Jens Hollunder

(Group member from 2008 until 2011)

+ 32 (0) 9 33 13 810

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent


  • 12/2008-... : Post-doc in Yves Van de Peer's group (Bioinformatics)
  • 06/2008-12/2008: Post-doc in Geert De Jaeger's (Functional Proteomics) and Yves Van der Peer's group (Bioinformatics)
  • 04/2007-06/2008: Post-doc in Martin Kuiper's group (Computational Biology)
  • 01/2007-04/2007: Post-doc in the group of Thomas Wilhelm (Theoretical Systems Biology)
  • 09/2005-01/2007: Assistant at the University of Applied Sciences Jena (statistics and mathematics)
  • 08/2003-05/2005: Additional studies in Bioinformatics (including bioinformatics, genetics, biochemistry, metabolic pathway analysis, and biological network analysis) at the University of Jena
  • 04/2003-01/2007: PhD. student in Thomas Wilhelm's group (Theoretical Systems Biology) Dissertation: 'Identification and Characterization of Statistically Significant Substructures in Unordered Biological Data'
  • 03/2003: Diploma (Thesis: 'SMS - subtraction games with special moves')
  • 06/2001-03/2003: Tutor at the private lessons school "MegaKids" in Weimar (courses: mathematics, physics, chemistry, computer science, project work (game programming with Delphi, programming with Visual Basic, Macromedia Flash, Corel Draw, assembly of computers)
  • 02/2001-03/2003: Teacher at the Community Education Centre Jena (courses: Windows, Word, Excel, PowerPoint, Internet, OpenOffice, JavaScript, and VBS)
  • 10/2000-11/2001: Programmer at the software company "exquisite Technologies"
  • 09/2000-05/2001: Scientific assistant at the University of Jena
  • 05/2000-09/2000: Scientific assistant at the University of Weimar
  • 09/1998-03/2001: Additional studies in computer science
  • 04/1998-03/2003: Undergraduate studies in business mathematics (covers mathematics and business studies) at the University of Jena


  • Systems Biology
  • Network analysis
  • Proteomics (molecular machines, protein clustering, protein subcomplexes, functional modules)
  • Transcriptional and post-transcriptional gene regulation
  • Data integration and analysis
  • Patter recognition and data mining
  • miRNA and non-coding RNAs


  • Game theory
  • Artificial intelligence (construction of robotics)

Service as reviewer


Developed method

We have developed a new method for identification of statistically significant combinations of elements in different sets. Here we do not consider any order of elements (non-sequence data). Using our DASS (Discovery of All Significant Substructures) approach (Hollunder et al. DASS: efficient discovery and p-value calculation of substructures in unordered data. Bioinformatics 23,2007,77-83) we can calculate p-values for element combinations (e.g. closed (item)sets) also in huge data where computational shuffling (Monte Carlo random permutation test) doesn't work anymore.

Furthermore, we have developed a graphical user interface with additional analysis features facilitating usage of our methods. A correponding publication is submitted: DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data.


Computational Biology and Modelling of Biological Systems (Master of Biochemistry and Biotechnology, with Yves Van de Peer and Tom Michoel)


(16) Laukens, K., Hollunder, J., Hai Dang, T., De Jaeger, G., Kuiper, M., Witters, E., Verschoren, A., Van Leemput, K. (2010) Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics 11:360.

(15) Van Leene, J., Hollunder, J., Eeckhout, D., Persiau, G., Van De Slijke, E., Stals, H., Van Isterdael, G., Verkest, A., Neirynck, S., Buffel, Y., Inzé, D., Witters, E., De Jaeger, G. (2010) Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 6:397.

(14) Boruc, J., Van Den Daele, H., Hollunder, J., Rombauts, S., Mylle, E., Hilson, P., Inzé, D., De Veylder, L., Russinova, E. (2010) Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. The Plant Cell 22(4):1264-80.

(13) * Hollunder, J., * Friedel, M., Kuiper, M., Wilhelm, T. (2010) DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. Bioinformatics 26(7):987-9. *contributed equally

(12) Boyko, A., Blevins, T., Yao, Y., Golubov, A., Bilichak, A., Ilnytskyy, Y., Hollunder, J., Meins, F., Kovalchuk, I. (2010) Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins. PLoS One 5(3):e9514.

(11) De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., Inzé, D. (2010) CORNET: a user-friendly tool for data mining and integration. Plant Physiol. 152(3):1167-79.

(10) Wilhelm, T., Hollunder, J. (2007) Information theoretic description of networks. Physica A 385, 385-396.

(9) Hollunder, J., Beyer, A., Beyer, A., Wilhelm, T. (2007) Protein subcomplexes - molecular machines with highly specialized functions. IEEE Trans. Nanobiosci. 6, 86-93.

(8) Hollunder, J., Friedel, M., Beyer, A., Workman, C., Wilhelm, T. (2007) DASS: Efficient discovery and p-value calculation of substructures in unordered data. Bioinformatics 23, 77-83.

(7) Wilhelm, T., Hollunder, J., Beyer, A., Kim, J.R. (2006) General classification of networks. Proceedings of AISB (2006): Adaptation in Artificial and Biological Systems. T. Kovacs, J.A.R. Marshall (eds.)., Vol.III, 189-194. University of Bristol, Bristol, UK.

(6) Beyer, A., Workman, C., Hollunder, J., Radke, D., Moeller, U., Wilhelm, T., Ideker, T. (2006) Integrated assessment and prediction of transcription factor binding. PLoS Comput. Biology 2, e70.

(5) Nikolajewa, S., Beyer, A., Friedel, M., Hollunder, J., Wilhelm, T. (2005) Common pattern in type II restriction enzyme binding sites. Nucleic Acids Res. 33, 2726-2733.

(4) Hollunder, J., Beyer, A., Wilhelm, T. (2005) Exploiting combinatorial complexity - searching for new functional entities in the cell. Proceedings of the 1st Systems Biology Conference, FOSBE 2005, 363-366.

(3) Hollunder, J., Beyer, A., Wilhelm, T. (2005) Identification and characterization of protein subcomplexes in yeast. Proteomics 5, 2082-2089.

(2) Wilhelm, T., Hollunder, J., Beyer, A. (2004) Patterns in weighted networks. Proceedings of the 8th World Multiconference on Systemics, Cybernetics and Informatics Vol. III, 217-221.

(1) Beyer, A., Hollunder, J., Nasheuer, H.-P., Wilhelm, T. (2004) Posttranscriptional expression regulation in the Saccharomyces cerevisiae on a genome scale. Molecular and Cellular Proteomics 3, 1083-1092.

VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
+32 (0) 9 33 13807 (phone)
+32 (0) 9 33 13809 (fax)

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