Qualitative Uncertainty Models from Random Set Theory. - Olaf Wolkenhauer (IDA, 1997)

Possibilistic Testing of Distribution Functions for Change Detection. - Olaf Wolkenhauer; John M. Edmunds (Intell. Data Anal., 1997)

Data engineering - fuzzy mathematics in systems theory and data analysis. - Olaf Wolkenhauer (Wiley, 2001)

On Information Fusion in the Life-Sciences. - Olaf Wolkenhauer (Data Fusion and Perception, 2001)

Random Sets and Histograms. - Javier Nunez-Garcia; Olaf Wolkenhauer (FUZZ-IEEE, 2001)

Systems Biology: the Reincarnation of Systems Theory Applied in Biology?. - Olaf Wolkenhauer (Briefings Bioinform., 2001)

Random set system identification. - Javier Nunez-Garcia; Olaf Wolkenhauer (IEEE Trans. Fuzzy Syst., 2002)

How to Synthesize an Optimized Genetic-Switching System? A System-Theoretic Approach Based on SQP. - Kwang-Hyun Cho; Jong-Ho Cha; Olaf Wolkenhauer (CMSB, 2003)

Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway. - Kwang-Hyun Cho; Sung-Young Shin; Hyun Woo Kim; Olaf Wolkenhauer; Brian McFerran; Walter Kolch (CMSB, 2003)

Simulation Study of the TNF alpha Mediated NF-kappa B Signaling Pathway. - Kwang-Hyun Cho; Sung-Young Shin; Hyeon-Woo Lee; Olaf Wolkenhauer (CMSB, 2003)

Fuzzy Clustering of Short Time-Series and Unevenly Distributed Sampling Points. - Carla S. Möller-Levet; Frank Klawonn; Kwang-Hyun Cho; Olaf Wolkenhauer (IDA, 2003)

Level sets and minimum volume sets of probability density functions. - Javier Nunez-Garcia; Zoltán Kutalik; Kwang-Hyun Cho; Olaf Wolkenhauer (Int. J. Approx. Reason., 2003)

Experimental Design in Systems Biology, Based on Parameter Sensitivity Analysis Using a Monte Carlo Method: A Case Study for the TNFalpha-Mediated NF-kappa B Signal Transduction Pathway. - Kwang-Hyun Cho; Sung-Young Shin; Walter Kolch; Olaf Wolkenhauer (Simul., 2003)

Introduction to the Special Issue on Systems Biology and Simulation. - Kwang-Hyun Cho; Adelinde M. Uhrmacher; Olaf Wolkenhauer (Simul., 2003)

Modelling gene expression time-series with radial basis function neural networks. - Carla S. Möller-Levet; Kwang-Hyun Cho; Hujun Yin; Olaf Wolkenhauer (IJCNN, 2004)

Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis. - Zoltán Kutalik; Jacqueline Inwald; Steve V. Gordon; R. Glyn Hewinson; Philip D. Butcher; Jason Hinds; Kwang-Hyun Cho; Olaf Wolkenhauer (Bioinform., 2004)

From Networks to Systems to Complex Systems: A Signaling Pathway Coordination Case Study. - Radina P. Soebiyanto; Sree N. Sreenath; Mihajlo D. Mesarovic; Olaf Wolkenhauer (CDC/ECC, 2005)

A fully Bayesian model to cluster gene-expression profiles. - C. Vogl; Fátima Sánchez-Cabo; Gernot Stocker; Simon J. Hubbard; Olaf Wolkenhauer; Zlatko Trajanoski (ECCB/JBI, 2005)

Clustering of unevenly sampled gene expression time-series data. - Carla S. Möller-Levet; Frank Klawonn; Kwang-Hyun Cho; Hujun Yin; Olaf Wolkenhauer (Fuzzy Sets Syst., 2005)

Bioinformatics and The Virtual Cell. - Änne Glass; Thomas Karopka; Olaf Wolkenhauer (it Inf. Technol., 2006)

Information Technology in Systems Biology (Informationstechnologien in der Systembiologie). - Henning Schmidt; Mats Jirstrand; Olaf Wolkenhauer (it Inf. Technol., 2006)

Interpreting Rosen. - Olaf Wolkenhauer (Artif. Life, 2007)

SBML export interface for the systems biology toolbox for MATLAB. - Henning Schmidt; Gunnar Drews; Julio Vera; Olaf Wolkenhauer (Bioinform., 2007)

PLMaddon: a power-law module for the MatlabTM SBToolbox. - Julio Vera; Cheng Sun; Yvonne Oertel; Olaf Wolkenhauer (Bioinform., 2007)

Ein Beitrag zu einer Theorie lebender Zellen (A Contribution towards a Theory of Living Cells). - Olaf Wolkenhauer; Jan-Hendrik S. Hofmeyr (Autom., 2008)

The role of dynamic stimulation pattern in the analysis of bistable intracellular networks. - Thomas Millat; Sree N. Sreenath; Radina P. Soebiyanto; Jayant Avva; Kwang-Hyun Cho; Olaf Wolkenhauer (Biosyst., 2008)

Dynamic properties of a delayed protein cross talk model. - Svetoslav G. Nikolov; Julio Vera; Vladimir Kotev; Olaf Wolkenhauer; Valko Petrov (Biosyst., 2008)

A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. - Julio Vera; Julie Bachmann; Andrea C. Pfeifer; Verena Becker; Jose A. Hormiga; Néstor Torres Darias; Jens Timmer; Ursula Klingmüller; Olaf Wolkenhauer (BMC Syst. Biol., 2008)

Dynamics of receptor and protein transducer homodimerisation. - Julio Vera; Thomas Millat; Walter Kolch; Olaf Wolkenhauer (BMC Syst. Biol., 2008)

A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. - Xin Lai 002; Svetoslav G. Nikolov; Olaf Wolkenhauer; Julio Vera (Comput. Biol. Chem., 2009)

Exploration of homodimer receptor: homodimer protein interactions. - Julio Vera; Taesoo Kwon; Ulf Schmitz; Walter Kolch; Olaf Wolkenhauer (Int. J. Bioinform. Res. Appl., 2009)

Non-coding RNA detection methods combined to improve usability, reproducibility and precision. - Peter Raasch; Ulf Schmitz; Nadja Patenge; Julio Vera; Bernd Kreikemeyer; Olaf Wolkenhauer (BMC Bioinform., 2010)

Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics. - Svetoslav G. Nikolov; Xin Lai 002; Ulf W. Liebal; Olaf Wolkenhauer; Julio Vera (Int. J. Syst. Sci., 2010)

Agent-based Simulation of Molecular Processes - An Application to Actin-polymerisation. - Stefan Pauleweit; J. Barbara Nebe; Olaf Wolkenhauer (SIMULTECH, 2011)

Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation. - Stefan Pauleweit; J. Barbara Nebe; Olaf Wolkenhauer (SIMULTECH (Selected Papers), 2011)

A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture. - Sylvia Haus; Sara Jabbari; Thomas Millat; Holger Janssen; Ralf-Jörg Fischer; Hubert Bahl; John R. King; Olaf Wolkenhauer (BMC Syst. Biol., 2011)

Modeling the Calvin-Benson cycle. - Jiri Jablonsky; Hermann Bauwe; Olaf Wolkenhauer (BMC Syst. Biol., 2011)

A stem cell niche dominance theorem. - Olaf Wolkenhauer; Darryl Shibata; Mihajlo D. Mesarovic (BMC Syst. Biol., 2011)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks. - Svetoslav G. Nikolov; Julio Vera; Ulf Schmitz; Olaf Wolkenhauer (Theory Biosci., 2011)

Considerations of graph-based concepts to manage of computational biology models and associated simulations. - Ron Henkel; Nicolas Le Novère; Olaf Wolkenhauer; Dagmar Waltemath (GI-Jahrestagung, 2012)

Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease. - Angelyn Lao; Vanessa Schmidt; Yvonne Schmitz; Thomas E. Willnow; Olaf Wolkenhauer (BMC Syst. Biol., 2012)

Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells. - Katja Rateitschak; Felix Winter; Falko Lange; Robert Jaster; Olaf Wolkenhauer (PLoS Comput. Biol., 2012)

Improving the reuse of computational models through version control. - Dagmar Waltemath; Ron Henkel; Robert Hälke; Martin Scharm; Olaf Wolkenhauer (Bioinform., 2013)

Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. - Ulf W. Liebal; Thomas Millat; Jon Marles-Wright; Richard J. Lewis; Olaf Wolkenhauer (BMC Syst. Biol., 2013)

Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes. - Padhraig Gormley; Kang Li 002; Olaf Wolkenhauer; George W. Irwin; Dajun Du (Cogn. Comput., 2013)

