SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
+49 381 498-7571
olaf.wolkenhauer@uni-rostock.de
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.
Projects
Research Projects
A platform for trimming and extracting genome-scale metabolic models (GEMs)
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.
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.
The AIR is to provide an interactive platform connecting scientific and medical communities.
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.
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).
~ 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.
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 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 |
Services
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 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
- "Auf der Suche nach Regeln und Ausnahmen" an essay about the interaction of cells within a larger group of cells was published in the Laborjournal (in German)
- Interview for systembiologie.de (pdf)
- Interview for the Systems Medicine Web Hub (pdf)
- Interview for the BMBF (in German) (pdf)
- An autobiographical article describing my path from engineering to biomedicine (IET Systems Biology, 2014)
- An essay (in German) on my origins in northern Germany and a book (published with Quickborn, Hamburg) I have written in "Plattdeutsch" - a language of northern Germany, spoken by a tiny minority along the coasts of the north and baltic seas. See also this newspaper article for a description 'op platt' (Kieler Nachrichten, 16. November 2012).
- Some "philosophical" musings on systems theory and systems biology can be found in an interview with The Reasoner, Vol. 5, Nr. 9, September 2011.
- A science policy briefing on Systems Biology for Medical Applications that I prepared for the European Science Foundation (see also Advancing systems biology for medical applications).
- In remembrance of Allan Muir.
- Collection of some of my favorite quotations, aphorisms and thoughts that have motivated and influenced my thinking.
- A review (pdf) of D. Ellerman: Adjoints and emergence: applications of a new theory of adjoint functors. Axiomathes (2007) 17:19-39.
- The Beauty of Mathematics - A Rough Sketch for a Proof (pdf), essay.
- Selbstorganisation: Eine charakterische Eigenschaft lebender Systeme (November 2007): Video, 8 min, 7 mb (wma) oder Pdf-Datei (pdf).
- An article in the Kiteboarding magazine, with my thoughts about surfing and music, describing why and how one can find happiness by living the moment (In German).
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:
- Elektron Music Production Tips
- Graphical representation of Octatrack Concepts
- Graphical representation of the Analog Four Structure
- Graphical representation of the Analog Rytm Sound Architecture
- Graphical representation of Analog Rytm Concepts
- Sheets for note taking with the Analog Rytm
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: