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
Books
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Inflammation Resolution and Chronic Diseases
Tripathi A, Dwivedi A, Gupta S, Poojan S (eds.)
ISBN 13 (print): 978-981-97-0156-8
ISBN 13 (online): 978-981-97-0157-5
DOI: 10.1007/978-981-97-0157-5
URL: https://link.springer.com/book/10.1007/978-981-97-0157-5
![](assets/images/5/Systems%20Biology%20of%20MicroRNAs%20in%20Cancer-002091c5.jpg)
Systems Biology of MicroRNAs in Cancer (Advances in Experimental Medicine and Biology, 1385, Band 1385)
Schmitz U, Wolkenhauer O, Vera-González J
![](assets/images/e/3-s2.0-C20171022560-cov200h-f616daab.gif)
Systems Medicine - Integrative, Qualitative, and Computational Approaches
Wolkenhauer O (Editor-in-Chief)
Academic Press 2020
ISBN 13 (online): 978-0-12-816078-7
URL: https://www.sciencedirect.com/referencework/9780128160787/systems-medicine
![](assets/images/3/springer2-bf4c8eea.jpg)
Computational Biology of Non-Coding RNA
Lai X, Gupta SK, Vera J (eds.)
Springer (2019), part of the Methods in Molecular Biology book series (MIMB, volume 1912)
![](assets/images/a/systems-medicine-498b50c4.png)
Systems Medicine
Schmitz U, Wolkenhauer O, (eds.)
Springer (2016), Series Title Methods in Molecular Biology
ISBN 13 (print): 9781493932825
ISBN 13 (online): 9781493932832
URL: http://link.springer.com/book/10.1007/978-1-4939-3283-2
![](assets/images/8/SBI_Books_microRNACancerRegulation_01-3afd6abe.jpg)
MicroRNA Cancer Regulation - Advanced Concepts, Bioinformatics and Systems Biology Tools
Schmitz U, Wolkenhauer O, Vera J (eds.)
Series: Advances in Experimental Medicine and Biology, Vol. 774
Springer 2012.
ISBN 13 (print): 9789400755895
URL: http://www.springer.com/biomed/cancer/book/978-94-007-5589-5
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Nich lang schnacken - Ein plattdeutsches Konversationshandbuch
Wolkenhauer O
Quickborn-Verlag 2012.
ISBN 10 (print): 3876513774
ISBN 13 (print): 9783876513775
![](assets/images/a/SBI_Books_EncyclopediaOfSystemsBiology-ca4ca978.jpg)
Encyclopedia of Systems Biology
Dubitzky W, Wolkenhauer O, Yokata H, Cho K-H (eds.)
Springer 2013.
ISBN 13 (print): 9781441998620
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Stochastic Approaches for Systems Biology
Ullah M, Wolkenhauer O
ISBN 10 (print): 1461404770
Amazon: Buy it now
URL: http://www.springer.com/mathematics/probability/book/978-1-4614-0477-4
Software
The following .zip archives contain all the files needed to reproduce plots in the book.
- Matlab files (includes .m scripts and functions, and .mat data files; file names are the same as used in the book. For example, the function make2MA on page 174 is listed in the archive as make2MA.m . The scripts in the archive can be looked for understanding how to use various functions mentioned in the book.)
- Cain files (includes .xml and .svg files produced with http://cain.sourceforge.net)
Errata
The following file lists typos and errors found in the book.
Errata.pdf
![](assets/images/3/SBI_Books_SystemsBiology-3e1eef2f.jpg)
Systems Biology
Wolkenhauer O, Wellstead P, Cho KH (eds.)
Portland Press (Essays in Biochemistry Series), 2008
ISBN 10 (print): 1855781700
![](assets/images/0/SBI_Books_DataEngineering-5bda4ff7.jpg)
Data Engineering: Fuzzy Mathematics in System Theory and Data Analysis
Wolkenhauer O
John Wiley and Sons 2001.
