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
2024
E2F1-induced autocrine IL-6 inflammatory loop mediates cancer-immune cell crosstalk that regulates metastatic properties in melanoma
Dhar P, Singh KP, Gupta S, Peringot D, Spitschak A, Pützer BM
AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6814.
2021
Combining uniform manifold approximation with localized affine shadowsampling improves classification of imbalanced datasets
Bej S, Srivastava P, Wolfien M, Wolkenhauer O
2021 International Joint Conference on Neural Networks (IJCNN), 2021, pp. 1-8,
2020
Artificial Intelligence, Machine learning, and Radiomics
Papp L, Wolfien M, Ladefoged CN, Spielvogel CP
ENMG 2020 Edition - Contribution of a chapter in the "European Nuclear Medicine Guide"
2019
Vertrauen oder Kontrolle? Meine Gesundheitsdaten und ich
Martin Scharm
Invited talk and panel discussion in the series "Vier Augen. Lebenswissenschaften in der Kontroverse" (2019)
Venue: Alfried Krupp Wissenschaftskolleg Greifswald
URL: https://www.wiko-greifswald.de/programm/vortraege/aktuelle-schwerpunkte/vier-augen/
2016
Challenges and opportunities for system biology standards and tools in medical research
M König, A Oellrich, D Waltemath, ... O Wolkenhauer
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
Venue: Halle, Germany
An integrative computational framework for personalized detection of tumor epitopes in melanoma immunotherapy
Jaitly T, Schaft N, Doerrie J, Gross S, Schuler-Thurner B, Wolkenhauer O, Schuler G, Taher L, Gupta S, Vera J
PeerJ Preprints 4:e2385v1
Model Management in Systems Biology: Challenges – Approaches – Solutions
Scharm M
A talk in the FAIRDOM webinar series 2016
2015
Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit
Scharm M and Waltemath D
Article in Proceedings of the Workshop on Data management in Life Sciences, BTW, Hamburg, germany (2015)
Venue: Hamburg, Germany
2014
The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results.
Scharm M, Wendland F, Peters M, Wolfien M, Theile T, and Waltemath D
Open Access demo paper in Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences (2014)
Attribute Exploration with Proper Premises and Incomplete Knowledge Applied to the Free Radical Theory of Ageing
Wollbold J, Köhling R, Borchmann D
Identifying, interpreting, and communicating changes in XML-encoded models of biological systems
Scharm M, Wolkenhauer O, and Waltemath D
Demo paper in Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Lisbon, Portugal (2014)
Venue: Lisbon, Portugal
2013
Predicting targets of synergistic microRNA regulation
Schmitz U, Gupta S, Lai X, Vera J, Wolkenhauer O
German Conference on Bioinformatics 2013, Göttingen, Germany
Venue: Göttingen, Germany
New candidate oncomiRs for malignant melanoma
Bhattacharya A, Schmitz U, Raatz Y, Schönherr M, Kunz M
International Investigative Dermatology (IID) in Edinburgh, UK
Venue: Edinburgh, UK
Modelling and simulation of dynamics in cells
Millat T, Wolkenhauer O
Systems Biology: From Molecules & Modeling to Cells, Gosau, Austria, 12 March - 18 March 2005
Venue: Gosau, Austria
Butyrate re-assimilation in C. acetobutylicum re-evaluated using modelling
Millat T
7th Annual SysMo-Conference, Berlin, Germany, 6 February - 8 February 2013
Venue: Berlin, Germany
2012
Continuous states on a grid enable an efficient simulation of diffusion in environments with excluded volumes
Kossow C, Rybacki S, Millat T, Rateitschak K, Uhrmacher AM, Wolkenhauer O
Biotec Forum ''Bioinformatics and Computational Biology'', Dresden, Germany, 06 December - 07 December 2012
Venue: Dresden, Germany
Regulated Trafficking of APP by SORLA in Alzheimers Disease
Lao A, Schmidt V, Schmitz Y, Willnow T, Wolkenhauer O
Systems Medicine International Conference (SYSMED), Dublin, Ireland, 9 September - 13 September 2012
Venue: Dublin, Ireland
Mathematical Modelling of the pH-induced Metabolic Shift in C. acetobutylicum Unravels a Heterogeneous Phase Transition
Millat T
Clostridium XII, Nothingham, UK, 9 September - 12 September 2012
Venue: Nothingham, UK
The regulation of microRNA target hubs
Schmitz U, Lai X, Vera J, Wolkenhauer O
International Workshop on Small RNA in Cancer, Inflammation, and Aging, Copenhagen, Denmark, September 3 - 4 , 2012.
Venue: Copenhagen, Denmark
A systems biology approach to study the cellular function of microRNAs
Lai X, Schmitz U, Vera J, Wolkenhauer O
International Workshop on Small RNA in Cancer, Inflammation, and Aging, Copenhagen, Denmark, September 3 - 4, 2012.
Venue: Copenhagen, Denmark
Considerations of graph-based concepts to manage computational biology models and associated simulations
R Henkel, N Le Novère, O Wolkenhauer, D Waltemath
Article in Proceedings of the 2012 INFORMATIK conference, Jahrestagung der GI e.V., Braunschweig (2012).
Virtual experiments for reusable models
Cooper J, Mirams G, Slaymaker M, Simpson A, Vik JO, Waltemath D (2013)
Proceedings of the 2012 VPH Conference, London, UK.
Access to PDF version through Researchgate (or contact us for further details about the manuscript)
Venue: London, UK
Multi-compartmental modeling of APP processing influenced by SORLA in Alzheimers disease
Lao A, Schmidt V, Schmitz Y, Willnow T, Wolkenhauer O
13th International Conference on Systems Biology (ICSB), Toronto, Canada, 19 August - 23 August 2012
Venue: Toronto, Canada
The role of micro RNA regulation in the early inflammatory response: miR-146a and NFkB signaling in lung inflammation
Lai X, Schulz C, Dolniak B, Wolkenhauer O, Schmeck B, Vera J, Sittka A
Symposium on Remodeling, Repair and Regeneration in Lung Diseases, Marburg, Germany, June 21-23, 2012
Best poster award
Venue: Marburg, Germany
Efficient Two-Dimensional Pattern Matching with Scaling and Rotation and Higher-Order Interpolation
Hundt C, Wendland F (2012)
In: J. Kärkkäinen & J. Stoye (Eds.), Combinatorial Pattern Matching (CPM 2012), LNCS, vol. 7354, pp. 124-137. Heidelberg: Springer.
Modelling partners in crime in pancreatic cancer - Application of a cellular automaton model
Christina Kossow
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
Venue: Wismar, Germany
Identification of gene-based biosignatures for radiation biodosimetry
Boldt S, Knops K, Kriehuber R, Wolkenhauer O
58. Biometrisches Kolloquium, Berlin, Germany, March 2012
Venue: Berlin, Germany
2011
Análisis de los fenómenos de adhesión celular en los estadios tempranos de cáncer de colon mediante un modelo de lógica multi-valuada extendida
Guebel DV, Schmitz U, Wolkenhauer O, Vera J
Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina, 13-16 September, 2011
Venue: Buenos Aires, Argentina
The pH-induced metabolic shift from acidogenesis to solventogenesis in Clostridium acetobutylicum
Millat T
5th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations, Rüdesheim, Germany, 12 September - 16 September 2011
Venue: Rüdesheim, Germany
Protein diversity of the stressosome - Stress sensitivity and Response magnitude
Liebal U, Millat T, Marles-Wright J, Lewis R, Wolkenhauer O
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
Mathematical modelling points out regulatory mechanisms of interferon-gamma induced STAT1 serine phosphorylation and MUC4 expression in pancreatic cancer cells
Kossow C, Jose D, Jaster R, Wolkenhauer O, Rateitschak K
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
Mathematical modelin of protein aggregation and transport in Alzheimer's disease
Winter F, Krohn M, Lange C, Pahnke J, Wolkenhauer O, Rateitschak K
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
Mathematical Modeling of APP Processing influenced by SORLA in Alzheimers Disease
Lao A, Schmitz Y, Schmidt V, Rateitschak K, Wolf J, Willnow T, Wolkenhauer O
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
Mathematical modelling of the Wnt pathway: the influence of nucleo-cytoplasmic shuttling of beta-catenin and its antagonists APC, Axin and GSK3
Schmitz Y, Rateitschak K, Wolkenhauer O
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
On the regulation of microRNA target hubs: a Systems Biology perspective
Lai X, Schmitz U, Gupta S, Kunz M, Wolkenhauer O, Vera J
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
The role of micro RNA regulation in the early inflammatory response: miR-146a and NFkB signaling in lung inflammation
Lai X, Schulz C, Sittka A, Dolniak B, Wolkenhauer O, Schmeck B and Vera J
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
Automated analysis of flow cytometry data from heterogeneous bacterial populations
Millat T, Rubenis O, Liebal U, Wolkenhauer O, de Jong I, Kuipers O
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
Protein Diversity of the Stressosome - Stress Sensitivity and Response Magnitude
Liebal UW, Millat T, Marles-Wright J, Lewis R, Wolkenhauer O
12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011
Venue: Heidelberg/Mannheim, Germany
Identification of radiation-specific gene expression changes in human PBL after ex vivo irradiation suitable for biodosimetric applications
Knops K, Boldt S, Wolkenhauer O, Kriehuber R
14th International Congress of Radiation Research, Warsaw, Poland, August 2011
Venue: Warsaw, Poland
Gene expression analysis in Jurkat cells after exposure to I-123-iododeoxyuridine, Gamma-rays and Alpha-particles
Unverricht-Yeboah M, Boldt S , Giesen U, Pomplun E, Wolkenhauer O, Kriehuber R
14th International Congress of Radiation Research, Warsaw, Poland, August 2011
Venue: Warsaw, Poland
Agent-based simulation of molecular processes
Pauleweit S, Nebe J B, Wolkenhauer O
SIMULTECH 2011, Noordwijkerhout, Netherlands, July 2011
Venue: Noordwijkerhout, Netherlands
Role of micro RNA 372 in melanoma progression
Bhattacharya A, Schmitz U, Schonherr M, Raatz Y, Kunz M
Experimental Dermatology (2011), Volume 20, Issue 2, 196.
2010
A p-value and fold-change driven gene selection method for radiation dose prediction
Boldt S, Knops K, Kriehuber R, Wolkenhauer O
EPRBioDose, Mandelieu-La-Napoule, France, October 2010
Venue: Mandelieu-La-Napoule, France
Gene expression pattern analysis in human PBLs as a tool for radiation biodosimetry
Knops K, Boldt S, Wolkenhauer O, Kriehuber R
EPRBioDose, Mandelieu-La-Napoule, France, October 2010
Venue: Mandelieu-La-Napoule, France
An extensive Boolean network for analysing the signalling events in early stages of humen colon cancer
Guebel DV, Schmitz U, Wolkenhauer O, Vera J
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, October 2010.
Venue: Edinburgh, UK
The dynamics of the phosphorelay and the initiation of sporulation in Bacillus subtilis - a systematic study
Millat, Liebal U, Wolkenhauer O, de Jong I, Kuipers O
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10 October - 15 October 2010
Venue: Edinburgh, UK
Systems Biology of Clostridium acetobutylicum and the Optimization of Butanol Production
Jabbari S, Haus S, Millat T, Wolkenhauer O, King JR
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10 October - 15 October 2010
Venue: Edinburgh, UK
Modelling the pH-dependent metabolic shift in Clostridum acetobutylicum
Thomas Millat, Sylvia Haus, Olaf Wolkenhauer, Ralf-Jörg Fischer, Holger Janssen, Hubert Bahl, Sara Jabari, John King
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010
Venue: Edinburgh, UK
How integrals over dynamic signals can unravel characteristic properties of signal transduction pathways
Thomas Millat, Simone Frey, Olaf Wolkenhauer
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010
Venue: Edinburgh, UK
Modelling the pH-dependent metabolic shift in Clostridum acetobutylicum
Millat T, Haus S, Wolkenhauer O, Fischer RJ, Janssen H, Bahl H, Jabari S, King J
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10 October - 15 October 2010
Venue: Edinburgh, UK
A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in S. cerevisiae
Simone Frey, Kristin Sott, Maria Smedh, Thomas Millat, Peter Dahl, Olaf Wolkenhauer, Mattias Goksör
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010
Venue: Edinburgh, UK
Mathematical modelling of nucleo-cytoplasmic shuttling of beta-catenin and its antagonist APC
Schmitz Y, Wolkenhauer O, Rateitschak K
11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010
Venue: Edinburgh, UK
Interferon gamma stimulated STAT1 signalling in pancreatic stellate cells: From experimental data to mathematical models, Workshop "Modelling in BioMedicine"
Rateitschak K, Lange F, Fitzner B, Wolkenhauer O, Jaster R
11th International Conference on Systems Biology, Edinburgh, UK, 10.10.-15.10.2010
Venue: Edinburgh, UK
Analysis and simulation of electrical interactions of implants with biosystems
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]
44. DGBMT Jahrestagung, Rostock, Germany, 05-08 October 2010
Venue: Rostock, Germany
see program for the full list of authors: DGBMT program
MicroRNAs in malignant melanoma progression
Schmitz U, Bhattacharya A, Gupta S, Schultz J, Kunz M, Wolkenhauer O
German Conference on Bioinformatics, Braunschweig, Germany, September 2010
Venue: Braunschweig, Germany
Radiation responsive genes in human lymphocytes as a tool for radiation biodosimetry
Knops K, Boldt S, Wolkenhauer O, Kriehuber R
GBS Tagung, Hamburg, Germany, September 2010
Venue: Hamburg, Germany
A stem cell niche dominance theorem
Wolkenhauer O, Shibata D, Mesarovic MD
(PGSSCR 2010-O-057) 010 Vol. 6 (2): p36 JSRM Code: 006020700063
Mathematical modelling of APP processing influenced by SORLA in Alzheimer's disease
Schmidt V, Lao A, Rateitschak K, Wolkenhauer O, Willnow T
Honolulu, Hawaii, 10.07-15.07.2010
Venue: Honolulu, Hawaii
Quantitative analysis of the SNF1-pathway in Saccharomyces cerevisiae
Garcia-Salcedo R, Frey S, Beltran G, Bosch D, Elbing K, Tian Y, Manchala S, Rateitschak K, Wolkenhauer O, Hohmann S
