Molecular basis of gene regulation of diseases – Carsten Daub's research group

We focus on understanding the molecular basis of gene regulation of diseases, specifically related to inflammation. Our work includes genome-wide gene expression analysis from human patient samples employing various RNA-Sequencing. Bioinformatics analysis identifies elements responsible for the observed expression differences in the diseased patients and the associated clinical phenotypes.

Examples include transcription factors (TFs), closely related but distinct alternative promoters resulting in the same protein but employing different sets of regulatory TFs, expression of anti-sense RNA to modulate the sense-RNA and the regulatory role of enhancers, expressed repeat elements and miRNAs. We are also involved in several genome annotation consortia.

Development of sequencing technologies and sequencing library methods for genome, metagenome, transcriptome and epigenome data is moving at a breathtaking pace. We are working with the development of corresponding bioinformatics data analysis technologies for these genomics data. For example, our group identified gene enhancers in transcriptome data and assigned gene regulatory roles to these enhancers in diseases and development.

diagram and data with dots in different colours
Spatial Transcriptomics data is used to identify cancer gene expression signatures and to classify cancer sub-types in breast tissue. Illustration: Niyaz Yoosuf Image modified from the original article, open access under the terms of Creative Commons Attribution 4.0 International License

Understanding the molecular basis of perturbed gene regulation in diseases is one aspect of our research. We are using genome-wide analysis technologies based on high-throughput sequencing extensively. Developing the necessary bioinformatics tools together with best-practice analysis methods constitutes an important aspect.

For the last ten years, we have been working on obesity-related type 2 diabetes and on asthma. Close collaboration with clinical research groups has been of key importance. We usually join the projects during the design phase where we contribute to the experimental design in terms of cohort stratification, statistical power, selection of tissue types, annotation of samples and data as well as selecting the high-throughput analysis technologies used. Addressing the specific biomedical questions of the projects by analysing the sequencing data together with the clinical data constitutes one of the main aspects of our work. Very close interaction with the clinicians is of outmost importance in connecting the findings of the data analysis to the biology underlying the disease.

a group photo taken inside a building, people standing next to each other
Carsten Daub's group, from left to right: Matthias Hörtenhuber, Kelvin Kwok, Tahmina Akhter, Carsten Daub, Rasha Fahad, Marine Tessarech, Irene Stevens and Abdul Kadir Mukarram.

We contributed to genome annotation projects for the zebrafish as part of the DANIO-CODE consortium and for the dog as part of the DoGA consortium. We first developed a sample and data annotation framework since both consortia are consolidating data from various sources. Main goals include improved genome annotation and adding gene enhancers. We work with Spatial Transcriptomics (ST) data, where we used the ST data in a gene independent way and employed machine learning methods to identify breast cancer signatures.


Selected publications

Staff and contact

Group leader

All members of the group

Previous group members

Audrey Piraud, Summer intern (2022)

Sabina Gansberger, Master student (2022)

Matthias Hörtenhuber, PhD student (2015-2022)

Abdul Kadir Mukarram, PhD Student (2015-2021)

Enrichetta Mileti, PhD Student (2014-2021)

Fiona Roß, Master Student (2021)

Kelvin Kwok, Postdoc (2017-2021)

Ahmad Ali, Master student (2020)

Filip Runebou Läärä, Master student (2020)

Irene Stevens, Bioinformatics Lab Technician (2018-2019)

Marine Tessarech, Master student (2019)

Michaël Dong, Bioinformatics Lab Technician (2016-2018)

Amitha Raman, Lab engineer (2013-2018)

Niyaz Yoosuf, Postdoc (2014-2018)

Jiarui Mi, Master student (2017-2018)

Marta Dias, Erasmus master student (2015-2016)

Johanna Labate, Erasmus summer student (2015)

Olga Hrydziuszko, Postdoc (2012-2014)

Nancy Yu, Postdoc (2012-2014)

Wenjing Kang, Masters student (Feb-June 2014)

Jacqueline Nowak, Masters student (April-August 2014)

Kubra Altinel, Erasmus summer student (2014)

Bioinformatics and Systems Biology (methods development, see 10203) Cancer and Oncology Endocrinology and Diabetes
Content reviewer:
Sara Bruce