systems biology, bioinformatics, data engineering

Publications
Journals

2010

S. Nikolov, J. Vera, R. Herwig, O. Wolkenhauer, V. Petrov: "Dynamics of microRNA regulation of cancer network". Comptes rendus de l’Acad´emie bulgare des Sciences Tome 63, No 1, 2010

K. Rateitschak, O. Wolkenhauer: Thresholds in transient dynamics of signal transduction pathways. Accepted for publication in Journal of Theoretical Biology 2010

K. Rateitschak, A. Karger, B. Fitzner, F. Lange, O. Wolkenhauer, and R. Jaster: Mathematical modelling of interferon-gamma signalling in pancreatic stellate cells reflects and predicts dynamics of STAT1 pathway activity. Cellular Signalling, 22 (2010) 97–105. doi:10.1016/j.cellsig.2009.09.019
J. Vera, J. Schultz, S. Ibrahim, O. Wolkenhauer, M. Kunz. Dynamical effects of epigenetic silencing of 14-3-3s expression. Molecular Biosystems, 2010, 6, 254 - 263, doi: 10.1039/b907863k.

2009

O.Wolkenhauer et al.: Systems biologists seek fuller integration of systems biology approaches in new cancer research program. Cancer Res; 70(1); 12-3. PMID: 20028868
J. Schultz, S.M. Ibrahim, J. Vera, M. Kunz. 14-3-3sigma gene silencing during melanoma progression and its role in cell cycle control and cellular senescence. Molecular Cancer, 8:53, 2009.
M. Ullah and O. Wolkenhauer: Stochastic approaches in systems biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 9999 (2009). doi:10.1002/wsbm.78
X. Lai, S. Nikolov, O. Wolkenhauer and J. Vera: A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. (2009) Comput. Biol. Chem, Vol.33(4), pp. 312-324.
O. Wolkenhauer, D. Fell, P. De Meyts, N. Bluethgen, H. Herzel, N. Le Noveere, T. Hoefer, K. Schuerrle and I. van Leeuwen: SysBioMed report: Advancing systems biology for medical application. IET Syst. Biol., 2009, Vol. 3, Iss. 3, pp. 131–136 doi: 10.1049/iet-syb.2009.0005
S. Nikolov, X. Lai, W. Liebal, O. Wolkenhauer and J. Vera: Integration of Sensitivity and Bifurcation Analysis to Detect Critical Processes in a Model Combining Signalling and Cell Population Dynamics. International Journal of Systems Science,2009, 41:1, 81—105. DOI: 10.1080/00207720903147746
D.V. Guebel, M. Canovas, N.V. Torrres: Model Identification in presence of incomplete information by Generalized Principal Component Analysis: Application to the determination of the common and specific responses to Escherichia coli to multiple responses in a continuous, high-cellular density culture. (2009) Biotechnology Bioengineering,Volume 104 Issue 4, Pages 785 - 795.
J. Vera, Alberto Marin-Sanguino and N. Torres.: Optimization of biochemical systems through mathematical programming: methods and applications. (2009) Computers & Operations Research.Volume 37, Issue 8, August 2010, Pages 1427-1438.doi:10.1016/j.cor.2009.02.021
S. Nikolov, X. Lai, O. Wolkenhauer and J. Vera: Time delay and protein modulation analysis in a model of RNA silencing. Communications of SIWN (CoSIWN) (ISSN 1757-4439), Vol. 6, April 2009, pp. 111-117. Appendix.
R. Aebersold et al. (including O. Wolkenhauer): Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research. Molecular Oncology 3 (2009) 9-17, doi:10.1016/j.molonc.2008.11.003.
J. Vera, T.Kwon, U.Schmitz, W.Kolch, O. Wolkenhauer: Exploration of homodimer receptor - homodimer protein interactions. International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 5, No.4 pp. 447 - 457, 2009, doi: 10.1504/IJBRA.2009.027518.
M. Ullah, O.Wolkenhauer: Investigating the two-moment characterisation of subcellular biochemical networks. Journal of Theoretical Biology, Vol. 260, No.3, pp. 340 - 352, October 2009, doi:10.1016/j.jtbi.2009.05.022
S. Nikolov, J. Vera, O. Rath, W. Kolch, O.Wolkenhauer: The role of inhibitory proteins as modulators of oscillations in NFkB signalling. IET Systems Biology3(2):59-76 (2009).
S. Nikolov, X. Lai, O. Wolkenhauer and J. Vera:: Time delay and Epo dose modulation in a multilevel model for erythropoiesis. Bioautomation, vol. 12, pp. 53-69, 2009.

