Publikationen
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2025 |
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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, Asaanth Sivajohan, Saerom Youn, Kevin Lane, Jin Chun, Xinliang Wang, Yunchao Gu, Sixu Lu, Young-tack Oh, Hyunjin Park, Chia-Yen Lee, Hung Yeh, Kai-Wen Cheng, Haoyu Wang, Jin Ye, Junjun He, Lixu Gu, Dominik Müller, Iñaki Soto-Rey, Frank Kramer, Hidehisa Arai, Yuma Ochi, Takami Okada, Luca Giancardo, Gwenolé Quellec and Fabrice Mériaudeau. 2025. RFMiD: retinal image analysis for multi-disease detection challenge. Medical Image Analysis 99, 103365. DOI: 10.1016/j.media.2024.103365 |
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2024 |
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Gabriele Maria Lehner, Laura Gockeln, Bettina Marie Naber, Janis Raphael Thamm, Sandra Schuh, Gabriel Duttler, Anna Rottenkolber, Dennis Hartmann, Frank Kramer and Julia Welzel. 2024. Differences in the annotation between facial images and videos for training an artificial intelligence for skin type determination. Skin Research and Technology 30, 3, e13632. DOI: 10.1111/srt.13632 |
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Sergio García-García, Santiago Cepeda, Dominik Müller, Alejandra Mosteiro, Ramón Torné, Silvia Agudo, Natalia de la Torre, Ignacio Arrese and Rosario Sarabia. 2024. Mortality prediction of patients with subarachnoid hemorrhage using a deep learning model based on an initial brain CT scan. Brain Sciences 14, 1, 10. DOI: 10.3390/brainsci14010010 |
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Antonios Bayas, Ulrich Mansmann, Begum Irmak Ön, Verena S. Hoffmann, Achim Berthele, Mark Mühlau, Markus C. Kowarik, Markus Krumbholz, Makbule Senel, Verena Steuerwald, Markus Naumann, Julia Hartberger, Martin Kerschensteiner, Eva Oswald, Christoph Ruschil, Ulf Ziemann, Hayrettin Tumani, Ioannis Vardakas, Fady Albashiti, Frank Kramer, Iñaki Soto-Rey, Helmut Spengler, Gerhard Mayer, Hans Armin Kestler, Oliver Kohlbacher, Marlien Hagedorn, Martin Boeker, Klaus Kuhn, Stefan Buchka, Florian Kohlmayer, Jan S. Kirschke, Lars Behrens, Hanna Zimmermann, Benjamin Bender, Nico Sollmann, Joachim Havla, Bernhard Hemmer, Ansgar Berlis, Benedikt Wiestler, Tania Kümpfel, Klaus Seelos, Jutta Dünschede, Roswitha Kemmner, Meinrad Beer, Jennifer Dietrich and Jonas Schaller. 2024. Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing–remitting multiple sclerosis, the ProVal-MS study. Neurological Research and Practice 6, 1, 15. DOI: 10.1186/s42466-024-00310-x |
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Sebastian Lutz, Alicia D'Angelo, Sonja Hammerl, Maximilian Schmutz, Rainer Claus, Nina M. Fischer, Frank Kramer and Zaynab Hammoud. in press. Unveiling the digital evolution of molecular tumor boards. Targeted Oncology . DOI: 10.1007/s11523-024-01109-1 |
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Elisabeth Veronica Mess, Frank Kramer, Julia Krumme, Nico Kanelakis and Alexandra Teynor. in press. Use of creative frameworks in healthcare to solve data and information problems: a scoping review. JMIR Human Factors . DOI: 10.2196/55182 |
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Johann Frei, Florian J. Auer, Steffen Netzband, Yevgeniia Ignatenko and Frank Kramer. 2024. Web-based prototype for graphical exploration of FHIR® questionnaire responses. AMIA Annual Symposium Proceedings 2023, 351-358. |
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Melitta B. Köpke, Stefan Schiele, Verena Schmid, R. Haidinger, B. Weilter, S. Seitz, E. Schumacher-Wulff, U.-S. Albert, T. Baumgartner, Christoph Aulmann, Hasan Alkomiet, Christian Dannecker, S. Corradini, J. Ettl, N. Harbeck, Ludwig Christian Hinske, M. Kiechle, Miriam Kunz, O. Koelbl, O. Ortmann, Anna Rubeck, Frank Kramer, Miriam Reicherts, A. Woeckel, P. Fasching, M. Beckmann and Nina Ditsch. 2024. Zufriedenheit bei Brustkrebserkrankten mit Erstgespräch bei Behandlung während der Corona-Pandemie – Subgrupenanalyse der WAVES-Studie [Abstract]. Geburtshilfe und Frauenheilkunde 84, 6, E35-E36. DOI: 10.1055/s-0044-1787395 |
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2023 |
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Sebastian Lutz, Florian Auer, Dennis Hartmann, Hryhorii Chereda, Tim Beißbarth and Frank Kramer. in press. Adaptation of Graph Convolutional Neural Networks and graph layer-wise relevance propagation to the Spektral library with application to gene expression data of colorectal cancer patients. preprint. DOI: 10.1101/2023.01.26.525010 |
