Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Conferences

Rateitschak K, Schmidt S, Carlo AS, Sporbertm A, Lao A, Wolkenhauer O, Willnow T
Mathematical modeling of neurodegenerative processes in alzheimer's diesease

First status seminar of the Helmholtz alliance on systems biology, Potsdam, June 2008

Willnow T, Schmidt V, Lao A, Rateitschak K, Wolkenhauer O
Protein networks controlling amyloidogenic processing

Second status seminar and meeting of the advisory board of the Helmholtz Alliance on Systems Biology, DKFZ, Heidelberg, Germany, 26.10.-27.10.2009

Liebal U, Millat T, Marles-Wright J, Lewis R, Wolkenhauer O
Protein diversity of the stressosome - Stress sensitivity and Response magnitude

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim (Germany), 28 August - 1 September 2011

Kossow C, Jose D, Jaster R, Wolkenhauer O, Rateitschak K
Mathematical modelling points out regulatory mechanisms of interferon-gamma induced STAT1 serine phosphorylation and MUC4 expression in pancreatic cancer cells

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim (Germany), 28 August - 1 September 2011

Millat T, Haus S, Wolkenhauer O, Fischer RJ, Janssen H, Bahl H, Jabari S, King J
Modelling the pH-dependent metabolic shift in Clostridum acetobutylicum

11th International Conference on Systems Biology (ICSB), Edinburgh (UK), 10 October - 15 October 2010

Simone Frey, Kristin Sott, Maria Smedh, Thomas Millat, Peter Dahl, Olaf Wolkenhauer, Mattias Goksör
A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in S. cerevisiae

11th International Conference on Systems Biology (ICSB), Edinburgh (UK), 10-15 October 2010

Schmitz Y, Wolkenhauer O, Rateitschak K
Mathematical modelling of nucleo-cytoplasmic shuttling of beta-catenin and its antagonist APC

11th International Conference on Systems Biology (ICSB), Edinburgh (GB), 10-15 October 2010

Garcia-Salcedo R, Frey S, Beltran G, Bosch D, Elbing K, Tian Y, Manchala S, Rateitschak K, Wolkenhauer O, Hohmann S
Quantitative analysis of the SNF1-pathway in Saccharomyces cerevisiae

35thFEBS Congress 2010, Göteborg (Gothenburg), Sweden. June 26 - July 1, 2010

Wolkenhauer O, Shibata D, Mesarovic MD
A stem cell niche dominance theorem

(PGSSCR 2010-O-057) 010 Vol. 6 (2): p36 JSRM Code: 006020700063

Schmitz U, Bhattacharya A, Gupta S, Schultz J, Kunz M, Wolkenhauer O
MicroRNAs in malignant melanoma progression

German Conference on Bioinformatics, Braunschweig, Germany, 2010

Rateitschak K, Lange F, Fitzner B, Wolkenhauer O, Jaster R
Interferon gamma stimulated STAT1 signalling in pancreatic stellate cells: From experimental data to mathematical models

Conference on Systems Biology of Mammalian Cells-SBMC2010, Freiburg, Germany, 3-5 June 2010

Rateitschak K, Lange F, Fitzner B, Wolkenhauer O, Jaster R
Interferon gamma stimulated STAT1 signalling in pancreatic stellate cells: From experimental data to mathematical models

11th International Conference on Systems Biology, Edinburgh, UK, 10.10.-15.10.2010

Rateitschak K, Lange F, Fitzner B, Wolkenhauer O, Jaster R
Interferon gamma stimulated STAT1 signalling in pancreatic stellate cells: From experimental data to mathematical models, Workshop "Modelling in BioMedicine"

11th International Conference on Systems Biology, Edinburgh, UK, 10.10.-15.10.2010

Schmidt V, Lao A, Rateitschak K, Wolkenhauer O, Willnow T
Mathematical modelling of APP processing influenced by SORLA in Alzheimer's disease

Honolulu Hawaii, 10.07-15.07.2010

Garcia-Salcedo R, Frey S, Beltran G, Bosch D, Elbing K, Tian Y, Manchala S, Rateitschak K, Wolkenhauer O, Hohmann S
Quantitative analysis of the SNF1-pathway in Saccharomyces cerevisiae

35thFEBS Congress 2010, Göteborg (Gothenburg), Sweden. June 26 - July 1, 2010

Lai X, Vera J, Wolkenhauer O
Modeling miRNA regulation in signaling networks: miR-34a regulation of p53/Sirt1 module

Conference on Systems Biology of Mammalian Cells-SBMC2010, Freiburg, Germany, 3-5 June 2010

Raasch P, Schmitz U, Patenge N, Vera J, Kreikemeyer B, Wolkenhauer O
Local Genomic Properties as Indicators of Functional Elements

3. Gemeinsame Tagung der DGHM und der VAAM, Hannover, Germany, 28.03.-31.03.2010

Lao A, Schmidt V, Rateitschak K, Wolkenhauer O, Willnow T
Mathematical modelling of APP processing influenced by SORLA in Alzheimer's disease

Mid-term review of the Helmholtz Alliance on Systems Biology, DKFZ, Heidelberg, Germany, 13.01.-14.01.2010

Lange F, Fitzner B, Jaster R, Karger A, Wolkenhauer O, Rateitschak K
Charakterisierung intrazellulärer Signalwege in pankreatischen Sternzellen mit Hilfe mathematischer Modellierung

30. Jahrestagung des Deutschen Pankreasclub, Heidelberg, Germany, November 2009

Lai X, Nikolov S, Wolkenhauer O, Vera J
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis

The 2009 International Workshop on "Computational and Integrative Biology" (CIB 2009), Hangzhou, China, 18.09.-20.09.2009

Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R
Interferon gamma stimulated Stat1 signaling pathway in pancreatic stellate cells: From experimental data to mathematical models

4. ESCEC Symposium, Rüdesheim, Germany, 09.2009

Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R
Interferon gamma stimulated Stat1 signaling pathway in pancreatic stellate cells: From experimental data to mathematical models

Transatlantic Summer School Cancer Systems Biology, Rostock, Germany, June 2009

Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R
Interferon gamma stimulated Stat1 signaling pathway in pancreatic stellate cells: From experimental data to mathematical models

German Symposium on Systems Biology, Heidelberg, Germany, May 2009

Willnow T, Schmidt V, Lao A, Rateitschak K, Wolkenhauer O
Protein networks controlling amyloidogenic processing

Second status seminar and meeting of the advisory board of the Helmholtz Alliance on Systems Biology, DKFZ, Heidelberg, Germany, 26.10.-27.10.2009

Haus S, Jabbari S, Millat T, Wolkenhauer O, King JR
The Effect of pH on the Metabolic Shift in AB Fermentation in Clostridium acetobutylicum

10th International Conference on Systems Biology (ICSB), Stanford (USA), 30 August - 4 September 2009

Liebal U, Kim JR, Wolkenhauer O, Cho KH
Dynamic Behavior Determines the Design Strategy of Metabolic Regulation Networks

10th International Conference on Systems Biology, Stanford, USA, 30.8.-4.09.2009

Lao A, Schmidt V, Rateitschak K, Willnow T, Wolkenhauer O
Mathematical modelling of APP processing influenced by SORLA in Alzheimer's disease

Spring school 2009 on Systems Biology, Kloster Seeon, Germany, 06.04.-09.04.2009

Wolkenhauer O, Lao A, Omholt S, Martens H
Systems Approaches in Molecular and Cell Biology: Making Sense out of Data; Providing Meaning to Models

Independent Component Analysis, Wavelets, Neural Networks, Biosystems and Nanoengineering VII, Orlando, USA, 13.04.2009;
DOI: 10.1117/12.822742 ... More

Rateitschak K, Wolkenhauer O
Thresholds in transient dynamics of signal transduction pathways

Cancer workshop, University of Nottingham, Nottingham, UK, January 2008

Rateitschak K, Schmidt V, Carlo AS, Sporbertm A, Lao A, Wolkenhauer O, Willnow T
Mathematical modeling of neurodegenerative processes in alzheimer's diesease

First status seminar of the Helmholtz alliance on systems biology. Potsdam, Germany, June 2008

Rateitschak K, Karger A, Fitzner B, Wolkenhauer O, Jaster R
Nonlinear dynamics of biochemical networks in pancreatic cancer: From experimental data to mathematical models

First FORSYS symposium. Berlin, Germany, June 2008

Schmitz Y, Bader BM, Weiss DG, Wolkenhauer O, Rateitschak K
Elucidating the role of nucleo-cytoplasmic shuttling of beta-catenin antagonists by mathematical modelling

Summer School on Systems Biology for Medical Applications, Tenerife, Spain, 30.09.-02.10.2008

Karger A, Rateitschak K, Fitzner B, Wolkenhauer O, Jaster R
Threshold properties of Interferon-gamma stimulated Jak2-Stat1 signaling in pancreatic stellate cells: From experimental data to mathematical models

2nd International workshop on systems biology, Hamilton, Ireland, August 2008

Winter F, Krohn M, Lange C, Wolkenhauer O, Rateitschak K, Pahnke J
A power-law model to describe the aggregation of Beta-Amyloid and its transport across the Blood-Brain barrier based on quantitative data from Alzheimer mouse models

2nd International workshop on systems biology, Hamilton, Ireland, August 2008

Lai X, Liebal U, Nikolov S, Wolkenhauer O, Vera J
Use of sensitivity analysis to detect critical biochemical processes in a mathematical model linking intracellular and cell population dynamics in erythropoiesis

