Olaf Wolkenhauer

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 32

Top Topics

Imbalanced Datasets

Systems Biology

Frequent Patterns

Top Venues

Briefings Bioinform.

Publications

Rahul Bordoloi, Clémence Réda, Orell Trautmann, Saptarshi Bej, Olaf Wolkenhauer
Multivariate Functional Linear Discriminant Analysis for the Classification of Short Time Series with Missing Data. CoRR (2024)
Clémence Réda, Jill-Jênn Vie, Olaf Wolkenhauer
stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering. J. Open Source Softw. 9 (94) (2024)
Kristian Schultz, Saptarshi Bej, Waldemar Hahn, Markus Wolfien, Prashant Srivastava, Olaf Wolkenhauer
ConvGeN: A convex space learning approach for deep-generative oversampling and imbalanced classification of small tabular datasets. Pattern Recognit. 147 (2024)
Manjunath Mahendra, Chaithra Umesh, Saptarshi Bej, Kristian Schultz, Olaf Wolkenhauer
Convex space learning for tabular synthetic data generation. CoRR (2024)
Julio Vera, Xin Lai, Andreas Baur, Michael Erdmann, Shailendra K. Gupta, Cristiano Guttà, Lucie Heinzerling, Markus V. Heppt, Philipp Maximilian Kazmierczak, Manfred Kunz, Christopher Lischer, Brigitte M. Pützer, Markus Rehm, Christian Ostalecki, Jimmy Retzlaff, Stephan Witt, Olaf Wolkenhauer, Carola Berking
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Briefings Bioinform. 23 (6) (2022)
Prashant Srivastava, Saptarshi Bej, Kristian Schultz, Kristina Y. Yordanova, Olaf Wolkenhauer
Attention Retrieval Model for Entity Relation Extraction From Biological Literature. IEEE Access 10 (2022)
Kristian Schultz, Saptarshi Bej, Waldemar Hahn, Markus Wolfien, Prashant Srivastava, Olaf Wolkenhauer
Convex space learning improves deep-generative oversampling for tabular imbalanced classification on smaller datasets. CoRR (2022)
Saptarshi Bej, Kristian Schulz, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer
A Multi-Schematic Classifier-Independent Oversampling Approach for Imbalanced Datasets. IEEE Access 9 (2021)
Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer
LoRAS: an oversampling approach for imbalanced datasets. Mach. Learn. 110 (2) (2021)
Saptarshi Bej, Kristian Schultz, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer
A multi-schematic classifier-independent oversampling approach for imbalanced datasets. CoRR (2021)
Saptarshi Bej, Anne-Marie Galow, Robert David, Markus Wolfien, Olaf Wolkenhauer
Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling. BMC Bioinform. 22 (1) (2021)
Saptarshi Bej, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer
Combining uniform manifold approximation with localized affine shadowsampling improves classification of imbalanced datasets. IJCNN (2021)
Nivedita Singh, Martin Eberhardt, Olaf Wolkenhauer, Julio Vera, Shailendra K. Gupta
An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. BMC Bioinform. 21 (1) (2020)
Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi
GEMtractor: extracting views into genome-scale metabolic models. Bioinform. 36 (10) (2020)
Maxwell Lewis Neal, Matthias König, 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, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20 (2) (2019)
Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer
LoRAS: An oversampling approach for imbalanced datasets. CoRR (2019)
Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel
Identifying frequent patterns in biochemical reaction networks: a workflow. Database J. Biol. Databases Curation 2018 (2018)
Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath
Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC Syst. Biol. 12 (1) (2018)
Krishna P. Singh, Lokesh Baweja, Olaf Wolkenhauer, Qamar Rahman, Shailendra K. Gupta
Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide. J. Comput. Aided Mol. Des. 32 (3) (2018)
Minoo Ashtiani, Ali Salehzadeh-Yazdi, Zahra Razaghi-Moghadam, Holger Hennig, Olaf Wolkenhauer, Mehdi Mirzaie, Mohieddin Jafari
A systematic survey of centrality measures for protein-protein interaction networks. BMC Syst. Biol. 12 (1) (2018)
Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath, Olaf Wolkenhauer
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Comput. Biol. 14 (2) (2018)
Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 6 (2018)
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, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 5 (2017)
