rBiopaxParser - an R package to parse, modify and visualize BioPAX data. - Frank Kramer 001; Michaela Bayerlová; Florian Klemm; Annalen Bleckmann; Tim Beißbarth (Bioinform., 2013)

Comparative study on gene set and pathway topology-based enrichment methods. - Michaela Bayerlová; Klaus Jung; Frank Kramer 001; Florian Klemm; Annalen Bleckmann; Tim Beißbarth (BMC Bioinform., 2015)

Building pathway graphs from BioPAX data in R. - Nirupama Benis; Dirkjan Schokker; Frank Kramer 001; Mari A. Smits; María Suárez-Diez (F1000Research, 2016)

ndexr - an R package to interface with the network data exchange. - Florian Auer; Zaynab Hammoud; Alexandr Ishkin; Dexter Pratt; Trey Ideker; Frank Kramer 001 (Bioinform., 2018)

New perspectives: systems medicine in cardiovascular disease. - Frank Kramer 001; Steffen Just; Tanja Zeller (BMC Syst. Biol., 2018)

Utilizing Molecular Network Information via Graph Convolutional Neural Networks to Predict Metastatic Event in Breast Cancer. - Hryhorii Chereda; Annalen Bleckmann; Frank Kramer 001; Andreas Leha; Tim Beißbarth (GMDS, 2019)

Automated Chest CT Image Segmentation of COVID-19 Lung Infection based on 3D U-Net. - Dominik Müller; Iñaki Soto Rey; Frank Kramer 001 (CoRR, 2020)

Multi-Disease Detection in Retinal Imaging Based on Ensembling Heterogeneous Deep Learning Models. - Dominik Müller; Iñaki Soto Rey; Frank Kramer 001 (GMDS, 2021)

CARE REGIO - Digital Transformation and Technology in Nursing Care. - Dominik Fuchs; Ann-Kathrin Waibel; Maximilian Karthan; Nadine Seifert; Michael Örtl; Sabrina Bethge; Gina Fischer; Luca Waschbüsch; Steffen Netzband; Frank Kramer 001; Andreas Mahler; Alexandra Teynor; et al. (ICIMTH, 2021)

Perspective on Code Submission and Automated Evaluation Platforms for University Teaching. - Florian Auer; Johann Frei; Dominik Müller; Frank Kramer 001 (MedInfo, 2021)

COVID-19 Image Segmentation Based on Deep Learning and Ensemble Learning. - Philip Meyer; Dominik Müller; Iñaki Soto Rey; Frank Kramer 001 (MIE, 2021)

MIScnn: a framework for medical image segmentation with convolutional neural networks and deep learning. - Dominik Müller; Frank Kramer 001 (BMC Medical Imaging, 2021)

Assessing the Role of Random Forests in Medical Image Segmentation. - Dennis Hartmann; Dominik Müller; Iñaki Soto Rey; Frank Kramer 001 (CoRR, 2021)

Classification of Viral Pneumonia X-ray Images with the Aucmedi Framework. - Pia Schneider; Dominik Müller; Frank Kramer 001 (CoRR, 2021)

Adaptation of HL7 FHIR for the Exchange of Patients' Gene Expression Profiles. - Florian Auer; Zhibek Abdykalykova; Dominik Müller; Frank Kramer 001 (ICIMTH, 2022)

Implementation of Gene Expression Profiles in the HL7 FHIR Standard. - Florian Auer; Zhibek Abdykalykova; Dominik Müller; Frank Kramer 001 (MIE, 2022)

MISeval: A Metric Library for Medical Image Segmentation Evaluation. - Dominik Müller; Dennis Hartmann; Philip Meyer; Florian Auer; Iñaki Soto Rey; Frank Kramer 001 (MIE, 2022)

An Analysis on Ensemble Learning Optimized Medical Image Classification With Deep Convolutional Neural Networks. - Dominik Müller; Iñaki Soto Rey; Frank Kramer 001 (IEEE Access, 2022)

Towards a Guideline for Evaluation Metrics in Medical Image Segmentation. - Dominik Müller; Iñaki Soto Rey; Frank Kramer 001 (CoRR, 2022)

GERNERMED++: Transfer Learning in German Medical NLP. - Johann Frei; Ludwig Frei-Stuber; Frank Kramer 001 (CoRR, 2022)

Annotated Dataset Creation through General Purpose Language Models for non-English Medical NLP. - Johann Frei; Frank Kramer 001 (CoRR, 2022)

Standardized Medical Image Classification across Medical Disciplines. - Simone Mayer; Dominik Müller; Frank Kramer 001 (CoRR, 2022)

MISm: A Medical Image Segmentation Metric for Evaluation of weak labeled Data. - Dennis Hartmann; Verena Schmid; Philip Meyer; Iñaki Soto Rey; Dominik Müller; Frank Kramer 001 (CoRR, 2022)

Data-dependent visualization of biological networks in the web-browser with NDExEdit. - Florian Auer; Simone Mayer; Frank Kramer 001 (PLoS Comput. Biol., 2022)

GERNERMED: An open German medical NER model. - Johann Frei; Frank Kramer 001 (Softw. Impacts, 2022)

Abstract: AUCMEDI - Von der Insellösung zur einheitlichen und automatischen Klassifizierung von Medizinischen Bildern. - Dominik Müller; Dennis Hartmann; Iñaki Soto Rey; Frank Kramer 001 (Bildverarbeitung für die Medizin, 2023)

Data and Information Problems in Health Care and How Creative Methods Might Solve Them. - Elisabeth Veronica Mess; Julia Krumme; Frank Kramer 001; Alexandra Teynor (ICIMTH, 2023)

Evaluation of the Availability of Nursing Quality Indicators in German FHIR Implementations. - Steffen Netzband; Katharina Ott; Florian Auer; Frank Kramer 001 (ICIMTH, 2023)

The RCX Extension Hub: A Resource for Implementations Extending the R Adaption of the Cytoscape Exchange Format. - Florian Auer; Nadja Bramkamp; Simone Mayer; Dominik Müller; Frank Kramer 001 (MIE, 2023)

Towards Automated COVID-19 Presence and Severity Classification. - Dominik Müller; Silvan Mertes; Niklas Schröter; Fabio Hellmann; Miriam Elia; Bernhard Bauer 001; Wolfgang Reif; Elisabeth André; Frank Kramer 001 (MIE, 2023)

Annotated dataset creation through large language models for non-english medical NLP. - Johann Frei; Frank Kramer 001 (J. Biomed. Informatics, 2023)

GERNERMED++: Semantic annotation in German medical NLP through transfer-learning, translation and word alignment. - Johann Frei; Ludwig Frei-Stuber; Frank Kramer 001 (J. Biomed. Informatics, 2023)

Creating Ontology-annotated Corpora from Wikipedia for Medical Named-entity Recognition. - Johann Frei; Frank Kramer 001 (BioNLP@ACL, 2024)

GottBERT: a pure German Language Model. - Raphael Scheible; Johann Frei; Fabian Thomczyk; Henry He; Patric Tippmann; Jochen Knaus; Victor Jaravine; Frank Kramer 001; Martin Boeker (EMNLP, 2024)

Predicting Overall Survival of Glioblastoma Patients Using Deep Learning Classification Based on MRIs. - Katharina Ott; Santiago Cepeda; Dennis Hartmann; Frank Kramer 001; Dominik Müller (GMDS, 2024)

A Web-Based Questionnaire Builder to Facilitate form Management for the Electronic Data Capture with REDCap. - Florian Auer; Frank Kramer 001 (MIE, 2024)

Assessing the Performance of Deep Learning for Automated Gleason Grading in Prostate Cancer. - Dominik Müller; Philip Meyer; Lukas Rentschler; Robin Manz; Daniel Hieber; Jonas Bäcker; Samantha Cramer; Christoph Wengenmayr; Bruno Märkl; Ralf Huss; Frank Kramer 001; Iñaki Soto Rey; et al. (MIE, 2024)

Towards a FHIR-Based Framework for Analyzing Nursing-Related Data in Smaller Sized Care Facilities. - Steffen Netzband; Dominik Müller; Stefanie Meyer; Jeton Iseni; Frank Kramer 001 (MIE, 2024)

Deep Learning Based Automatic Fibroglandular Tissue Segmentation in Breast Magnetic Resonance Imaging Screening. - Guelsuem Pehlivan; Carl Mathis Wild; Julia Baumgartl; Dennis Hartmann; Nina Ditsch; Frank Kramer 001; Dominik Müller (MIE, 2024)

Development Process of an Interdisciplinary Framework to Approach Data and Information Problems in Healthcare - Preliminary Results. - Elisabeth Veronica Mess; Andreas Halbritter; Viktor Werlitz; Julia Krumme; Dominik Merli; Frank Kramer 001; Alexandra Teynor (ICHI, 2025)

RFMiD: Retinal Image Analysis for multi-Disease Detection challenge. - Samiksha Pachade; Prasanna Porwal; Manesh Kokare; Girish Deshmukh; Vivek Sahasrabuddhe; Zhengbo Luo; Feng Han; Zitang Sun; Li Qihan; Sei-ichiro Kamata; Edward Ho; Edward Wang; et al. (Medical Image Anal., 2025)

Infherno: End-to-end Agent-based FHIR Resource Synthesis from Free-form Clinical Notes. - Johann Frei; Nils Feldhus; Lisa Raithel; Roland Roller; Alexander Meyer; Frank Kramer 001 (CoRR, 2025)