Olaf Wolkenhauer

95 papers A* 1B 5C 1Journal 76Unranked 9

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Anomaly Detection via Mean Shift Density Enhancement. CoRR Pritam Kar, Rahul Bordoloi, Olaf Wolkenhauer, Saptarshi Bej
2026	J	`jnl`	Convex space learning for tabular synthetic data generation. Neurocomputing Manjunath Mahendra, Chaithra Umesh, Kristian Schultz, Olaf Wolkenhauer, Saptarshi Bej
2026	J	`jnl`	Embedding Learning on Multiplex Networks for Link Prediction. CoRR Orell Trautmann, Olaf Wolkenhauer, Clémence Réda
2026	A*	`conf`	Multivariate Functional Linear Discriminant Analysis for Partially-Observed Time Series (Abstract Reprint). AAAI Rahul Bordoloi, Clémence Réda, Orell Trautmann, Saptarshi Bej, Olaf Wolkenhauer
2025	J	`jnl`	Dependency-aware synthetic tabular data generation. CoRR Chaithra Umesh, Kristian Schultz, Manjunath Mahendra, Saptarshi Bej, Olaf Wolkenhauer
2025	J	`jnl`	Detection of pre-ictal epileptic events using a self-attention based neural network from raw Neonatal EEG data. Comput. Biol. Medicine Kondaveeti Tejaswi, Madala Vikas, Himala Praharsha, Pranshu Mandal, Sujan Chakraborty, Olaf Wolkenhauer, Saptarshi Bej
2025	J	`jnl`	FUSE: Fast Semi-Supervised Node Embedding Learning via Structural and Label-Aware Optimization. CoRR Sujan Chakraborty, Rahul Bordoloi, Anindya Sengupta, Olaf Wolkenhauer, Saptarshi Bej
2025	J	`jnl`	Joint embedding-classifier learning for interpretable collaborative filtering. BMC Bioinform. Clémence Réda, Jill-Jênn Vie, Olaf Wolkenhauer
2025	J	`jnl`	Multivariate functional linear discriminant analysis for partially-observed time series. Mach. Learn. Rahul Bordoloi, Clémence Réda, Orell Trautmann, Saptarshi Bej, Olaf Wolkenhauer
2025	J	`jnl`	Preserving logical and functional dependencies in synthetic tabular data. Pattern Recognit. Chaithra Umesh, Kristian Schultz, Manjunath Mahendra, Saptarshi Bej, Olaf Wolkenhauer
2024	J	`jnl`	Bitter peptide prediction using graph neural networks. J. Cheminformatics Prashant Srivastava, Alexandra Steuer, Francesco Ferri, Alessandro Nicoli, Kristian Schultz, Saptarshi Bej, Antonella Di Pizio, Olaf Wolkenhauer
2024	J	`jnl`	ConvGeN: A convex space learning approach for deep-generative oversampling and imbalanced classification of small tabular datasets. Pattern Recognit. Kristian Schultz, Saptarshi Bej, Waldemar Hahn, Markus Wolfien, Prashant Srivastava, Olaf Wolkenhauer
2024	J	`jnl`	Convex space learning for tabular synthetic data generation. CoRR Manjunath Mahendra, Chaithra Umesh, Saptarshi Bej, Kristian Schultz, Olaf Wolkenhauer
2024	J	`jnl`	Multivariate Functional Linear Discriminant Analysis for the Classification of Short Time Series with Missing Data. CoRR Rahul Bordoloi, Clémence Réda, Orell Trautmann, Saptarshi Bej, Olaf Wolkenhauer
2024	J	`jnl`	Preserving logical and functional dependencies in synthetic tabular data. CoRR Chaithra Umesh, Kristian Schultz, Manjunath Mahendra, Saptarshi Bej, Olaf Wolkenhauer
2024	J	`jnl`	stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering. J. Open Source Softw. Clémence Réda, Jill-Jênn Vie, Olaf Wolkenhauer
2022	J	`jnl`	Attention Retrieval Model for Entity Relation Extraction From Biological Literature. IEEE Access Prashant Srivastava, Saptarshi Bej, Kristian Schultz, Kristina Y. Yordanova, Olaf Wolkenhauer
2022	J	`jnl`	Convex space learning improves deep-generative oversampling for tabular imbalanced classification on smaller datasets. CoRR Kristian Schultz, Saptarshi Bej, Waldemar Hahn, Markus Wolfien, Prashant Srivastava, Olaf Wolkenhauer
2022	J	`jnl`	Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Briefings Bioinform. 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
2021	J	`jnl`	A Multi-Schematic Classifier-Independent Oversampling Approach for Imbalanced Datasets. IEEE Access Saptarshi Bej, Kristian Schulz, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer
2021	J	`jnl`	A multi-schematic classifier-independent oversampling approach for imbalanced datasets. CoRR Saptarshi Bej, Kristian Schultz, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer
2021	J	`jnl`	Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling. BMC Bioinform. Saptarshi Bej, Anne-Marie Galow, Robert David, Markus Wolfien, Olaf Wolkenhauer
2021	B	`conf`	Combining uniform manifold approximation with localized affine shadowsampling improves classification of imbalanced datasets. IJCNN Saptarshi Bej, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer
2021	J	`jnl`	LoRAS: an oversampling approach for imbalanced datasets. Mach. Learn. Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer
2020	J	`jnl`	An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. BMC Bioinform. Nivedita Singh, Martin Eberhardt, Olaf Wolkenhauer, Julio Vera, Shailendra K. Gupta
2020	J	`jnl`	GEMtractor: extracting views into genome-scale metabolic models. Bioinform. Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi
2019	J	`jnl`	Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 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
2019	J	`jnl`	LoRAS: An oversampling approach for imbalanced datasets. CoRR Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer
2018	J	`jnl`	A systematic survey of centrality measures for protein-protein interaction networks. BMC Syst. Biol. Minoo Ashtiani, Ali Salehzadeh-Yazdi, Zahra Razaghi-Moghadam, Holger Hennig, Olaf Wolkenhauer, Mehdi Mirzaie, Mohieddin Jafari
2018	J	`jnl`	Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC Syst. Biol. Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath
2018	J	`jnl`	Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel
2018	J	`jnl`	Identifying frequent patterns in biochemical reaction networks: a workflow. Database J. Biol. Databases Curation Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel
2018	J	`jnl`	Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide. J. Comput. Aided Mol. Des. Krishna P. Singh, Lokesh Baweja, Olaf Wolkenhauer, Qamar Rahman, Shailendra K. Gupta
2018	J	`jnl`	Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Comput. Biol. Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath, Olaf Wolkenhauer
2017	J	`jnl`	Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel
2017	J	`jnl`	The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 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
2016	J	`jnl`	An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinform. Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath
2016	J	`jnl`	COMODI: an ontology to characterise differences in versions of computational models in biology. J. Biomed. Semant. Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer
2016	—	`conf`	Challenges and opportunities for system biology standards and tools in medical research. ODLS Matthias König, Anika Oellrich, Dagmar Waltemath, Richard J. B. Dobson, Tim J. P. Hubbard, Olaf Wolkenhauer
2016	J	`jnl`	Finding patterns in biochemical reaction networks. PeerJ Prepr. Ron Henkel, Fabienne Lambusch, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Dagmar Waltemath
2016	J	`jnl`	How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE Trans. Biomed. Eng. Dagmar Waltemath, Olaf Wolkenhauer
2016	J	`jnl`	Personalized cancer immunotherapy using Systems Medicine approaches. Briefings Bioinform. Shailendra K. Gupta, Tanushree Jaitly, Ulf Schmitz, Gerold Schuler, Olaf Wolkenhauer, Julio Vera
2016	J	`jnl`	TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinform. Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stefan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer
2016	J	`jnl`	The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions. Briefings Bioinform. Ulf Schmitz, Hojjat Naderi-Meshkin, Shailendra K. Gupta, Olaf Wolkenhauer, Julio Vera
