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
Inflammation Resolution and Chronic Diseases
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
Systems Biology of MicroRNAs in Cancer (Advances in Experimental Medicine and Biology, 1385, Band 1385)
Systems Medicine - Integrative, Qualitative, and Computational Approaches
Academic Press 2020
ISBN 13 (online): 978-0-12-816078-7
URL: https://www.sciencedirect.com/referencework/9780128160787/systems-medicine
Computational Biology of Non-Coding RNA
Springer (2019), part of the Methods in Molecular Biology book series (MIMB, volume 1912)
Systems Medicine
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
MicroRNA Cancer Regulation - Advanced Concepts, Bioinformatics and Systems Biology Tools
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
Nich lang schnacken - Ein plattdeutsches Konversationshandbuch
Quickborn-Verlag 2012.
ISBN 10 (print): 3876513774
ISBN 13 (print): 9783876513775
Encyclopedia of Systems Biology
Springer 2013.
ISBN 13 (print): 9781441998620
Stochastic Approaches for Systems Biology
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
Systems Biology
Portland Press (Essays in Biochemistry Series), 2008
ISBN 10 (print): 1855781700
Data Engineering: Fuzzy Mathematics in System Theory and Data Analysis
John Wiley and Sons 2001.
ISBN 10 (print): 0471416568
Possibility Theory with Applications to Data Analysis
Research Studies Press 1998.
ISBN 10 (print): 086380229X
Chapters in Books
A Current Perspective of Medical Informatics Developments for a Clinical Translation of (Non-coding)RNAs and Single-Cell Technologies
Springer (2025), chapter in Computational Biology of Non-Coding RNA (editors: Lai X, Gupta S, Vera Gonzalez J). Methods in Molecular Biology, vol 2883.
ISBN 13 (print): 978-107-16-4289-4
ISBN 13 (online): 978-107-16-4290-0
DOI: 10.1007/978-1-0716-4290-0_2
URL: https://link.springer.com/protocol/10.1007/978-1-0716-4290-0_2
Mechanistic Understanding of Inflammation Resolution Using the Atlas of Inflammation Resolution (AIR)
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
Mechanistic Understanding of Inflammation Resolution Using the Atlas of Inflammation Resolution (AIR)
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
Are Multi-Component Drugs Better in Resolving the Inflammation Compared to the Single-Component Drugs?
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
Inflammation Resolution Mediators: Future Prospects
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
Systembiologie
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
Single-Cell RNA Sequencing Procedures and Data Analysis
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
Network Biology Approaches in Ophthalmological Diseases: A Case Study of Glaucoma
In Systems Medicine: Integrative, qualitative and computational approaches (2020)
Envisioning the Application of Systems Biology in Cancer Immunology
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
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices
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
Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.
Workflow Development for the Functional Characterization of ncRNAs
Springer (2019), chapter in Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912.
Applications of genome-scale metabolic models and data integration in systems medicine
Nova (2019), chapter in Focus on Systems Theory Research
ISBN 13 (online): 9781536145618
Integrative workflow for network analysis
A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression.
From Microscopes to Macroscopes: Advancing Biomedical Research Through Systems Approaches
Chapter in Philosophy of Systems Biology (Springer)
Part of the series History, Philosophy and Theory of the Life Sciences pp 257-265
Biochemical pathway modeling tools for drug target detection in Cancer and other complex diseases
In Michael Johnson editor: Methods in Enzymology, Vol. 487,
Burlington: Academic Press, 2010, pp 319-370.
Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive
In: Systems Medicine, Methods in Molecular Biology (2016) 1386: 135-179.
Published by Springer.
ISBN 13 (print): 9781493932825
Network-Assisted Disease Classification and Biomarker Discovery
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
RNA Systems Biology for Cancer: From Diagnosis to Therapy
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
Mehrebenensysteme in der Systembiologie
Wissenschaft und Kunst der Modellierung. De Gruyter 2015.
Envisioning the Application of Systems Biology in Cancer
In Cancer Immunology, N.Rezaei (ed.), 429-449, Springer 2015
ISBN 13 (print): 9783662440063
Explanation and Organizing Principles in Systems Biology
In Explanation in Biology, P-A Braillard, C Malaterre (eds), 249-264, Springer 2015
ISBN 13 (print): 9789401798228
Mehrebenensysteme in der Biomedizin
In Wissenschaft und Kunst der Modellierung, B.Thalheim, I.Nissen (eds), 455-474, De Gruyter 2015
ISBN 13 (print): 9781501510403
Modelle und ihre Befragbarkeit als Grundlage biomedizinischer Erkenntnis
Erwägen-Wissen-Ethik. Vol 26 Nr 3 (2015), 420-422
Cancer Systems Biology: Current Achievements in – Omics Data Analysis, Network Reconstruction and Mathematical Modelling
In: eLS. John Wiley & Sons Ltd, Chichester.
Reproducibility of model-based results in systems biology
In: Systems Biology: Integrative Biology and Simulation Tools 1, pp 301-320. Prokop A, Csukas B (eds) Springer (2013)
Interdisciplinarity as both necessity and hurdle for progress in the life sciences
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
Modeling Colorectal Cancer: A Stability Analysis Approach
in: Medical Advancements in Aging and Regenerative Technologies; Daskalaki A
Clinical Tools and Applications: 53-75
IGI Global 2013
Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation
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
The pH-induced metabolic shift from acidogenesis to solventogenesis in Clostridium acetobutylicum - From experiments to models
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
Computational microRNA biology
in: Encyclopedia of Systems Biology; Dubitzky W, Wolkenhauer O, Yokata H, Cho K-H (eds.); Springer 2012.
