuously extended under my supervision.
• My Freiburg RNA tools webserver is a flexible front-end of the tools developed within our group.
• The Graph Grammar Library (GGL) and its chemoinformatics application are developed with the Vienna TBI group.
• I am one of the distributors of the Energy Landscape Library (ELL) and the BIU library.
• My CPSP-tools enable studies for HP-type protein models in complex 3D-lattices.
• The LatPack is made for studies in arbitrary lattice protein models.
• LatFit allows for lattice approximations/fits or real protein structures in PDB format.
• To avoid ugly learning by trying: my HowTo-site.
• For Constraint Programming I am using and extending the Gecode C++ library.
• For some usefull free tools have a look here.
• And if you want to get away from electronics, check out Bela Bender's outdoor page.

Collaborations

To be successful you need a team. Therefore I am happy to collaborate with ...


• Dominik F. Stangler and Hans-Peter Kahle of the Forest Growth group - University of Freiburg (Germany) on the alignment of tree growth data and its mapping onto environmental factors.
• Fabrizio Costa from University of Exeter (England) on machine learning in chemistry and bioinformatics.
• Christoph Flamm from University of Vienna (Austria) on graph grammars and their applications.
• Michael T. Wolfinger, Gregor Entzian and Sebastian Will from University of Vienna (Austria) about energy landscapes of RNA molecules.
• ... and of course with the team of my group!

Publications and Teaching

• Here is my list of publications also available via ORCID or Google Scholar.
• An introductory talk on Lattice proteins, CPSP approach, and applications I presented.
  
  
• At the Bioinformatics group at the University Freiburg:
  
  • Together with Prof. Backofen I presented the special lecture on 'RNA Bioinformatics' ( SS'19, SS'18, SS'16, SS'15, SS'14 ),
  • and the basic lectures 'Bioinformatics I' ( WS'19, WS'18, WS'17, WS'16, SS'13 ) and 'Bioinformatics II' ( SS'17, WS'15, WS'13, WS'12 ),
  • I was responsible for the exercise course of the special lecture on 'Protein folding and energy landscapes' ( SS'09 ),
  • as well as the exercise course of the 'Bioinformatics I' lecture ( SS'11, SS'10 ).
  • I was supervising a Java programming course on bioinformatics algorithms ( WS'09, '08, '07, '06 ) and a Perl course ( SS'08 )
  • Further, I am the mentor of several theses and student projects.
  
  
• My teaching is guided by the insights I gained during the training for my certificate of university didactics of Baden-Württemberg.
  
  
• I was honored with the E-Learning-Förderpreis 2015 of the University of Freiburg for my E-learning-based restructuring of our RNA bioinformatics lecture in SS'15. ( uni.fr pr, tf, blog, and Badische Zeitung, Regiotrends )