Current Research in Systems Biology and Bioinformatics

Seminars are normally presented on TUESDAYs at 13:00 in Ulmenstr. 69, Building 3 (Haus 3), Room 410 (SR410). Be aware that we choose fitting dates for our guest speakers. Seminars are a mix of presentations from PhD students and academic visitors. If you are willing to attend the research seminar from outside Rostock, please contact Tom Gebhardt (Tel.: 0381-498-7575; Email: prior to the announced seminar.

Seminars in our group are structured into two types of talks:

  • Research Presentation

Members and students of our research group present their work and the talk is strictly limited to 20 minute presentation plus 10 minute discussion. A typical structure for the presentation should follow the outline: What's the context? What's the question asked? Why is it exciting? What has been done? What are the results, conclusions and achievements.

  • Research Discussion

The aim of this kind of talk is to stir up discussions about a topic of interest, not necessarily limited to a certain project. The talk is limited to 10 minutes only with up to 30 minutes for discussion and debate.
For more information concerned by the speakers, please see here.

* t.b.a. = to be announced

Summer semester 2018

Tom Gebhardt


Dr. Suchi Smita


Andrea Bagnacani


Dr. Shailendra Gupta


, Ulmencampus, Haus 3, Raum 410

Prof. Bernhard Thalheim


Saptarshi Bej


Dr. Pål Westermark


David Brauer


Martin Scharm


Identifying White Blood Cells using Machine Learning - Mariam Nassar

Identifying the number of different white blood cells (WBC) in human blood is an established clinical routine, where WBC are labeled with fluorescent markers.
A novel approach based on machine learning will be presented, where WBC are identified label-free, i.e., without any markers.
We developed an open-source workflow that seamlessly connects the recorded images from the instruments with machine learning. The goal is a presentation of the results relevant for clinicians.
This enables fast, cheap and highly accurate identification of WBC, without destroying the cells and leaves marker channels free to answer other biological questions.

, Ulmencampus, Haus 3, Raum 410

Computer Simulation of the Metastatic Progression and Treatment Interventions - Bertin Hoffmann

Growth and spreading behaviour of tumours and metastases are still subject of intensive research regarding the most effective treatment intervention in individual cases. It is difficult to evaluate experimental data regarding different treatment strategies and its individual characteristics for their clinical relevance. Our collaboration developed a computer model which allows a quantitative comparison of effects of treatment interventions with clinical and experimental data.

The computer model is based on a discrete event simulation protocol. Analytical functions describe the growth of primary tumour and distant metastases, a rate function models the intravasation events of the primary tumour and its metastases. Events describe the behaviour of the emitted malignant cells until the formation of new metastases.

We analysed data from experiments with untreated groups of mice from human small cell lung cancer lines OH-1 and extracted information about the growing and spreading behaviour. On this basis we modelled experimental data from groups of mice, which were treated with chemotherapy and radiation therapy. Our results reveal that the fractal dimension of the primary tumour vasculature changes during treatment. That indicates that the therapy affects the blood vessels’ geometry. We proved that by quantitative histological analysis showing that the blood vessel density is depleted during treatment.

, Ulmencampus, Haus 3, Raum 410

A SNP calling workflow for the analysis of RNA-Sequencing data

Markus Wolfien will give a brief introduction about the GATK4 Single Nucleotide Variant (SNP) caller and will show a detailed workflow for the analysis of RNA-Sequencing datasets.

Faiz Khan


, Ulmencampus, Haus 3, Raum 410

Can cells cause behaviors of organisms? - Dr. Beate Krickel

Why philosophers think that interlevel-causation is problematic and how we can solve these problems.

Please read the abstract for more information.

, Ulmencampus, Haus 3, Raum 410

Coupled within- to between-host dynamics indicate vaccination-outbreak conflicts in a viral infectious disease - Dr. Alexis Almocera

The complex processes governing an infectious disease remain an incomplete but significant area in systems medicine. Problems on the emerging dynamics at the interface of viral replication and transmission motivate the analysis of multiscale models, especially from a mathematical standpoint. A coupled system, which comprises ordinary differential equations, links within- and between-host scales by means of disease-induced transmission. Bifurcation analysis captures the dynamical relationship between the two scales by evaluating the predicted epidemic size as a function of viral replication. The analysis further suggests that conflicts can arise between effective vaccination and outbreak prevention.

, Ulmencampus, Haus 3, Raum 410

Translating molecular activity into multidimensional waves - Dr. Patrick Schopohl

If you like to prepare yourself for this short notice seminar, please have a look at the this or this documentary.