The 6th Conference on Computational Methods in Systems Biology (CMSB), Rostock-Warnemünde, Germany, October 2008

Frey S, Schmidt H, Rateitschak K, Beltran G, Garcia-Salcedo R, Elbing K, Bosch D, Ye T, Hohmann S, Wolkenhauer O
Modelling Snf1 regulation in Saccharomyces cerevisiae

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Bittig A, Carling D, Wolkenhauer O
A Mathematical Model of the Regulation of AMPK Activation

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Schmidt H
Hierarchical Modelling of Metabolism: From Methodology to Application

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Egea JA, Schmidt H, Banga JR
A new tool for parameter estimation in nonlinear dynamic biological systems using global optimization

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Liebal U, Schmidt H
Sensitivity Analysis based Adaptive Search-Space Reduction for Parameter Estimation Applications

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Bittig A, Schmidt H
Format Overflow? Handling of Modeling Projects in Systems Biology

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Dell'Orco D, Fanelli F, Schmidt H
Dynamic modeling of phototransduction biochemistry in vertebrate rods: from dark/light adaptation to disease

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Wolkenhauer, O, Vera J
Computational Systems Biology of Cell Signalling - COSBICS

9th International Conference on Systems Biology,Göteborg (Gothenburg), Sweden, August 2008

Bader BM, Schmitz Y, Redlich B, Rateitschak K, Wolkenhauer O, Weiss DG
Quantitative 3D image analysis to study the beta-catenin translocation during differentiation of human neural progenitor cells

2nd International Congress on Stem Cells and Tissue Formation, Dresden, Germany, July 2008

Rateitschak K, Wolkenhauer O
Thresholds in transient dynamics of signal transduction pathways

Joint Receptor Tyrosine Kinase (RTK) Consortium & British Society for Proteome Research/European Bioinformatics Institute Workshop, Hinxton Hall Conference Centre Cambridge, UK, 23-24 July 2007

Wolkenhauer O, Bittig A, Hofmeyr J
A principal limitation of virtual cell simulations using differential equation models

Winter Simulation Conference (WSC '06), December 2006

Frey S, Millat T, Rateitschak K, Wolkenhauer O
Quantitative measures to characterize properties of signal transduction pathways

Winter Simulation Conference (WSC '06), December 2006

Rateitschak K, Wolkenhauer O
Tresholds in transient dynamics of signal transduction pathways

Proc. ICSB 2006, Yokohama (Japan), 2006

Bachmann J, Fleck C, Maiwald T, Vera J, Wolkenhauer O, Timmer J, Klingmüller U
Modelling of negative feedback loops regulating the JAK2/STAT5 signal transduction pathway

Proc. ICSB 2006, Yokohama, Japan, 2006

Vera J, Bachmann J, Pfeifer A, Hormiga JA, Torres Darias NV, Klingmüller U, Wolkenhauer O
A power-law model with delay to describe the dynamic behaviour of Jak2-Stat5 pathway: from the modelling strategy to the analysis of the properties

1st International Symposium on Systems Biology: From genomes to in silico and back. Murcia, Spain, June 2006

Gleim R, Mehler A, Dehmer M
Web Corpus Mining by Instance of Wikipedia, to appear

Proceedings of the EACL 2006 Workshop on Web as Corpus, Trento, Italy, 03.04.-07.04.2006

Assmus H, Wolkenhauer O
Huntingtin and its Interaction Network: A Computer Model

Bmb+f NGFN II conference, Bonn, Germany, November 2005

Wolkenhauer O
A Pledge for more theory in cell signalling experiments: when fishing for drug targets is not sufficient

Ernst Schering Foundation Workshop "Systems Biology - Applications and Perspectives". Berkeley, USA, November 2005

Rateitschak K, Wolkenhauer O
Steady state - limit cycle - steady state transitions in gene transcription networks with distributed time delay

International Conference for Systems Biology (ICSB), Boston, USA, October 2005

Wolkenhauer O
What is required for a successful molecular fishing expedition?

2nd ESF Functional Genomics and Disease Conference, Oslo, Sweden, September 2005

Wolkenhauer O
The Systems in Systems Biology

2nd Systems Biology conference, Maynooth, Ireland, August 2005

Wellstead P, Mason O, O'Connor WT, Cho KH, Bullinger E, Wolkenhauer O, Duncan S
Towards a Systems Understanding of the Cerebral Motor Circuit

Foundations of Systems Biology and Engineering (FOSBE), UCSB, August 2005

Mesarovic M, Sreenath SN, Wolkenhauer O
Multilevel, hierarchical systems paradigm of Systems Biology

Foundations of Systems Biology and Engineering (FOSBE), UCSB, August 2005

Soebiyanto RP, Sreenath SN, Mesarovic MD, Wolkenhauer O
From Networks to Systems to Complex Systems: A Signaling Pathway Coordination Case Study

44th IEEE Conference on Decision and Control and European Control Conference ECC 2005, Seville, Spain, 12-15 December 2005

Vogl C, Sanchez-Cabo F, Stocker G, Hubbard S, Wolkenhauer O, Trajanoski Z
A fully Bayesian model to cluster gene expression profiles

ECC05

Wolkenhauer O
There is nothing more practical than a good theory

Complexity, Stellenbosch, South Africa, June 2005

Wolkenhauer O, Ullah M
The Role of Theory, Modelling and Simulation in Systems Biology

Towards a Philosophy of Systems Biology, Amsterdam, Netherlands, May 2005

Millat T, Wolkenhauer O
Assumptions in Dynamic Modelling of Biochemical Networks and their Consequences

FEBS Systems Biology Workshop, Gosau, Austria, March 2005

Wolkenhauer O, Ullah M
The role of feedback in the control and regulation of intracellular networks

Biochemical Society, Sheffield, UK, January 2005

Möller-Levet CS, Yin H, Cho KH, Wolkenhauer O
Modelling gene expression time-series with radial basis function neural networks

IEEE Int. Conf. on Neural Networks. Conf. Proc. 2, 1191-1195, 2004

Kutalik Z, Razaz M, Inwald J, Gordon SV, Wolkenhauer O
A novel statistical approach in comparative genomics to reveal new immunogenic antigens in M. Bovis

1st International Conference on Basic and Clinical Immunogenomics, Budapest, Hungary, 03-07 October 2004

Cho KH, Shin SY, Kolch W, Wolkenhauer O
Modeling and Analysis of Two Feedback Loop Dynamics in Ras/Raf-1/MEK/ERK Signaling Pathway

International Conference on Systems Biology (ICSB) 2004, Heidelberg, Germany, October 2004

Cho KH, Johansson KH, Wolkenhauer O
A System-Theoretic Modeling Framework for Cellular Processes

International Conference on Systems Biology (ICSB) 2004, Heidelberg, Germany, October 2004

Ullah M, Cho KH, Kolch W, Wolkenhauer O
Choosing an appropriate modelling framework: How deterministic are random processes?

International Conference on Systems Biology (ICSB) 2004, Heidelberg, Germany, October 2004

Sanchez-Cabo F, Hackl H, Hubbard S, Stocker G, Trajanoski Z, Wolkenhauer O, Vogl C
A Fully Bayesian Model to Cluster Gene Expression Profiles

Intelligent Systems in Molecular Biology (ISMB), July 2004

Wolkenhauer O
Dynamic Pathway Modelling

Proceeding of the Sixteenth International Symposium on Mathematical Theory of Networks and Systems (MTNS), July 2004

Wolkenhauer O, Kolch W, Cho KH
Dynamic Pathway Modelling: from models to cells

Proceeding of the 3rd Workshop on Computation of Biochemical Pathways and Genetic Networks. 6-7 October 2003

Cho KH, Shin SY, Kolch W, Wolkenhauer O
Mathematical Modeling of Ras/Raf-1/MEK/ERK Signal Pathway: Qualitative Analysis of the Positive Feedback Mechanism

ICSB2003, St. Louis, USA

Möller-Levet C, Klawonn F, Cho KH, Wolkenhauer O
Fuzzy clustering of short time series and unevenly distributed sampling points

IDA'2003, August 2003

Sanchez-Cabo F, Trajanoski Z, Cho KH, Wolkenhauer O
A Graphical User Interface to Normalize Microarray Data

DSC'2003, March 2003

Cho KH, Shin SY, Lee HW, Wolkenhauer O
Investigations in the Analysis and Modelling of the TNFalpha Mediated NF-kappaB Signaling Pathway

ICSB2002, Stockholm, Sweden, 2002

Cho KH, Shin SY, Lee HW, Wolkenhauer O
Simulation Study of the TNF Mediated NF- B Signaling Pathway

CSMB'2003, LNCS 2602, page 171, Springer Verlag

Cho KH, Cha JH, Wolkenhauer O
How to Synthesize an Optimized Genetic l-Switching System? A System-Theoretic Approach Based on SQP

CSMB'2003, page 170, LNCS 2602, Springer Verlag

Taillefond N, Wolkenhauer O
Fuzzy Clustering and Classification for Automated Leak Detection Systems

IFAC'2002 Proceedings, Barcelona, Spain, 2002

Nunez-Garcia J, Wolkenhauer O
Random Sets and Histograms

Proceedings of the 10th IEEE International Conference on Fuzzy Systems, Vol. 2, Melbourne, Australia, December 2001

Babuska R, Wolkenhauer O
An Introduction to Fuzzy Systems

UK Control 2000, Cambridge, UK, 2000

Babuska R, Wolkenhauer O
Fuzzy Systems Identification and Control

UK Control 2000, Cambridge, UK, 2000

Wolkenhauer O, Babuska R
Fuzzy Relational Biology: A Factor-Space Approach to Genome Analysis

Computation in Cells, pages 53-58, April 2000

Wolkenhauer O, Garcia-Sanz M
A Random Sets Statistical Approach to Systems Identification

AIDA'99, pages 388-392, June 1999

Wolkenhauer O, Labib AW
An Adaptable Maintenance Model Using a Fuzzy System and Possibility Theory

EUFIT'98, pages 1570-1573, September 1998

Wolkenhauer O, Edmunds J
Qualitative Uncertainty Models using Random Set Theory

IDA'97, pages 609-620, August 1997

Wolkenhauer O, Edmunds J
Local Uncertainty Models for the Analysis of Time Series Data

EUFIT'97, pages 1774-1778, September 1997

Wolkenhauer O
On the Combination of Probabilistic and Fuzzy Concepts in Signal-based Data Analysis

EUFIT'97, pages 1279-1283, September 1997

2016

M König, A Oellrich, D Waltemath, ... O Wolkenhauer
Challenges and opportunities for system biology standards and tools in medical research

Open Access article in Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, F Loebe, M Boeker, H Herre, L Jansen, D Schober (eds.), Halle, Germany (2016)
URL: http://ceur-ws.org/Vol-1692/paperC.pdf (PDF)

Jaitly T, Schaft N, Doerrie J, Gross S, Schuler-Thurner B, Wolkenhauer O, Schuler G, Taher L, Gupta S, Vera J
An integrative computational framework for personalized detection of tumor epitopes in melanoma immunotherapy

PeerJ Preprints 4:e2385v1
doi.org/10.7287/peerj.preprints.2385v1

M Scharm
Model Management in Systems Biology: Challenges – Approaches – Solutions

A talk in the FAIRDOM webinar series 2016
recordings: fair-dom.org/knowledgehub/webinars-2/martin-scharm/
slides: slideshare.net/binfalse/model-management-in-systems-biology-challenges-approaches-solutions

2015

M Scharm and D Waltemath
Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit

Article in Proceedings of the Workshop on Data management in Life Sciences, BTW, Hamburg (2015)
URL: http://www.btw-2015.de/res/proceedings/Workshops/DMS/Scharm-Extracting_reproducible_sim.pdf (PDF)

2014

M Scharm, F Wendland, M Peters, M Wolfien, T Theile, D Waltemath
The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results.

Open Access demo paper in Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences (2014)
URL: http://ceur-ws.org/Vol-1320/paper_19.pdf
PeerJ Preprint: https://peerj.com/preprints/639/

Wollbold J, Köhling R, Borchmann D
Attribute Exploration with Proper Premises and Incomplete Knowledge Applied to the Free Radical Theory of Ageing

In: Glodeanu C, Kaytoue M, Sacarea C: Formal Concept Analysis. LNCS 8478, Springer 2014, p. 268-283.

M Scharm, O Wolkenhauer, D Waltemath
Identifying, interpreting, and communicating changes in XML-encoded models of biological systems

Demo paper in Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Lisbon, Portugal (2014)
URL: http://dils2014.inesc-id.pt/data/uploads/paper_42.pdf

2013

Schmitz U, Gupta S, Lai X, Vera J, Wolkenhauer O
Predicting targets of synergistic microRNA regulation

German Conference on Bioinformatics 2013, Göttingen.

Bhattacharya A, Schmitz U, Raatz Y, Schönherr M, Kunz M
New candidate oncomiRs for malignant melanoma

International Investigative Dermatology (IID) in Edinburgh, UK

Millat T
Butyrate re-assimilation in C. acetobutylicum re-evaluated using modelling

7th Annual SysMo-Conference, Berlin (Germany), 6 February - 8 February 2013

2012

Christina Kossow
Modelling partners in crime in pancreatic cancer - Application of a cellular automaton model

Talk at Department of Mechanical and Process Engineering, Engineering Faculty, Hochschule Wismar-University of Applied Sciences: Technology, Business and Design, Wismar (Germany), 15.03.2012

Kossow C, Rybacki S, Millat T, Rateitschak K, Uhrmacher AM, Wolkenhauer O
Continuous states on a grid enable an efficient simulation of diffusion in environments with excluded volumes

Biotec Forum ''Bioinformatics and Computational Biology'', Dresden (Germany), 06 December - 07 December 2012

Millat T
Mathematical Modelling of the pH-induced Metabolic Shift in C. acetobutylicum Unravels a Heterogeneous Phase Transition

