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Olaf 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
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
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
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
Attention Retrieval Model for Entity Relation Extraction From Biological Literature. IEEE Access 10: 22429-22440 (2022) - [j54]Julio Vera
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
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
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
LoRAS: an oversampling approach for imbalanced datasets. Mach. Learn. 110(2): 279-301 (2021) - [c14]Saptarshi Bej, Prashant Srivastava, Markus Wolfien
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
GEMtractor: extracting views into genome-scale metabolic models. Bioinform. 36(10): 3281-3282 (2020) - [j49]Nivedita Singh
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
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019) - [i4]Saptarshi Bej, Narek Davtyan, Markus Wolfien
LoRAS: An oversampling approach for imbalanced datasets. CoRR abs/1908.08346 (2019) - 2018
- [j47]Fabienne Lambusch
Identifying frequent patterns in biochemical reaction networks: a workflow. Database J. Biol. Databases Curation 2018: bay051 (2018) - [j46]Martin Scharm
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
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
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
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
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 6: e1479 (2018) - 2017
- [j42]Björn A. Grüning
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
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 5: e1479 (2017) - 2016
- [j41]Ulf Schmitz
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
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
COMODI: an ontology to characterise differences in versions of computational models in biology. J. Biomed. Semant. 7: 46 (2016) - [j37]Markus Wolfien
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
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
Annotation-based feature extraction from sets of SBML models. J. Biomed. Semant. 6: 20 (2015) - [p2]Tom Theile
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
Improving the reuse of computational models through version control. Bioinform. 29(6): 742-748 (2013) - [j31]Ulf W. Liebal
Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. BMC Syst. Biol. 7: 3 (2013) - [j30]Padhraig Gormley
Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes. Cogn. Comput. 5(1): 106-118 (2013) - 2012
- [j29]Angelyn Lao
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
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
A stem cell niche dominance theorem. BMC Syst. Biol. 5: 4 (2011) - [j26]Sylvia Haus, Sara Jabbari
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
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011) - [j23]Svetoslav G. Nikolov, Julio Vera
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
Non-coding RNA detection methods combined to improve usability, reproducibility and precision. BMC Bioinform. 11: 491 (2010) - [j21]Svetoslav G. Nikolov, Xin Lai
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
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
Exploration of homodimer receptor: homodimer protein interactions. Int. J. Bioinform. Res. Appl. 5(4): 447-457 (2009) - 2008
- [j18]Olaf Wolkenhauer
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
Dynamic properties of a delayed protein cross talk model. Biosyst. 91(1): 51-68 (2008) - [j16]Thomas Millat
The role of dynamic stimulation pattern in the analysis of bistable intracellular networks. Biosyst. 92(3): 270-281 (2008) - [j15]Julio Vera
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. BMC Syst. Biol. 2: 38 (2008) - [j14]Julio Vera
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
SBML export interface for the systems biology toolbox for MATLAB. Bioinform. 23(10): 1297-1298 (2007) - [j11]Julio Vera
PLMaddon: a power-law module for the MatlabTM SBToolbox. Bioinform. 23(19): 2638-2640 (2007) - 2006
- [j10]Änne Glass, Thomas Karopka
Bioinformatics and The Virtual Cell. it Inf. Technol. 48(1): 44-51 (2006) - [j9]Henning Schmidt, Mats Jirstrand
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
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
A fully Bayesian model to cluster gene-expression profiles. ECCB/JBI 2005: 136 - 2004
- [j7]Zoltán Kutalik
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
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
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
Simulation Study of the TNF alpha Mediated NF-kappa B Signaling Pathway. CMSB 2003: 171 - [c3]Carla S. Möller-Levet, Frank Klawonn
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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