2008

J.Vera, T.Millat, W.Kolch, O.Wolkenhauer: Dynamics of receptor and protein transducer homodimerisation. BMC Systems Biology, 2008 2:92.
S.Frey, Th.Millat, S.Hohmann, O.Wolkenhauer: How quantitative measures unravel design principles in multi-stage phosphorylation cascades. Journal of Theoretical Biology, 254 (2008) 27-36. doi:10.1016/j.jtbi.2008.04.037
J.Vera, J.Bachmann, A.Pfeifer, V.Becker, J.Hormiga, N.Torres Darias, J.Timmer, U.Klingmuller, O.Wolkenhauer: A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. BMC Systems Biology 2008, 2:38, doi:10.1186/1752-0509-2-38
J.Pahnke, O.Wolkenhauer, M.Krohn, L.D.K.Walker: Clinico-pathologic function of cerebral ABC transporters – implications for the pathogenesis of Alzheimer’s disease. Current Alzheimer Research, 5(4), 396-405, 2008.
S.Gerber, H.E.Assmus, B.M.Bakker, E.Klipp. Drug-efficacy depends on the inhibitor type and the target position in a metabolic - A systematic study. J.Theoret.Biol. 252(3), 442-455, 2008
H.Schmidt, M.Madsen, S.Danø, G.Cedersund: Complexity Reduction of Biochemical Rate Expressions. Bioinformatics, 15;24(6):848-54, 2008, doi:10.1093/bioinformatics/btn035.
D.Dell'Orco, H.Schmidt: Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in the ROS-disc membrane. Journal of Physical Chemistry, 112:14, 4419-4426 (2008).
O.Wolkenhauer, J.H. Hofmeyr: Ein Beitrag zu einer Theorie lebender Zellen. at - Automatisierungstechnik, Jahrgang 56 (2008) Heft 5, 225-232. DOI 10.1524/auto.2008.0707
S.Nikolov, J.Vera, O.Wolkenhauer, V.Petrov: Dynamic properties of a delayed protein cross talk model. BioSystems, 91, 51–68, January 2008.
T.Millat, S.N.Sreenath, R.P.Soebiyanto, J.Avva, K.-H.Cho, and Olaf Wolkenhauer: The role of dynamic stimulation pattern in the analysis of bistable intracellular networks. BioSystems 92(3), 270-281 (2008). doi:10.1016/j.biosystems.2008.03.007

2007

O.Wolkenhauer: Defining Systems Biology: An Engineering Perspective. IET Systems Biology, Vol. 1, No. 4, 204-206, 2007.
S.Nikolov, G.Georgiev, V.Kotev, O.Wolkenhauer: Stability Analysis of a time delay model for the JAK-STAT signalling pathway. Series on Biomechanics, Vol.23, No.1, 2007, 52-65
S.Nikolov, E.Yankulova, O.Wolkenhauer, V.Petrov: Principal Difference Between Stability and Structural Stability (Robustness) as Used in Systems Biology. Nonlinear Dynamics, Psychology, and Life Sciences, Vol. 11, No. 4, 413-433, 2007.
J.Vera, C.Sun, Y.Oertel, O.Wolkenhauer: PLMaddon: a power-law module for the Matlab SBToolbox. Bioinformatics, Vol. 23 no. 19, 2638–2640, 2007
O.Wolkenhauer: Interpreting Rosen. Artificial Life 13: 1-2 (2007)
S.Nikolov, J.Vera, O.Wolkenhauer, V.Petrov: Investigation of dynamic behaviour of receptor tyrosin kinase and protein tyrosine phospatase reaction network using mathematical model. International Electronic Journal of Bioautomation (IEJB), 8(1):105-114, 2007
S.Nikolov, J.Vera, O.Wolkenhauer, E.Yankulova and V.Petrov: Chaos in a delayed protein cross talk model with periodic forcing (2007). Comptes rendus de l’Academie bulgare des Sciences, Vol.60, No 2, 127-132, 2007
H.Schmidt, G.Drews, J.Vera, O.Wolkenhauer: SBML Export Interface for Systems Biology Toolbox for Matlab. Bioinformatics, 23, 1297-1298, 2007
S.N.Sreenath, R.Soebyanto, M.D.Mesarovic, O.Wolkenhauer: Coordination of Crosstalk between MAPK-PKC Pathways: An Exploratory Study. IET Systems Biology, 33-40, Vol. 1, Issue 1, January 2007.
V.Petrov, E.Nikolova, and O.Wolkenhauer: Reduction of Nonlinear Dynamic Systems with an Application to Signal Transduction Pathways. IET Systems Biology, 2-9, Vol. 1, Issue 1, January 2007.
K.Rateitschak, O.Wolkenhauer: Intracellular delay limits cyclic changes in gene expression. Mathematical Biosciences. 2007 Feb, 205(2):163-79. Epub Aug 2006 doi:10.1016/j.mbs.2006.08.010
J.Vera, E. Balsa-Canto, P.Wellstead, J.R.Banga, O.Wolkenhauer: Power-Law Models of Signal Transduction Pathways. Cellular Signalling. 19 (2007): 1531-1541 (PMID: 17399948).
R.Hoffrogge, S.Beyer, R.Hübner, S.Mikkat, E.Mix, C.Scharf, U.Schmitz, S.Pauleweit, M.Berth, I.Z.Zbrzycki, H.Christoph, J.Pahnke, O.Wolkenhauer, A.Uhrmacher, U.Völker, R.Rolfs: 2-DE profiling of GDNF overexpression-related proteome changes in differentiating ST14A rat progenitor cells. Proteomics 2007, 7, 33-46.
T.Millat, E.Bullinger, J.Rohwer, O.Wolkenhauer: Approximations and their Consequences in Dynamic Modelling of Signal Transduction Pathways. Mathematical Biosciences 47 (2007) 40-57. doi 10.1016/j.mbs.2006.08.01.
O.Wolkenhauer, J.-H.Hofmeyr: An Abstract Cell Model that describes the Self-Organization of Cell Function in Living Systems. Journal of Theoretical Biology 246 (2007) 461-476. doi:10.1016/j.jtbi.2007.01.005 (8 Min Einführung (in German), 7MB WMA Datei)
M.Ullah, O.Wolkenhauer: Family tree of Markov models in systems biology . IET Systems Biology. 1(4): 247-254, 2007

2006

C.Lange, E.Mix, K.Rateitschak, A.Rolfs: Wnt Signal Pathways and Neural Stem Cell Differentiation. Neurodegenerative Dis. 2006; 3: 76-86
H.E.Assmus, R.Herwig, K.-H.Cho, O.Wolkenhauer: Dynamics of biological systems: the role of systems biology in medical research. Expert Rev. Mol. Diagn. 6(6), 891-902, 2006
S.-Y.Shin, S.-M.Choo,D.Kim, S.-J.Baek, O.Wolkenhauer, K.-H.Cho: Switching Feedback Mechanisms Realize the Dual Role of MCIP in the Regulation of Calcineurin Activity. FEBS Letters 580 (2006) 5965-5973.
M.Dehmer, Emmert-Streib F., Kilian J.: A Similarity Measure for Graphs with low computational complexity, to appear: Applied Mathematics and Computation, Elsevier, 2006
M.Dehmer, Mehler A.: A new Method of Measuring Similarity for a Special Class of Directed Graphs, to appear: Tatra Mountains Mathematical Publications, 2006
M.Dehmer: On the Location of Zeros for complex Polynomials, Journal of Inequalities in Pure and Applied Mathematics, Vol. 7, Issue 1, 2006
F.Emmert-Streib, Dehmer M., Liu J., Mühlhäuser M.: Ranking Genes from DNA Microarray Data of Cervical Cancer by a local Tree Comparison, International Journal of Biomedical Science, 2006
M.Dehmer, Emmert-Streib F., Mehler A., Kilian J.: Measuring the Structural Similarity of Webbased Documents: A novel Approach, International Journal of Computational Intelligence 3:1, 2006
M.Dehmer, Emmert-Streib F., Mehler A.: Mining Graph Patterns in Web-based Systems, submitted to International Journal of Intelligent Information Technologies, January 2006
M.Dehmer, F.Emmert-Streib, O. Wolkenhauer:Perspectives of Graph Mining Techniques. Rostocker Informatik Berichte 30(2) (2006) 47-56 (ISSN 0233-0784)
H.Schmidt, M.Jirstrand, O.Wolkenhauer: Information Technology in Systems Biology. it - Information Technology, 3/2006, 133-139.
P.Wellstead, R.Middleton, O.Wolkenhauer: Feedback Medicine: Control Systems Concepts in Personalised, Predictive Medicine and Combinatorial Intervention. arXiv:q-bio.TO/0603032 v1 27 March 2006.
A.Glass, T.Koropka, O.Wolkenhauer: Bioinformatics and The Virtual Cell, it - Information Technology, Vol.48, Nr.1, 44-51, February 2006.
M.Ullah, H.Schmidt, K-H.Cho and O.Wolkenhauer: Deterministic Modelling and Stochastic Simulation of Pathways using MATLAB IEE Proc Systems Biology, Vol.153, No.2, 53-60, March 2006. SUPPLEMENTARY MATERIAL.

2005

K.-H.Cho, O.Wolkenhauer: Systems Biology: Discovering the Dynamic Behavior of Biochemical Networks. BioSystems Review, Vol.1, No.1, 9-17, March 2005.
C.Vogl, F.Sanchez-Cabo, G.Stocker, S.Hubbard, O.Wolkenhauer, Z.Trajanoski: A fully Bayesian model to cluster gene expression profiles. Bioinformatics, 21 Suppl 2: ii130-ii136. PMID: 16204092, 2005.
K.-H.Cho, S.-M. Choo, P.Wellstead, and O.Wolkenhauer: A Unified Framework for Unraveling the Interaction Model Structure of a Biochemical Network using Stimulus-Response Data. FEBS Letters, 579 (2005) 4520-4528.
V.Petrov, E.Nikolova, O.Wolkenhauer: A driver identification of the Ras/Raf/MEK/ERK signal transduction pathway. Comptes Rendus d. l'Acad. Bulg. Sci., Tome 58, No. 6, 639-644, 2005.
O.Wolkenhauer, M.Mesarovic: Feedback Dynamics and Cell Function: Why Systems Biology is called Systems Biology. Molecular BioSystems, Royal Society of Chemistry. Vol.1, No.1, 14-16, May 2005.
O.Wolkenhauer, M.Ullah, P.Wellstead, K.H.Cho: The Dynamic Systems Approach to Control and Regulation of IntraCellular Networks. FEBS Letters 579 (2005), 1846-1853.
O.Wolkenhauer, S.Sreenath, P.Wellstead, M.Ullah, K.H.Cho: A Systems- and Signal-Oriented Approach to IntraCellular Dynamics.Biochemical Society Transactions, Vol.33, Part 3, 507-515, 2005.
C.Moller-Levet, F.Klawonn, K.-H.Cho, H.Yin and O.Wolkenhauer: Clustering of unevenly sampled gene expression time-series data. Fuzzy Sets and Systems 152(1):49-66, 2005.
K.-H.Cho, K.H. Johansson, O.Wolkenhauer: A Hybrid Systems Framework for Cellular Processes. BioSystems, Vol.80, 273-282, 2005.

Before 2005

Z.Kutalik, Razaz, M., Inwald, J., Gordon, S.V. and Wolkenhauer, O.: A novel statistical approach in comparative genomics to reveal new immunogenic antigens in M. bovis. Tissue Antigens, 64 (4), 427-427, 2004.
O.Wolkenhauer, M.Ullah, W.Kolch, K.-H.Cho: Modelling and Simulation of IntraCellular Dynamics: Choosing an Appropriate Framework. IEEE Transactions on NanoBioScience, Vol. 3, No. 3, 200-207, September 2004. Supplementary material.
H.Hackl, F.Sanchez-Cabo, A.Sturn, O.Wolkenhauer, Z.Trajanoski: Analysis of DNA microarray data. Curr. Top. Med. Chem., 4:1355-1368, 2004.
K.-H.Cho and O.Wolkenhauer: Analysis and modelling of signal transduction pathways in systems biology. Biochemical Society Transactions. Vol.31, Part 6, 1503-1509, 2003.
J.Nunez-Garcia, V.Mersinias, K.-H.Cho, C.P.Smith and O.Wolkenhauer: The statistical distribution of the intensity of pixels within spots of DNA microarrays: what is the appropriate single-value representative?. Applied Bioinformatics 2003:2(4), 229-239.
Z.Kutalik, K.-H.Cho, and O.Wolkenhauer: Optimal Sampling Time Selection for Parameter Estimation in Signal Transduction Pathway Modelling. BioSystems 75 (2004) 43-55. Supplementary material.
K.-H.Cho, S.-Y.Shin, W.Kolch, and O.Wolkenhauer: Experimental Design in Systems Biology Based on Parameter Sensitivity Analysis with Monte Carlo Simulation: A Case Study for the TNFalpha Mediated NF-kappaB Signal Transduction Pathway. Simulation, Vol. 79, No. 11-12, December 2003.
F.Sanchez-Cabo, K.-H.Cho, J.Hinds and O.Wolkenhauer: Assessing the efficiency of dye-swap normalization to remove systematic bias from two-color microarray data. Accepted for publication in Applied Bioinformatics. Supplementary material.
C.Moller-Levet, K.-H.Cho, and O.Wolkenhauer: Microarray Data Clustering based on Temporal Variation: FCV with TSD Preclustering © Open Mind Journals. Applied Bioinformatics 2(1), 35-45, 2003. Supplementary material.
Z.Kutalik, J.Inwald, S.V.Gordon, R.G.Hewinson, P.Butcher, J.Hinds, K.-H.Cho, and O.Wolkenhauer: Advanced Significance Analysis of microarray data based on weighted resampling: A comparative study and application to gene deletions in Mycobacterium bovis. Bioinformatics. Supplementary material, Vol. 20, No. 3, 357-363, 2004.
J.Nunez-Garcia, Z.Kutalik, K.-H.Cho and O.Wolkenhauer: Level Sets and Minimum Volume Sets of Probability Density Functions. Approximate Reasoning Vol. 34, 25-47, September 2003.
K-H.Cho, J-H.Cha, and O.Wolkenhauer: Optimization of Genetic Switching Systems based on SQP: A Synthetic lambda-switch System. Submitted for publication.
K-H.Cho, S-Y Shin, H-W Lee, and O.Wolkenhauer: Investigations in the Analysis and Modelling of the TNFalpha Mediated NF-kappaB Signaling Pathway. Genome Research 13:2413-2422, 2003.
O.Wolkenhauer, H.Kitano, K-H.Cho: An introduction to systems biology. IEEE Control Systems Magazine, Vol.23, No.4, 38-48, August 2003.
O.Wolkenhauer, C.Moller-Levet, and F.Sanchez-Cabo: The Curse of Normalisation. Comparative and Functional Genomics, 3: 375-379, Copyright Wiley, 2002.
Y.Cai, C.J.T.Dodson, A.Doig and O.Wolkenhauer: Information Theoretic Analysis of Protein Sequences shows that Amino Acids Self Cluster. Journal of Theoretical Biology (2002), 218, 409-418, Copyright Academic Press .
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O.Wolkenhauer: Mathematical Modelling in the Post-Genome Era: Understanding Genome Expression and Regulation - A Systems Theoretic Approach. BioSystems, Vol. 65, No. 1, 1-18, February 2002, Elsevier Science.
J.Nunez-Garcia and O.Wolkenhauer: Random-Set System Identification. IEEE Transactions on Fuzzy Systems. Vol.10, No.3, 287-296, June 2002.
K.S.Sidhu, P.Sangvanich, F.L.Brancia, A.G.Sullivan, S.J.Gaskell, O.Wolkenhauer, S.G.Oliver and S.J.Hubbard: Bioinformatic Assessment of Mass Spectrometric Chemical Derivatisation Techniques for Proteome Database Searching. Proteomics, 1, 1368 - 1377, 2001.
O.Wolkenhauer: Systems Biology: the reincarnation of systems theory applied in biology? Briefings in Bioinformatics, Copyright Henri Stewart Publications, Vol. 2, No. 3, 258-270, 2001.
O.Wolkenhauer and J.Edmunds: Dynamic Systems Reliability Evaluation using Uncertainty Techniques for Performance Monitoring. IEE Proc.- Control Theory Appl., Vol.144, No.1, pages 103-108, Jan 1997.
O.Wolkenhauer and J.Edmunds: Possibilistic Testing of Distribution Functions for Change Detection. Intelligent Data Analysis, Elsevier Science. Vol.1 (2), 119-127, 1997.
O.Wolkenhauer and J.Edmunds: A Critique of Fuzzy Logic in Control. IJEEE (International Journal of Electrical Engineering Education), Vol. 34, No.3, 235-242, July 1997.