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, stochastic processes and category theory. The results of my work support basic biological and medical research.

Profil auf Deutsch; Profile in English

Projects

Research Projects

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).

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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.

 

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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.

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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.

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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.

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SYSTERACT: Systematic Rebuilding of Actinomycetes for Natural Product Formation

The main objective of the SYSTERACT project is through an integrated and interdisciplinary approach to develop the model actinomycete Streptomyces coelicolor into a "Superhost" for the efficient heterologous production of bioactive compounds, enabling a faster discovery of new antibiotics from environmental microbial resources (microbial strains and metagenomes). Central to this approach will be an iterative Systems Biology process, combining microbiology, genetics, biochemistry, and fermentation technology with modelling.

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A systems methodology to assess the risk of tumor relapse in melanoma by the profiling of plasma extracellular vesicles - 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.

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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.

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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

Services

My academic work includes various advisory functions to ministries, research institutions, award committees and a wide range of funding bodies in Germany, Europe and across the world. Over the years, I have coordinated several research consortia in the UK, Germany and for the European Commission.

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 a one day course on Science Communication through which I share my experience as an academic. The course has been booked by various universities and institutes as part of their doctoral and postdoctoral training programmes.

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 but most university degrees and PhD programmes provide no or very limited training in science communication.

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. The concept is not specific to a particular field and is well suited for researchers and students in the engineering, biomedical, biological, medical and physical sciences.

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: