Prof. Olaf Wolkenhauer

I am making sense out of data; Providing meaning to models.

Research interest

I am a data scientist, using mathematics and computational tools to make sense of data. My work focusses on understanding how the functioning of cellular systems emerges from the interactions between the system’s parts, and how these emergent properties of a system as a whole enable or constrain the behaviour of its parts. Despite technological advances, that allow us to identify and characterise cellular components, the principles by which cells and tissues realise their function, remain poorly understood. My approach combines data-driven modelling with model-driven experimentation, using a wide range of computational and mathematical tools, including machine learning, statistics, systems theory, and stochastic processes. The results of my work support basic biological and medical research.

Profil auf Deutsch; Profile in English


Research Projects

Sarcopenia Map

In collaboration with the Division of Gastroenterology at the Rostock University Medical Center (as part of the EnErGie project) we are developing an in-depth, standardized, and computationally encoded disease map of the molecular interactions regulating muscle growth and function. We integrated the two disease states intestinal dysfunctions (ID) and liver cirrhosis (LC) into the map to investigate their contribution to the loss of muscle function (sarcopenia).



A benchmark of context-specific models for the assessment of cancer metabolic heterogeneity.



A platform for trimming and extracting genome-scale metabolic models (GEMs)


MelAutim - Systems medicine investigation of melanoma and autoimmunity in the context of immune therapies

The MelAutim project aims to uncover the molecular and cellular mechanisms for the interaction of cancer and autoimmunity. In particular, it aims to identify factors that are involved in the development of new or the exacerbation of existing autoimmune diseases during immunotherapy.


SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke
Machine Learning on Imbalanced datasets

In real world scenarios, datasets are often imbalanced. That is, the datasets meant for supervised learning, divides into classes, where in some classes there are a very large number of instancess, compared to the others. Training machine learning algorithms on such data is challenging. We have developed an algorithm that overcomes problems of widely used algorithms.



A European standardization framework for data integration and data-driven in silico models for personalised medicine.



AIR: Atlas of Inflammation Resolution

The AIR is to provide an interactive platform connecting scientific and medical communities.


iPlacenta: A Systems Biology Approach towards Phenotype-Specific Interactomes for Placental Function

Pre-eclampsia (PE) is a complex disorder occurring during pregnancy and the postpartum affecting almost 5-8% of all pregnancies and often occurs with other complications. Its pathology is largely unknown. To improve the diagnosis and treatment outcomes, a deeper understanding of the determinants of pathophysiology is urgently needed.


iRhythmics: Programming pacemaker cells for in vitro drug testing

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.


BESTER: Bioprocesses for the optimized, integrated production of butyl esters from sustainable resources

The BESTER project will develop new bioprocesses for the production of butyl esters for the bio-based chemicals market. The in situ enzymatic esterification of butyric acid (HBu) and butanol (BuOH), produced by C. acetobutylicum, to butyl butyrate (BuB) with simultaneous extraction of the ester has been successfully shown by TU Delft (NL), using a single bioreactor setup (5g/L BuB yield).


The TOTO Project: Towards a Theory of Tissue Organisation

 ~ In biology, the exception is the rule. ~

 ~ With our work, we are not really interested in the unique, but in what is general in the unique.~

With this project, we want to address a biological and a methodological challenge. First, we wish to clarify how the functioning of cells, and the functioning of a tissue relate to each other. Do cells exercise a degree of autonomy, or is their behavior completely determined by the functioning of the tissue? Such questions are important in understanding the emergence and progression of diseases. For example, it remains unclear whether the causative origin of colon cancer is a cell, or a consequence of tissue organization.



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.


A systems methodology to assess the risk of tumor relapse in melanoma - MelEVIR

The aim of the project is to develop, test and prepare for translation into clinical practice a systems-biology-based diagnostic tool for assessing the probability of tumor relapse in melanoma patients, based on the profiling of pEVs. In the methodology proposed, in vitro and clinical data are integrated using data-driven mathematical modeling. The insights obtained from patient data analysis, reconstruction of biochemical networks, and model simulations are used to a) select a set of microRNAs, long non-coding RNAs, and proteins present in pEVs of patients to be measured in a blood test as surrogates of immune system activity against MRD and b) assess the probability of tumor relapse in the close future.



The TriplexRNA is a database of cooperating microRNAs and their mutual targets.

The database collects predicted and experimentally validated RNA triplexes, and provides an interactive interface for highligting targets of concerted RNA regulation within known disease pathways.


Academic background

2017– to date Adjunct Professor, Chhattisgarh Swami Vivekanand Technical University, India
2005 Fellow of the Stellenbosch Institute for Advanced Study (STIAS), Stellenbosch, South Africa
2004 – to date Adjunct Professor, Dept. of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, USA
2003 – to date Full Professor (C4/W3), Dept. of Systems Biology & Bioinformatics, Faculty of Computer Science and Electrical Engineering, University of Rostock, Germany
2003 – 2006 Visiting Reader, School of Mathematics, The University of Manchester, UK
2002 – 2003 Senior Lecturer. Joint appointment between the Dept. of Biomolecular Sciences and the Dept. of Electrical Engineering, University of Manchester Institute of Science and Technology (UMIST), UK
1999 – 2000 Senior Research Fellow (by invitation), Faculty of Information Technology and Systems, Delft University of Technology, Netherlands
1997 – 2000

Lecturer, Lucas Varity Research Lectureship, Control Systems Centre, UMIST, Manchester, UK

1997 Ph.D. Dissertation title: Possibility Theory with Applications to Data Analysis. Control Systems Centre, University of Manchester Institute of Science and Technology (UMIST), UK
1994 – 1997 Research Associate, Control Systems Centre, UMIST, Manchester, UK
1993 Research Assistant, Institute of Biomedical Engineering, Medical Academy Carl Gustav Carus, Dresden, Germany
1993 – 1994 B.Eng. (hons) 1st School of Systems Engineering, University of Portsmouth, UK
1991 – 1993 Teacher, Stiftung für Berufliche Bildung, Hamburg
1989 – 1993 Dipl.Ing. (FH) Control Engineering, Dept of Electrical Engineering and Computer Science. University of Applied Sciences, Hamburg, Germany
1985 – 1988 Industrial apprentice, completed with distinction. AEG Systems Technology, Hamburg


My work involves various advisory functions to ministries, funding bodies, award committees and consultancy for companies. Over the years, I have coordinated several research consortia in the UK, Germany and for the European Commission. I am the member of scientific advisory boards for several systems biology institutes and initiatives across Europe.

I am the founding editor of the first international journal in Systems Biology. I have written four books, including the research monograph “Possibility Theory with Applications to Data Analysis” (Wiley), the textbooks “Data Engineering” (Wiley) and “Stochastic Approaches for Systems Biology” (Springer). Another, more unusual book is an introductory conversation handbook for 'Plattdeutsch' (lower German) an old language that is spoken by only few people. I have edited other books, including a volume on “Systems Biology” (Portland Press), the Encyclopaedia of Systems Biology (Springer), a book on MicroRNA Cancer Regulation (Springer) and in 2016 a book on Systems Medicine (Springer). I am also the editor of the upcoming Encyclopaedia of Systems Medicine.

Awards and Distinctions

2016– 2019 Elected member of the DFG review panel Foundations of Medicine and Biology, German Research Foundation (DFG)
2009 SPIE Pioneer Award
1994 IBM Computing Prize for best Final Year Project

Teaching Experience

My teaching focusses on data analysis and mathematical modelling with applications in the life sciences, i.e., Bioinformatics, Systems Biology, Systems Medicine. We have more than 15 years of experience in teaching interdisciplinary courses at graduate level. Our students are coming from biology, medicine, physics, mathematics, engineering and computer science. Over the years, I have also enjoyed the organisation and teaching at various international summer and winter schools.

I am also offering three seminars, through which I share my experience and try to support young scientists. The seminars have been booked by various Universities, doctoral training centres, graduate schools and research institutes.

Productivity, Project and Time Management for Scientists
To-Do lists, reminder apps, multiple calendars, meeting protocols, „zero-inbox“ strategies: A career goal for every one of us, should be, not to require project, time management strategies and productivity tools. Unfortunately, most of us have to handle multiple projects at work, and at home. The question is how to be most productive and effective? The seminar will help you getting more things done, avoid errors, focus on what’s important, including fulfilment, and have more effective project meetings.

Effective Scientific Communication
Scientific data do not speak for themselves but require an argument to be accepted as facts. For facts to be trusted and results being accepted, we must communicate them effectively. Therefore, scientists are, to some extent, only as clever as others think they are. The communication of scientific results is therefore at least as important as their generation. In this course, we learn a strategy to effectively communicate research in paper abstracts, in grant applications, through websites as well as in oral and poster presentations. Our analysis reveals strategies to structure and formulate texts. These findings contribute to a more successful communication of the participant’s work and identify strategies for effective forms of writing.

Successful writing of grant proposals
In this seminar I would like to share my experience as an applicant and reviewer for DFG, BMBF and EU funding. Why? (i) Because I find it difficult to write successful proposals.  (ii) Because I was elected to the DFG Review panel on the Foundations of Medicine and Biology, rewarding the trust I have gained. (iii) Because as a young scientist I would have liked to receive help for this important part of my work. The seminar is therefore aimed at all those for whom writing applications for third-party funding is an opportunity to learn. My experiences are of course limited and not universally valid. For colleagues from the engineering and natural sciences, as well as medicine, however, one or the other valuable reference could be there. The format of the seminar is not a lecture, but a discussion with hopefully many questions of the participants. The most important experience in twenty years of reviewing is the observation that proposals for research projects is a form of science communication that has a number of similarities with other forms of communication (publications, posters, websites ...). I will present this structure of successful proposals and give concrete advice on how to submit them.

Other Interests and Activities

As part of my training as an Elektronaut I prepared some How to guides, Cheat sheets and notes that may be of help to other Elektron musicians:

I don't play chess but I am interested in the question of how complexity emerges from simplicity. Here are some notes I prepared while reading chess books and which may be useful for a novice: