| Jahr Year | Titel/Autor:in Title/Author | Publikationstyp Publication Type |
|---|---|---|
| 2024 | Dataset of miRNA-disease relations extracted from textual data using transformer-based neural networks Madan, Sumit; Kühnel, Lisa; Fröhlich, Holger; Hofmann-Apitius, Martin; Fluck, Juliane |
Zeitschriftenaufsatz Journal Article |
| 2024 | Transformer models in biomedicine Madan, Sumit; Lentzen, Manuel; Brandt, Johannes; Rueckert, Daniel; Hofmann-Apitius, Martin; Fröhlich, Holger |
Review |
| 2024 | Personalized drug recommendation with pretrained GNNs on a large biomedical knowledge graph Von Arnim, Georg Philip |
Master Thesis |
| 2023 | A natural language processing system for the efficient updating of highly curated pathophysiology mechanism knowledge graphs Babaiha, Negin Sadat; Elsayed, Hassan; Zhang, Bide; Kaladharan, Abish; Sethumadhavan, Priya; Schultz, Bruce; Klein, Jürgen; Freudensprung, Bruno; Lage-Rupprecht, Vanessa; Tom Kodamullil, Alpha; Jacobs, Marc; Geissler, Stefan; Madan, Sumit; Hofmann-Apitius, Martin |
Zeitschriftenaufsatz Journal Article |
| 2023 | MultiGML: Multimodal graph machine learning for prediction of adverse drug events Krix, Sophia; DeLong, Lauren; Madan, Sumit; Domingo Fernández, Daniel; Ahmad, Ashar; Gul, Sheraz; Zaliani, Andrea; Fröhlich, Holger |
Zeitschriftenaufsatz Journal Article |
| 2023 | The Epilepsy Ontology: a community-based ontology tailored for semantic interoperability and text mining Sargsyan, Astghik; Wegner, Philipp; Gebel, Stephan; Kaladharan, Abish; Sethumadhavan, Priya; Lage-Rupprecht, Vanessa; Darms, Johannes; Schultz, Bruce; Klein, Jürgen; Jacobs, Marc; Madan, Sumit; Hofmann-Apitius, Martin; Tom Kodamullil, Alpha |
Zeitschriftenaufsatz Journal Article |
| 2023 | A Transformer-Based Model Trained on Large Scale Claims Data for Prediction of Severe COVID-19 Disease Progression Lentzen, Manuel; Linden, Thomas; Veeranki, Sai Pavan Kumar; Madan, Sumit; Kramer, Diether; Leodolter, Werner; Fröhlich, Holger |
Zeitschriftenaufsatz Journal Article |
| 2022 | Accurate prediction of virus-host protein-protein interactions via a Siamese neural network using deep protein sequence embeddings Madan, Sumit; Demina, Victoria; Stapf, Marcus; Ernst, Oliver; Fröhlich, Holger |
Zeitschriftenaufsatz Journal Article |
| 2022 | Modeling approaches for early warning and monitoring of pandemic situations as well as decision support Botz, Jonas; Wang, Danqi; Lambert, Nicolas; Wagner, Nicolas; Génin, Marie; Thommes, Edward; Madan, Sumit; Coudeville, Laurent; Fröhlich, Holger |
Review |
| 2022 | Deep Learning-based Detection of Psychiatric Attributes from German Mental Health Records Madan, Sumit; Zimmer, Fabian Julius; Balabin, Helena; Schaaf, Sebastian; Fröhlich, Holger; Fluck, Juliane; Neuner, Irene; Mathiak, Klaus; Hofmann-Apitius, Martin; Sarkheil, Pegah |
Zeitschriftenaufsatz Journal Article |
| 2022 | Critical assessment of transformer-based AI models for German clinical notes Lentzen, Manuel; Madan, Sumit; Lage-Rupprecht, Vanessa; Kühnel, Lisa; Fluck, Juliane; Jacobs, Marc; Mittermaier, Mirja; Witzenrath, Martin; Brunecker, Peter; Hofmann-Apitius, Martin; Weber, Joachim; Fröhlich, Holger |
Zeitschriftenaufsatz Journal Article |
