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The research focus of our institute is on regulatory networks of cells and organisms. By applying a range of bioinformatics methods, we hope to contribute to unravel the underlying principles and, at the same time, to develop a couple of tools which may prove useful to the systems biology community. Like our research, our teaching in bioinformatics is very much biology-driven. In this sense, we try to convey the importance and the principles of bioinformatics to students in medicine, biology and computer sciences.


November 02, 2016

Available as Ebook now:

Systems Biology of Transcription Regulation

Ekaterina Shelest, Edgar Wingender, Joerg Linde (editors)
Published by Frontiers Media SA (ISBN 9782889199679)
doi: 10.3389/978-2-88919-967-9

Free download

August 12, 2016

Enhancer-promoter interaction mediated by transcription factors c-Fos and NF-Y:

We addressed the question how transcription factors (TFs) bind to their target genes through non-canonical sequence elements. We found that the TFs c-Fos, a regulator that conveys a variety of stimuli to gene activation processes, and NF-Y, which is rather considered as a house-keeping factor, may mediate a novel kind of cell-specific enhancer-promoter interaction.

A systematic analysis of c-Fos bound genomic intervals has revealed that many c-Fos targets are characterized by CCAAT boxes rather than classical c-Fos (AP-1) binding motifs. A functional class of promoters contains a defined arrangement of two CCAAT boxes and an AP-1 motif in the nearby enhancers:

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


April 19, 2016

MicroRNA promoter allocation:

Applying a newly designed computational workflow, we could reliably identify the transcription start sites for microRNAs in the human genome. The workflow and the results obtained have been published today in Bioinformatics:

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

This work was part of a highly productive collaboration of our group with the group of Prof. Jin Wang at the Nanjig University (NJU) and became part of Xu Hua's PhD thesis. It was supported by the German Centre for Cardiovascular Research, the China Scholarship Council, the National Science Foundation of China, and the NJU-Yangzhou Institute of Optoelectronics.


April 05, 2016

Metastasizing cancer:

We subjected the transcriptomes of two colorectal cancer cell lines differing in their potential to metastasize to a typical "upstream analysis", i.e. an integrated promoter and pathway analysis. Both cell lines significantly differed in certain pathways and their cross-talks, e.g. between Wnt-signaling and certain nuclear receptor pathways. They also exhibit different master regulators, in particular subtle differences among the MAP kinase pathways activated.

As the paper below, this study was published in a special issue of the Frontiers in Genetics on the research topic "Systems Biology of Transcription Regulation".

This work again showed the great synergy brought about by collaboration between experimental and computational biologists. It was supported by the BMBF-funded project MetastaSys, "Investigating the systems biology of metastasis".


March 23, 2016

Heart development:

Stem cell differentiation into cardiomyocytes depends on clusters of transcription factors (TFs) that specify the individual stages of this process. The number of TF clusters varies according to an hourglass model. Our study was published in a special issue of the Frontiers in Genetics on the research topic "Systems Biology of Transcription Regulation".

This work was a joint effort of experimental and computational biologists, supported by the German Centre for Cardiovascular Research.


March 01, 2016

New project launched: MyPathSem

Today, a new project has been launched, entitled MyPathSem – A data integration platform for generating patient-specific signaling pathways for personalized treatment decisions in clinical applications. It is supported by the German Ministry of Education and Research (BMBF) through the funding program "i:DSem – Integrative Datensemantik in der Systemmedizin".


December 07, 2015


The basic idea: we consider the genome as a document, genes as sentences, individual sequence elements as words, and apply mathematical concepts proven in linguistics.

PC-TraFF stands for "Potentially Collaborating Transcription Factor Finder". It is an information-theoretic method to identify, in a given set of genes, pairs of transcription factor binding sites. The corresponding transcription factors can be reasonably hypothesized to functionally interact in the regulation of these genes. When applied to breast cancer-associated genes, PC-TraFF found interacting TF pairs, some of them already known, others giving rise to interesting hypotheses for further validation.

July 02, 2015

A further refined version of Anirban Bhar's triclustering approach, EMOA-delta-TRIMAX, has been published. We acknowledge support by Erasmus Mundus and the ExITox project, funded by BMBF.

May 21, 2015

Anirban Bhar's triclustering approach provided the basis for illustrating the toxic  effect of naphthalene on lung and liver tissue. The work was part of our contribution to the ExITox project.

March 24, 2015

Our team member Anirban Bhar successfully passed his PhD defense. See here for his novel triclustering approach.

Congratulations, Anirban!

February 25, 2015

"Basic concepts of bioinformatics":
Lecture by E. Wingender at the Grodno State Medical University, Belarus

February 16, 2015

Project coordination meeting on Cardiovascular Bioinformatics with Dr. Shizuka Uchida and his team from Goethe University Frankfurt a.M.

January 28, 2015

New classification of human and rodent transcription factors published!

Featured paper

Compared with the different kinds of intracellular (metabolic, signaling, or gene regulatory) networks, intercellular networks are much less investigated at a systems level. On the other hand, the relevance of such cell-cell networks in particular for biomedicla research projects is quite obvious. – To facilitate corresponding investigations, we have set up a specialized information resource: EndoNet. The name was triggered by the fact that in the beginning, we were very much focussing on human hormonal (endocrine) communication pathways. – In this paper, which appeared in BMC Systems Biology 8:49 (2014), we have reported on the latest state of this resource, its contents as well as new functionalities.

EndoNet itself can be found here.

December 10, 2015



Prof. Dr. Edgar Wingender

Institute of Bioinformatics

Phone : +49 - (0)551 - 39 14912

Goldschmidtstr. 1


37077 Göttingen