35thFEBS Congress 2010, Göteborg (Gothenburg), Sweden. June 26 - July 1, 2010
Venue: Gothenburg, Sweden
Quantitative analysis of the SNF1-pathway in Saccharomyces cerevisiae
Garcia-Salcedo R, Frey S, Beltran G, Bosch D, Elbing K, Tian Y, Manchala S, Rateitschak K, Wolkenhauer O, Hohmann S
35thFEBS Congress 2010, Göteborg (Gothenburg), Sweden. June 26 - July 1, 2010
Venue: Gothenburg, Sweden
Interferon gamma stimulated STAT1 signalling in pancreatic stellate cells: From experimental data to mathematical models
Rateitschak K, Lange F, Fitzner B, Wolkenhauer O, Jaster R
Conference on Systems Biology of Mammalian Cells-SBMC2010, Freiburg, Germany, 3-5 June 2010
Venue: Freiburg, Germany
Modeling miRNA regulation in signaling networks: miR-34a regulation of p53/Sirt1 module
Lai X, Vera J, Wolkenhauer O
Conference on Systems Biology of Mammalian Cells-SBMC2010, Freiburg, Germany, 3-5 June 2010
Venue: Freiburg, Germany
Local Genomic Properties as Indicators of Functional Elements
Raasch P, Schmitz U, Patenge N, Vera J, Kreikemeyer B, Wolkenhauer O
3. Gemeinsame Tagung der DGHM und der VAAM, Hannover, Germany, 28.03.-31.03.2010
Venue: Hannover, Germany
Using a modelling approach to elucidate unexpected reporter gene signals for sigmaB activity in B. Subtilis
Liebal U, Sappa PK, Millat T, Steil L, Völker U, Wolkenhauer O
Conference on Systems Biology of Microorganisms, Paris, France, 22 March - 24 March 2010
Venue: Paris, France
Mathematical modelling of APP processing influenced by SORLA in Alzheimer's disease
Lao A, Schmidt V, Rateitschak K, Wolkenhauer O, Willnow T
Mid-term review of the Helmholtz Alliance on Systems Biology, DKFZ, Heidelberg, Germany, 13.01.-14.01.2010
Venue: Heidelberg, Germany
2009
Charakterisierung intrazellulärer Signalwege in pankreatischen Sternzellen mit Hilfe mathematischer Modellierung
Lange F, Fitzner B, Jaster R, Karger A, Wolkenhauer O, Rateitschak K
30. Jahrestagung des Deutschen Pankreasclub, Heidelberg, Germany, November 2009
Venue: Heidelberg, Germany
Protein networks controlling amyloidogenic processing
Willnow T, Schmidt V, Lao A, Rateitschak K, Wolkenhauer O
Second status seminar and meeting of the advisory board of the Helmholtz Alliance on Systems Biology, DKFZ, Heidelberg, Germany, 26.10.-27.10.2009
Venue: Heidelberg, Germany
A Data Analysis Workflow for the Identification of Expression Signatures Functioning as Molecular Biodosimeters
Boldt S, Knops K, Kriehuber R, Wolkenhauer O
German Conference of Bioinformatics, Halle (Saale), Germany, September 2009
Venue: Halle (Saale), Germany
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis
Lai X, Nikolov S, Wolkenhauer O, Vera J
The 2009 International Workshop on "Computational and Integrative Biology" (CIB 2009), Hangzhou, China, 18.09.-20.09.2009
Venue: Hangzhou, China
Interferon gamma stimulated Stat1 signaling pathway in pancreatic stellate cells: From experimental data to mathematical models
Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R
4. ESCEC Symposium, Rüdesheim, Germany, 09.2009
Venue: Rüdesheim, Germany
Gene Expression pattern analysis as a tool for radiation biodosimetry
Knops K, Boldt S, Wolkenhauer O, Kriehuber R
ERRS, Prague, Czech Republic, August 2009
Venue: Prague, Czech Republic
Systems Biology - How Modelling and Simulation improve our understanding of complex biological systems
Millat T
Systems Biology of Neurodegenerative Diseases, Kuopio, Finland, 16 June - 18 June 2009
Venue: Kuopio, Finland
Interferon gamma stimulated Stat1 signaling pathway in pancreatic stellate cells: From experimental data to mathematical models
Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R
Transatlantic Summer School Cancer Systems Biology, Rostock, Germany, June 2009
Venue: Rostock, Germany
Interferon gamma stimulated Stat1 signaling pathway in pancreatic stellate cells: From experimental data to mathematical models
Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R
