Jens Hollunder
CV
Research
Interest
Service as reviewerBioinformaticsDeveloped methodWe 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. TeachingComputational Biology and Modelling of Biological Systems (Master of Biochemistry and Biotechnology, with Yves Van de Peer and Tom Michoel)Papers(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. |
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