2015	J	`jnl`	Annotation-based feature extraction from sets of SBML models. J. Biomed. Semant. Rebekka Alm, Dagmar Waltemath, Markus Wolfien, Olaf Wolkenhauer, Ron Henkel
2015	J	`jnl`	Combining computational models, semantic annotations and simulation experiments in a graph database. Database J. Biol. Databases Curation Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath
2015	—	`ch.`	Mehrebenensysteme in der Biomedizin. Wissenschaft und Kunst der Modellierung Tom Theile, Olaf Wolkenhauer
2014	—	`conf`	Annotation-Based Feature Extraction from Sets of SBML Models. DILS Rebekka Alm, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel
2014	J	`jnl`	Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis. BMC Syst. Biol. Johannes Wollbold, Robert Jaster, Sarah Müller, Katja Rateitschak, Olaf Wolkenhauer
2013	J	`jnl`	Improving the reuse of computational models through version control. Bioinform. Dagmar Waltemath, Ron Henkel, Robert Hälke, Martin Scharm, Olaf Wolkenhauer
2013	J	`jnl`	Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes. Cogn. Comput. Padhraig Gormley, Kang Li, Olaf Wolkenhauer, George W. Irwin, Dajun Du
2013	J	`jnl`	Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. BMC Syst. Biol. Ulf W. Liebal, Thomas Millat, Jon Marles-Wright, Richard J. Lewis, Olaf Wolkenhauer
2012	—	`conf`	Considerations of graph-based concepts to manage of computational biology models and associated simulations. GI-Jahrestagung Ron Henkel, Nicolas Le Novère, Olaf Wolkenhauer, Dagmar Waltemath
2012	J	`jnl`	Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease. BMC Syst. Biol. Angelyn Lao, Vanessa Schmidt, Yvonne Schmitz, Thomas E. Willnow, Olaf Wolkenhauer
2012	J	`jnl`	Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells. PLoS Comput. Biol. Katja Rateitschak, Felix Winter, Falko Lange, Robert Jaster, Olaf Wolkenhauer
2011	J	`jnl`	A model-based strategy to investigate the role of Theory Biosci. Svetoslav G. Nikolov, Julio Vera, Ulf Schmitz, Olaf Wolkenhauer
2011	J	`jnl`	A stem cell niche dominance theorem. BMC Syst. Biol. Olaf Wolkenhauer, Darryl Shibata, Mihajlo D. Mesarovic
2011	J	`jnl`	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. Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R. King, Olaf Wolkenhauer
2011	C	`conf`	Agent-based Simulation of Molecular Processes - An Application to Actin-polymerisation. SIMULTECH Stefan Pauleweit, J. Barbara Nebe, Olaf Wolkenhauer
2011	J	`jnl`	Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 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
2011	J	`jnl`	Modeling the Calvin-Benson cycle. BMC Syst. Biol. Jiri Jablonsky, Hermann Bauwe, Olaf Wolkenhauer
2011	—	`conf`	Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation. SIMULTECH (Selected Papers) Stefan Pauleweit, J. Barbara Nebe, Olaf Wolkenhauer
2010	J	`jnl`	Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics. Int. J. Syst. Sci. Svetoslav G. Nikolov, Xin Lai, Ulf W. Liebal, Olaf Wolkenhauer, Julio Vera
2010	J	`jnl`	Non-coding RNA detection methods combined to improve usability, reproducibility and precision. BMC Bioinform. Peter Raasch, Ulf Schmitz, Nadja Patenge, Julio Vera, Bernd Kreikemeyer, Olaf Wolkenhauer
2009	J	`jnl`	A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. Comput. Biol. Chem. Xin Lai, Svetoslav G. Nikolov, Olaf Wolkenhauer, Julio Vera
2009	J	`jnl`	Exploration of homodimer receptor: homodimer protein interactions. Int. J. Bioinform. Res. Appl. Julio Vera, Taesoo Kwon, Ulf Schmitz, Walter Kolch, Olaf Wolkenhauer
2008	J	`jnl`	A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. BMC Syst. Biol. Julio Vera, Julie Bachmann, Andrea C. Pfeifer, Verena Becker, Jose A. Hormiga, Néstor Torres Darias, Jens Timmer, Ursula Klingmüller, Olaf Wolkenhauer
2008	J	`jnl`	Dynamic properties of a delayed protein cross talk model. Biosyst. Svetoslav G. Nikolov, Julio Vera, Vladimir Kotev, Olaf Wolkenhauer, Valko Petrov
