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ORCIDOlaf Wolkenhauer
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- affiliation: University of Rostock, Germany
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2020 – today
- 2024
[j58]Prashant Srivastava, Alexandra Steuer, Francesco Ferri, Alessandro Nicoli, Kristian Schultz, Saptarshi Bej, Antonella Di Pizio, Olaf Wolkenhauer:
Bitter peptide prediction using graph neural networks. J. Cheminformatics 16(1): 111 (2024)- [j57]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): 5973 (2024) - [j56]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: 110138 (2024) - [i8]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 abs/2402.13103 (2024) - [i7]Manjunath Mahendra, Chaithra Umesh, Saptarshi Bej, Kristian Schultz, Olaf Wolkenhauer:
Convex space learning for tabular synthetic data generation. CoRR abs/2407.09789 (2024) - 2022
- [j55]Prashant Srivastava, Saptarshi Bej, Kristian Schultz, Kristina Y. Yordanova, Olaf Wolkenhauer:
Attention Retrieval Model for Entity Relation Extraction From Biological Literature. IEEE Access 10: 22429-22440 (2022) - [j54]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) - [i6]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 abs/2206.09812 (2022) - 2021
- [j53]Saptarshi Bej, Kristian Schulz, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer:
A Multi-Schematic Classifier-Independent Oversampling Approach for Imbalanced Datasets. IEEE Access 9: 123358-123374 (2021) - [j52]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): 557 (2021) - [j51]Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer:
LoRAS: an oversampling approach for imbalanced datasets. Mach. Learn. 110(2): 279-301 (2021) - [c14]Saptarshi Bej, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer:
Combining uniform manifold approximation with localized affine shadowsampling improves classification of imbalanced datasets. IJCNN 2021: 1-8 - [i5]Saptarshi Bej, Kristian Schultz, Prashant Srivastava, Markus Wolfien, Olaf Wolkenhauer:
A multi-schematic classifier-independent oversampling approach for imbalanced datasets. CoRR abs/2107.07349 (2021) - 2020
- [j50]Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi:
GEMtractor: extracting views into genome-scale metabolic models. Bioinform. 36(10): 3281-3282 (2020) - [j49]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): 329 (2020)
2010 – 2019
- 2019
- [j48]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): 540-550 (2019) - [i4]Saptarshi Bej, Narek Davtyan, Markus Wolfien, Mariam Nassar, Olaf Wolkenhauer:
LoRAS: An oversampling approach for imbalanced datasets. CoRR abs/1908.08346 (2019) - 2018
- [j47]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: bay051 (2018) - [j46]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): 53:1-53:10 (2018) - [j45]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): 80:1-80:17 (2018) - [j44]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): 487-496 (2018) - [j43]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) - [i3]Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel:
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 6: e1479 (2018) - 2017
- [j42]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): W560-W566 (2017) - [i2]Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel:
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 5: e1479 (2017) - 2016
- [j41]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): 380-392 (2016) - [j40]Shailendra K. Gupta, Tanushree Jaitly, Ulf Schmitz, Gerold Schuler, Olaf Wolkenhauer, Julio Vera:
Personalized cancer immunotherapy using Systems Medicine approaches. Briefings Bioinform. 17(3): 453-467 (2016) - [j39]Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath:
An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinform. 32(4): 563-570 (2016) - [j38]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: 46 (2016) - [j37]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: 21 (2016) - [j36]Dagmar Waltemath, Olaf Wolkenhauer:
How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE Trans. Biomed. Eng. 63(10): 1999-2006 (2016) - [c13]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: 1-6 - [i1]Ron Henkel, Fabienne Lambusch, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Dagmar Waltemath:
Finding patterns in biochemical reaction networks. PeerJ Prepr. 4: e1479 (2016) - 2015
- [j35]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) - [j34]Rebekka Alm, Dagmar Waltemath, Markus Wolfien, Olaf Wolkenhauer, Ron Henkel:
Annotation-based feature extraction from sets of SBML models. J. Biomed. Semant. 6: 20 (2015) - [p2]Tom Theile, Olaf Wolkenhauer:
Mehrebenensysteme in der Biomedizin. Wissenschaft und Kunst der Modellierung 2015: 455-474 - 2014
- [j33]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: 101 (2014) - [c12]Rebekka Alm, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel:
Annotation-Based Feature Extraction from Sets of SBML Models. DILS 2014: 81-95 - 2013
- [j32]Dagmar Waltemath, Ron Henkel, Robert Hälke, Martin Scharm, Olaf Wolkenhauer:
Improving the reuse of computational models through version control. Bioinform. 29(6): 742-748 (2013) - [j31]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: 3 (2013) - [j30]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): 106-118 (2013) - 2012
- [j29]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: 74 (2012) - [j28]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) - [c11]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: 1545-1551 - 2011
- [j27]Olaf Wolkenhauer, Darryl Shibata, Mihajlo D. Mesarovic:
A stem cell niche dominance theorem. BMC Syst. Biol. 5: 4 (2011) - [j26]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: 10 (2011) - [j25]Jiri Jablonsky, Hermann Bauwe, Olaf Wolkenhauer:
Modeling the Calvin-Benson cycle. BMC Syst. Biol. 5: 185 (2011) - [j24]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) - [j23]Svetoslav G. Nikolov, Julio Vera, Ulf Schmitz, Olaf Wolkenhauer:
A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks. Theory Biosci. 130(1): 55-69 (2011) - [c10]Stefan Pauleweit, J. Barbara Nebe, Olaf Wolkenhauer:
Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation. SIMULTECH (Selected Papers) 2011: 183-191 - [c9]Stefan Pauleweit, J. Barbara Nebe, Olaf Wolkenhauer:
Agent-based Simulation of Molecular Processes - An Application to Actin-polymerisation. SIMULTECH 2011: 276-282 - 2010
- [j22]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: 491 (2010) - [j21]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): 81-105 (2010)
2000 – 2009
- 2009
- [j20]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): 312-324 (2009) - [j19]Julio Vera, Taesoo Kwon, Ulf Schmitz, Walter Kolch, Olaf Wolkenhauer:
Exploration of homodimer receptor: homodimer protein interactions. Int. J. Bioinform. Res. Appl. 5(4): 447-457 (2009) - 2008
- [j18]Olaf Wolkenhauer, Jan-Hendrik S. Hofmeyr:
Ein Beitrag zu einer Theorie lebender Zellen (A Contribution towards a Theory of Living Cells). Autom. 56(5): 225-232 (2008) - [j17]Svetoslav G. Nikolov, Julio Vera, Vladimir Kotev, Olaf Wolkenhauer, Valko Petrov:
Dynamic properties of a delayed protein cross talk model. Biosyst. 91(1): 51-68 (2008) - [j16]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): 270-281 (2008) - [j15]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: 38 (2008) - [j14]Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer:
Dynamics of receptor and protein transducer homodimerisation. BMC Syst. Biol. 2: 92 (2008) - 2007
- [j13]Olaf Wolkenhauer:
Interpreting Rosen. Artif. Life 13(3): 291-292 (2007) - [j12]Henning Schmidt, Gunnar Drews, Julio Vera, Olaf Wolkenhauer:
SBML export interface for the systems biology toolbox for MATLAB. Bioinform. 23(10): 1297-1298 (2007) - [j11]Julio Vera, Cheng Sun, Yvonne Oertel, Olaf Wolkenhauer:
PLMaddon: a power-law module for the MatlabTM SBToolbox. Bioinform. 23(19): 2638-2640 (2007) - 2006
- [j10]Änne Glass, Thomas Karopka, Olaf Wolkenhauer:
Bioinformatics and The Virtual Cell. it Inf. Technol. 48(1): 44-51 (2006) - [j9]Henning Schmidt, Mats Jirstrand, Olaf Wolkenhauer:
Information Technology in Systems Biology (Informationstechnologien in der Systembiologie). it Inf. Technol. 48(3): 133-139 (2006) - 2005
- [j8]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): 49-66 (2005) - [c8]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: 4851-4856 - [c7]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: 136 - 2004
- [j7]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): 357-363 (2004) - 2003
- [j6]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): 25-47 (2003) - [j5]Kwang-Hyun Cho, Adelinde M. Uhrmacher, Olaf Wolkenhauer:
Introduction to the Special Issue on Systems Biology and Simulation. Simul. 79(12): 673 (2003) - [j4]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): 726-739 (2003) - [c6]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: 127-141 - [c5]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: 170 - [c4]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: 171 - [c3]Carla S. Möller-Levet, Frank Klawonn, Kwang-Hyun Cho, Olaf Wolkenhauer:
Fuzzy Clustering of Short Time-Series and Unevenly Distributed Sampling Points. IDA 2003: 330-340 - 2002
- [j3]Javier Nunez-Garcia, Olaf Wolkenhauer:
Random set system identification. IEEE Trans. Fuzzy Syst. 10(3): 287-296 (2002) - 2001
- [b1]Olaf Wolkenhauer:
Data engineering - fuzzy mathematics in systems theory and data analysis. Wiley 2001, ISBN 978-0-471-41656-2, pp. I-XXXII, 1-263 - [j2]Olaf Wolkenhauer:
Systems Biology: the Reincarnation of Systems Theory Applied in Biology?. Briefings Bioinform. 2(3): 258-270 (2001) - [c2]Javier Nunez-Garcia, Olaf Wolkenhauer:
Random Sets and Histograms. FUZZ-IEEE 2001: 1183-1186 - [p1]Olaf Wolkenhauer:
On Information Fusion in the Life-Sciences. Data Fusion and Perception 2001: 121-134
1990 – 1999
- 1997
- [j1]Olaf Wolkenhauer, John M. Edmunds:
Possibilistic Testing of Distribution Functions for Change Detection. Intell. Data Anal. 1(1-4): 119-127 (1997) - [c1]Olaf Wolkenhauer:
Qualitative Uncertainty Models from Random Set Theory. IDA 1997: 609-620
Coauthor Index
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