Kwang-hyun Cho, Sung-young Shin, Hyun-woo Kim, Olaf Wolkenhauer, Brian Mcferran, Walter Kolch
modeling of the influence of RKIP
Dynamics of receptor and protein transducer homodimerisation (2008)
Vera, Julio, Millat, Thomas, Kolch, Walter, Wolkenhauer, Olaf
Abstract Background Signalling pathways are complex systems in which not only simple monomeric molecules interact, but also more complex structures that include constitutive or induced protein...
Investigating the two-moment characterisation of subcellular biochemical networks (2008)
Ullah, Mukhtar, Wolkenhauer, Olaf
While ordinary differential equations (ODEs) form the conceptual framework for modelling many cellular processes, specific situations demand stochastic models to capture the influence of noise. The...
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway (2008)
Vera, Julio, Bachmann, Julie, Pfeifer, Andrea C, Becker, Verena, Hormiga, Jose A, Darias, Nestor, ...
Abstract Background The amplification of signals, defined as an increase in the intensity of a signal through networks of intracellular reactions, is considered one of the essential properties in...
ACCEPTED MANUSCRIPT Power-Law Models of Signal Transduction Pathways (2008)
Julio Vera, Eva Balsa-canto, Peter Wellstead, Julio R. Banga, Olaf Wolkenhauer, Julio Vera A, ...
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo...
Contents 1 Approximate Reasoning 4 1.1 Modus Pone" ...................... 6 1.2 CompositionalRule ofInfe["]T ............. 7 1.3 Fuzzy Implication OpeTwL"b .............. 9 2...
Fuzzy Relatial Biology - A Factor-Space Approach to Genome Analysis (2007)
Olaf Wolkenhauer, Robert Babuska, Control Systems Centre
With thestaggeramount of gene and prd( sequenceinfor( that is now available it is evident that the dynamics of biologicalr egulator mechanisms cannot beunder( od bymer identifying components,...
Fuzzy Regression Models - Fuzzy Clustering and Switching Regression (2007)
Contents 1 SwitchcN Regression 3 1.1 MixtureD ensity Estimation ............... 4 1.2 Fuzzy c-Regression Models ................ 5 1.3 Fuzzy c-Regression Algorithm .............. 7 2 Example: pH...
Fuzzy System Identification - Takagi-Sugeno Modelling and Identification (2007)
Contents 1 Model Structures 3 1.1 Linguistic Model ..................... 4 1.2 Fuzzy System as Basis Func=wD Approximator .... 5 1.3 Takagi-Sugeno Model ................... 7 1.4 IdentificX(wh of...
Fuzzy vs Statistical Classifiers - Bayesian Classifier, Singleton Fuzzy Model (2007)
Contents 1 Learning Objectives 3 2 Multivariate Analysis 4 3 Classification, Discrimination 5 4 Probabilistic Classifier 7 4.1 Kernel Densl y Es=PL[jgG ................ 8 5 Fuzzy Classifier 12 5.1...
Fuzzy Control - PI vs. Fuzzy PI-Control (2007)
Contents 1 Learning Objectives 4 2 Feedback Control 5 3Fuzzy PI-Controller 6 4 Example: First-Order System with Dead-Time 15 4.1 FuzzyRulew'kw ..................... 17 4.2 Ce tre AveSwk...
A Graphical Users Interface to Normalize Microarray Data (2007)
Kurt Hornik, Friedrich Leisch, Achim Zeileis (eds, Fatima Sanchez Cabo, Zlatko Trajanoski, Kwang-hyun Cho, ...
Microarray technology is becoming an essential tool in functional genomics. The possibility of monitoring the expression level of thousands of genes simultaneously, as the response to a particular...
A Graphical Users Interface to Normalize Microarray Data (2007)
Fatima Sanchez Cabo, Zlatko Trajanoski, Kwang-hyun Cho, Olaf Wolkenhauer
Microarray technology is becoming an essential tool in functional genomics. The possibility of monitoring the expression level of thousands of genes simultaneously, as the response to a particular...
Random Sets and Histograms (2007)
Javier Nuñez-garcia, Olaf Wolkenhauer
A probability density function verifies more demanding properties than a possibility measure. Probabilistic models ensure a predictable asymptotic behaviour. This should not be taken to suggest...
Optimal Sampling Time Selection for Parameter Estimation in (2007)
Dynamic Pathway Modelling, Zoltan Kutalik, Kwang-hyun Cho, Stevev. Gordon, Olaf Wolkenhauer
Systems Biology is an emerging research area, which considers mathematical representations of inter- and intra-cellular dynamics. Among the many research problems that have been addressed, dynamic...
understanding genome expression (2007)
Mathematical modelling in the post-genome era:
Functional Models and Probability Density Functions. (2007)
Javier Nuñez-garcia, Olaf Wolkenhauer
Abstract. There exist many approaches to discern a functional relationship between two variables. A functional model is useful for two reasons: Firstly, if the function is a relatively simple model...
A System-Theoretic Epistemology of Genomics (2007)
The text is organised as follows. In the first part, there are six main propositions, preceded by a definition. Referring mainly to the philosophy of Arthur Schopenhauer, the first proposition...
PLMaddon: a power-law module for the MatlabTM SBToolbox (2007)
Vera, Julio, Sun, Cheng, Oertel, Yvonne, Wolkenhauer, Olaf
Summary: PLMaddon is a General Public License (GPL) software module designed to expand the current version of the SBToolbox (a Matlab ™ toolbox for systems biology; www.sbtoolbox.org) with a set of...
SBML export interface for the systems biology toolbox for MATLAB (2007)
Schmidt, Hening, Drews, Gunnar, Vera, Julio, Wolkenhauer, Olaf
Summary: In this application note, we present an Systems biology markup language (SBML) export interface for the Systems Biology Toolbox for MATLAB. This interface allows modelers to automatically...
Approximations and their consequences for dynamic modelling of signal transduction pathways (2007)
Millat, Thomas, Bullinger, Eric, Rohwer, Johann, Wolkenhauer, Olaf
Signal transduction is the process by which the cell converts one kind of signal or stimulus into another. This involves a sequence of biochemical reactions, carried out by proteins. The dynamic...
A family tree of Markov models in systems biology (2006)
Ullah, Mukhtar, Wolkenhauer, Olaf
Motivated by applications in systems biology, we seek a probabilistic framework based on Markov processes to represent intracellular processes. We review the formal relationships between different...
Wellstead, Peter, Middleton, Rick, Wolkenhauer, Olaf
In its broadest definition, systems biology is the application of a `systems' way of thinking about and doing cell biology. By implication, this also invites us to consider a systems approach in the...
Intracellular delay limits cyclic changes in gene expression (2006)
Rateitschak, Katja, Wolkenhauer, Olaf
Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kB gene expression, we improve these models through a distributed delay formulation of the time...
The Curse of Normalization (2006)
Olaf Wolkenhauer, Carla Möller-Levet, Fatima Sanchez-Cabo
Despite its enormous promise to further our understanding of cellular processes involved in the regulation of gene expression, microarray technology generates data for which statistical...
Gutachter Prof, Dr. Rudolf Kruse, Prof Dr, Hans-joachim Lenz, Prof Dr, Olaf Wolkenhauer
angenommen durch die Fakultät für Informatik
Modelling and simulation of intracellular dynamics: Choosing an appropriate framework (2004)
Olaf Wolkenhauer, Mukhtar Ullah, Walter Kolch, Kwang-hyun Cho
Abstract--- Systems biology, that is, mathematical modelling and simulation of biochemical reaction networks in intracellular processes has gained renewed interest in recent years. For most...
A Study of the Statistical Distribution of the Intensity of (2004)
Pixels Within Spots, Javier Nuñez-garcia, Vassilios Mersinias, Kwang-hyun Cho, Colin P. Smith, Olaf Wolkenhauer
In this paper we open a discussion about an important issue found in the analysis of data from spotted DNA microarrays: how to summarise into a single value the distribution for the intensity values...
Kutalik, Zoltan, Inwald, Jacqueline, Gordon, Steve V., Hewinson, R. Glyn, Butcher, Philip, Hinds, Jason, ...
Motivation: When analyzing microarray data, non-biological variation introduces uncertainty in the analysis and interpretation. In this paper we focus on the validation of significant differences in...
Kwang-hyun Cho, Walter Kolch, Olaf Wolkenhauer
Mathematical modeling and dynamic simulation of signal transduction pathways is a central theme in systems biology and is increasingly attracting attention in the postgenomic era. The estimation of...
Fuzzy clustering of short time series and unevenly distributed sampling points (2003)
Frank Klawonn, Kwang-hyun Cho, Olaf Wolkenhauer
Abstract. This paper proposes a new algorithm in the fuzzy-c-means family, which is designed to cluster time-series and is particularly suited for short time-series and those with unevenly spaced...
Level sets and minimum volume sets of probability density functions (2003)
Javier Nuñez-garcia, Zoltan Kutalik, Kwang-hyun Cho, Olaf Wolkenhauer
Summarizing the whole support of a random variable into minimum volume sets of its probability density function is studied in the paper. We prove that the level sets of a probability density function...
DNA Microarray Data Clustering Based on Temporal (2003)
Variation Fcv With, Kwang-hyun Cho, Olaf Wolkenhauer
The aim of this paper is to present a new clustering algorithm for short time-series gene expression data that is able to characterize temporal relations in the clustering environment (i.e.,...
A Graphical Users Interface to Normalize Microarray Data (2003)
Fatima Sanchez Cabo, Zlatko Trajanoski, Kwang-hyun Cho, Olaf Wolkenhauer
Microarray technology is becoming an essential tool in functional genomics. The possibility of monitoring the expression level of thousands of genes simultaneously, as the response to a particular...
Mathematical modeling of the influence of RKIP on the ERK signaling pathway (2003)
Kwang-hyun Cho, Sung-young Shin, Hyun-woo Kim, Olaf Wolkenhauer, Brian Mcferran, Walter Kolch
Abstract. This paper investigates the influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signaling pathway through mathematical modeling and...
Cho, Kwang-Hyun, Shin, Sung-Young, Lee, Hyeon-Woo, Wolkenhauer, Olaf
In this study, we propose a system-theoretic approach to the analysis and quantitative modeling of the TNFα-mediated NF-κB-signaling pathway. Tumor necrosis factor α (TNFα) is a potent...
Cho, Kwang-Hyun, Shin, Sung-Young, Lee, Hyeon-Woo, Wolkenhauer, Olaf
In this study, we propose a system-theoretic approach to the analysis and quantitative modeling of the TNFα-mediated NF-κB-signaling pathway. Tumor necrosis factor α (TNFα) is a potent...
Fuzzy Relational Biology - A Factor-Space Approach to Genome Analysis (2002)
Contents 1 Biology for System Scientists 4 2 System Th:NJ for Biologists 8 3 Knowledge Representation 9 4 Reasoning about Data 18 5 Formalities 22 6 Conclusions 26 7 Appendix 28 ## ## # # Back View 3...
Department of Mathematics, (2002)
Yudong Cai, Andrew J. Doig, Olaf Wolkenhauer
Information theoretic analysis of protein sequences shows that amino acids self cluster
The Curse of Normalization (2002)
Olaf Wolkenhauer, Carla Möller-Levet, Fatima Sanchez-Cabo
Despite its enormous promise to further our understanding of cellular processes involved in the regulation of gene expression, microarray technology generates data for which statistical...
Systems biology: The reincarnation of systems theory applied in biology? (2001)
With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International...
A System-Theoretic Epistemology of Genomics (2000)
The text isorg33)Cj as follows. In the first part, there are six main propositions, preceded by a definition.Referring mainly to the philosophy of Arthur Schopenhauer, the first proposition provides...
Fuzzy Relational Biology - A Factor-Space Approach to Genome Analysis (2000)
objects may for example be answers to a question or concepts. Components are understood as interconnected objects or concepts. The factor f : U X(f) as a mapping from U to X(f) can also be understood...
Investigations Into the Analysis and Modeling of the TNFα-Mediated NF-κB-Signaling Pathway
Cho, Kwang-Hyun, Shin, Sung-Young, Lee, Hyeon-Woo, Wolkenhauer, Olaf
In this study, we propose a system-theoretic approach to the analysis and quantitative modeling of the TNFα-mediated NF-κB-signaling pathway. Tumor necrosis factor α (TNFα) is a potent...
Investigations Into the Analysis and Modeling of the TNFα-Mediated NF-κB-Signaling Pathway
Cho, Kwang-Hyun, Shin, Sung-Young, Lee, Hyeon-Woo, Wolkenhauer, Olaf
In this study, we propose a system-theoretic approach to the analysis and quantitative modeling of the TNFα-mediated NF-κB-signaling pathway. Tumor necrosis factor α (TNFα) is a potent...
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway
Vera, Julio, Bachmann, Julie, Pfeifer, Andrea C, Becker, Verena, Hormiga, Jose A, Darias, Nestor V Torres, ...
Wolkenhauer, Olaf, Möller-Levet, Carla, Sanchez-Cabo, Fatima
Despite its enormous promise to further our understanding of cellular processes involved in the regulation of gene expression, microarray technology generates data for which statistical...