Annotation-Based Feature Extraction from Sets of SBML Models. - Rebekka Alm; Dagmar Waltemath; Olaf Wolkenhauer; Ron Henkel (DILS, 2014)

Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis. - Johannes Wollbold; Robert Jaster; Sarah Müller; Katja Rateitschak; Olaf Wolkenhauer (BMC Syst. Biol., 2014)

Mehrebenensysteme in der Biomedizin. - Tom Theile; Olaf Wolkenhauer (Wissenschaft und Kunst der Modellierung, 2015)

Combining computational models, semantic annotations and simulation experiments in a graph database. - Ron Henkel; Olaf Wolkenhauer; Dagmar Waltemath (Database J. Biol. Databases Curation, 2015)

Annotation-based feature extraction from sets of SBML models. - Rebekka Alm; Dagmar Waltemath; Markus Wolfien; Olaf Wolkenhauer; Ron Henkel (J. Biomed. Semant., 2015)

Challenges and opportunities for system biology standards and tools in medical research. - Matthias König 003; Anika Oellrich; Dagmar Waltemath; Richard J. B. Dobson; Tim J. P. Hubbard; Olaf Wolkenhauer (ODLS, 2016)

Personalized cancer immunotherapy using Systems Medicine approaches. - Shailendra K. Gupta; Tanushree Jaitly; Ulf Schmitz; Gerold Schuler; Olaf Wolkenhauer; Julio Vera (Briefings Bioinform., 2016)

The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions. - Ulf Schmitz; Hojjat Naderi-Meshkin; Shailendra K. Gupta; Olaf Wolkenhauer; Julio Vera (Briefings Bioinform., 2016)

An algorithm to detect and communicate the differences in computational models describing biological systems. - Martin Scharm; Olaf Wolkenhauer; Dagmar Waltemath (Bioinform., 2016)

COMODI: an ontology to characterise differences in versions of computational models in biology. - Martin Scharm; Dagmar Waltemath; Pedro Mendes 001; Olaf Wolkenhauer (J. Biomed. Semant., 2016)

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. - Markus Wolfien; Christian Rimmbach; Ulf Schmitz; Julia Jeannine Jung; Stefan Krebs; Gustav Steinhoff; Robert David; Olaf Wolkenhauer (BMC Bioinform., 2016)

Finding patterns in biochemical reaction networks. - Ron Henkel; Fabienne Lambusch; Olaf Wolkenhauer; Kurt Sandkuhl; Christian Rosenke; Dagmar Waltemath (PeerJ Prepr., 2016)

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. - Dagmar Waltemath; Olaf Wolkenhauer (IEEE Trans. Biomed. Eng., 2016)

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. - Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani; Markus Wolfien; Steffen Lott; et al. (Nucleic Acids Res., 2017)

Identifying frequent patterns in biochemical reaction networks: a workflow. - Fabienne Lambusch; Dagmar Waltemath; Olaf Wolkenhauer; Kurt Sandkuhl; Christian Rosenke; Ron Henkel (Database J. Biol. Databases Curation, 2018)

A systematic survey of centrality measures for protein-protein interaction networks. - Minoo Ashtiani; Ali Salehzadeh-Yazdi; Zahra Razaghi-Moghadam; Holger Hennig; Olaf Wolkenhauer; Mehdi Mirzaie; Mohieddin Jafari (BMC Syst. Biol., 2018)

Evolution of computational models in BioModels Database and the Physiome Model Repository. - Martin Scharm; Tom Gebhardt; Vasundra Touré; Andrea Bagnacani; Ali Salehzadeh-Yazdi; Olaf Wolkenhauer; Dagmar Waltemath (BMC Syst. Biol., 2018)

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide. - Krishna P. Singh; Lokesh Baweja; Olaf Wolkenhauer; Qamar Rahman; Shailendra K. Gupta (J. Comput. Aided Mol. Des., 2018)

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. - Vasundra Touré; Nicolas Le Novère; Dagmar Waltemath; Olaf Wolkenhauer (PLoS Comput. Biol., 2018)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

GEMtractor: extracting views into genome-scale metabolic models. - Martin Scharm; Olaf Wolkenhauer; Mahdi Jalili; Ali Salehzadeh-Yazdi (Bioinform., 2020)

An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. - Nivedita Singh; Martin Eberhardt; Olaf Wolkenhauer; Julio Vera; Shailendra K. Gupta (BMC Bioinform., 2020)