Construction and analysis of Molecular Interaction Map(MIM) for Colorectal Cancer(CRC)

Winter semester 2017/2018

, Ulmencampus, Haus 3, Raum 410

Deep Learning in Biology for Next Generation Sequencing Data - DeepBioSeq

Dr. Holger Henning and Markus Wolfien

DeepBioSeq - Deep Learning in Biology for Next Generation Sequencing Data


, Ulmencampus, Haus 3, Raum 410

Argyris Arnellos

Short text


Summer semester 2017

Prof. Julio Vera-González (University of Erlangen-Nürnberg)

Surfing oceans of data in Neurobiology with networks and mathematical modelling. The case of oligodendrocytes


Dr. Anu Jauhan

Systems Pharmacology for Drug Discovery and Development: Paradigm Shift or Flash in the Pan?


Andrea Bagnacani

Towards automating and publishing reusable workflow analyses in Galaxy.

Markus Wolfien

Customized workflow development and omics data integration concepts in Systems Medicine.

Shailendra Gupta

Identification of molecular signatures and therapeutic targets underlying E2F1 mediated epithelial to mesenchymal transition

Ali Salehzadeh-Yazdi

Metabolic Modelling (Applications & Challenges)

Holger Hennig

Deepometry: Workflow for applying deep learning in bioimaging analysis

Matti Hoch

Bachelor thesis - practice session

Etienne Rolland

Internship: Extension of the TriplexRNA, Workflow to construct a circular RNA to upregulate pathways of interest

Dr. Olga Krebs (HITS)

Karrierewege für Informatiker in den Lebenswissenschaften

Prof. Béatrice Desvergne & Prof. Olaf Wolkenhauer

Modelling of human metabolism


Are you interested in giving a talk at our research seminar? Please contact Tom Gebhardt (


Are you interested in giving a talk at our research seminar? Please contact Tom Gebhardt (

Winter semester 2016/2017

Tom Theile

spatio-temporal modeling

Markus Wolfien

Customized workflow development with Galaxy

Anton Kulaga

Gene circuits modelling with KAPPA rule based language

Holger Hennig

Causality vs. correlation: how to infer stem cell decision making and gene regulation from time lapse microscopy data

Sherry Freiesleben


Prof. Julio Vera-González

A comprehensive network on macrophage regulations

Ali Salehzadeh-Yazdi

SYSTERACT: Systematic Rebuilding of Actinomycetes for Natural Product Formation

Björn Anderson (Lübeck)

Safe and Dynamic Networking in Operating Room and Hospital

Summer semester 2016

Andrea Bagnacani


Vasundra Toure

Practices for drawing biological networks using the SBGN standard

Suchi Smita

Investigation of toxicity profile of various combustion aerosols by integrative network approaches

Tom Gebhardt

Improve the visualization of differences between model versions

Holger Hennig

Label-free analysis for high-throughput imaging flow cytometry using machine learning

Sherry Freiesleben

COLLAR - Current status of microarray gene expression analysis

Birgit Berger

A Summary of the IdaMo Summer School

Markus Wolfien

Next Generation Sequencing Data Analysis to Reveal Structural DNA Variations

Tobias Plewka

Cyber-Physical-Systems - Characteristics Analysis

Andrea Bagnacani

The Semantic Lancet Project: a Linked Open Dataset for Scholarly Publishing

Adrien Barton

Dispositions in the Lifesciences

Shailendra Gupta

Systems Biology of E2F Signalling in Tumor Progression and Metastasis

Fritz Beise

Basics in layouting e-books with Adobe InDesign

Winter semester 2015/2016

Steffen Möller

Title:- "eQTL: intertwining disease decomposition and drug repositioning" Expression QTL (eQTL) further annotate disease-associated genetic loci with co-observed changes in the transcriptome. With drugs selected to compensate the disturbance caused for single loci, for a genotyped patient of a multifactorial disease one may derive a recipe for a drug cocktail. This presentation reviews resources available today and emergent algorithms, exemplified on murine data for experimental autoimmune encephalomyelitis, a mouse model for neuroinflammation.

Steffen Möller

eQTL: intertwining disease decomposition and drug repositioning

Martin Scharm


Sherry Freiesleben

A consensus-based approach to identify networks underlying DNA damage responses using microarrays

Steffen Moller & Mohamed Hamed

Integrative computational approaches for studying complex diseases

Tom Theile

Understanding bone tissue - How do small cells organise large structures?

Daniel Koch

Modeling and simulation of chronic myeloid leukemia using causal Bayesian networks

Ron Henkel

Creating a Habitat for Computational Biological Models

Prof. Olaf Wolkenhauer

Muhammad Ali and the Principle of Life: Modelling Whole-Part Relationships in Living Systems

Felix Winter

Mathematical modelling of brain energy metabolism reveals Alzheimer's-specific shape alterations in the BOLD function

Florian Wendland

Hybrid stochastic simulation for multi-scale and multi-level models

Markus Wolfien

New insights into the regulation of the heart rate at the molecular and meta-level

Summer semester 2015

Prof. Dr. Blagoj Ristevski (St. Kliment Ohridski University - Bitola)

Reverse Engineering of Micro-RNA Mediated and Gene Regulatory Networks and Netwoks Properties.

