Markus Wolfien

To analyse, evaluate and annotate RNA sequencing data, we develop connective workflows.

Research interest

Omics data integration concepts in Systems Medicine

"I am interested in developing computational data analysis workflows to investigate biological phenomena."

Application of computer science in the life science plays an increasingly important role. A key challenge is to adapt, compare, benchmark and integrate the most appropriate computational tools into data analysis workflows. In my research, I focus on the needs of experimental researchers and develop flexible workflows for the analysis of low and high throughput data such as blood measurements, protein expression, RNA sequencing data and environmental information. One major task in this project is to develop state-of-the-art approaches to analyse Next Generation Sequencing data. For this reason, we develop a Transparent, Reproducible and Automated PipeLine, short TRAPLINE, to analyze and evaluate RNA-Seq data which needs less computational knowledge than other tools and, therefore, is ready to use workflow for experimentalists. I am combining state-of-the-art tools including R, Python, Galaxy and Docker as well as further downstream analysis approaches such as network analyses or machine learning (classical ML and Deep Learning). We already applied and validated our developed methodologies in interdisciplinary collaborations. Exemplarily, pre-clinical and clinical data of stem cell derived cardiac cell types have been investigated to demonstrate the value of such integrative data analysis workflows, contributing towards a better understanding within the field of cardio vascular diseases and cardiac repair. My work highly facilitates the use of Systems Medicine approaches in a clinical setting and thus supporting improved diagnosis, prevention and therapy.

My posters and videos can be accessed via figshare.



Research Projects

DeepMRI: Analysis of phase III clinical trial data, including MRI image classification using artificial intelligence

Regenerative therapies using stem cells for the repair of heart tissue have been at the forefront of preclinical and clinical development during the past 16 years. To build upon this progress, the Phase III clinical trial PERFECT was designed to assess clinical safety and efficacy of intramyocardial CD133+ bone marrow stem cell treatment combined with coronary artery bypass graft for induction of cardiac repair.


DeepBioSeq: Deep Learning for Next Generation Sequencing Data

Deep learning technologies are making an impact, particularly with image analysis and object detection. Applications to Next Generation Sequencing data are however still at an early stage ...


GB-XMap: Assessing the risk of gut-brain cross-diseases

Investigating the gut-brain-axis

The gut–brain axis (GBA) provides a bidirectional homeostatic communication between the gastrointestinal tract and the central nervous system. The interdisciplinary collaboration is going to fully explore a first comprehensive GBA cross-disease map of genetic, expression and regulatory changes associated with ulcerative colitis and schizophrenia disease entities.


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.


de.STAIR: Structured Analysis and Integration of RNA-Seq Experiments

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. We provide easy access to comprehensive analysis of RNA-Seq experiments as a service. To do so, we leverage on the Galaxy framework, and organise dedicated workshops, training programs, and screencasts to make Life Scientists familiar with computational approaches to biological problems.


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.


Academic background

In 2008 I started my Bachelor studies of Biosystems Engineering at the Otto-von-Guericke University (OvGU) Magdeburg to gain knowledge about basic concepts in molecular biology, computer science and engineering. For one year I worked at the Institute of Experimental Internal Medicine at the cellular infection biology unit to investigate H. pylori by means of imaging technologies. After finishing my B.Sc. in 2012, I changed my study focus at the Master level to Medical Biotechnology in Rostock. During a research assistant position at the Dept. of Systems Biology and Bioinformatics (SBI), I got first impressions about computational analyses and mathematical modeling. In 2014 I completed my Master’s thesis and since then I remain working at the Dept. as a PhD candidate and scientific employee.

Further details of my recent work can be obtained further below; my posters and videos can be accessed via figshare. Beside my research activities, I enjoy snowboarding in the winter and sports activities like climbing and playing American football during summer.


2014 - present

PhD Program: Molecular Mechanisms of Regenerative Processes

Thesis title: Customized workflow development and omics data integration concepts in Systems Medicine
University of Rostock, Rostock/Germany

2012 - 2014

Master's degree in Medical Biotechnology

Thesis title: Next Generation Sequencing Data Analysis of Stem Cell Derived Cardiomyocyte Cell Types
University of Rostock, Rostock/Germany

2008 - 2012

Bachelor's degree in Biosystems Engineering

Thesis title: Verification of translocation of RelA in H.pylori infected cells through immunofluorescence
OvGU Magdeburg, Magdeburg/Germany


Selected publications

Cardiac Function Improvement and Bone Marrow Response Outcome Analysis of the Randomized Perfect Phase III Clinical Trial of Intramyocardial CD133 + Application After Myocardial Infarction

Steinhoff G, Nesteruk J, Wolfien M, ... , Hennig H, ... , Wolkenhauer O

EBioMedicine 22, 208-224 (2017)

Cardiac cell therapies for the treatment of acute myocardial infarction: A Meta-Analysis from mouse studies

Lang C, Wolfien M, Langenbach A, Müller P, Wolkenhauer O, Yavari A, Ince H, Steinhoff G, Krause B, David R, Glass Ä

Cellular Physiology and Biochemistry

Community-driven data analysis training for biology

Batut B, Hiltemann S, Bagnacani A, …, Wolfien M, ..., Gruening B

Cell Systems

Mammalian γ2 AMPK regulates intrinsic heart rate

Yavari A, ..., Wolfien M, ..., Wolkenhauer O, ..., Ashrafian H

Nature Communications

Stem cells and heart disease - brake or accelerator?

Steinhoff G, Nesteruk J, Wolfien M, Große J, Ruch U, Vasudevan P, Müller P

Advanced Drug Delivery Reviews

(Re-)Programming of Subtype Specific Cardiomyocytes

Hausburg F, Jung JJ, Hoch M, Wolfien M, Yavari A, Rimmbach C, David R

Advanced Drug Delivery Reviews

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR

Journal of Biotechnology

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Gruening BA, ..., Bagnacani A, Wolfien M, ..., Wolkenhauer O, ..., Backofen R

Nucleic Acids Research

Toward community standards and software for whole-cell modeling

Waltemath D, Karr JT, Bergmann FT, Chelliah V ... Scharm M et al.

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

TRAPLINE: A standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation

Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stephan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer (2016)

BMC Bioinformatics

Annotation-Based Feature Extraction from Sets of SBML Models

R Alm, D Waltemath, M Wolfien, O Wolkenhauer et al.

Open Access article in J Biomedical Semantics 6:20 (2015)

Ca2+/calmodulin-dependent kinase II contributes to inhibitor of nuclear factor-kappa B kinase complex activation in Helicobacter pylori infection.

Maubach G, O Sokolova, M Wolfien, HJ Rothkötter, M Naumann

Int J Cancer. Epub ahead of print 5 March 2013. IF: 5,444

The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results.

Scharm M, Wendland F, Peters M, Wolfien M, Theile T, and Waltemath D

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

Next Generation Sequencing Data Analysis of Stem Cell Derived Cardiomyocyte Cell Types

Markus Wolfien


M.Sc. within the study degree of Medical Biotechnology

Education and Work Experience

2017 edX course: "Data Analytics in Health – From Basics to Business" (KULeuvenX)
2016 edX course: "Genomic Medicine Gets Personal" (GeorgetownX)
2015 edX course: "Medicine in the Digital Age" (RiceX)
2015 edX course: "Case Study: RNA-seq data analysis" (HarvardX)


2015 - present Member of the European Association of Systems Medicine (EASyM)
2014 - present Member of the structured curriculum Molecular Mechanisms of Regenerative Processes (MMRP)


Awards and Distinctions

2017 Posterpreis "Junge Wissenschaft 2016" - IV. Interdisziplinären Kongresses für Junge Wissenschaft und Praxis

Teaching Experience

2016 - present Providing de.NBI Trainings for RNA-Sequencing data analysis
SS18 Introduction to Computer Science
WS16/17 Introduction to High Performance Computing
SS17 Introduction to Computer Science
WS16/17 Introduction to High Performance Computing
SS16 Introduction to Computer Science
WS15/16 Introduction to Functional Programming