German Symposium on Systems Biology, Heidelberg, Germany, May 2009
Venue: Heidelberg, Germany
Systems Approaches in Molecular and Cell Biology: Making Sense out of Data, Providing Meaning to Models
Wolkenhauer O, Lao A, Omholt S, Martens H
Independent Component Analysis, Wavelets, Neural Networks, Biosystems and Nanoengineering VII, Orlando, USA, 13.04.2009
DOI: 10.1117/12.822742
Venue: Orlando, USA
Mathematical modelling of APP processing influenced by SORLA in Alzheimer's disease
Lao A, Schmidt V, Rateitschak K, Willnow T, Wolkenhauer O
Spring school 2009 on Systems Biology, Kloster Seeon, Germany, 06.04.-09.04.2009
Venue: Kloster Seeon, Germany
Dynamic Motifs in Pathway Modelling
Millat T
Rijksuniversiteit Groningen, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), Department of Genetics, Molecular Genetics, Haren, The Netherlands, 3 April 2009
Venue: Haren, The Netherlands
2008
Detecting Differential Gene Expression in ALL Cell Lines Treated with the Multikinase Inhibitor Sorafenib
Boldt, Glass, Schult, Junghanß, Wolkenhauer
Systems Biology for Medical Applications, Summer School, Costa Adeje, Soain, 30 October 2008
Venue: Costa Adeje, Soain
A JAVA framework to integrate ncRNA detection methods
Raasch P, Schmitz U, Kreikemeyer B, Wolkenhauer O
Systems Biology for Medical Applications Summer School, Costa Adeje, Spain, 30 October 2008
Venue: Costa Adeje, Spain
Mathematical Modelling and Simulation of Cellular Processes
Wolkenhauer O, Millat T
Vorlesungsreihe Biosystem-Material-Interaktion an der Interdisziplinären
Fakultät der Universität Rostock, Rostock, Germany, 27 October 2008
Venue: Rostock, Germany
Sorafenib inhibits proliferation in B- and T- Lymphoblastic cell lines via the PI3k/AKT Pathway
Schult C, Dahlhaus M, Glass A, Boldt S, Ruck S, Sawitzky M, Lange M, Amoroso F, Freund M, Neri L, Junghanss C
Ash, San Francisco, USA, 2008
Venue: San Francisco, USA
Use of sensitivity analysis to detect critical biochemical processes in a mathematical model linking intracellular and cell population dynamics in erythropoiesis
Lai X, Liebal U, Nikolov S, Wolkenhauer O, Vera J
The 6th Conference on Computational Methods in Systems Biology (CMSB), Rostock-Warnemünde, Germany, October 2008
Venue: Rostock-Warnemünde, Germany
Software Supporting Collaborations
Stefan Pauleweit
Summer School on Systems Biology for Medical Applications, Tenerife, Spain, 30.09.-02.10.2008
Venue: Tenerife, Spain
Elucidating the role of nucleo-cytoplasmic shuttling of beta-catenin antagonists by mathematical modelling
Schmitz Y, Bader BM, Weiss DG, Wolkenhauer O, Rateitschak K
Summer School on Systems Biology for Medical Applications, Tenerife, Spain, 30.09.-02.10.2008
Venue: Tenerife, Spain
Analysis of a Model of sigB Activation Following Glucose Starvation
Liebal U, Millat T, Wolkenhauer O, Sappa PK, Steil L, Völker U
10th International Conference on Systems Biology (ICSB), Stanford, USA, 30 August -4 September 2009
Venue: Stanford, USA
The Metabolic Shift of Clostridium acetobutylicum - The Role of pH-Dependent Enzyme Activities
Millat T, Haus S, Wolkenhauer O, Fischer RJ, Janssen H, Bahl H
10th International Conference on Systems Biology (ICSB), Stanford, USA, 30 August - 4 September 2009
Venue: Stanford, USA
The Effect of pH on the Metabolic Shift in AB Fermentation in Clostridium acetobutylicum
Haus S, Jabbari S, Millat T, Wolkenhauer O, King JR
10th International Conference on Systems Biology (ICSB), Stanford, USA, 30 August - 4 September 2009
Venue: Stanford, USA
Dynamic Behavior Determines the Design Strategy of Metabolic Regulation Networks
Liebal U, Kim JR, Wolkenhauer O, Cho KH
10th International Conference on Systems Biology, Stanford, USA, 30.8.-4.09.2009
Venue: Stanford, USA
Modular education for interdisciplinary Systems Biology
Stalidzans E, Mozga I, Roos C, Fernandez E, Font J, Vanags J, Remm M, Schmitz U, Wolkenhauer O
9th International Conference on Systems Biology, Gothenburg, Sweden, 2008.
Venue: Gothenburg, Sweden
COSMIC - Systems biology of Clostridium acetobutylicim - A possible answer to dwindling crude oil reserves
Millat T, COSMIC consortium
9th International Conference on Systems Biology (ICSB), Gothenborg, Sweden, 23 August - 27 August 2008
Venue: Gothenburg, Sweden
Modeling of ABE Fermentation in Clostridium acetobutylicum
Haus S, Millat T, Wolkenhauer O
9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008
Venue: Gothenburg, Sweden
How Quantitative Measures unravel Design Principles in multi-stage Phosphorylation Cascades
Frey S, Millat T, Hohmann S, Wolkenhauer O
9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008
Venue: Gothenburg, Sweden
The Role of Dynamic Stimulation Pattern in the Analysis of Bistable Intracellular Systems
Millat T, Sreenath SN, Soebiyanto RP, Avva J, Cho KH, Wolkenhauer O
9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008
Venue: Gothenburg, Sweden
Threshold properties of Interferon-gamma stimulated Jak2-Stat1 signaling in pancreatic stellate cells: From experimental data to mathematical models
Karger A, Rateitschak K, Fitzner B, Wolkenhauer O, Jaster R
2nd International workshop on systems biology, Hamilton, Ireland, August 2008
Venue: Hamilton, Ireland
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
Winter F, Krohn M, Lange C, Wolkenhauer O, Rateitschak K, Pahnke J
2nd International workshop on systems biology, Hamilton, Ireland, August 2008
Venue: Hamilton, Ireland
Modelling Snf1 regulation in Saccharomyces cerevisiae
Frey S, Schmidt H, Rateitschak K, Beltran G, Garcia-Salcedo R, Elbing K, Bosch D, Ye T, Hohmann S, Wolkenhauer O
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
A Mathematical Model of the Regulation of AMPK Activation
Bittig A, Carling D, Wolkenhauer O
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
Hierarchical Modelling of Metabolism: From Methodology to Application
Schmidt H
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
A new tool for parameter estimation in nonlinear dynamic biological systems using global optimization
Egea JA, Schmidt H, Banga JR
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
Sensitivity Analysis based Adaptive Search-Space Reduction for Parameter Estimation Applications
Liebal U, Schmidt H
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
Format Overflow? Handling of Modeling Projects in Systems Biology
Bittig A, Schmidt H
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
Computational Systems Biology of Cell Signalling - COSBICS
Wolkenhauer, O, Vera J
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
Dynamic modeling of phototransduction biochemistry in vertebrate rods: from dark/light adaptation to disease
Dell'Orco D, Fanelli F, Schmidt H
9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008
Venue: Gothenburg, Sweden
pH-Dependent Modelling of ABE Fermentation in Clostridium acetobutylicum
Haus S, Millat T, Wolkenhauer O
SysMo Evaluation Conference, Bad Honnef, Germany, 1 July - 2 July 2008
Venue: Bad Honnef, Germany
Modelling Aspects of Stress Response mediated by sigB
Liebal UW, Hildisch H, Millat T, Völker U, Wolkenhauer O
SysMo Evaluation Conference, Bad Honnef, Germany, 1 July - 2 July 2008
Venue: Bad Honnef, Germany
Quantitative 3D image analysis to study the beta-catenin translocation during differentiation of human neural progenitor cells
Bader BM, Schmitz Y, Redlich B, Rateitschak K, Wolkenhauer O, Weiss DG
2nd International Congress on Stem Cells and Tissue Formation, Dresden, Germany, July 2008
Venue: Dresden, Germany
Mathematical modeling of neurodegenerative processes in alzheimer's diesease
Rateitschak K, Schmidt V, Carlo AS, Sporbertm A, Lao A, Wolkenhauer O, Willnow T
First status seminar of the Helmholtz alliance on systems biology. Potsdam, Germany, June 2008
Venue: Potsdam, Germany
Nonlinear dynamics of biochemical networks in pancreatic cancer: From experimental data to mathematical models
Rateitschak K, Karger A, Fitzner B, Wolkenhauer O, Jaster R
First FORSYS symposium. Berlin, Germany, June 2008
Venue: Berlin, Germany
Thresholds in transient dynamics of signal transduction pathways
Rateitschak K, Wolkenhauer O
Cancer workshop, University of Nottingham, Nottingham, UK, January 2008
Venue: Nottingham, UK
2007
Exploring cell signalling homodimer receptor-homodimer protein interactions and their dynamical consequences
Vera J, Millat T, Kwon T, Schmitz U, Wolkenhauer O
German Conference on Bioinformatics, Potsdam, Germany, 26 September - 28 September 2007
Venue: Potsdam, Germany
Thresholds in transient dynamics of signal transduction pathways
Rateitschak K, Wolkenhauer O
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
Venue: Cambridge, UK
Von der Notwendigkeit der mathematischen Modellierung in den Biowissenschaften
Wolkenhauer O, Millat T, Assmuss, H
Interdisziplinäre Ringvorlesung - Modellierung und Simulation - Techniken und gesellschaftliche Implikationen, Rostock, Germany, 19 April 2007
Venue: Rostock, Germany
Bistable Systems - a dynamic view
Millat T
Winter School on Systems Biology for Medical Applications, Puerto de la Cruz, Tenerife, Spain, 26 February - 2 March 2007
Venue: Tenerife, Spain
2006
A principal limitation of virtual cell simulations using differential equation models
Wolkenhauer O, Bittig A, Hofmeyr J
Winter Simulation Conference (WSC '06), December 2006
Quantitative measures to characterize properties of signal transduction pathways
Frey S, Millat T, Rateitschak K, Wolkenhauer O
Winter Simulation Conference (WSC '06), December 2006
Tresholds in transient dynamics of signal transduction pathways
Rateitschak K, Wolkenhauer O
Proc. ICSB 2006, Yokohama, Japan, 2006
Venue: Yokohama, Japan
Modelling of negative feedback loops regulating the JAK2/STAT5 signal transduction pathway
Bachmann J, Fleck C, Maiwald T, Vera J, Wolkenhauer O, Timmer J, Klingmüller U
Proc. ICSB 2006, Yokohama, Japan, 2006
Venue: Yokohama, Japan
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
Vera J, Bachmann J, Pfeifer A, Hormiga JA, Torres Darias NV, Klingmüller U, Wolkenhauer O
1st International Symposium on Systems Biology: From genomes to in silico and back. Murcia, Spain, June 2006
Venue: Murcia, Spain
2005
From Networks to Systems to Complex Systems: A Signaling Pathway Coordination Case Study
Soebiyanto RP, Sreenath SN, Mesarovic MD, Wolkenhauer O
44th IEEE Conference on Decision and Control and European Control Conference ECC 2005, Seville, Spain, 12-15 December 2005
Venue: Seville, Spain
Huntingtin and its Interaction Network: A Computer Model
Assmus H, Wolkenhauer O
Bmb+f NGFN II conference, Bonn, Germany, November 2005
Venue: Bonn, Germany
A Pledge for more theory in cell signalling experiments: when fishing for drug targets is not sufficient
Wolkenhauer O
Ernst Schering Foundation Workshop "Systems Biology - Applications and Perspectives". Berkeley, USA, November 2005
Venue: Berkeley, USA
Steady state - limit cycle - steady state transitions in gene transcription networks with distributed time delay
Rateitschak K, Wolkenhauer O
International Conference for Systems Biology (ICSB), Boston, USA, October 2005
Venue: Boston, USA,
What is required for a successful molecular fishing expedition?
Wolkenhauer O
2nd ESF Functional Genomics and Disease Conference, Oslo, Sweden, September 2005
Venue: Oslo, Sweden
A fully Bayesian model to cluster gene expression profiles
Vogl C, Sanchez-Cabo F, Stocker G, Hubbard S, Wolkenhauer O, Trajanoski Z
ECC05
From Experiments to Models: Assumptions, Approximations and their Consequences
Millat T
SYMBIONIC 2005, Course on Methods, Data Handling and Standards in Neuronal Systems Biology, Trieste, Italy, 31 August - 3 September 2005
Venue: Trieste, Italy
Dynamics Motifs in Pathway Modelling
Millat T
SYMBIONIC 2005, Course on Methods, Data Handling and Standards in Neuronal Systems Biology, Trieste, Italy, 31 August - 3 September 2005
Venue: Trieste, Italy
Towards a Systems Understanding of the Cerebral Motor Circuit
Wellstead P, Mason O, O'Connor WT, Cho KH, Bullinger E, Wolkenhauer O, Duncan S
Foundations of Systems Biology and Engineering (FOSBE), UCSB, August 2005
Multilevel, hierarchical systems paradigm of Systems Biology
Mesarovic M, Sreenath SN, Wolkenhauer O
Foundations of Systems Biology and Engineering (FOSBE), UCSB, August 2005
The Systems in Systems Biology
Wolkenhauer O
2nd Systems Biology conference, Maynooth, Ireland, August 2005
There is nothing more practical than a good theory
Wolkenhauer O
Complexity, Stellenbosch, South Africa, June 2005
Venue: Stellenbosch, South Africa
The Role of Theory, Modelling and Simulation in Systems Biology
Wolkenhauer O, Ullah M
Towards a Philosophy of Systems Biology, Amsterdam, Netherlands, May 2005
Venue: Amsterdam, Netherlands
Web Corpus Mining by Instance of Wikipedia, to appear
Gleim R, Mehler A, Dehmer M
Proceedings of the EACL 2006 Workshop on Web as Corpus, Trento, Italy, 03.04.-07.04.2006
Venue: Trento, Italy
Assumptions in Dynamic Modelling of Biochemical Networks and their Consequences
Millat T, Wolkenhauer O
FEBS Systems Biology Workshop, Gosau, Austria, March 2005
Venue: Gosau, Austria,
The role of feedback in the control and regulation of intracellular networks
Wolkenhauer O, Ullah M
Biochemical Society, Sheffield, UK, January 2005
Venue: Sheffield, UK
2004
A novel statistical approach in comparative genomics to reveal new immunogenic antigens in M. Bovis
Kutalik Z, Razaz M, Inwald J, Gordon SV, Wolkenhauer O
1st International Conference on Basic and Clinical Immunogenomics, Budapest, Hungary, 03-07 October 2004
Venue: Budapest, Hungary
Modeling and Analysis of Two Feedback Loop Dynamics in Ras/Raf-1/MEK/ERK Signaling Pathway
Cho KH, Shin SY, Kolch W, Wolkenhauer O
International Conference on Systems Biology (ICSB) 2004, Heidelberg, Germany, October 2004
Venue: Heidelberg, Germany
A System-Theoretic Modeling Framework for Cellular Processes
Cho KH, Johansson KH, Wolkenhauer O
International Conference on Systems Biology (ICSB) 2004, Heidelberg, Germany, October 2004
Choosing an appropriate modelling framework: How deterministic are random processes?