ISBN 10 (print): 0471416568
![](assets/images/e/SBI_Books_PossibilityTheory-8cc0764c.jpg)
Possibility Theory with Applications to Data Analysis
Wolkenhauer O
Research Studies Press 1998.
ISBN 10 (print): 086380229X
Chapters in Books
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Mechanistic Understanding of Inflammation Resolution Using the Atlas of Inflammation Resolution (AIR)
Müller RLJ, Cavallo C, Gupta SS, Hoch M, Gupta S
In: Tripathi, A., Dwivedi, A., Gupta, S., Poojan, S. (eds) Inflammation Resolution and Chronic Diseases. Springer, Singapore.
ISBN 13 (print): 978-981-97-0156-8
ISBN 13 (online): 978-981-97-0157-5
DOI: 10.1007/978-981-97-0157-5_13
URL: https://link.springer.com/chapter/10.1007/978-981-97-0157-5_13
![](assets/images/e/978-981-97-0157-5-b360bdb9.png)
Mechanistic Understanding of Inflammation Resolution Using the Atlas of Inflammation Resolution (AIR)
Müller RLJ, Cavallo C, Gupta SS, Hoch M, Gupta S
In: Tripathi, A., Dwivedi, A., Gupta, S., Poojan, S. (eds) Inflammation Resolution and Chronic Diseases. Springer, Singapore.
ISBN 13 (print): 978-981-97-0156-8
ISBN 13 (online): 978-981-97-0157-5
DOI: 10.1007/978-981-97-0157-5_13
URL: https://link.springer.com/chapter/10.1007/978-981-97-0157-5_13
![](assets/images/e/978-981-97-0157-5-b360bdb9.png)
Are Multi-Component Drugs Better in Resolving the Inflammation Compared to the Single-Component Drugs?
Cavallo C, Hoch M, Gupta S
In: Tripathi, A., Dwivedi, A., Gupta, S., Poojan, S. (eds) Inflammation Resolution and Chronic Diseases. Springer, Singapore.
ISBN 13 (print): 978-981-97-0156-8
ISBN 13 (online): 978-981-97-0157-5
DOI: 10.1007/978-981-97-0157-5_10
URL: https://link.springer.com/chapter/10.1007/978-981-97-0157-5_10
![](assets/images/e/978-981-97-0157-5-b360bdb9.png)
Inflammation Resolution Mediators: Future Prospects
Müller RLJ, Hoch M, Gupta S
In: Tripathi, A., Dwivedi, A., Gupta, S., Poojan, S. (eds) Inflammation Resolution and Chronic Diseases. Springer, Singapore.
ISBN 13 (print): 9789819701568
ISBN 13 (online): 9789819701575
DOI: 10.1007/978-981-97-0157-5_9
URL: https://link.springer.com/book/10.1007/978-981-97-0157-5
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Systembiologie
Wolkenhauer O, Gebhardt T.
In: Bioanalytik; Kurreck J, Engels JW, Lottspeich Fr (Eds), Springer 2022, 1145 - 1153
URL: https://link.springer.com/book/10.1007/978-3-662-61707-6
ISBN 13 (print): 978-3-662-61706-9
![](assets/images/4/bio-2114e19e.png)
Single-Cell RNA Sequencing Procedures and Data Analysis
Wolfien M, David R, Galow AM
Exon Publications, Brisbane, Australia (2021), chapter in Bioinformatics.
ISBN 13 (online): 978-0-6450017-1-6
DOI: 10.36255/exonpublications.bioinformatics.2021.ch2
URL: https://exonpublications.com/index.php/exon/article/view/265
![](assets/images/e/3-s2.0-C20171022560-cov200h-f616daab.gif)
Network Biology Approaches in Ophthalmological Diseases: A Case Study of Glaucoma
Choudhari JK, Chatterjee T, Gupta SK, Garcia-Garcia JG, Vera J
In Systems Medicine: Integrative, qualitative and computational approaches (2020)
![](assets/images/8/978-3-030-30845-2-ec6c5db4.jpg)
Envisioning the Application of Systems Biology in Cancer Immunology
Jaitly T, Gupta SK, Wolkenhauer O, Schuler G, Vera J
In: Rezaei N. (eds) Cancer Immunology. Springer, Cham. (2020)
ISBN 13 (print): 978-3-030-30844-5
ISBN 13 (online): 978-3-030-30845-2
DOI: 10.1007/978-3-030-30845-2_27
URL: https://link.springer.com/chapter/10.1007/978-3-030-30845-2_27
![](assets/images/9/978-1-4939-9736-7-b7b3c930.jpg)
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices
Scharm M, Stanford NJ, Dobson PD et al.