ISBN 13 (print): 9781441998620
Mathematical modelling of the pH-induced metabolic shift in Clostridium acetobutylicum
in: Systems Biology of Clostridium acetobutylicum, Dürre P (ed.), Imperial College Press, 2014, 103-130.
ISBN 13 (print): 9781783264407
Bifurcation Analysis of a Model Accounting for the 14-3-3s Signalling Compartmentalisation
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
Bioinformatics Analysis of High-Throughput Experiments
in: Recent Trends in Biotechnology. Volume 2; Singh M P, Agrawal A, Sharma B (eds.); Nova Science Publishers 2011.
ISBN 13 (print): 9781617617973
Modeling of Cellular Processes: Methods, Data, and Requirements
in: Data Mining in Proteomics; Hamacher M, Eisenacher M, Stephan C (eds.); Springer 2011.
ISBN 13 (print): 9781607019864
Modelling miRNA regulation in cancer signalling systems: miR-34a regulation of the p53/Sirt1 signalling module
in: Computational Modelling of Signalling Networks; Liu X, Betterton M (eds.); Humana 2012.
ISBN 13 (print): 9781617798230
Qualitative Uncertainty Models using Random Set Theory
in: Advances in Intelligent Data Analysis; Liu X, Cohen P, Berthold M (eds.); Springer LNCS 1280, 1997.
ISBN 10 (print): 3540633464
Interferon-g stimulated STAT1 signalling: from experimental data to a predictive mathematical model
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
Quantifying properties of cell signaling cascades
in: Control Theory and Systems Biology; Iglesias P A, Ingalls B (eds.); MIT press 2009.
ISBN 13 (print): 9780262013345
Methods in In Silico Biology: Modeling Feedback and Dynamics
in: Systems Biology for Drug Discovery and Development; Young D, Michelson S (eds); Wiley 2011.
ISBN 13 (print): 9780470261231
The Complexity of Cell-Biological Systems
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
Reverse Engineering of Biological Networks
in: Methods in Bioengineering: Systems Analysis of Biological Networks; Jayaraman A, Hahn J (eds.); Artech House 2009.
ISBN 13 (print): 9781596934061
Enriching biotechnology with recent bioinformatics tools and protocols
in: Recent trends in Biotechnology; Singh MP, Agrawal A, Sharma B (eds.); Nova Science Publishers Inc. 2011.
ISBN 13 (print): 9781608761487
Case study in systematic modelling: Thiamine uptake in Yeast S. cerevisiae, book chapter, Essays
In: Biochemistry - Systems Biology, Portland Press, accepted (2008)
Systems and Control Theory for Medical Systems Biology
in: Handbook of Research on Systems Biology Applications in Medicine; A. Daskalak (ed.); IGI Publishers; November 2008.
ISBN 10 (print): 1605660760
A system biology approach to understand functional activity of cell communication systems
in: Methods in Nano Cell Biology; Ramaswamy B (ed.); Elsevier 2008.
ISBN 13 (print): 9781597492706
A plea for more theory in molecular biology
In: Systems Biology - Applications and Perspectives; Bringmann P, Butcher EC, Parry P, Weiss B (eds.); Springer 2007.
ISBN 13 (print): 9783540313380
A power-law model to describe the dynamics of the JAK2-STAT5 signalling pathway
in: Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine; Cánovas M, Iborra JL, Manjón A (eds.); Fundacion Cajamurcia 2006.
ISBN 13 (print): 9788461111350
Identification of enzyme targets in metabolic diseases by modelling and optimisation. The case of hyperuricemia in humans
in: Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine; Cánovas M, Iborra JL, Manjón A (eds.); Fundacion Cajamurcia 2006.
ISBN 13 (print): 9788461111350
Bifurcation threshold in the MAPK cascade is independent of the Hill coefficient
in: Irreversible Prozesse und Selbstorganisation; Pöschel ET, Malchow H, Schimansky-Geier L (eds.); Logos Verlag Berlin 2006.
ISBN 13 (print): 9783832513504
All Models are Wrong
in: Systems Biology - Philosophical Foundations; Boogard F, Bruggeman F, Hofmeyr J, Westerhoff H (eds.); Elsevier 2006.
ISBN 10 (print): 0444520856
Mathematical Systems Biology: Genomic Cybernetics
in: Computations in Cells and Tissues: Perspectives and Tools of Thought; Paton R (ed.); Springer 2004.
ISBN 10 (print): 3540003584
Mathematical Modelling of the Influence of RKIP on the ERK Signalling Pathway
in: Computational Methods in Systems Biology; Priami C (ed.); Springer 2003.
ISBN 10 (print): 3540006052
Fuzzy Clustering of Short Time-Series and Unevenly Distributed Sampling Points
In: Advances in Intelligent Data Analysis V; Berthold MR, Lenz HJ, Bradley E, Kruse R, Borgelt C (eds.); Springer 2003.
ISBN 10 (print): 3540408134
Information Fusion in Genomics: Qualitative vs Quantitative
in: Data Fusion and Perception; Della Riccia G, Lenz HJ, Kruse R (eds.); Springer 2001.
ISBN 10 (print): 3211836837
Random-Sets: Theory and Applications
in: Granular Computing: An Emerging Paradigm; Pedrycz W (ed.); Springer 2001.
ISBN 10 (print): 3790813877