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

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