Ullah M, Cho KH, Kolch W, Wolkenhauer O
International Conference on Systems Biology (ICSB) 2004, Heidelberg, Germany, October 2004
Modelling gene expression time-series with radial basis function neural networks
Möller-Levet CS, Yin H, Cho KH, Wolkenhauer O
IEEE Int. Conf. on Neural Networks. Conf. Proc. 2, 1191-1195, 2004
A Fully Bayesian Model to Cluster Gene Expression Profiles
Sanchez-Cabo F, Hackl H, Hubbard S, Stocker G, Trajanoski Z, Wolkenhauer O, Vogl C
Intelligent Systems in Molecular Biology (ISMB), July 2004
Dynamic Pathway Modelling
Wolkenhauer O
Proceeding of the Sixteenth International Symposium on Mathematical Theory of Networks and Systems (MTNS), July 2004
2003
Mathematical Modeling of Ras/Raf-1/MEK/ERK Signal Pathway: Qualitative Analysis of the Positive Feedback Mechanism
Cho KH, Shin SY, Kolch W, Wolkenhauer O
ICSB2003, St. Louis, USA
Venue: St. Louis, USA
Dynamic Pathway Modelling: from models to cells
Wolkenhauer O, Kolch W, Cho KH
Proceeding of the 3rd Workshop on Computation of Biochemical Pathways and Genetic Networks. 6-7 October 2003
Fuzzy clustering of short time series and unevenly distributed sampling points
Möller-Levet C, Klawonn F, Cho KH, Wolkenhauer O
IDA'2003, August 2003
A Graphical User Interface to Normalize Microarray Data
Sanchez-Cabo F, Trajanoski Z, Cho KH, Wolkenhauer O
DSC'2003, March 2003
Simulation Study of the TNF Mediated NF- B Signaling Pathway
Cho KH, Shin SY, Lee HW, Wolkenhauer O
CSMB'2003, LNCS 2602, page 171, Springer Verlag
How to Synthesize an Optimized Genetic l-Switching System? A System-Theoretic Approach Based on SQP
Cho KH, Cha JH, Wolkenhauer O
CSMB'2003, page 170, LNCS 2602, Springer Verlag
2002
Investigations in the Analysis and Modelling of the TNFalpha Mediated NF-kappaB Signaling Pathway
Cho KH, Shin SY, Lee HW, Wolkenhauer O
ICSB2002, Stockholm, Sweden, 2002
Venue: Stockholm, Sweden
Fuzzy Clustering and Classification for Automated Leak Detection Systems
Taillefond N, Wolkenhauer O
IFAC'2002 Proceedings, Barcelona, Spain, 2002
Venue: Barcelona, Spain
2001
Random Sets and Histograms
Nunez-Garcia J, Wolkenhauer O
Proceedings of the 10th IEEE International Conference on Fuzzy Systems, Vol. 2, Melbourne, Australia, December 2001
Venue: Melbourne, Australia
2000
An Introduction to Fuzzy Systems
Babuska R, Wolkenhauer O
UK Control 2000, Cambridge, UK, 2000
Venue: Cambridge, UK
Fuzzy Systems Identification and Control
Babuska R, Wolkenhauer O
UK Control 2000, Cambridge, UK, 2000
Venue: Cambridge, UK
Fuzzy Relational Biology: A Factor-Space Approach to Genome Analysis
Wolkenhauer O, Babuska R
Computation in Cells, pages 53-58, April 2000
1999
A Random Sets Statistical Approach to Systems Identification
Wolkenhauer O, Garcia-Sanz M
AIDA'99, pages 388-392, June 1999
1998
An Adaptable Maintenance Model Using a Fuzzy System and Possibility Theory
Wolkenhauer O, Labib AW
EUFIT'98, pages 1570-1573, September 1998
1997
Local Uncertainty Models for the Analysis of Time Series Data
Wolkenhauer O, Edmunds J
EUFIT'97, pages 1774-1778, September 1997
On the Combination of Probabilistic and Fuzzy Concepts in Signal-based Data Analysis
Wolkenhauer O
EUFIT'97, pages 1279-1283, September 1997
Qualitative Uncertainty Models using Random Set Theory
Wolkenhauer O, Edmunds J
IDA'97, pages 609-620, August 1997
1996
Possibilistic Change Detection: The Onset of Oscillations
Wolkenhauer O
EUFIT'96, pages 1610-1613, September 1996
Dynamic Reliability Evaluation and Performance Monitoring
Wolkenhauer O
EUFIT'96, pages 951-955, September 1996