Clostridium XII, Nothingham (UK), 9 September - 12 September 2012

Lao A, Schmidt V, Schmitz Y, Willnow T, Wolkenhauer O
Multi-compartmental modeling of APP processing influenced by SORLA in Alzheimers disease

13th International Conference on Systems Biology (ICSB), Toronto (Canada), 19 August - 23 August 2012

Lao A, Schmidt V, Schmitz Y, Willnow T, Wolkenhauer O
Regulated Trafficking of APP by SORLA in Alzheimers Disease

Systems Medicine International Conference (SYSMED), Dublin (Ireland), 9 September - 13 September 2012

Lai X, Schmitz U, Vera J, Wolkenhauer O
A systems biology approach to study the cellular function of microRNAs

International Workshop on Small RNA in Cancer, Inflammation, and Aging, Copenhagen (Denmark), September 3 - 4, 2012.

Schmitz U, Lai X, Vera J, Wolkenhauer O
The regulation of microRNA target hubs

International Workshop on Small RNA in Cancer, Inflammation, and Aging, Copenhagen (Denmark), September 3 - 4 , 2012.

R Henkel, N Le Novère, O Wolkenhauer, D Waltemath
Considerations of graph-based concepts to manage computational biology models and associated simulations

Article in Proceedings of the 2012 INFORMATIK  conference, Jahrestagung der GI e.V., Braunschweig (2012).
URL: http://cs.emis.de/LNI/Proceedings/Proceedings208/1545.pdf

Cooper J, Mirams G, Slaymaker M, Simpson A, Vik JO, Waltemath D (2013)
Virtual experiments for reusable models

Proceedings of the 2012 VPH Conference, London.
Access to PDF version through Researchgate (or contact us for further details about the manuscript)

Hundt C, Wendland F (2012)
Efficient Two-Dimensional Pattern Matching with Scaling and Rotation and Higher-Order Interpolation

In: J. Kärkkäinen & J. Stoye (Eds.), Combinatorial Pattern Matching (CPM 2012), LNCS, vol. 7354, pp. 124-137. Heidelberg: Springer.
doi:10.1007/978-3-642-31265-6_10

Lai X, Schulz C, Dolniak B, Wolkenhauer O, Schmeck B, Vera J, Sittka A
The role of micro RNA regulation in the early inflammatory response: miR-146a and NFkB signaling in lung inflammation

Symposium on Remodeling, Repair and Regeneration in Lung Diseases, Marburg (Germany), June 21-23, 2012
Best poster award

Boldt S, Knops K, Kriehuber R, Wolkenhauer O
Identification of gene-based biosignatures for radiation biodosimetry

58. Biometrisches Kolloquium, Berlin (Germany), March 2012

2011

Millat T
The pH-induced metabolic shift from acidogenesis to solventogenesis in Clostridium acetobutylicum

5th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations, Rüdesheim (Germany), 12 September - 16 September 2011

Guebel DV, Schmitz U, Wolkenhauer O, Vera J
Análisis de los fenómenos de adhesión celular en los estadios tempranos de cáncer de colon mediante un modelo de lógica multi-valuada extendida

Facultad de Medicina, Universidad de Buenos Aires, 13-16 September, 2011

 

Winter F, Krohn M, Lange C, Pahnke J, Wolkenhauer O, Rateitschak K
Mathematical modelin of protein aggregation and transport in Alzheimer's disease

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim (Germany), 28 August - 1 September 2011

Schmitz Y, Rateitschak K, Wolkenhauer O
Mathematical modelling of the Wnt pathway: the influence of nucleo-cytoplasmic shuttling of beta-catenin and its antagonists APC, Axin and GSK3

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim (Germany), 28 August - 1 September 2011

Lao A, Schmitz Y, Schmidt V, Rateitschak K, Wolf J, Willnow T, Wolkenhauer O
Mathematical Modeling of APP Processing influenced by SORLA in Alzheimers Disease

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim (Germany), 28 August - 1 September 2011

Lai X, Schmitz U, Gupta S, Kunz M, Wolkenhauer O, Vera J
On the regulation of microRNA target hubs: a Systems Biology perspective

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Lai X, Schulz C, Sittka A, Dolniak B, Wolkenhauer O, Schmeck B and Vera J
The role of micro RNA regulation in the early inflammatory response: miR-146a and NFkB signaling in lung inflammation

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Millat T, Rubenis O, Liebal U, Wolkenhauer O, de Jong I, Kuipers O
Automated analysis of flow cytometry data from heterogeneous bacterial populations

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Liebal UW, Millat T, Marles-Wright J, Lewis R, Wolkenhauer O
Protein Diversity of the Stressosome - Stress Sensitivity and Response Magnitude

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Knops K, Boldt S, Wolkenhauer O, Kriehuber R
Identification of radiation-specific gene expression changes in human PBL after ex vivo irradiation suitable for biodosimetric applications

14th International Congress of Radiation Research, Warschau, 2011

Unverricht-Yeboah M, Boldt S , Giesen U, Pomplun E, Wolkenhauer O, Kriehuber R
Gene expression analysis in Jurkat cells after exposure to I-123-iododeoxyuridine, Gamma-rays and Alpha-particles

14th International Congress of Radiation Research, Warschau, 2011

Pauleweit S, Nebe J B, Wolkenhauer O
Agent-based simulation of molecular processes

SIMULTECH 2011, Noordwijkerhout, Netherlands, July 2011

Bhattacharya A, Schmitz U, Schonherr M, Raatz Y, Kunz M
Role of micro RNA 372 in melanoma progression

Experimental Dermatology (2011), Volume 20, Issue 2, 196.

2010

Boldt S, Knops K, Kriehuber R, Wolkenhauer O
A p-value and fold-change driven gene selection method for radiation dose prediction

EPRBioDose, Mandelieu-La-Napoule, 2010

Knops K, Boldt S, Wolkenhauer O, Kriehuber R
Gene expression pattern analysis in human PBLs as a tool for radiation biodosimetry

EPRBioDose, Mandelieu-La-Napoule, 2010

Knops K, Boldt S, Wolkenhauer O, Kriehuber R
Radiation responsive genes in human lymphocytes as a tool for radiation biodosimetry

GBS Tagung, Hamburg, 2010

Guebel DV, Schmitz U, Wolkenhauer O, Vera J
An extensive Boolean network for analysing the signalling events in early stages of humen colon cancer

11th International Conference on Systems Biology (ICSB), Edinburgh, October 2010.

Thomas Millat, Sylvia Haus, Olaf Wolkenhauer, Ralf-Jörg Fischer, Holger Janssen, Hubert Bahl, Sara Jabari, John King
Modelling the pH-dependent metabolic shift in Clostridum acetobutylicum

11th International Conference on Systems Biology (ICSB), Edinburgh (UK), 10-15 October 2010

Jabbari S, Haus S, Millat T, Wolkenhauer O, King JR
Systems Biology of Clostridium acetobutylicum and the Optimization of Butanol Production

11th International Conference on Systems Biology (ICSB), Edinburgh (UK), 10 October - 15 October 2010

Millat, Liebal U, Wolkenhauer O, de Jong I, Kuipers O
The dynamics of the phosphorelay and the initiation of sporulation in Bacillus subtilis - a systematic study

11th International Conference on Systems Biology (ICSB), Edinburgh (UK), 10 October - 15 October 2010

Thomas Millat, Simone Frey, Olaf Wolkenhauer
How integrals over dynamic signals can unravel characteristic properties of signal transduction pathways

11th International Conference on Systems Biology (ICSB), Edinburgh (UK), 10-15 October 2010

van Rienen U, Appali R, Bader R, Baumann W, Beck U, Behrend D, Benecke R, Biala K, Birkholz H, Burkel E, Engel K, Ewald H, Gimsa J, Gimsa U, Gongadze E, Grünbaum A, Haba Y, Liese F, Liu B, Lüder M, Pauleweit S, Mittelmeier W, Mix E, Nebe JB,....[+12]
Analysis and simulation of electrical interactions of implants with biosystems

44. DGBMT Jahrestagung, Rostock, Germany, 05-08 October 2010
(see program for the full list of authors: DGBMT program)

Liebal U, Sappa PK, Millat T, Steil L, Völker U, Wolkenhauer O
Using a modelling approach to elucidate unexpected reporter gene signals for sigmaB activity in B. Subtilis

Conference on Systems Biology of Microorganisms, Paris (France), 22 March - 24 March 2010

2009

Millat T
Systems Biology - How Modelling and Simulation improve our understanding of complex biological systems

Systems Biology of Neurodegenerative Diseases, Kuopio (Finland), 16 June - 18 June 2009

Millat T
Dynamic Motifs in Pathway Modelling

Rijksuniversiteit Groningen, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), Department of Genetics, Molecular Genetics, Haren (The Netherlands), 3 April 2009

Boldt S, Knops K, Kriehuber R, Wolkenhauer O
A Data Analysis Workflow for the Identification of Expression Signatures Functioning as Molecular Biodosimeters

German Conference of Bioinformatics, Halle, 2009

Knops K, Boldt S, Wolkenhauer O, Kriehuber R
Gene Expression pattern analysis as a tool for radiation biodosimetry

ERRS, Prag, 2009

Liebal U, Millat T, Wolkenhauer O, Sappa PK, Steil L, Völker U
Analysis of a Model of sigB Activation Following Glucose Starvation

10th International Conference on Systems Biology (ICSB), Stanford (USA), 30 August -4 September 2009