2008	J	`jnl`	Dynamics of receptor and protein transducer homodimerisation. BMC Syst. Biol. Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer
2008	J	`jnl`	Ein Beitrag zu einer Theorie lebender Zellen (A Contribution towards a Theory of Living Cells). Autom. Olaf Wolkenhauer, Jan-Hendrik S. Hofmeyr
2008	J	`jnl`	The role of dynamic stimulation pattern in the analysis of bistable intracellular networks. Biosyst. Thomas Millat, Sree N. Sreenath, Radina P. Soebiyanto, Jayant Avva, Kwang-Hyun Cho, Olaf Wolkenhauer
2007	J	`jnl`	Interpreting Rosen. Artif. Life Olaf Wolkenhauer
2007	J	`jnl`	PLMaddon: a power-law module for the Matlab Bioinform. Julio Vera, Cheng Sun, Yvonne Oertel, Olaf Wolkenhauer
2007	J	`jnl`	SBML export interface for the systems biology toolbox for MATLAB. Bioinform. Henning Schmidt, Gunnar Drews, Julio Vera, Olaf Wolkenhauer
2006	J	`jnl`	Bioinformatics and The Virtual Cell. it Inf. Technol. Änne Glass, Thomas Karopka, Olaf Wolkenhauer
2006	J	`jnl`	Information Technology in Systems Biology (Informationstechnologien in der Systembiologie). it Inf. Technol. Henning Schmidt, Mats Jirstrand, Olaf Wolkenhauer
2005	—	`conf`	A fully Bayesian model to cluster gene-expression profiles. ECCB/JBI C. Vogl, Fátima Sánchez-Cabo, Gernot Stocker, Simon J. Hubbard, Olaf Wolkenhauer, Zlatko Trajanoski
2005	J	`jnl`	Clustering of unevenly sampled gene expression time-series data. Fuzzy Sets Syst. Carla S. Möller-Levet, Frank Klawonn, Kwang-Hyun Cho, Hujun Yin, Olaf Wolkenhauer
2005	—	`conf`	From Networks to Systems to Complex Systems: A Signaling Pathway Coordination Case Study. CDC/ECC Radina P. Soebiyanto, Sree N. Sreenath, Mihajlo D. Mesarovic, Olaf Wolkenhauer
2004	J	`jnl`	Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis. Bioinform. Zoltán Kutalik, Jacqueline Inwald, Steve V. Gordon, R. Glyn Hewinson, Philip D. Butcher, Jason Hinds, Kwang-Hyun Cho, Olaf Wolkenhauer
2004	B	`conf`	Modelling gene expression time-series with radial basis function neural networks. IJCNN Carla S. Möller-Levet, Kwang-Hyun Cho, Hujun Yin, Olaf Wolkenhauer
2003	J	`jnl`	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. Kwang-Hyun Cho, Sung-Young Shin, Walter Kolch, Olaf Wolkenhauer
2003	B	`conf`	Fuzzy Clustering of Short Time-Series and Unevenly Distributed Sampling Points. IDA Carla S. Möller-Levet, Frank Klawonn, Kwang-Hyun Cho, Olaf Wolkenhauer
2003	—	`conf`	How to Synthesize an Optimized Genetic-Switching System? A System-Theoretic Approach Based on SQP. CMSB Kwang-Hyun Cho, Jong-Ho Cha, Olaf Wolkenhauer
2003	J	`jnl`	Introduction to the Special Issue on Systems Biology and Simulation. Simul. Kwang-Hyun Cho, Adelinde M. Uhrmacher, Olaf Wolkenhauer
2003	J	`jnl`	Level sets and minimum volume sets of probability density functions. Int. J. Approx. Reason. Javier Nunez-Garcia, Zoltán Kutalik, Kwang-Hyun Cho, Olaf Wolkenhauer
2003	—	`conf`	Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway. CMSB Kwang-Hyun Cho, Sung-Young Shin, Hyun Woo Kim, Olaf Wolkenhauer, Brian McFerran, Walter Kolch
2003	—	`conf`	Simulation Study of the TNF alpha Mediated NF-kappa B Signaling Pathway. CMSB Kwang-Hyun Cho, Sung-Young Shin, Hyeon-Woo Lee, Olaf Wolkenhauer
2002	J	`jnl`	Random set system identification. IEEE Trans. Fuzzy Syst. Javier Nunez-Garcia, Olaf Wolkenhauer
2001	—	`book`	Data engineering - fuzzy mathematics in systems theory and data analysis. Olaf Wolkenhauer
2001	—	`ch.`	On Information Fusion in the Life-Sciences. Data Fusion and Perception Olaf Wolkenhauer
2001	B	`conf`	Random Sets and Histograms. FUZZ-IEEE Javier Nunez-Garcia, Olaf Wolkenhauer
2001	J	`jnl`	Systems Biology: the Reincarnation of Systems Theory Applied in Biology?. Briefings Bioinform. Olaf Wolkenhauer
1997	J	`jnl`	Possibilistic Testing of Distribution Functions for Change Detection. Intell. Data Anal. Olaf Wolkenhauer, John M. Edmunds
1997	B	`conf`	Qualitative Uncertainty Models from Random Set Theory. IDA Olaf Wolkenhauer