Shailendra K. Gupta, Tanushree Jaitly, Ulf Schmitz, Gerold Schuler, Olaf Wolkenhauer, Julio Vera
Personalized cancer immunotherapy using Systems Medicine approaches. Briefings Bioinform. 17 (3) (2016)
Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer
COMODI: an ontology to characterise differences in versions of computational models in biology. J. Biomed. Semant. 7 (2016)
Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath
An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinform. 32 (4) (2016)
Matthias König, Anika Oellrich, Dagmar Waltemath, Richard J. B. Dobson, Tim J. P. Hubbard, Olaf Wolkenhauer
Challenges and opportunities for system biology standards and tools in medical research. ODLS (2016)
Ron Henkel, Fabienne Lambusch, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Dagmar Waltemath
Finding patterns in biochemical reaction networks. PeerJ Prepr. 4 (2016)
Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stefan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinform. 17 (2016)
Ulf Schmitz, Hojjat Naderi-Meshkin, Shailendra K. Gupta, Olaf Wolkenhauer, Julio Vera
The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions. Briefings Bioinform. 17 (3) (2016)
Dagmar Waltemath, Olaf Wolkenhauer
How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE Trans. Biomed. Eng. 63 (10) (2016)
Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath
Combining computational models, semantic annotations and simulation experiments in a graph database. Database J. Biol. Databases Curation 2015 (2015)
Rebekka Alm, Dagmar Waltemath, Markus Wolfien, Olaf Wolkenhauer, Ron Henkel
Annotation-based feature extraction from sets of SBML models. J. Biomed. Semant. 6 (2015)
Johannes Wollbold, Robert Jaster, Sarah Müller, Katja Rateitschak, Olaf Wolkenhauer
Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis. BMC Syst. Biol. 8 (2014)
Rebekka Alm, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel
Annotation-Based Feature Extraction from Sets of SBML Models. DILS (2014)
Padhraig Gormley, Kang Li, Olaf Wolkenhauer, George W. Irwin, Dajun Du
Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes. Cogn. Comput. 5 (1) (2013)
Dagmar Waltemath, Ron Henkel, Robert Hälke, Martin Scharm, Olaf Wolkenhauer
Improving the reuse of computational models through version control. Bioinform. 29 (6) (2013)
Ulf W. Liebal, Thomas Millat, Jon Marles-Wright, Richard J. Lewis, Olaf Wolkenhauer
Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. BMC Syst. Biol. 7 (2013)
Angelyn Lao, Vanessa Schmidt, Yvonne Schmitz, Thomas E. Willnow, Olaf Wolkenhauer
Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease. BMC Syst. Biol. 6 (2012)
Katja Rateitschak, Felix Winter, Falko Lange, Robert Jaster, Olaf Wolkenhauer
Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells. PLoS Comput. Biol. 8 (12) (2012)
Ron Henkel, Nicolas Le Novère, Olaf Wolkenhauer, Dagmar Waltemath
Considerations of graph-based concepts to manage of computational biology models and associated simulations. GI-Jahrestagung (2012)
Stefan Pauleweit, J. Barbara Nebe, Olaf Wolkenhauer
Agent-based Simulation of Molecular Processes - An Application to Actin-polymerisation. SIMULTECH (2011)
Jiri Jablonsky, Hermann Bauwe, Olaf Wolkenhauer
Modeling the Calvin-Benson cycle. BMC Syst. Biol. 5 (2011)
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, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7 (4) (2011)
Svetoslav G. Nikolov, Julio Vera, Ulf Schmitz, Olaf Wolkenhauer
regulation in cancer signalling networks. Theory Biosci. 130 (1) (2011)
Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R. King, Olaf Wolkenhauer
A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture. BMC Syst. Biol. 5 (2011)
Olaf Wolkenhauer, Darryl Shibata, Mihajlo D. Mesarovic
A stem cell niche dominance theorem. BMC Syst. Biol. 5 (2011)
Stefan Pauleweit, J. Barbara Nebe, Olaf Wolkenhauer
Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation. SIMULTECH (Selected Papers) (2011)
Svetoslav G. Nikolov, Xin Lai, Ulf W. Liebal, Olaf Wolkenhauer, Julio Vera
Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics. Int. J. Syst. Sci. 41 (1) (2010)
Peter Raasch, Ulf Schmitz, Nadja Patenge, Julio Vera, Bernd Kreikemeyer, Olaf Wolkenhauer