Suchi Smita

Integration of multi-omics and chemometric data to acess the impact of aerosols exposure

Tom Theile

Modeling Bone-Remodeling. The Influence of Microcracks

Felix Winter

Modelling metabolic markers of dementia

Markus Wolfien

Automated NGS data analysis and evaluation

Prof Dr Ralf Schnabel (Head of the Institute for GeneticsTechnical University Braunschweig)

Phainothea:Creation of form by cell focussing in the C. elegans embryo

Dr. Dagmar Waltemath

Notions of similarity for systems biology models

Muhammad Haseeb

Mathematical Modeling of Crosstalk between Wnt Signaling and Cell Cycle Pathways

Aakash Chavan Ravindranath

Data integration and modelling techniques to study protein and compound activity towards drug discovery

Ulf Schmitz

An investigation of microRNA target regulation mechanisms - rehearsal for PhD defence

Dr. Alberto de la Fuente (From Leibniz Institute for Farm Animal Biology (FBN) Dummersdorf)

Silence on the relevant literature and errors in implementation?

Florian Wendland

Pathway-based Prediction of Dynamics in Cancer Cell Populations

Martin Scharm

M2CAT: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit

Winter semester 2014/2015

Dagmar Waltemath

Coming soon: de.NBI and SBGN-ED

Dr. Michael Linnenbacher

HRO collection as tools for individual cancer network biology.

Faiz M. Khan and Stephan Marquardt

Unraveling the regulatory core of E2F1-mediated tumor aggressiveness using integrated network analysis methods

Murali Chodisetti

Next-Generation Sequencing in Acute Lymphoblastic Leukemia

Raheleh Amirkhah

Prediction of miRNA targets in colorectal cancer using machine learning method

Dr. Sonja Strunz

Gene Co-Expression Networks Reflecting the Transcriptional Responses to Radiation Exposure

Tom Theile

Modeling Bone Growth Using Agent-based-Simulations - Understanding the role of Osteocytes

Dr. Johannes Wollbold

Formal concept analysis methods for systems biology: representing knowledge, analyzing and validating models

Prof. M.J. Bottema

Spatio-Temporal Structure of Cancellous Bone

Markus Wolfien

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

Summer semester 2014

, room 410

Dr. Johaness Wollbold

Constructing a knowledge base for the Free Radical Theory of Ageing

Prof. Maureen O'Malley (University of Sydney)

What has philosophy to do with systems biology, and what has systems biology to do with philosophy?

Sonja Strunz (PhD Defence Rehearsal)

Transcriptional Responses to Radiation Exposure Facilitate the Discovery of Biomarkers Functioning as Radiation Biodosimeters


Winter semester 2013/2014

Markus Wolfien (Student in SEMS project)

Standardising Karr's Whole Cell Model

Prof. Dr. rer. nat. Robert David (Reference and Translation Center for Cardiac Stem Cell Therapy (RTC) Rostock)

Cardiac Cell Types from Stem Cells.

Siavash Ghavami

Accounting for randomness in measurement and sampling of cancer cell population dynamics

Dr. Katja Rateitschak

Pancreatic cancer reloaded

Sherry Freiesleben

Identification of microRNA networks in multiple sclerosis

Daniel Arend

Long-Term Preservation and Management of Scientific Primary Data

Bingquan Bao (Master defence)

Multi-scale hybrid model of biological system used as predictors of anti-caner therapy outcoume

Summer semester 2013

Noman al Hassan (Master defence)

Identification and analysis of putatively cooperating microRNAs

Mustafa Baig Mirza (Master defence)

Extending the multi-valued logic approach for modeling biochemical reaction networks

Tim Kacprowski (Ernst-Moritz-Arndt-Universität Greifswald Interfakultäres Institut für Genetik und Funktionelle Genomforschung)

Ranking Molecules - from Disease Gene Prioritization to Omics Data Analyses

Dr. Georg Homuth (Ernst-Moritz-Arndt-Universität Greifswald Interfakultäres Institut für Genetik und Funktionelle Genomforschung)

Whole-Blood Transcriptome Profiling of Population-based Cohorts Reveals Major Gene Expression Changes Correlated with Body Mass Index

Sherry Freiesleben

Investigation of microRNA expression in multiple sclerosis

, Building 1, Room 126

Peter Nonnenmann (FIAS)

Ellerman's heteromorphic adjoint functors & Wolkenhauer's tissue organization

Yang Du

BiomvRCNS: copy number study and segmentation for multivariate biological data