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Johann Frei and Frank Kramer. 2023. Annotated dataset creation through large language models for non-english medical NLP. Journal of Biomedical Informatics 145, 104478. DOI: 10.1016/j.jbi.2023.104478 |
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Elisabeth Veronica Mess, Julia Krumme, Frank Kramer and Alexandra Teynor. 2023. Data and information problems in health care and how creative methods might solve them. In John Mantas, Parisis Gallos, Emmanouil Zoulias, Arie Hasman, Mowafa S. Househ, Martha Charalampidou and Andriana Magdalinou (Ed.). Healthcare transformation with informatics and artificial intelligence. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 305), 335-338. DOI: 10.3233/shti230498 |
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Steffen Netzband, Volker Hammen and Frank Kramer. 2023. Data-driven nursing research: an overview of underlying concepts and enablers. In Ralf Huss (Ed.). Digital medicine: bringing digital solutions to medical practice. Jenny Stanford Publishing, New York, NY, 171-184. DOI: 10.1201/9781003386070-9 |
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Timo Fuchs, Lena Kaiser, Dominik Müller, Laszlo Papp, Regina Fischer and Johannes Tran-Gia. 2023. Enhancing interoperability and harmonisation of nuclear medicine image data and associated clinical data. Nuklearmedizin - NuclearMedicine 62, 6, 389-398. DOI: 10.1055/a-2187-5701 |
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Steffen Netzband, Katharina Ott, Florian Auer and Frank Kramer. 2023. Evaluation of the availability of nursing quality indicators in German FHIR implementations. In John Mantas, Parisis Gallos, Emmanouil Zoulias, Arie Hasman, Mowafa S. Househ, Martha Charalampidou and Andriana Magdalinou (Ed.). Healthcare transformation with informatics and artificial intelligence. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 305), 299-302. DOI: 10.3233/shti230488 |
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Dominik Müller. 2023. Frameworks in medical image analysis with deep neural networks. Dissertation, Universität Augsburg. . |
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Johann Frei, Ludwig Frei-Stuber and Frank Kramer. 2023. GERNERMED++: semantic annotation in German medical NLP through transfer-learning, translation and word alignment. Journal of Biomedical Informatics 147, 104513. DOI: 10.1016/j.jbi.2023.104513 |
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Johann Frei and Frank Kramer. 2023. German medical named entity recognition model and data set creation using machine translation and word alignment: algorithm development and validation. JMIR Formative Research 7, e39077. DOI: 10.2196/39077 |
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Dennis Hartmann, Verena Schmid, Philip Meyer, Florian Auer, Iñaki Soto-Rey, Dominik Müller and Frank Kramer. 2023. MISM: a medical image segmentation metric for evaluation of weak labeled data. Diagnostics 13, 16, 2618. DOI: 10.3390/diagnostics13162618 |
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Sergio García, Santiago Cepeda, Dominik Müller, Alejandra Mosteiro-Cadaval, Ramon Torne, Silvia Agudo, Natalia de la Torre, Ignacio Arrese and Rosario Sarabia. 2023. Neurological outcome prediction in patients with subarachnoid hemorrhage using a model based on initial CT scan, clinical data and neural networks [Abstract]. Brain and Spine 3, Supplement 1, 101995. DOI: 10.1016/j.bas.2023.101995 |
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Florian Auer, Nadja Bramkamp (Beckmann), Simone Mayer, Dominik Müller and Frank Kramer. 2023. The RCX extension hub: a resource for implementations extending the R adaption of the cytoscape exchange format. In Maria Hägglund, Madeleine Blusi, Stefano Bonacina, Lina Nilsson, Inge Cort Madsen, Sylvia Pelayo, Anne Moen, Arriel Benis, Lars Lindsköld and Parisis Gallos (Ed.). Caring is sharing – exploiting the value in data for health and innovation. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 302), 1075-1076. DOI: 10.3233/shti230352 |
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Dominik Mueller, Silvan Mertes, Niklas Schroeter, Fabio Hellmann, Miriam Elia, Bernhard Bauer, Wolfgang Reif, Elisabeth André and Frank Kramer. 2023. Towards automated COVID-19 presence and severity classification. In Maria Hägglund, Madeleine Blusi, Stefano Bonacina, Lina Nilsson, Inge Cort Madsen, Sylvia Pelayo, Anne Moen, Arriel Benis, Lars Lindsköld and Parisis Gallos (Ed.). Caring is sharing – exploiting the value in data for health and innovation. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 302), 917-921. DOI: 10.3233/shti230309 |
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Nina Ditsch, Melitta B. Köpke, R. Haidinger, R. Würstlein, B. Welter, S. Seitz, E. Schumacher-Wulff, U. S. Albert, T. Baumgartner, C. Aulmann, Alkomiet Hasan, Christian Dannecker, S. Corradini, J. Ettl, N. Harbeck, Ludwig Christian Hinske, M. Kiechle, Miriam Kunz, O. Koelbl, O. Ortmann, Stefan Schiele, Verena Schmid, M. Weiss, A. Wöckel, P. Fasching and M. W. Beckmann. 2023. Ärztliches "Sich Zeit nehmen" befürwortet – erste Ergebnisse der WAVES-Studie im Rahmen der Diagnosemitteilung Brustkrebs [Abstract]. Geburtshilfe und Frauenheilkunde 83, 6, 758-759. DOI: 10.1055/s-0043-1768873 |
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2022 |
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Florian Auer, Zhibek Abdykalykova, Dominik Müller and Frank Kramer. 2022. Adaptation of HL7 FHIR for the exchange of patients' gene expression profiles. In John Mantas, Parisis Gallos, Emmanouil Zoulias, Arie Hasman, Mowafa S. Househ, Mowafa S. Househ, Marianna Diomidous, Joseph Liaskos and Martha Charalampidou (Ed.). Advances in informatics, management and technology in healthcare. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 295), 332-335. DOI: 10.3233/shti220730 |
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Dominik Müller, Inaki Soto-Rey and Frank Kramer. 2022. An analysis on ensemble learning optimized medical image classification with deep convolutional neural networks. IEEE Access 10, 66467-66480. DOI: 10.1109/access.2022.3182399 |
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Dominik Fuchs, Ann-Kathrin Waibel, Maximilian Karthan, Nadine Seifert, Michael Örtl, Sabrina Bethge, Gina Fischer, Luca Waschbüsch, Steffen Netzband, Frank Kramer, Andreas Mahler, Alexandra Teynor, Dominik Merli, Elisabeth Veronica Mess, Jennifer Öttinger, Stefanie Schmid, Amelie Scheu, Walter Swoboda and Petra Friedrich. 2022. CARE REGIO – digital transformation and technology in nursing care. In John Mantas, Arie Hasman, Mowafa S. Househ, Parisis Gallos, Emmanouil Zoulias and Joseph Liaskos (Ed.). Informatics and Technology in Clinical Care and Public Health. IOS Press (Studies in Health Technology and Informatics ; 289), 286-289. DOI: 10.3233/shti210915 |
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Florian Auer, Simone Mayer and Frank Kramer. 2022. Data-dependent visualization of biological networks in the web-browser with NDExEdit. PLoS Computational Biology 18, 6, 1010205. DOI: 10.1371/journal.pcbi.1010205 |
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Johann Frei, Iñaki Soto-Rey and Frank Kramer. 2022. DrNote: an open medical annotation service. PLOS Digital Health 1, 8, e0000086. DOI: 10.1371/journal.pdig.0000086 |
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Sebastian Hofmann. 2022. Forschungsklausel statt Broad Consent: Sekundärnutzung von Patientendaten ohne Einwilligung, dafür mit Opt-out. Datenschutz und Datensicherheit - DuD 46, 12, 756-761. DOI: 10.1007/s11623-022-1691-7 |
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Johann Frei and Frank Kramer. 2022. GERNERMED: an open German medical NER model. Software Impacts 11, 100212. DOI: 10.1016/j.simpa.2021.100212 |
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Georg Emons, Noam Auslander, Peter Jo, Julia Kitz, Azadeh Azizian, Yue Hu, Clemens F. Hess, Claus Roedel, Ulrich Sax, Gabriela Salinas, Philipp Stroebel, Frank Kramer, Tim Beissbarth, Marian Grade, Michael Ghadimi, Eytan Ruppin, Thomas Ried and Jochen Gaedcke. 2022. Gene-expression profiles of pretreatment biopsies predict complete response of rectal cancer patients to preoperative chemoradiotherapy. British Journal of Cancer 127, 4, 766-775. DOI: 10.1038/s41416-022-01842-2 |
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Seyed-Ahmad Ahmadi, Johann Frei, Gerome Vivar, Marianne Dieterich and Valerie Kirsch. 2022. IE-Vnet: deep learning-based segmentation of the inner ear's total fluid space. Frontiers in Neurology 13, 663200. DOI: 10.3389/fneur.2022.663200 |