Springer (2019), chapter in Yeast Systems Biology.
Methods in Molecular Biology.
ISBN 10 (online): 978-1-4939-9736-7
DOI: 10.1007/978-1-4939-9736-7_17
URL: https://link.springer.com/protocol/10.1007%2F978-1-4939-9736-7_17
![](assets/images/3/springer2-bf4c8eea.jpg)
Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
Bagnacani A, Wolfien M, Wolkenhauer O
Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.
![](assets/images/3/springer2-bf4c8eea.jpg)
Workflow Development for the Functional Characterization of ncRNAs
Wolfien M, Brauer DL, Bagnacani A, Wolkenhauer O
Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.
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Applications of genome-scale metabolic models and data integration in systems medicine
Salehzadeh-Yazdi A, Wolfien M, Wolkenhauer O
Nova (2019), chapter in Focus on Systems Theory Research
ISBN 13 (online): 9781536145618
![](assets/images/a/essay_in_Biochemistry-062126b8.jpg)
Integrative workflow for network analysis
Faiz M. Khan, Shailendra K. Gupta, Olaf Wolkenhauer
![](assets/images/1/Springer%20Protocols2.jpg-6e6f7b10.png)
A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression.
Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O
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From Microscopes to Macroscopes: Advancing Biomedical Research Through Systems Approaches
Olaf Wolkenhauer
Chapter in Philosophy of Systems Biology (Springer)
Part of the series History, Philosophy and Theory of the Life Sciences pp 257-265
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Biochemical pathway modeling tools for drug target detection in Cancer and other complex diseases
Marin-Sanguino A, Gupta SK, Voit EO, Vera J
In Michael Johnson editor: Methods in Enzymology, Vol. 487,
Burlington: Academic Press, 2010, pp 319-370.
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Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive
Eberhardt M, Lai X, Tomar N, Gupta SK, Schmech B, Steinkasserer A, Schuler G, Vera J
In: Systems Medicine, Methods in Molecular Biology (2016) 1386: 135-179.
Published by Springer.
ISBN 13 (print): 9781493932825
![](assets/images/a/systems-medicine-498b50c4.png)
Network-Assisted Disease Classification and Biomarker Discovery
S. Strunz, O. Wolkenhauer, A. de la Fuente
In Springer (2016), Systems Medicine, pp 353-374
ISBN 13 (print): 9781493932825
ISBN 13 (online): 9781493932832
URL: http://link.springer.com/protocol/10.1007/978-1-4939-3283-2_16
![](assets/images/a/systems-medicine-498b50c4.png)
RNA Systems Biology for Cancer: From Diagnosis to Therapy
R. Amirkhah, A. Farazmand, O. Wolkenhauer, U. Schmitz
In Springer (2016), Systems Medicine, pp 305-330
ISBN 13 (print): 9781493932825
ISBN 13 (online): 9781493932832
URL: http://link.springer.com/protocol/10.1007/978-1-4939-3283-2_14
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Mehrebenensysteme in der Systembiologie
Theile T, Wolkenhauer O
Wissenschaft und Kunst der Modellierung. De Gruyter 2015.
![](assets/images/8/2_01-cac2acb7.png)
Envisioning the Application of Systems Biology in Cancer
J.Vera, S.Gupta, O.Wolkenhauer, G.Schuler (2015)
In Cancer Immunology, N.Rezaei (ed.), 429-449, Springer 2015
ISBN 13 (print): 9783662440063
![](assets/images/5/book_01-cffbde58.png)
Explanation and Organizing Principles in Systems Biology
T.Breidenmoser, O.Wolkenhauer (2015)
In Explanation in Biology, P-A Braillard, C Malaterre (eds), 249-264, Springer 2015
ISBN 13 (print): 9789401798228
![](assets/images/2/3-0565eb91.png)
Mehrebenensysteme in der Biomedizin
T.Theile, O.Wolkenhauer (2015)
In Wissenschaft und Kunst der Modellierung, B.Thalheim, I.Nissen (eds), 455-474, De Gruyter 2015
ISBN 13 (print): 9781501510403
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Modelle und ihre Befragbarkeit als Grundlage biomedizinischer Erkenntnis
Wolkenhauer, O
Erwägen-Wissen-Ethik. Vol 26 Nr 3 (2015), 420-422
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Cancer Systems Biology: Current Achievements in – Omics Data Analysis, Network Reconstruction and Mathematical Modelling
Vera J, Wolkenhauer O, Schmitz U (2014)
In: eLS. John Wiley & Sons Ltd, Chichester.
![](assets/images/f/SB_Book_Springer_title_01-ef7d4e5a.jpg)
Reproducibility of model-based results in systems biology
D Waltemath, R Henkel, F Winter, O Wolkenhauer
In: Systems Biology: Integrative Biology and Simulation Tools 1, pp 301-320. Prokop A, Csukas B (eds) Springer (2013)
![](assets/images/d/9789400758445_p0_v1_s260x420-e9681c0a.png)
Interdisciplinarity as both necessity and hurdle for progress in the life sciences
Wolkenhauer O, Hofmeyr J (2013)
in: Andersen H, Dieks D, Gonzales WJ, Uebel T, Wheeler G, eds.
New Challenges to Philosophy of Science - The Philosophy of Science in a European perspective 4. Springer Verlag, 2013, 225-235
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Modeling Colorectal Cancer: A Stability Analysis Approach
Nikolow S, Ullah M, Nenov M, Gonzales JV, Raasch P, Wolkenhauer O
in: Medical Advancements in Aging and Regenerative Technologies; Daskalaki A
Clinical Tools and Applications: 53-75
IGI Global 2013
![](assets/images/e/978-3-642-34335-3-db84e069.jpg)
Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation
Pauleweit S, Nebe BJ, Wolkenhauer O
in: Simulation and Modeling Methodologies, Technologies and Applications; Nuno P, Janusz K, Joaquim F (eds.); series: Advances in Intelligent Systems and Computing.
ISBN 13 (print): 9783642343353
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The pH-induced metabolic shift from acidogenesis to solventogenesis in Clostridium acetobutylicum - From experiments to models
Millat T, Janssen H, Bahl H, Fischer R-J, Wolkenhauer O
in: Proceedings of the 5th Internation ESCEC Symposium on "Experimental Standard Conditions of Enzyme Characterization", Kettner, C (ed.); Logos Verlag Berlin 2013.
ISBN 13 (print): 9783832533670
![](assets/images/a/SBI_Books_EncyclopediaOfSystemsBiology-ca4ca978.jpg)
Computational microRNA biology
Schmitz U, Vera J
in: Encyclopedia of Systems Biology; Dubitzky W, Wolkenhauer O, Yokata H, Cho K-H (eds.); Springer 2012.
ISBN 13 (print): 9781441998620
![](assets/images/c/ClostridiumModelling_01-bbd17365.jpg)
Mathematical modelling of the pH-induced metabolic shift in Clostridium acetobutylicum
Millat T, Haus S, Wolkenhauer O
in: Systems Biology of Clostridium acetobutylicum, Dürre P (ed.), Imperial College Press, 2014, 103-130.
ISBN 13 (print): 9781783264407
![](assets/images/b/nikolov-1fe10ef0.jpg)
Bifurcation Analysis of a Model Accounting for the 14-3-3s Signalling Compartmentalisation
Nikolov S, Vera J, Wolkenhauer O
in: Quality Assurance in Healthcare Service Delivery, Nursing, and Personalized Medicine: Technologies and Processes. Lazakidou A, Daskalaki A (eds.); Medical Information Science Reference 2011.
ISBN 10 (print): 161350120X
![](assets/images/d/nova-0e481faf.jpg)
Bioinformatics Analysis of High-Throughput Experiments
Gupta S, Schmitz U
in: Recent Trends in Biotechnology. Volume 2; Singh M P, Agrawal A, Sharma B (eds.); Nova Science Publishers 2011.
ISBN 13 (print): 9781617617973
![](assets/images/8/millat-9781607619864_01-de20c832.jpg)
Modeling of Cellular Processes: Methods, Data, and Requirements
Millat T, Wolkenhauer O, Fischer, RJ, Bahl, H
in: Data Mining in Proteomics; Hamacher M, Eisenacher M, Stephan C (eds.); Springer 2011.
ISBN 13 (print): 9781607019864
![](assets/images/0/ISBN_978-1-61779-832-0-764effc2.jpg)
Modelling miRNA regulation in cancer signalling systems: miR-34a regulation of the p53/Sirt1 signalling module
Lai X, Wolkenhauer O, Vera J
in: Computational Modelling of Signalling Networks; Liu X, Betterton M (eds.); Humana 2012.
ISBN 13 (print): 9781617798230
![](assets/images/6/wolkenhauer-3540633464-29764719.jpg)
Qualitative Uncertainty Models using Random Set Theory
Wolkenhauer O
in: Advances in Intelligent Data Analysis; Liu X, Cohen P, Berthold M (eds.); Springer LNCS 1280, 1997.
ISBN 10 (print): 3540633464
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Interferon-g stimulated STAT1 signalling: from experimental data to a predictive mathematical model
Rateitschak K, Jaster R, Wolkenhauer O
in: Proceedings of the 4th International Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations; Hicks MG , Kettner C (eds.); Logos Berlin 2010.
ISBN 13 (print): 9783832526067
![](assets/images/1/frey-9780262013345-35912f5b.jpg)
Quantifying properties of cell signaling cascades
Frey S, Wolkenhauer O, Millat T
in: Control Theory and Systems Biology; Iglesias P A, Ingalls B (eds.); MIT press 2009.
ISBN 13 (print): 9780262013345
![](assets/images/7/wolkenhauer-9780470261231-d0e210e2.jpg)
Methods in In Silico Biology: Modeling Feedback and Dynamics
Wolkenhauer O, Wellstead P
in: Systems Biology for Drug Discovery and Development; Young D, Michelson S (eds); Wiley 2011.
ISBN 13 (print): 9780470261231
![](assets/images/4/wolkenhauer-9780444520760-551b27b6.jpg)
The Complexity of Cell-Biological Systems
Wolkenhauer O, Muir A
in: Philosophy of Complex Systems Vol. 10; 345-385; Hooker CA (ed.); series: Handbook of the Philosophy of Science; North-Holland 2011.
ISBN 13 (print): 9780444520760
![](assets/images/1/assmus-9781596934061-8cde1c29.jpg)
Reverse Engineering of Biological Networks
Assmus HE, Boldt S, Wolkenhauer O
in: Methods in Bioengineering: Systems Analysis of Biological Networks; Jayaraman A, Hahn J (eds.); Artech House 2009.
ISBN 13 (print): 9781596934061
![](assets/images/4/gupta-9781608761487-283548fa.jpg)
Enriching biotechnology with recent bioinformatics tools and protocols
Gupta SK, Smita S, Rahman Q
in: Recent trends in Biotechnology; Singh MP, Agrawal A, Sharma B (eds.); Nova Science Publishers Inc. 2011.
ISBN 13 (print): 9781608761487
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Case study in systematic modelling: Thiamine uptake in Yeast S. cerevisiae, book chapter, Essays
Ericsson A, Mojzita D, Schmidt H, Hohmann S
In: Biochemistry - Systems Biology, Portland Press, accepted (2008)
![](assets/images/d/wellstead-1605660760-8375e30c.jpg)
Systems and Control Theory for Medical Systems Biology
Wellstead P, Sreenath S, Cho KH, Wolkenhauer O
in: Handbook of Research on Systems Biology Applications in Medicine; A. Daskalak (ed.); IGI Publishers; November 2008.
ISBN 10 (print): 1605660760
![](assets/images/f/gonzalez-methods_in_cell_biology-679d4184.gif)
A system biology approach to understand functional activity of cell communication systems
Vera J, Wolkenhauer O
in: Methods in Nano Cell Biology; Ramaswamy B (ed.); Elsevier 2008.
ISBN 13 (print): 9781597492706
![](assets/images/d/wolkenhauer-9783540313380-25718ec3.jpg)
A plea for more theory in molecular biology
Wolkenhauer O, Mesarovic M, Wellstead P
In: Systems Biology - Applications and Perspectives; Bringmann P, Butcher EC, Parry P, Weiss B (eds.); Springer 2007.
ISBN 13 (print): 9783540313380
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A power-law model to describe the dynamics of the JAK2-STAT5 signalling pathway
Vera J, Bachmann J, Pfeifer AC, Hormiga JA, Torres Darias NV, Klingmüller U, Wolkenhauer O
in: Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine; Cánovas M, Iborra JL, Manjón A (eds.); Fundacion Cajamurcia 2006.
ISBN 13 (print): 9788461111350
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Identification of enzyme targets in metabolic diseases by modelling and optimisation. The case of hyperuricemia in humans
Vera J, Torres NV, Curto R, Cascante M
in: Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine; Cánovas M, Iborra JL, Manjón A (eds.); Fundacion Cajamurcia 2006.
ISBN 13 (print): 9788461111350
![](assets/images/b/rateitschak-9783832513504-405f27c7.jpg)
Bifurcation threshold in the MAPK cascade is independent of the Hill coefficient
Rateitschak K, Kschischo M
in: Irreversible Prozesse und Selbstorganisation; Pöschel ET, Malchow H, Schimansky-Geier L (eds.); Logos Verlag Berlin 2006.
ISBN 13 (print): 9783832513504
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All Models are Wrong
Wolkenhauer O, Ullah M
in: Systems Biology - Philosophical Foundations; Boogard F, Bruggeman F, Hofmeyr J, Westerhoff H (eds.); Elsevier 2006.
ISBN 10 (print): 0444520856
![](assets/images/b/wolkenhauer-3540003584-5c8c0280.jpg)
Mathematical Systems Biology: Genomic Cybernetics
Wolkenhauer O, Kolch W, Cho KH
in: Computations in Cells and Tissues: Perspectives and Tools of Thought; Paton R (ed.); Springer 2004.
ISBN 10 (print): 3540003584
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Mathematical Modelling of the Influence of RKIP on the ERK Signalling Pathway
Cho HH, Shin SY, Kim HW, Wolkenhauer O, McFerran B, Kolch W
in: Computational Methods in Systems Biology; Priami C (ed.); Springer 2003.
ISBN 10 (print): 3540006052
![](assets/images/5/moeller-levet-9783540408130-0508e383.jpg)
Fuzzy Clustering of Short Time-Series and Unevenly Distributed Sampling Points
Moeller-Levet C S, Klawonn F, Cho K H, Wolkenhauer O
In: Advances in Intelligent Data Analysis V; Berthold MR, Lenz HJ, Bradley E, Kruse R, Borgelt C (eds.); Springer 2003.
ISBN 10 (print): 3540408134
![](assets/images/b/wolkenhauer-3211836837-7fe01833.jpg)
Information Fusion in Genomics: Qualitative vs Quantitative
Wolkenhauer O
in: Data Fusion and Perception; Della Riccia G, Lenz HJ, Kruse R (eds.); Springer 2001.
ISBN 10 (print): 3211836837
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Random-Sets: Theory and Applications
Nunez-Garcia J, Wolkenhauer O
in: Granular Computing: An Emerging Paradigm; Pedrycz W (ed.); Springer 2001.
ISBN 10 (print): 3790813877