LOgo SBI Uni Rostock

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

Books

Books

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

Systems Biology of MicroRNAs in Cancer (Advances in Experimental Medicine and Biology, 1385, Band 1385)

Schmitz U, Wolkenhauer O, Vera-González J

ISBN 10 (print): 3031083555

ISBN 13 (print): 978-3031083556

Amazon: Buy it now

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

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

URL: http://link.springer.com/book/10.1007/978-1-4939-3283-2

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

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

Data Engineering: Fuzzy Mathematics in System Theory and Data Analysis

Wolkenhauer O

John Wiley and Sons 2001.

ISBN 10 (print): 0471416568

Possibility Theory with Applications to Data Analysis

Wolkenhauer O

Research Studies Press 1998.

ISBN 10 (print): 086380229X

Chapters in Books

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

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

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

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

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

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

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)

DOI: 10.1016/B978-0-12-801238-3.11586-7

URL: https://www.sciencedirect.com/science/article/pii/B9780128012383115867?via%3Dihub

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

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

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.

DOI: 10.1007/978-1-4939-8982-9_8

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.

DOI: 10.1007/978-1-4939-8982-9_5

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

 

DOI: 10.1042/EBC20180005

Pubmed: 30366988

URL: http://essays.biochemistry.org/content/62/4/549

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

Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O

DOI: 10.1007/978-1-4939-7456-6_12

Pubmed: 29119509

URL: https://link.springer.com/search?facet-content-type=%22Book%22&package=12345&facet-start-year=2018&facet-end-year=2018

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

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

URL: http://link.springer.com/protocol/10.1007/978-1-4939-3283-2_16

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

Mehrebenensysteme in der Systembiologie

Theile T, Wolkenhauer O

Wissenschaft und Kunst der Modellierung. De Gruyter 2015.

URL: http://www.researchgate.net/publication/276205166_Wissenschaft_und_Kunst_der_Modellierung_%28Science_and_Art_of_Modelling%29_-_Kieler_Zugang_zur_Definition_Nutzung_und_Zukunft

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.

DOI: 10.1002/9780470015902.a0025237

URL: http://www.els.net

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)

DOI: 10.1007/978-94-007-6803-1_10

URL: http://link.springer.com/chapter/10.1007/978-94-007-6803-1_10

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

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

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

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

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

URL: http://www.ncbi.nlm.nih.gov/pubmed/19195559

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

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

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

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

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

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

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

Downloads & more:

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

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

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