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Florian Auer, Zhibek Abdykalykova, Dominik Müller and Frank Kramer. 2022. Implementation of gene expression profiles in the HL7 FHIR standard. In Brigitte Séroussi, Patrick Weber, Ferdinand Dhombres, Cyril Grouin, Jan-David Liebe, Sylvia Pelayo, Andrea Pinna, Bastien Rance, Lucia Sacchi, Adrien Ugon, Arriel Benis and Parisis Gallos (Ed.). Challenges of trustable AI and added-value on health. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 294), 417-418. DOI: 10.3233/shti220490 |
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Dominik Müller, Dennis Hartmann, Philip Meyer, Florian Auer, Iñaki Soto-Rey and Frank Kramer. 2022. MISeval: a metric library for medical image segmentation evaluation. In Brigitte Séroussi, Patrick Weber, Ferdinand Dhombres, Cyril Grouin, Jan-David Liebe, Sylvia Pelayo, Andrea Pinna, Bastien Rance, Lucia Sacchi, Adrien Ugon, Arriel Benis and Parisis Gallos (Ed.). Challenges of trustable AI and added-value on health. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 294), 33-37. DOI: 10.3233/shti220391 |
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Florian Auer, Simone Mayer and Frank Kramer. in press. MetaRelSubNetVis: referenceable network visualizations based on integrated patient data with group-wise comparison. preprint. DOI: 10.1101/2022.04.18.488628 |
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Adrian Pfleiderer, Dominik Müller and Frank Kramer. in press. Nucleus segmentation and analysis in breast cancer with the MIScnn framework. preprint. DOI: 10.48550/arXiv.2206.08182 |
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Florian Auer, Johann Frei, Dominik Müller and Frank Kramer. 2022. Perspective on code submission and automated evaluation platforms for university teaching. In Paula Otero, Philip Scott, Susan Z. Martin and Elaine Huesing (Ed.). MEDINFO 2021: one world, one health – global partnership for digital innovation. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 290), 912-916. DOI: 10.3233/shti220212 |
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Florian Auer and Frank Kramer. 2022. RCX — an R package adapting the Cytoscape Exchange format for biological networks. Bioinformatics Advances 2, 1, vbac020. DOI: 10.1093/bioadv/vbac020 |
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Florian Auer, Hryhorii Chereda, Júlia Perera-Bel and Frank Kramer. in press. Reproducible data integration and visualization of biological networks in R. preprint. DOI: 10.1101/2022.04.15.488519 |
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Dominik Müller, Iñaki Soto-Rey and Frank Kramer. 2022. Towards a guideline for evaluation metrics in medical image segmentation. BMC Research Notes 15, 1, 210. DOI: 10.1186/s13104-022-06096-y |
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2021 |
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Dennis Hartmann, Dominik Müller, Iñaki Soto-Rey and Frank Kramer. in press. Assessing the role of random forests in medical image segmentation. preprint. DOI: 10.48550/arXiv.2103.16492 |
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Philip Meyer, Dominik Müller, Iñaki Soto-Rey and Frank Kramer. 2021. COVID-19 image segmentation based on deep learning and ensemble learning. In John Mantas, Lăcrămioara Stoicu-Tivadar, Catherine Chronaki, Arie Hasman, Patrick Weber, Parisis Gallos, Mihaela Crişan-Vida, Emmanouil Zoulias and Oana Sorina Chirila (Ed.). Public health and informatics. IOS Press, Amsterdam (Studies in Health Technology and Informatics ; 281), 518-519. DOI: 10.3233/shti210223 |
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Manuel Manfred Nietert, Liza Vinhoven, Florian Auer, Sylvia Hafkemeyer and Frauke Stanke. 2021. Comprehensive analysis of chemical structures that have been tested as CFTR activating substances in a publicly available database CandActCFTR. Frontiers in Pharmacology 12, 689205. DOI: 10.3389/fphar.2021.689205 |
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Hryhorii Chereda, Annalen Bleckmann, Kerstin Menck, Júlia Perera-Bel, Philip Stegmaier, Florian Auer, Frank Kramer, Andreas Leha and Tim Beißbarth. 2021. Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer. Genome Medicine 13, 1, 42. DOI: 10.1186/s13073-021-00845-7 |