Millat T, Haus S, Wolkenhauer O, Fischer RJ, Janssen H, Bahl H
The Metabolic Shift of Clostridium acetobutylicum - The Role of pH-Dependent Enzyme Activities

10th International Conference on Systems Biology (ICSB), Stanford (USA), 30 August - 4 September 2009

2008

Millat T, COSMIC consortium
COSMIC - Systems biology of Clostridium acetobutylicim - A possible answer to dwindling crude oil reserves

9th International Conference on Systems Biology (ICSB), Gothenborg (Sweden), 23 August - 27 August 2008

Haus S, Millat T, Wolkenhauer O
pH-Dependent Modelling of ABE Fermentation in Clostridium acetobutylicum

SysMo Evaluation Conference, Bad Honnef (Germany), 1 July - 2 July 2008

Liebal UW, Hildisch H, Millat T, Völker U, Wolkenhauer
Modelling Aspects of Stress Response mediated by sigB

SysMo Evaluation Conference, Bad Honnef (Germany), 1 July - 2 July 2008

Wolkenhauer O, Millat T
Mathematical Modelling and Simulation of Cellular Processes

Vorlesungsreihe Biosystem-Material-Interaktion an der Interdisziplinären
Fakultät der Universität Rostock, Rostock (Germany), 27 October 2008

Schult C, Dahlhaus M, Glass A, Boldt S, Ruck S, Sawitzky M, Lange M, Amoroso F, Freund M, Neri L, Junghanss C
Sorafenib inhibits proliferation in B- and T- Lymphoblastic cell lines via the PI3k/AKT Pathway

Ash, San Francisco, 2008

Boldt, Glass, Schult, Junghanß, Wolkenhauer
Detecting Differential Gene Expression in ALL Cell Lines Treated with the Multikinase Inhibitor Sorafenib

Systems Biology for Medical Applications, Summer School, Costa Adeje, 2008

Stefan Pauleweit
Software Supporting Collaborations

Summer School on Systems Biology for Medical Applications, Tenerife, Spain, 30.09.-02.10.2008

Raasch P, Schmitz U, Kreikemeyer B, Wolkenhauer O
A JAVA framework to integrate ncRNA detection methods

Systems Biology for Medical Applications Summer School, Costa Adeje, Spain, 2008.

Stalidzans E, Mozga I, Roos C, Fernandez E, Font J, Vanags J, Remm M, Schmitz U, Wolkenhauer O
Modular education for interdisciplinary Systems Biology

9th International Conference on Systems Biology, Gothenburg, 2008.

Haus S, Millat T, Wolkenhauer O
Modeling of ABE Fermentation in Clostridium acetobutylicum

9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008

Frey S, Millat T, Hohmann S, Wolkenhauer O
How Quantitative Measures unravel Design Principles in multi-stage Phosphorylation Cascades

9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008

Millat T, Sreenath SN, Soebiyanto RP, Avva J, Cho KH, Wolkenhauer O
The Role of Dynamic Stimulation Pattern in the Analysis of Bistable Intracellular Systems

9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008

2007

Wolkenhauer O, Millat T, Assmuss, H
Von der Notwendigkeit der mathematischen Modellierung in den Biowissenschaften

Interdisziplinäre Ringvorlesung - Modellierung und Simulation - Techniken
und gesellschaftliche Implikationen, Rostock (Germany), 19 April 2007

Millat T
Bistable Systems - a dynamic view

Winter School on Systems Biology for Medical Applications, Puerto de la Cruz, Tenerife (Spain), 26 February - 2 March 2007

Vera J, Millat T, Kwon T, Schmitz U, Wolkenhauer O
Exploring cell signalling homodimer receptor-homodimer protein interactions and their dynamical consequences

German Conference on Bioinformatics, Potsdam (Germany), 26 September - 28 September 2007

2005

Millat T, Wolkenhauer O
Modelling and simulation of dynamics in cells

Systems Biology: From Molecules & Modeling to Cells, Gosau (Austria), 12 March - 18 March 2005

Millat T
From Experiments to Models: Assumptions, Approximations and their Consequences

SYMBIONIC 2005, Course on Methods, Data Handling and Standards in Neuronal Systems Biology, Trieste (Italy), 31 August - 3 September 2005

Millat T
Dynamics Motifs in Pathway Modelling

SYMBIONIC 2005, Course on Methods, Data Handling and Standards in Neuronal Systems Biology, Trieste (Italy), 31 August - 3 September 2005

2004 and older

Wolkenhauer O
Possibilistic Change Detection: The Onset of Oscillations

EUFIT'96, pages 1610-1613, September 1996

Wolkenhauer O
Dynamic Reliability Evaluation and Performance Monitoring

EUFIT'96, pages 951-955, September 1996