Dr. Steffen Möller

Photo of Dr. Steffen  Möller

Head of Bioinformatics Group

Proteome Center Rostock
Schillingallee 69
18057 Rostock

+49 381 4 94 49 30
+49 381 4 94 49 32

Research interests

In general, this is any computational tool that supports biological research. The work I personally liked most is

  • GPCR coupling prediction
  • Intergenomics on disease-associated chromosomal loci
  • many more on agents and transmembrane proteins

Current activities involve the computer aided interpretation of what we get from genome-wide SNP studies. And it was these thoughts that guided me into the field of grid computing. Something that albeit having published on is less of a science but more of a promotional nature is my involvement with the Debian Linux distribution. This is bunch of enthusiastic people who mutually help each other and (en passent the world) in maintaining their research infrastructure. This comprises both general IT and bioinformatics applications.

Active Projects

  • EU project "Know ARC" on grid computing. A single look on the Nordu Grid monitor says more than a 1 000 words. I am investigating how grid technologies can become more applicable for bioinformatics:
  • Dynamic Runtime Environments
  • Embedding grid jobs in bioinformatics workflow suite Taverna
  • Expression QTL analysis in a murine model of Multiple Sclerosis 


  • Apical-basolateral distribution of epithelial membrane proteins
  • sugaR - R package for plotting a diabetes diary


For my first degree in the early nineties of the last century I was joining some fun competitions that I like to think back about:

  • National Programming Contest, U Texas, Austin, TX, USA
  • 1995 Shocc - Shortest C Contest, Kaiserslautern, Germany

and I had helped with the 1994 MICE (Most Intelligent Corn Eater) competition in Hildesheim, Germany. Since then I contributed to two projects that were rewarded: 

  • 2005 - Intergenomics on QTL (German QUECKENSTEDT Award for research in multiple sclerosis)
  • 2006 - prediction of a pical-basolateral sorting in kidney epithelia (Jugend forscht)



  • Kandaswamy, K. K., Chou, K., Martinetz, T., Möller, S., Suganthan, P. N., Sridharan, S., and Pugalenthi, G.: AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties: Journal of Theoretical Biology, vol. 270, no. 1, pp. 56-62, 2011


  • Kandaswamy, K. K., Pugalenthi, G., Hartmann, E., Kalies, K., Möller, S., Suganthan, P., and Martinetz, T.: SPRED: A machine learning approach for the identification of classical and non-classical secretory proteins in mammalian genomes: Biochemical and biophysical research communications, vol. 391, no. 3, pp. 1306-1311, 2010
    BibTeX PDF
  • Kandaswamy, K. K., Pugalenthi, G., Möller, S., Hartmann, E., Kalies, K., .N.Suganthan, ., and Martinetz, T.: Prediction of apoptosis protein locations with Genetic Algorithms and Support Vector Machines through a new mode of pseudo amino acid composition: Protein Peptide Letters, vol. 17, pp. 1473-1479, 2010


  • Zhou, X., Krabbenhöft, H., Niinimäki, M., Depeuringe, A., Möller, S., and Müller, H.: An Easy Setup for Parallel Medical Image Processing: Using Taverna and ARC: Stud Health Technol Inform., vol. 147, pp. 41-50, 2009


  • Krabbenhöft, H. N., Möller, S., and Bayer, D.: Integrating ARC Grid Middleware with Taverna Workflows: Bioinformatics, vol. 24, no. 9, pp. 1221-1222, 2008
  • Schwarz, D. F., Hädicke, O., Erdmann, J., Ziegler, A., Bayer, D., and Möller, S.: SNPtoGO: characterizing SNPs by enriched GO terms: Bioinformatics, vol. 24, no. 1, pp. 146-148, 2008
    BibTeX Website


