Publications 2012-2013

Eggeling, R., Gohr, A., Bourguignon, P.-Y., Wingender, E. and Grosse, I.:
Inhomogeneous Parsimonious Markov Models

Lecture Notes in Computer Science, LNAI 8188, 321-336 (2013). link

Deyneko, I. V., Kel, A. E., Kel-Margoulis, O. V., Deineko, E. V., Wingender, E. and Weiss, S.:
MatrixCatch – a novel tool for the recognition of composite regulatory elements in promoters

BMC Bioinformatics 14, 241 (2013). link

Sugii, M., Wingender, E. and Matsuno, H.:
Petri net modeling of oscillatory processes in the activation of cell cycle proteins

Proceedings of the 28th International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2013), June 30-July 3, 2013, Yeosu, Korea, pp. 76-79 (2013). pdf

Dönitz, J., Großmann, D., Schild, I., Schmitt-Engel, C., Bradler, S., Prpic, N.-M. and Bucher, G.:
TrOn: An anatomical ontology for the beetle Tribolium castaneum

PLoS ONE 8, e70695 (2013). link

Fuchs, M., Beissbarth, T., Wingender, E. and Jung, K.:
Connecting high-dimensional mRNA and miRNA expression data for  binary medical classification problems

Comput. Methods Programs Biomed. 111, 592-601 (2013). link

Bhar, A., Haubrock, M., Mukhopadhyay, A., Maulik, U., Bandyopadhyay, S. and Wingender, E.:
Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell

Algorithms Mol. Biol. 8, 9 (2013). link

Stegmaier, P., Kel, A., Wingender, E. and Borlak, J.:
A discriminative approach for unsupervised clustering of DNA sequence motifs
PLoS Comput. Biol. 9, e1002958 (2013). link

Wingender, E.:
Criteria for an updated classification of human transcription factor DNA-binding domains
J. Bioinform. Comput. Biol. 11, 1340007 (2013). link

Wingender, E., Schoeps, T. and Dönitz, J.:
TFClass: An expandable hierarchical classification of human transcription factors
Nucleic Acids Res. 41, D165-D170 (2013). link

Haubrock, M., Li, J. and Wingender, E.:
Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks
BMC Syst. Biol. 6 Suppl. 2, S15 (2012). link

Dönitz, J. and Wingender, E.:
The ontology-based answers (OBA) service: A connector for embedded usage of ontologies in applications
Front. Gene. 3, 197 (2012). link

Gültas, M., Haubrock, M., Tüysüz, N. and Waack, S.:
Coupled Mutation Finder: A new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations
BMC Bioinformatics 13, 225 (2012). link

Bhar, A., Haubrock, M., Mukhopadhyay, A., Maulik, U., Bandyopadhyay, S. and Wingender, E.:
delta-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data
Raphael, B. and Tang, J. (eds.) Algorithms in Bioinformatics, 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012, Proceedings, LNBI 7534, 165-177 (2012). link

Li, J., Hua, X., Haubrock, M., Wang, J. and Wingender, E.:
The architecture of the gene regulatory networks of different tissues
Bioinformatics 28, i509-514 (2012). link