Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Markus Wolfien

Image: Markus Wolfien

Current Projects

Complex DNA lesions and their impact on cellular radiation response (Collar)
The investigations will deepen our knowledge on the impact of radiation-induced complex DNA lesions with spinoffs for radiation protection and the development of new, advanced tumor therapy strategies.
Structured Analysis and Integration of RNA-Seq Experiments - de.STAIR
RNA sequencing (RNA-Seq) has become a widely used tool to study quantitative and qualitative aspects of the transcriptome. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. Our aim is to enable a comprehensive analysis of RNA-Seq experiments as a service. To enable maximum usefulness, interconnectivity, and accessibility for the developed approaches and services, we will provide dedicated workshops, training programs and screen casts for bioinformaticians and other life scientists and, ultimately, lower the barriers to RNA-Seq data analysis as a whole.
KNOWYODA - KNow and OWn YOur DAta
KNOWYODA delivers high quality tools to manage and analyse health data for the private user. KNOWYODA is a secure, personal, digital memory focussing on health related data. We develop cutting edge methodologies to support patients and the public visualise and interpret their data.

Research Interest

Next Generation Sequencing and beyond

"I am interested to develop NGS data analysis approaches to investigate biological phenomena."

One major task in this project is to develop state-of-the-art approaches to analyze Next Generation Sequencing data. For this reason, we develope a Transparent, Reproducible and Automated PipeLine, short TRAPLINE, to analyze and evaluate RNAseq data which needs less computational knowledge than other tools and, therefore, is ready to use workflow for experimentalists. One of our specialized use cases is about the transcriptomic differences between induced sino-atrial bodies (iSaBs) in comparison to antibiotic-selected cardiac bodies (aCaBs).  Furthermore, I will focus the challenge of functional characterization & prediction of lncRNAs to investigate their influences towards iSaBs generation.

Additionally, I perform meta-analysis approaches, namely Random-effects & HLM, to evolve the experimental design of pre-clinical and clinical models that were used to analyze the regeneration of the heart after infarction.

Posters and videos can be accessed via figshare.


Academic Background

PhD Program: Molecular Mechanisms of Regenerative Processes
University of Rostock, Rostock/Germany

Master's degree in Medical Biotechnology
University of Rostock, Rostock/Germany

Bachelor's degree in Biosystems Engineering 

Otto von Guericke University Magdeburg, Magdeburg/Germany


Yavari A, ..., Wolfien M, ..., Wolkenhauer O, ..., Ashrafian H
Mammalian γ2 AMPK regulates intrinsic heart rate

Nature Communications

Hausburg F, Jung JJ, Hoch M, Wolfien M, Yavari A, Rimmbach C, David R
(Re-)Programming of Subtype Specific Cardiomyocytes

Advanced Drug Delivery Reviews

Steinhoff G, Nesteruk J, Wolfien M, Kundt G, The PERFECT Trial Investigators Group, ... , Hennig H, ... , Wolkenhauer O
Cardiac Function Improvement and Bone Marrow Response Outcome Analysis of the Randomized Perfect Phase III Clinical Trial of Intramyocardial CD133 + Application After Myocardial Infarction


Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR
Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

Journal of Biotechnology

Gruening BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Nucleic Acids Research

Lang C, Wolfien M, Langenbach A, Müller P, Wolkenhauer O, Yavari A, Ince H, Steinhoff G, Krause B, David R, Glass Ä
Cardiac cell therapies for the treatment of acute myocardial infarction: A Meta-Analysis from mouse studies

Cellular Physiology and Biochemistry
doi: 10.1159/000477324

D Waltemath, JR Karr, FT Bergmann, V Chelliah et al.
Toward community standards and software for whole-cell modeling

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14 (2016)

Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stephan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer (2016)
TRAPLINE: A standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation

BMC Bioinformatics
doi: 10.1186/s12859-015-0873-9
open access

R Alm, D Waltemath, M Wolfien, O Wolkenhauer et al.
Annotation-Based Feature Extraction from Sets of SBML Models

Open Access article in J Biomedical Semantics 6:20 (2015)
DOI: 10.1186/s13326-015-0014-4

M Scharm, F Wendland, M Peters, M Wolfien, T Theile, D Waltemath
The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results.

Open Access demo paper in Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences (2014)
PeerJ Preprint:

Contact Details

Dept. of Systems Biology and Bioinformatics,
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
Room 413

phone: +49 381 498-7577
fax: +49 381 498-7572
mail: markus.wolfien(at)

Collaborators & Partners

Federal Ministry for Education and Research (BMBF)
Mecklenburg Vorpommern
Prof. Robert David
Reference and Translation Center for Cardiac Stem Cell Therapy, Rostock, Germany
Prof. Gustav Steinhoff
Reference and Translation Center for Cardiac Stem Cell Therapy, Rostock, Germany
Georg Iliakis
Institute of Medical Radiation Biology, Medical School, University of Duisburg-Essen, Duisburg-Essen/Germany