  • Bayer, D., Bhimdi, T., Oechsler, G., Orellana, F., Wäänänen, A., Kónya, B., and Möller, S.: Dynamic Runtime Environments for Grid Computing: Cracow`07 Grid Workshop, Cracow, Poland, pp. 155-162, 2007
  • Eddelbuettel, D., Vernazobres, D., Gebhardt, A., and Möller, S.: apt-get install cran bioc: On automated builds of 1700 R packages for Debian: useR conference, Ames, Iowa, 2007
    BibTeX Website
  • Merelli, E., Armano, G., Cannata, N., Corradini, F., d`Inverno, M., Doms, A., Lord, P., Martin, A., Milanesi, L., Möller, S., Schroeder, M., and Luck, M.: Agents in bioinformatics, computational and systems biology.: Briefings in Bioinformatics, vol. 8, no. 1, pp. 45-59, 2007
  • Möller, S., Bayer, D., Vernazobres, D., Gebhardt, A., and Eddelbuettel, D.: Scientific Grid Computing via Community-Controlled Autobuilding of Software Packages Across Architectures: NETTAB, Pisa, Italy, 2007
    BibTeX Website


  • Goertsches, R., Serrano-Fernández, P., Möller, S., Koczan, D., and Zettl, U. K.: Multiple Sclerosis Therapy Monitoring Based on Gene Expression: Curr. Pharm. Des., vol. 12, no. 29, pp. 3761-3779, 2006
    BibTeX Website
  • Möller, S., Zettl, U. K., Goertsches, R., and Serrano-Fernández, P.: Comparative Genomics for the Investigation of Autoimmune Diseases: Curr. Pharm. Des., vol. 12, no. 29, pp. 3707-3722, 2006
    BibTeX Website
  • Öckinger, J., Serrano-Fernández, P., Möller, S., Ibrahim, S. M., Olsson, T., and Jagodic, M.: Definition of a 1.06 Mb region linked to neuroinflammation in humans, rats and mice: Genetics, vol. 173, no. 3, pp. 1539-1545, 2006
    BibTeX Website
  • Yu, X., Wernhoff, K. B. P., Koczan, D., Möller, S., Thiesen, H., and Ibrahim, S.: Fine mapping of collagen-induced arthritis quantitative trait loci in an advanced intercross line: J. Immunol., vol. 177, no. 10, pp. 7042-7049, 2006


  • Aidinis, V., Carninci, P., Armaka, M., Witke, W., Harokopos, V., Pavelka, N., Koczan, D., Argyropoulos, C., Thwin, M., Möller, S., Kazunori, W., Gopalakrishnakone, P., Ricciardi-Castagnoli, P., Thiesen, H., Hayashizaki, Y., and Kollias, G.: Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.: PLoS Genet., vol. 1, no. 4, , 2005
    BibTeX Website
  • Bartocci, E., Merelli, E., and Möller, S.: Integration of EnsEMBL with BioAgent.: Technical Report, no. TR02-2005, 2005
  • Gierer, P., Ibrahim, S. M., Mittlmeier, T., Koczan, D., Möller, S., Landes, J., Gradl, G., and Vollmar, B.: Gene expression profile and synovial microcirculation at early stages of collagen-induced arthritis: Arthritis Research and Therapy, no. 7, pp. R868-R876, 2005
    BibTeX Website PDF
  • Johannesson, M., Olsson, L. M., Lindqvist, A. K., Möller, S., Koczan, D., Wester-Rosenlof, L., Ibrahim, H. J. T. S., and Holmdahl, R.: Gene expression profiling of arthritis using a QTL chip reveals a complex gene regulation of the Cia5 region in mice: Genes Immun., vol. 6, pp. 575-583, 2005
    BibTeX Website
  • Möller, S., Serrano-Fernández, P., Watson, M., Koczan, D., Kotsikoris, V., Kunz, M., Blüggel, M., Pahnke, J., Illges, H., Mikkat, S., Thiesen, H., Glocker, M. O., Zettl, U. K., and Ibrahim, S. M.: Collection of soluble variants of membrane proteins for transcriptomics and proteomics.: In Silico Biol., vol. 5, no. 3, pp. 295-311, 2005
    BibTeX Website
  • Serrano-Fernández, P., Ibrahim, S. M., Koczan, D., Zettl, U. K., and Möller, S.: In silico fine-mapping: narrowing disease-associated loci by intergenomics: Bioinformatics, vol. 21, no. 8, pp. 1737-1738, 2005
    BibTeX Website
  • Tille, A. and Möller, S.: Debian-Med Free Software in Health Care: MAS*BIOMED Workshop, AAMAS, Utrecht, NL, Admano, G., Denzinger, J., Martin, A., Merelli, E., Miles, S., Tianfield, H., and Unland, R. (Ed.), pp. 72-85, 2005
    BibTeX Website PDF