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Dominik Müller and Frank Kramer. 2021. MIScnn: a framework for medical image segmentation with convolutional neural networks and deep learning. BMC Medical Imaging 21, 1, 12. DOI: 10.1186/s12880-020-00543-7 |
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Dominik Müller, Iñaki Soto-Rey and Frank Kramer. 2021. Multi-disease detection in retinal imaging based on ensembling heterogeneous deep learning models. In Rainer Röhrig, Tim Beißbarth, Jochem König, Claudia Ose, Geraldine Rauch, Ulrich Sax, Björn Schreiweis and Martin Sedlmayr (Ed.). German Medical Data Sciences 2021: Digital Medicine: Recognize – Understand – Heal. IOS Press (Studies in Health Technology and Informatics ; 283), 23-31. DOI: 10.3233/shti210537 |
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J. Eduardo Martinez-Hernandez, Zaynab Hammoud, Alessandra Mara de Sousa, Frank Kramer, Rubens L. do Monte-Neto, Vinicius Maracaja-Coutinho and Alberto J. M. Martin. 2021. Network-based approaches reveal potential therapeutic targets for host-directed antileishmanial therapy driving drug repurposing. Microbiology Spectrum 9, 2, e01018-21. DOI: 10.1128/spectrum.01018-21 |
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M. Storck, S. Sandmann, P. Bruland, M. P. Pereira, S. Steinke, C. Riepe, Iñaki Soto‐Rey, S. Garcovich, M. Augustin, C. Blome, S. Bobko, F. J. Legat, N. Potekaev, A. Lvov, L. Misery, W. Weger, A. Reich, E. Şavk, M. Streit, E. Serra‐Baldrich, J. C. Szepietowski, M. Dugas, S. Ständer and C. Zeidler. 2021. Pruritus intensity scales across Europe: a prospective validation study. Journal of the European Academy of Dermatology and Venereology 35, 5, 1176-1185. DOI: 10.1111/jdv.17111 |
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Dominik Müller, Iñaki Soto-Rey and Frank Kramer. 2021. Robust chest CT image segmentation of COVID-19 lung infection based on limited data. Informatics in Medicine Unlocked 25, 100681. DOI: 10.1016/j.imu.2021.100681 |
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2020 |
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Frank Kramer, Wolfgang Reif, Matthias Schmidt, Thomas Schneider, Karin Thieme and Theo Ungerer. 2020. Die Fakultät für Angewandte Informatik: partnerschaftliche Lösungen für globale Herausforderungen. In Hubert Zapf (Ed.). Wissenschaft, Kreativität, Verantwortung - 50 Jahre Universität Augsburg. Schnell & Steiner, Regensburg, 182-199. |
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Michael Örtl, Felix Holl, Marina Fotteler, Frank Kramer, Andreas Mahler, Dominik Merli, Elisabeth Veronica Mess, Stefanie Schmid, Alexandra Teynor, Petra Friedrich and Walter Swoboda. 2020. Digitalizing nursing in the Bavarian Swabia region of Germany: presentation of the joint project CARE REGIO. Studies in Health Technology and Informatics 272, 265-266. DOI: 10.3233/shti200545 |
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Zaynab Hammoud and Frank Kramer. 2020. Multilayer networks: aspects, implementations, and application in biomedicine. Big Data Analytics 5, 1, 2. DOI: 10.1186/s41044-020-00046-0 |
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Zaynab Hammoud and Frank Kramer. 2020. Multipath: an R package to generate integrated reproducible pathway models. Biology 9, 12, 483. DOI: 10.3390/biology9120483 |
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2019 |
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Vijayalakshmi Kari, Sanjay Kumar Raul, Jana Maria Henck, Julia Kitz, Frank Kramer, Robyn Laura Kosinsky, Nadine Übelmesser, Wael Yassin Mansour, Jessica Eggert, Melanie Spitzner, Zeynab Najafova, Holger Bastians, Marian Grade, Jochen Gaedcke, Florian Wegwitz and Steven A. Johnsen. 2019. The histone methyltransferase DOT1L is required for proper DNA damage response, DNA repair, and modulates chemotherapy responsiveness. Clinical Epigenetics 11, 1, 4. DOI: 10.1186/s13148-018-0601-1 |
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Hryhorii Chereda, Annalen Bleckmann, Frank Kramer, Andreas Leha and Tim Beissbarth. 2019. Utilizing molecular network information via graph convolutional neural networks to predict metastatic event in breast cancer. In Rainer Röhrig, Harald Binder, Hans-Ulrich Prokosch, Ulrich Sax, Irene Schmidtmann, Susanne Stolpe, Antonia Zapf (Eds.). German medical data sciences: shaping change – creative solutions for innovative medicine; proceedings of the 64th Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.) 2019 in Dortmund, Germany – GMDS 2019. IOS Press, Amsterdam, 181-186 DOI: 10.3233/SHTI190824 |
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2018 |
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Frank Kramer, Steffen Just and Tanja Zeller. 2018. New perspectives: systems medicine in cardiovascular disease. BMC Systems Biology 12, 1, 57. DOI: 10.1186/s12918-018-0579-5 |
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Zaynab Hammoud and Frank Kramer. 2018. mully: an R package to create, modify and visualize multilayered graphs. Genes 9, 11, 519. DOI: 10.3390/genes9110519 |
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Florian Auer, Zaynab Hammoud, Alexandr Ishkin, Dexter Pratt, Trey Ideker and Frank Kramer. 2018. ndexr — an R package to interface with the network data exchange. Bioinformatics 34, 4, 716-717. DOI: 10.1093/bioinformatics/btx683 |
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2017 |
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Peter Jo, Azadeh Azizian, Junius Salendo, Frank Kramer, Markus Bernhardt, Hendrik Wolff, Jens Gruber, Marian Grade, Tim Beißbarth, B. Ghadimi and Jochen Gaedcke. 2017. Changes of microrna levels in plasma of patients with rectal cancer during chemoradiotherapy. International Journal of Molecular Sciences 18, 6, 1140. DOI: 10.3390/ijms18061140 |
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Georg Emons, Melanie Spitzner, Sebastian Reineke, Janneke Möller, Noam Auslander, Frank Kramer, Yue Hu, Tim Beissbarth, Hendrik A. Wolff, Margret Rave-Fränk, Elisabeth Heßmann, Jochen Gaedcke, B. Michael Ghadimi, Steven A. Johnsen, Thomas Ried and Marian Grade. 2017. Chemoradiotherapy resistance in colorectal cancer cells is mediated by Wnt/β-catenin signaling. Molecular Cancer Research 15, 11, 1481-1490. DOI: 10.1158/1541-7786.mcr-17-0205 |
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Frank Kramer and Tim Beißbarth. 2017. Working with ontologies. In Jonathan M. Keith (Ed.). Bioinformatics, volume I: data, sequence analysis, and evolution. Springer, New York, NY, 123-135. DOI: 10.1007/978-1-4939-6622-6_6 |
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2016 |
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Jochen Kruppa, Frank Kramer, Tim Beißbarth and Klaus Jung. 2016. A simulation framework for correlated count data of features subsets in high-throughput sequencing or proteomics experiments. Statistical Applications in Genetics and Molecular Biology 15, 5, 401-414. DOI: 10.1515/sagmb-2015-0082 |
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Georg Emons, Melanie Spitzner, Sebastian Reineke, Frank Kramer, Margret Rave-Fraenk, Jochen Gaedcke, Michael Ghadimi, Thomas Ried and Marian Grade. 2016. Abstract 1653: a novel role for Wnt/β-catenin signaling in mediating resistance of colorectal cancer to chemoradiotherapy [Abstract]. Cancer Research 76, 14_Supplement, 1653. DOI: 10.1158/1538-7445.am2016-1653 |
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Nirupama Benis, Dirkjan Schokker, Frank Kramer, Mari A. Smits and Maria Suarez-Diez. 2016. Building pathway graphs from BioPAX data in R. F1000Research 5, 2414. DOI: 10.12688/f1000research.9582.2 |
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Azadeh Azizian, Ingo Epping, Frank Kramer, Peter Jo, Markus Bernhardt, Julia Kitz, Gabriela Salinas, Hendrik Wolff, Marian Grade, Tim Beißbarth, B. Ghadimi and Jochen Gaedcke. 2016. Prognostic value of MicroRNAs in preoperative treated rectal cancer. International Journal of Molecular Sciences 17, 4, 568. DOI: 10.3390/ijms17040568 |
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Silvia von der Heyde, Johanna Sonntag, Frank Kramer, Christian Bender, Ulrike Korf and Tim Beißbarth. 2016. Reconstruction of protein networks using reverse-phase protein array data. In Klaus Jung (Ed.). Statistical analysis in proteomics. Springer, New York, NY (Methods in Molecular Biology ; 1362), 227-246. DOI: 10.1007/978-1-4939-3106-4_15 |
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2015 |
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Michaela Bayerlová, Klaus Jung, Frank Kramer, Florian Klemm, Annalen Bleckmann and Tim Beißbarth. 2015. Comparative study on gene set and pathway topology-based enrichment methods. BMC Bioinformatics 16, 1, 334. DOI: 10.1186/s12859-015-0751-5 |
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Michaela Bayerlová, Florian Klemm, Frank Kramer, Tobias Pukrop, Tim Beißbarth and Annalen Bleckmann. 2015. Newly constructed network models of different WNT signaling cascades applied to breast cancer expression data. PLoS ONE 10, 12, e0144014. DOI: 10.1371/journal.pone.0144014 |
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Azadeh Azizian, Frank Kramer, Peter Jo, Hendrik A. Wolff, Tim Beißbarth, Robert Skarupke, Markus Bernhardt, Marian Grade, B. Michael Ghadimi and Jochen Gaedcke. 2015. Preoperative prediction of lymph node status by circulating mir‐18b and mir‐20a during chemoradiotherapy in patients with rectal cancer. World Journal of Surgery 39, 9, 2329-2335. DOI: 10.1007/s00268-015-3083-8 |
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2014 |
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Frank Kramer. 2014. Integration of pathway data as prior knowledge into methods for network reconstruction. Georg-August-Universität Göttingen, Göttingen. DOI: 10.53846/goediss-4729 |
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Frank Kramer, Michaela Bayerlová and Tim Beißbarth. 2014. R-based software for the integration of pathway data into bioinformatic algorithms. Biology 3, 1, 85-100. DOI: 10.3390/biology3010085 |
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Melanie Spitzner, Birte Roesler, Christian Bielfeld, Georg Emons, Jochen Gaedcke, Hendrik A. Wolff, Margret Rave‐Fränk, Frank Kramer, Tim Beissbarth, Julia Kitz, Jürgen Wienands, B. Michael Ghadimi, Reinhard Ebner, Thomas Ried and Marian Grade. 2014. STAT3 inhibition sensitizes colorectal cancer to chemoradiotherapy in vitro and in vivo. International Journal of Cancer 134, 4, 997-1007. DOI: 10.1002/ijc.28429 |
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H. Landmann, D. A. Proia, S. He, L. S. Ogawa, Frank Kramer, T. Beißbarth, M. Grade, J. Gaedcke, M. Ghadimi, U. Moll and M. Dobbelstein. 2014. UDP glucuronosyltransferase 1A expression levels determine the response of colorectal cancer cells to the heat shock protein 90 inhibitor ganetespib. Cell Death & Disease 5, 9, e1411. DOI: 10.1038/cddis.2014.378 |
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2013 |
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Predrag Radivojac, Wyatt T. Clark, Tal Ronnen Oron, Alexandra M. Schnoes, Tobias Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur, Gaurav Pandey, Jeffrey M. Yunes, Ameet S. Talwalkar, Susanna Repo, Michael L. Souza, Damiano Piovesan, Rita Casadio, Zheng Wang, Jianlin Cheng, Hai Fang, Julian Gough, Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm, Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones, Bhakti Limaye, Harshal Inamdar, Avik Datta, Sunitha K. Manjari, Rajendra Joshi, Meghana Chitale, Daisuke Kihara, Andreas M. Lisewski, Serkan Erdin, Eric Venner, Olivier Lichtarge, Robert Rentzsch, Haixuan Yang, Alfonso E. Romero, Prajwal Bhat, Alberto Paccanaro, Tobias Hamp, Rebecca Kaßner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos, Jari Björne, Tapio Salakoski, Andrew Wong, Hagit Shatkay, Fanny Gatzmann, Ingolf Sommer, Mark N. Wass, Michael J. E. Sternberg, Nives Škunca, Fran Supek, Matko Bošnjak, Panče Panov, Sašo Džeroski, Tomislav Šmuc, Yiannis A. I. Kourmpetis, Aalt D. J. van Dijk, Cajo J. F. ter Braak, Yuanpeng Zhou, Qingtian Gong, Xinran Dong, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Barbara Di Camillo, Stefano Toppo, Liang Lan, Nemanja Djuric, Yuhong Guo, Slobodan Vucetic, Amos Bairoch, Michal Linial, Patricia C. Babbitt, Steven E. Brenner, Christine Orengo, Burkhard Rost, Sean D. Mooney and Iddo Friedberg. 2013. A large-scale evaluation of computational protein function prediction. Nature Methods 10, 3, 221-227. DOI: 10.1038/nmeth.2340 |
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Amin Moghaddas Gholami, Hannes Hahne, Zhixiang Wu, Florian Auer, Chen Meng, Mathias Wilhelm and Bernhard Kuster. 2013. Global proteome analysis of the NCI-60 cell line panel. Cell Reports 4, 3, 609-620. DOI: 10.1016/j.celrep.2013.07.018 |
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Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos and Burkhard Rost. 2013. Homology-based inference sets the bar high for protein function prediction. BMC Bioinformatics 14, S3, S7. DOI: 10.1186/1471-2105-14-s3-s7 |
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Junius Salendo, Melanie Spitzner, Frank Kramer, Xin Zhang, Peter Jo, Hendrik A. Wolff, Julia Kitz, Silke Kaulfuß, Tim Beißbarth, Matthias Dobbelstein, Michael Ghadimi, Marian Grade and Jochen Gaedcke. 2013. Identification of a microRNA expression signature for chemoradiosensitivity of colorectal cancer cells, involving miRNAs-320a, -224, -132 and let7g. Radiotherapy and Oncology 108, 3, 451-457. DOI: 10.1016/j.radonc.2013.06.032 |
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A. Bleckmann, L. Siam, F. Klemm, E. Rietkötter, Chr. Wegner, Frank Kramer, T. Beissbarth, C. Binder, Chr. Stadelmann and T. Pukrop. 2013. Nuclear LEF1/TCF4 correlate with poor prognosis but not with nuclear β-catenin in cerebral metastasis of lung adenocarcinomas. Clinical & Experimental Metastasis 30, 4, 471-482. DOI: 10.1007/s10585-012-9552-7 |
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Frank Kramer, Michaela Bayerlová, Florian Klemm, Annalen Bleckmann and Tim Beißbarth. 2013. rBiopaxParser — an R package to parse, modify and visualize BioPAX data. Bioinformatics 29, 4, 520-522. DOI: 10.1093/bioinformatics/bts710 |
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2012 |
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Tanja Prenzel, Frank Kramer, Upasana Bedi, Sankari Nagarajan, Tim Beissbarth and Steven A. Johnsen. 2012. Cohesin is required for expression of the estrogen receptor-alpha (ESR1) gene. Epigenetics & Chromatin 5, 1, 13. DOI: 10.1186/1756-8935-5-13 |
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Amanda B. Hummon, Jason J. Pitt, Jordi Camps, Georg Emons, Susan B. Skube, Konrad Huppi, Tamara L. Jones, Tim Beissbarth, Frank Kramer, Marian Grade, Michael J. Difilippantonio, Thomas Ried and Natasha J. Caplen. 2012. Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells. Molecular Cancer 11, 1, 1. DOI: 10.1186/1476-4598-11-1 |
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Oleksandra Karpiuk, Zeynab Najafova, Frank Kramer, Magali Hennion, Christina Galonska, Annekatrin König, Nicolas Snaidero, Tanja Vogel, Andrei Shchebet, Yvonne Begus-Nahrmann, Moustapha Kassem, Mikael Simons, Halyna Shcherbata, Tim Beissbarth and Steven A. Johnsen. 2012. The histone H2B monoubiquitination regulatory pathway is required for differentiation of multipotent stem cells. Molecular Cell 46, 5, 705-713. DOI: 10.1016/j.molcel.2012.05.022 |
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2011 |
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Tanja Prenzel, Yvonne Begus-Nahrmann, Frank Kramer, Magali Hennion, Chieh Hsu, Theresa Gorsler, Corinna Hintermair, Dirk Eick, Elisabeth Kremmer, Mikael Simons, Tim Beissbarth and Steven A. Johnsen. 2011. Estrogen-dependent gene transcription in human breast cancer cells relies upon proteasome-dependent monoubiquitination of histone H2B. Cancer Research 71, 17, 5739-5753. DOI: 10.1158/0008-5472.can-11-1896 |
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Emil Kendziorra, Kerstin Ahlborn, Melanie Spitzner, Margret Rave-Fränk, Georg Emons, Jochen Gaedcke, Frank Kramer, Hendrik A. Wolff, Heinz Becker, Tim Beissbarth, Reinhard Ebner, B.Michael Ghadimi, Tobias Pukrop, Thomas Ried and Marian Grade. 2011. Silencing of the Wnt transcription factor TCF4 sensitizes colorectal cancer cells to (chemo-) radiotherapy. Carcinogenesis 32, 12, 1824-1831. DOI: 10.1093/carcin/bgr222 |
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F. Klemm, A. Bleckmann, L. Siam, H. N. Chuang, E. Rietkötter, D. Behme, M. Schulz, M. Schaffrinski, S. Schindler, L. Trümper, Frank Kramer, T. Beissbarth, C. Stadelmann, C. Binder and T. Pukrop. 2011. β-catenin-independent WNT signaling in basal-like breast cancer and brain metastasis. Carcinogenesis 32, 3, 434-442. DOI: 10.1093/carcin/bgq269 |
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2010 |
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Melanie Spitzner, Georg Emons, Frank Kramer, Jochen Gaedcke, Margret Rave-Fränk, Jens-Gerd Scharf, Peter Burfeind, Heinz Becker, Tim Beissbarth, B. Michael Ghadimi, Thomas Ried and Marian Grade. 2010. A gene expression signature for chemoradiosensitivity of colorectal cancer cells. International Journal of Radiation Oncology*Biology*Physics 78, 4, 1184-1192. DOI: 10.1016/j.ijrobp.2010.06.023 |