Combining uniform manifold approximation with localized affine shadowsampling improves classification of imbalanced datasets. - Saptarshi Bej; Prashant Srivastava; Markus Wolfien; Olaf Wolkenhauer (IJCNN, 2021)

A Multi-Schematic Classifier-Independent Oversampling Approach for Imbalanced Datasets. - Saptarshi Bej; Kristian Schulz; Prashant Srivastava; Markus Wolfien; Olaf Wolkenhauer (IEEE Access, 2021)

Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling. - Saptarshi Bej; Anne-Marie Galow; Robert David; Markus Wolfien; Olaf Wolkenhauer (BMC Bioinform., 2021)

A multi-schematic classifier-independent oversampling approach for imbalanced datasets. - Saptarshi Bej; Kristian Schultz; Prashant Srivastava; Markus Wolfien; Olaf Wolkenhauer (CoRR, 2021)

LoRAS: an oversampling approach for imbalanced datasets. - Saptarshi Bej; Narek Davtyan; Markus Wolfien; Mariam Nassar; Olaf Wolkenhauer (Mach. Learn., 2021)

Attention Retrieval Model for Entity Relation Extraction From Biological Literature. - Prashant Srivastava; Saptarshi Bej; Kristian Schultz; Kristina Y. Yordanova; Olaf Wolkenhauer (IEEE Access, 2022)

Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. - Julio Vera; Xin Lai 002; Andreas Baur; Michael Erdmann; Shailendra K. Gupta; Cristiano Guttà; Lucie Heinzerling; Markus V. Heppt; Philipp Maximilian Kazmierczak; Manfred Kunz; Christopher Lischer; Brigitte M. Pützer; et al. (Briefings Bioinform., 2022)

Convex space learning improves deep-generative oversampling for tabular imbalanced classification on smaller datasets. - Kristian Schultz; Saptarshi Bej; Waldemar Hahn; Markus Wolfien; Prashant Srivastava; Olaf Wolkenhauer (CoRR, 2022)

Multivariate Functional Linear Discriminant Analysis for the Classification of Short Time Series with Missing Data. - Rahul Bordoloi; Clémence Réda; Orell Trautmann; Saptarshi Bej; Olaf Wolkenhauer (CoRR, 2024)

Convex space learning for tabular synthetic data generation. - Manjunath Mahendra; Chaithra Umesh; Saptarshi Bej; Kristian Schultz; Olaf Wolkenhauer (CoRR, 2024)

stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering. - Clémence Réda; Jill-Jênn Vie; Olaf Wolkenhauer (J. Open Source Softw., 2024)

ConvGeN: A convex space learning approach for deep-generative oversampling and imbalanced classification of small tabular datasets. - Kristian Schultz; Saptarshi Bej; Waldemar Hahn; Markus Wolfien; Prashant Srivastava; Olaf Wolkenhauer (Pattern Recognit., 2024)

Bitter peptide prediction using graph neural networks. - Prashant Srivastava; Alexandra Steuer; Francesco Ferri; Alessandro Nicoli; Kristian Schultz; Saptarshi Bej; Antonella Di Pizio; Olaf Wolkenhauer (J. Cheminformatics, 2024)

Detection of pre-ictal epileptic events using a self-attention based neural network from raw Neonatal EEG data. - Kondaveeti Tejaswi; Madala Vikas; Himala Praharsha; Pranshu Mandal; Sujan Chakraborty; Olaf Wolkenhauer; Saptarshi Bej (Comput. Biol. Medicine, 2025)

Preserving logical and functional dependencies in synthetic tabular data. - Chaithra Umesh; Kristian Schultz; Manjunath Mahendra; Saptarshi Bej; Olaf Wolkenhauer (Pattern Recognit., 2025)

Multivariate functional linear discriminant analysis for partially-observed time series. - Rahul Bordoloi; Clémence Réda; Orell Trautmann; Saptarshi Bej; Olaf Wolkenhauer (Mach. Learn., 2025)

Dependency-aware synthetic tabular data generation. - Chaithra Umesh; Kristian Schultz; Manjunath Mahendra; Saptarshi Bej; Olaf Wolkenhauer (CoRR, 2025)

Joint embedding-classifier learning for interpretable collaborative filtering. - Clémence Réda; Jill-Jênn Vie; Olaf Wolkenhauer (BMC Bioinform., 2025)