Selected key publications / Publications by years / Publications by subjects / Book
See also my publication profile at MS Academic Search (although this is not fully up to date!).

Selected key publications:

Dönitz, J. and Wingender, E.: EndoNet: An information resource about the intercellular signaling network. BMC Syst. Biol. 8, 49 (2014). doi: 10.1186/1752-0509-8-49 (PubMed 24758335; Publisher: Abstract)

Gültas, M., Düzgün, G., Herzog, S., Jäger, S. J., Meckbach, C., Wingender, E. and Waack, S.: Quantum Coupled Mutation Finder: Predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming. BMC Bioinformatics 15, 96 (2014). doi: 10.1186/1471-2105-15-96 (PubMed 24694117; Publisher: Abstract)

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). (Publisher: Abstract)

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). doi:10.1186/1471-2105-14-241 (PubMed 23924163; Publisher: Abstract)

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). doi: 10.1016/j.cmpb.2013.05.013 (PubMed 23849930; Publisher: Abstract)

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). doi:10.1186/1748-7188-8-9 (PubMed 23521829; Publisher: Abstract)

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). doi:10.1371/journal.pcbi.1002958 (Publisher: Full text)

Wingender, E.: Criteria for an updated classification of human transcription factor DNA-binding domains. J. Bioinform. Comput. Biol. 11, 1340007 (2013). doi: 10.1142/S0219720013400076 (Publisher: Abstract; Full text (pdf, open access))

Wingender, E., Schoeps, T. and Dönitz, J.: TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170 (2013). doi: 10.1093/nar/gks1123 (PubMed 23180794; Nucleic Acids Res. Full text)

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). (BMC Syst. Biol. Full text)

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). (PubMed 23060901)

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). (PubMed 22962474)

Wang, J., Haubrock, M., Cao, K.-M., Hua, X., Zhang, C.-Y., Wingender, E. and Li, J.: Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network. BMC Bioinformatics 5, 199 (2011). (PubMed 22176772)

Ante, M., Wingender, E. and Fuchs, M.: Integration of gene expression data with prior knowledge for network analysis and validation. BMC Res. Notes 4, 520 (2011). (PubMed 22123172)

Stegmaier, P., Voss, N., Meier, T., Kel, A., Wingender, E. and Borlak, J.: Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PLoS ONE 6, e17738 (2011). (Link)

Stegmaier, P., Krull, M., Voss, N., Kel, A. and Wingender, E.: Molecular mechanistic associations of human diseases. BMC Syst. Biol. 4, 1024 (2010). (PubMed 18454847)

Goemann, B., Potapov, A. P., Ante, M. and Wingender, E.: Comparative analysis of topological patterns in different mammalian networks. Genome Inf. Ser. 23, 32-45 (2009). (link (pdf))

Potapov, A. P., Goemann, B. and Wingender, E.: The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks. BMC Bioinformatics 9, 227 (2008). (PubMed 18454847)

Wingender, E.: The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform. 9, 326-332 (2008). (PubMed 18436575)

Dönitz, J., Goemann, B., Lizé, M., Michael, H., Sasse, N., Wingender, E. and Potapov, A. P.: EndoNet: An information resource about regulatory networks of cell-to-cell communication. Nucleic Acids Res. 36, D689-D694 (2008). (PubMed 18045786)

Krull, M., Pistor, S., Voss, N., Kel, A., Reuter, I., Kronenberg, D., Michael, H., Schwarzer, K., Potapov, A., Choi, C., Kel-Margoulis, O. and Wingender, E.: TRANSPATH®: an Information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 34, D546-D551 (2006). (PubMed 16381929)

Matys, V., Kel-Margoulis, O. V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A. E. and Wingender, E.: TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108-D110 (2006). (PubMed 16381825)

Sauer, T., Shelest, E. and Wingender, E.: Evaluating phylogenetic footprinting for human-rodent comparisons. Bioinformatics 22, 430-437 (2006). (PubMed 16332706)

Kel, A. E., Gößling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V. and Wingender, E.: MATCH(TM): a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31, 3576-3579 (2003). (PubMed 12824369)

Wingender, E.: Classification scheme of eukaryotic transcription factors. Molekularnaya Biologiya 31, 584-600 (1997); Mol. Biol. Engl. Tr. 31, 483-497 (1997). (PubMed 9340487; Full text (pdf, 15MB))

Quandt, K., Frech, K., Karas, H., Wingender, E. and Werner, T.: MatInd and MatInspector - New fast and sensitive tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 23, 4878-4884 (1995). (PubMed 8532532)

Wingender, E.: Compilation of transcription regulating proteins. Nucleic Acids Res. 16, 1879-1902 (1988). (PubMed 3282223)

Scientific publications by years:

2011 - (as pdf)
2006 - 2010 (as pdf)
2001 - 2005 (as pdf)
1996 - 2000 (as pdf)
1991 - 1995 (as pdf)
1980 - 1990 (as pdf)

These lists are arranged in descending order, showing the most recent publication of each time interval at the top.

Scientific publications by subjects:

Bioinformatics, with the main subsections Databases, Regulatory sequence analysis, Network analysis / systems biology (as pdf)

Transcription regulation (experimental work / reviews; as pdf)

Chromatin structure (as pdf)

Bone growth / parathyroid hormone (as pdf)

General publications (as pdf)

Note that some publications may be assigned to more than one category.


E. Wingender
Gene Regulation in Eukaryotes
VCH Weinheim - New York - Basel - Cambridge, 1993 (ISBN 3-527-28460-5)

In case you are interested in this book, although it is rather outdated, you may wish to contact me; I still have some copies lying around ...
E. Wingender (editor)
Biological Petri Nets
IOS Press, Amsterdam, 2010 (ISBN 978-1-60750-703-1)