The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results. - Martin Scharm; Florian Wendland; Martin Peters; Markus Wolfien; Tom Theile; Dagmar Waltemath (SWAT4LS, 2014)

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

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)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (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)

Customized workflow development and omics data integration concepts in systems medicine - Markus Wolfien (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)

Word2Vec Embeddings for Categorical Values in Synthetic Tabular Generation. - Waldemar Hahn; Martin Sedlmayr; Markus Wolfien (CSCI, 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)

Context-Sensitive Common Data Models for Genetic Rare Diseases - A Concept. - Najia Ahmadi; Michele Zoch; Brita Sedlmayr; Katharina Schuler; Waldemar Hahn; Martin Sedlmayr; Markus Wolfien (ICIMTH, 2023)

Towards Standardizing Ophthalmic Data for Seamless Interoperability in Eye Care. - Katja Hoffmann; Yuan Peng 011; Tobias Schlosser; Gabriel Stolze; Holger Langner; Marcel Susky; Trixy Meyer; Marc Ritter; Danny Kowerko; Vinodh Kakkassery; Markus Wolfien; Martin Sedlmayr (GMDS, 2024)

Synthetic Data Generation in Hematology - Paving the Way for OMOP and FHIR Integration. - Najia Ahmadi; Katja Hoffmann; Jan-Niklas Eckardt; Martin Sedlmayr; Markus Wolfien (MIE, 2024)

A Concept for Integrating AI-Based Support Systems into Clinical Practice. - Katja Hoffmann; Richard Gebler; Sophia Grummt; Yuan Peng 011; Ines Reinecke; Markus Wolfien; Martin Sedlmayr (MIE, 2024)

A Hybrid-Approach for Privacy Preserving Record Linkage - A Case Study from Germany. - Igor Nesterow; Markus Wolfien (MIE, 2024)

Mimicking clinical trials with synthetic acute myeloid leukemia patients using generative artificial intelligence. - Jan-Niklas Eckardt; Waldemar Hahn; Christoph Röllig; Sebastian Stasik; Uwe Platzbecker; Carsten Müller-Tidow; Hubert Serve; Claudia D. Baldus; Christoph Schliemann; Kerstin Schäfer-Eckart; Maher Hanoun; Martin Kaufmann; et al. (npj Digit. Medicine, 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)

From Polar Bears to People: The Role of Ethnic Genetic Variation in Thermoregulation and Heat-Related Health Risk. - Alexandra Baumann; Jakob Thiel; Nina Haffer; Shailendra Gupta; Markus Wolfien (BIOSTEC (1), 2025)

Generating Reliable Synthetic Clinical Trial Data: The Role of Hyperparameter Optimization and Domain Constraints. - Waldemar Hahn; Jan-Niklas Eckardt; Christoph Röllig; Martin Sedlmayr; Jan Moritz Middeke; Markus Wolfien (CoRR, 2025)