Systems Medicine - Integrative, Qualitative, and Computational Approaches

Wolkenhauer O (Editor-in-Chief)

Academic Press 2020

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)

ISBN 13 (print): 9781493989812

ISBN 13 (online): 9781493989829

DOI: 10.1007/978-1-4939-8982-9

Systems Medicine

Schmitz U, Wolkenhauer O, (eds.)

Springer (2016), Series Title Methods in Molecular Biology

ISBN 13 (print): 9781493932825

ISBN 13 (online): 9781493932832


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.

Nich lang schnacken - Ein plattdeutsches Konversationshandbuch

Wolkenhauer O

Quickborn-Verlag 2012.

ISBN 10 (print): 3876513774

ISBN 13 (print): 9783876513775

Encyclopedia of Systems Biology

Dubitzky W, Wolkenhauer O, Yokata H, Cho K-H (eds.)

Springer 2013.

ISBN 13 (print): 9781441998620

Systems Biology

Wolkenhauer O, Wellstead P, Cho KH (eds.)

Portland Press (Essays in Biochemistry Series), 2008

ISBN 10 (print): 1855781700

BIB: Download file

Data Engineering: Fuzzy Mathematics in System Theory and Data Analysis

Wolkenhauer O

John Wiley and Sons 2001.

ISBN 10 (print): 0471416568

BIB: Download file

Possibility Theory with Applications to Data Analysis

Wolkenhauer O

Research Studies Press 1998.

ISBN 10 (print): 086380229X

BIB: Download file

Chapters in Books


Wolkenhauer O, Gebhardt T.

In: Bioanalytik; Kurreck J, Engels JW, Lottspeich Fr (Eds), Springer 2022, 1145 - 1153


ISBN 13 (print): 978-3-662-61706-9

Single-Cell RNA Sequencing Procedures and Data Analysis

Wolfien M, David R, Galow AM

Exon Publications, Brisbane, Australia (2021), chapter in Bioinformatics.

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)

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


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.

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.

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.

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

Integrative workflow for network analysis

Faiz M. Khan, Shailendra K. Gupta, Olaf Wolkenhauer


A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression.

Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O

From Microscopes to Macroscopes: Advancing Biomedical Research Through Systems Approaches

Olaf Wolkenhauer

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.

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

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


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


Mehrebenensysteme in der Systembiologie

Theile T, Wolkenhauer O

Wissenschaft und Kunst der Modellierung. De Gruyter 2015.

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

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

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

Modelle und ihre Befragbarkeit als Grundlage biomedizinischer Erkenntnis

Wolkenhauer, O

Erwägen-Wissen-Ethik. Vol 26 Nr 3 (2015), 420-422

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.

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)

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

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

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

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

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

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

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

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

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

DOI: 10.1007/978-1-60761-987-1_27

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

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

BIB: Download file

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

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

BIB: Download file

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

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

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

BIB: Download file

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

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)

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

BIB: Download file

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

BIB: Download file


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

BIB: Download file

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

BIB: Download file

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

BIB: Download file

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

BIB: Download file

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

BIB: Download file

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

BIB: Download file

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

BIB: Download file

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

BIB: Download file

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

BIB: Download file

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

BIB: Download file