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 email@example.com
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: firstname.lastname@example.org) prior to the announced seminar.
Seminars in our group are structured into two types of talks:
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.
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
Construction of disease networks and identification of common regulatory molecules in selected acute inflammatory indications.
Models - The third dimension of the sciences - Prof. Bernhard Thalheim
Models have become a universal tool in almost all sciences, in technology and also in normal life. For example, computer science cannot do without models in constructing or in explaining and describing systems or in teaching. Modeling is often done as a craft and seems a long way off to have a scientific basis. Models are instruments that fulfill certain functions in scenarios. Therefore they stand independently between data / observations / situations and theories. In an initiative lasting for almost a decade, a discussion forum about all faculties of the CAU together with partners - such as from Rostock – developed a model concept that does not resort to phenomena, but treats models as an independent research subject. In this talk, I will introduce the developed approach to the model concept, to the art and science of the models, to the modeling as a well-founded technique in both development and also when using models and modeling as systematic work towards a culture. Illustrative examples are models from the field of databases, business processes and archeology.
Disease specific network reconstruction from GWAS data
Protein and Gene interaction Networks are an integral part of Systems Biology today. Techniques like RNA sequencing and GWAS helps us to identify important genes and proteins relevant to a specific disease. The challenge is to extract important protein and gene identifiers from the Human interactome and create a network out of their interactions that is specific to a disease. We will explore how to create such a network using Cytoscape.
Research on Circadian Rhythms in mRNA Expression: Contributions from Mathematical Modeling and Data Analysis. - Dr. Pål Westermark
In animals, the biological circadian clock generates rhythms with a period of ~24 hours that synchronize to the ambient daily light-dark cycles. Genetic feedback loops in single cells are the primary generator of these rhythms, but they are also observable at the tissue and organ level, as well as in behavior. Thousands of genes in many cell types exhibit circadian rhythms in their expression: this is the clock output. Central questions include which cellular processes are affected by circadian gene expression, as well as whether there are underlying principles for circadian control of cellular pathways. We will give examples from our research activities in the study of the clock output in cells from various tissues in mice with focus on mRNA expression and statistics to investigate clock-controlled processes. We also discuss changes in circadian gene expression due to aging, their consequences and how to detect them. We will further give an example of how mathematical analysis helped us uncover some principles for circadian orchestration of metabolic pathways.
Functional Characterization of lncRNAs - David Brauer
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.
, 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.
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)
Causality vs. correlation: how to infer stem cell decision making and gene regulation from time lapse microscopy data
Prof. Julio Vera-González
A comprehensive network on macrophage regulations
SYSTERACT: Systematic Rebuilding of Actinomycetes for Natural Product Formation
Björn Anderson (Lübeck)
Safe and Dynamic Networking in Operating Room and Hospital
Summer semester 2016
Practices for drawing biological networks using the SBGN standard
Investigation of toxicity profile of various combustion aerosols by integrative network approaches
Improve the visualization of differences between model versions
Label-free analysis for high-throughput imaging flow cytometry using machine learning
COLLAR - Current status of microarray gene expression analysis
A Summary of the IdaMo Summer School
Next Generation Sequencing Data Analysis to Reveal Structural DNA Variations
Cyber-Physical-Systems - Characteristics Analysis
The Semantic Lancet Project: a Linked Open Dataset for Scholarly Publishing
Dispositions in the Lifesciences
Systems Biology of E2F Signalling in Tumor Progression and Metastasis
Basics in layouting e-books with Adobe InDesign
Winter semester 2015/2016
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.
eQTL: intertwining disease decomposition and drug repositioning
A consensus-based approach to identify networks underlying DNA damage responses using microarrays
Steffen Moller & Mohamed Hamed
Integrative computational approaches for studying complex diseases
Understanding bone tissue - How do small cells organise large structures?
Modeling and simulation of chronic myeloid leukemia using causal Bayesian networks
Creating a Habitat for Computational Biological Models
Prof. Olaf Wolkenhauer
Muhammad Ali and the Principle of Life: Modelling Whole-Part Relationships in Living Systems
Mathematical modelling of brain energy metabolism reveals Alzheimer's-specific shape alterations in the BOLD function
Hybrid stochastic simulation for multi-scale and multi-level models
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.
Integration of multi-omics and chemometric data to acess the impact of aerosols exposure
Modeling Bone-Remodeling. The Influence of Microcracks
Modelling metabolic markers of dementia
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
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
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?
Pathway-based Prediction of Dynamics in Cancer Cell Populations
M2CAT: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit