Publications 2016-2018

Meckbach, C., Wingender, E. and Gültas, M.:
Removing background co-occurrences of transcription factor binding sites greatly improves the prediction of specific transcription factor cooperations
Front. Genet. 9, 189 (2018)
doi: 10.3389/fgene.2018.00189  link

Hua, X., Tang, R., Xu, X., Wang, Z., Xu, Q., Chen, L., Wingender, E., Li, J., Zhang, C. and Wang, J.:
mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines
Nucleic Acids Res. 46, D168-D174 (2018)
doi: 10.1093/nar/gkx996  link

Wingender, E., Schoeps, T., Haubrock, M., Krull, M. and Dönitz, J.:
TFClass: expanding the classification of human transcription factors to their mammalian orthologs
Nucleic Acids Res. 46, D343-D347 (2018)
doi: 10.1093/nar/gkx987  link

Dönitz, J., Gerischer, L., Hahnke, S., Pfeiffer, S. and Bucher, G.:
Expanded and updated data and a query pipeline for iBeetle-Base
Nucleic Acids Res. 46, D831–D835 (2018)
doi: 10.1093/nar/gkx984  link

Stegmaier, P., Kel, A. and Wingender, E.:
geneXplainR: An R interface for the geneXplain platform
J. Open Source Softw. 2, 412 (2017)
doi: 10.21105/joss.00412  link

Tiburcy, M., Hudson, J. E., Balfanz, P., Schlick, S., Meyer, T., Chang Liao, M.-L., Levent, E., Raad, F., Zeidler, S., Wingender, E., Riegler, S., Wang, M., Gold, J. D., Kehat, I., Wettwer, E., Ravens, U., Dierickx, P., van Laake, L. W., Goumans, M. J., Khadjeh, S., Toischer, K., Hasenfuss, G., Couture, L. A., Unger, A., Linke, W. A., Araki, T., Neel, B., Keller, G., Gepstein, L., Wu, J. C. and Zimmermann, W.-H.:
Defined engineered human myocardium with advanced maturation for applications in heart failure modelling and repair
Circulation 135, 1832-1847 (2017)
doi:10.1161/CIRCULATIONAHA.116.024145  link

Kel, A.E., Stegmaier, P., Valeev, T., Koschmann, J., Poroikov, V., Kel-Margoulis, O.V. and Wingender, E.:
Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer
EuPA Open Proteomics 13, 1-13 (2016)
doi:10.1016/j.euprot.2016.09.002  link

Dang, T.K.L., Meckbach, C., Tacke, R., Waack, S. and Gültas, M.:
A novel sequence-based feature for the identification of DNA-binding sites in proteins using Jensen–Shannon Divergence
Entropy 18, 379 (2016)
doi:10.3390/e18100379  link

Shelest, E., Wingender, E. and Linde, J. (eds.):
Systems Biology of Transcription Regulation
Frontiers Media, Lausanne 2016 (ISBN 978-2-88919-967-9).
doi: 10.3389/978-2-88919-967-9  link

Shelest, E. and Wingender, E.:
Editorial: Systems biology of transcription regulation
Front. Genet. 7, 124 (2016).
doi: 10.3389/fgene.2016.00124  link

Haubrock, M., Hartmann, F. and Wingender, E.:
NF-Y binding site architecture defines a c-Fos targeted promoter class
PLoS ONE 11, e0160803 (2016)
doi:10.1371/journal.pone.0160803  link

Hua, X., Chen, L., Wang, J., Li, J. and Wingender, E.:
Identifying cell-specific microRNA transcriptional start sites
Bioinformatics 32, 2403-2410 (2016)
doi: 10.1093/bioinformatics/btw171  link

Wlochowitz, D., Haubrock, M., Arackal, J., Bleckmann, A., Wolff, A., Beissbarth, T., Wingender, E. and Gültas, M.:
Computational identification of key regulators in two different colorectal cancer cell lines
Front. Genet. 7, 42 (2016).
doi: 10.3389/fgene.2016.00042  link

Zeidler, S., Meckbach, C., Tacke, R., Raad, F. S., Roa, A., Uchida, S., Zimmermann, W. H., Wingender, E. and Gültas, M.:
Computational detection of stage-specific transcription factor clusters during heart development
Front. Genet. 7, 33 (2016).
doi: 10.3389/fgene.2016.00033  link

Schirmer, M.A., Lüske, C., Roppel, S., Schaudinn, A., Zimmer, C., Pflüger, R., Haubrock, M., Rapp, J., Güngör, C., Bockhorn, M., Hackert, T., Hank, T., Strobel, O., Werner, J., Izbicki, J.R., Johnsen, S.A., Gaedcke, J., Brockmöller, J. and Ghadimi, B.M.:
Relevance of Sp binding site polymorphism in WWOX for treatment outcome in pancreatic cancer

J. Natl. Cancer Inst. 108, djv387 (2016).
doi: 10.1093/jnci/djv387  link