Non-coding RNA detection methods combined to improve usability, reproducibility and precision. BMC Bioinform. 11 (2010)
Julio Vera, Taesoo Kwon, Ulf Schmitz, Walter Kolch, Olaf Wolkenhauer
Exploration of homodimer receptor: homodimer protein interactions. Int. J. Bioinform. Res. Appl. 5 (4) (2009)
Xin Lai, Svetoslav G. Nikolov, Olaf Wolkenhauer, Julio Vera
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. Comput. Biol. Chem. 33 (4) (2009)
Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer
Dynamics of receptor and protein transducer homodimerisation. BMC Syst. Biol. 2 (2008)
Julio Vera, Julie Bachmann, Andrea C. Pfeifer, Verena Becker, Jose A. Hormiga, Néstor Torres Darias, Jens Timmer, Ursula Klingmüller, Olaf Wolkenhauer
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. BMC Syst. Biol. 2 (2008)
Thomas Millat, Sree N. Sreenath, Radina P. Soebiyanto, Jayant Avva, Kwang-Hyun Cho, Olaf Wolkenhauer
The role of dynamic stimulation pattern in the analysis of bistable intracellular networks. Biosyst. 92 (3) (2008)
Svetoslav G. Nikolov, Julio Vera, Vladimir Kotev, Olaf Wolkenhauer, Valko Petrov
Dynamic properties of a delayed protein cross talk model. Biosyst. 91 (1) (2008)
Olaf Wolkenhauer, Jan-Hendrik S. Hofmeyr
Ein Beitrag zu einer Theorie lebender Zellen (A Contribution towards a Theory of Living Cells). Autom. 56 (5) (2008)
Olaf Wolkenhauer
Interpreting Rosen. Artif. Life 13 (3) (2007)
Julio Vera, Cheng Sun, Yvonne Oertel, Olaf Wolkenhauer
SBToolbox. Bioinform. 23 (19) (2007)
Henning Schmidt, Gunnar Drews, Julio Vera, Olaf Wolkenhauer
SBML export interface for the systems biology toolbox for MATLAB. Bioinform. 23 (10) (2007)
Änne Glass, Thomas Karopka, Olaf Wolkenhauer
Bioinformatics and The Virtual Cell. it Inf. Technol. 48 (1) (2006)
Henning Schmidt, Mats Jirstrand, Olaf Wolkenhauer
Information Technology in Systems Biology (Informationstechnologien in der Systembiologie). it Inf. Technol. 48 (3) (2006)
Carla S. Möller-Levet, Frank Klawonn, Kwang-Hyun Cho, Hujun Yin, Olaf Wolkenhauer
Clustering of unevenly sampled gene expression time-series data. Fuzzy Sets Syst. 152 (1) (2005)
C. Vogl, Fátima Sánchez-Cabo, Gernot Stocker, Simon J. Hubbard, Olaf Wolkenhauer, Zlatko Trajanoski
A fully Bayesian model to cluster gene-expression profiles. ECCB/JBI (2005)
Radina P. Soebiyanto, Sree N. Sreenath, Mihajlo D. Mesarovic, Olaf Wolkenhauer
From Networks to Systems to Complex Systems: A Signaling Pathway Coordination Case Study. CDC/ECC (2005)
Zoltán Kutalik, Jacqueline Inwald, Steve V. Gordon, R. Glyn Hewinson, Philip D. Butcher, Jason Hinds, Kwang-Hyun Cho, Olaf Wolkenhauer
Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis. Bioinform. 20 (3) (2004)
Kwang-Hyun Cho, Jong-Ho Cha, Olaf Wolkenhauer
How to Synthesize an Optimized Genetic-Switching System? A System-Theoretic Approach Based on SQP. CMSB (2003)
Javier Nunez-Garcia, Zoltán Kutalik, Kwang-Hyun Cho, Olaf Wolkenhauer
Level sets and minimum volume sets of probability density functions. Int. J. Approx. Reason. 34 (1) (2003)
Kwang-Hyun Cho, Sung-Young Shin, Hyun Woo Kim, Olaf Wolkenhauer, Brian McFerran, Walter Kolch
Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway. CMSB (2003)
Kwang-Hyun Cho, Adelinde M. Uhrmacher, Olaf Wolkenhauer
Introduction to the Special Issue on Systems Biology and Simulation. Simul. 79 (12) (2003)
Carla S. Möller-Levet, Frank Klawonn, Kwang-Hyun Cho, Olaf Wolkenhauer
Fuzzy Clustering of Short Time-Series and Unevenly Distributed Sampling Points. IDA (2003)
Kwang-Hyun Cho, Sung-Young Shin, Walter Kolch, Olaf Wolkenhauer
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. Simul. 79 (12) (2003)
Kwang-Hyun Cho, Sung-Young Shin, Hyeon-Woo Lee, Olaf Wolkenhauer
Simulation Study of the TNF alpha Mediated NF-kappa B Signaling Pathway. CMSB (2003)
Javier Nunez-Garcia, Olaf Wolkenhauer
Random set system identification. IEEE Trans. Fuzzy Syst. 10 (3) (2002)
Olaf Wolkenhauer
Systems Biology: the Reincarnation of Systems Theory Applied in Biology?. Briefings Bioinform. 2 (3) (2001)
Javier Nunez-Garcia, Olaf Wolkenhauer
Random Sets and Histograms. FUZZ-IEEE (2001)
Olaf Wolkenhauer
Qualitative Uncertainty Models from Random Set Theory. IDA (1997)
Olaf Wolkenhauer, John M. Edmunds
Possibilistic Testing of Distribution Functions for Change Detection. Intell. Data Anal. 1 (1-4) (1997)