SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
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.
The project addresses the generation and establishment of programmed pacemaker cells for an in vitro drug testing possibility to perform predictive tests. This may lead to an improved treatment of cardiac arrhythmias or an accurate identification of potential drug molecules at an early stage of development. Important benefits will arise in verifying the safety of a wide variety of medicines while reducing animal testing.
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.
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 ...
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 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.
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.
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.
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, motorcycling, 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
|2012 - 2014||
Master's degree in Medical Biotechnology
Thesis title: Next Generation Sequencing Data Analysis of Stem Cell Derived Cardiomyocyte Cell Types
|2008 - 2012||
Bachelor's degree in Biosystems Engineering
Thesis title: Verification of translocation of RelA in H.pylori infected cells through immunofluorescence
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
Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression
Mucha S, ... Bej S, ..., Wolfien M, ..., Wolkenhauer O, ..., Ellinghaus D
The Journal of Allergy and Clinical Immunology
LoRAS: An oversampling approach for imbalanced datasets
Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer
** Submitted in Springer Machine Learning (Decision pending after major revision)
Community-driven data analysis training for biology
Batut B, Hiltemann S, Bagnacani A, …, Wolfien M, ..., Gruening B
Mammalian γ2 AMPK regulates intrinsic heart rate
Yavari A, ..., Wolfien M, ..., Wolkenhauer O, ..., Ashrafian H
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)
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
Applications of genome-scale metabolic models and data integration in systems medicine
Salehzadeh-Yazdi A, Wolfien M, Wolkenhauer O
Nova (2019), chapter in Focus on Systems Theory Research
ISBN 13 (online): 9781536145618
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)
Education and Work Experience
|2019||edX course: "The FDA and Prescription Drugs: Current Controversies in Context" (HarvardX)|
|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)|
|2018 - 2021||GMDS Project group leader for Data Processing Workflows (GMDS)|
|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
|2019||Attendance of the Rostock's Eleven as a representative of the University of Rostock|
|2018||Attendance of a Science Slam in Bremen|
|2017||Posterpreis "Junge Wissenschaft 2016" - IV. Interdisziplinären Kongresses für Junge Wissenschaft und Praxis|
|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|