| 2021 | COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints Langnickel, L.; Baum, R.; Darms, J.; Madan, S.; Fluck, J. |
Konferenzbeitrag Conference Paper |
| 2021 | Information extraction from german clinical care documents in context of Alzheimer's disease Langnickel, Lisa; Krockauer, Kilian; Uebachs, Mischa; Schaaf, Sebastian; Madan, Sumit; Klockgether, Thomas; Fluck, Juliane |
Zeitschriftenaufsatz Journal Article |
| 2020 | Data-Driven Modeling of Knowledge Assemblies in Understanding Comorbidity Between Type 2 Diabetes Mellitus and Alzheimer's Disease Karki, Reagon; Madan, Sumit; Gadiya, Yojana; Domingo-Fernandez, Daniel; Kodamullil, Alpha Tom; Hofmann-Apitius, Martin |
Zeitschriftenaufsatz Journal Article |
| 2020 | The future of German MeSH: a new semi-automatic translation process and new services for search and annotation Langnickel, Lisa; Baum, Roman; Wollnik-Korn, Gabriele; Fischer-Wagener, Brigitte; Madan, Sumit; Fluck, Juliane |
Zeitschriftenaufsatz Journal Article |
| 2020 | CTO: A community-based clinical trial ontology and its applications in PubChemRDF and SCAIView Lin, A.Y.; Gebel, S.; Li, Q.L.; Madan, S.; Darms, J.; Bolton, E.; Smith, B.; Hofmann-Apitius, M.; He, Y.O.; Kodamullil, A.T. |
Konferenzbeitrag Conference Paper |
| 2020 | The COVID-19 Ontology Sargsyan, Astghik; Kodamullil, Alpha Tom; Baksi, Shounak; Darms, Johannes; Madan, Sumit; Gebel, Stephan; Keminer, Oliver; Jose, Geena Mariya; Balabin, Helena; DeLong, Lauren Nicole; Kohler, Manfred; Jacobs, Marc; Hofmann-Apitius, Martin |
Zeitschriftenaufsatz Journal Article |
| 2020 | SEAweb: The small RNA Expression Atlas web application Rahman, Raza-Ur; Liebhoff, Anna-Maria; Bansal, Vikas; Fiosins, Maksims; Rajput, Ashish; Sattar, Abdul; Magruder, Daniel S.; Madan, Sumit; Sun, Ting; Gautam, Abhivyakti; Heins, Sven; Liwinski, Timur; Bethune, Jörn; Trenkwalder, Claudia; Fluck, Juliane; Mollenhauer, Brit; Bonn, Stefan |
Zeitschriftenaufsatz Journal Article |
| 2020 | Systems Toxicology Approach for Testing Chemical Cardiotoxicity in Larval Zebrafish Li, Roman; Zupanic, Anze; Talikka, Marja; Belcastro, Vincenzo; Madan, Sumit; Dörpinghaus, Jens; Berg, Colette vom; Szostak, Justyna; Martin, Florian; Peitsch, Manuel C.; Hoeng, Julia |
Zeitschriftenaufsatz Journal Article |
| 2020 | Proposal of an Architecture for Terminology Management in a Research Project Mora, Sara; Madan, Sumit; Gebel, Stephan; Giacomini, Mauro |
Konferenzbeitrag Conference Paper |
| 2019 | The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track Madan, S.; Szostak, J.; Elayavilli, R.K.; Tsai, R.T.H.; Ali, M.; Qian, L.H.; Rastegar-Mojarad, M.; Hoeng, J.; Fluck, J. |
Zeitschriftenaufsatz Journal Article |
| 2018 | SCAIView - A semantic search engine for biomedical research utilizing a microservice architecture Dörpinghaus, J.; Klein, J.; Darms, J.; Madan, S.; Jacobs, M. |
Konferenzbeitrag Conference Paper |
| 2018 | A semantic data integration methodology for translational neurodegenerative disease research Madan, S.; Fiosins, M.; Bonn, S.; Fluck, J. |
Konferenzbeitrag Conference Paper |
| 2017 | Overview of BEL track: Extraction of complex relationships and their conversion to BEL Madan, Sumit; Szostak, Justyna; Dörpinghaus, Jens; Hoeng, Julia; Fluck, Juliane |
Konferenzbeitrag Conference Paper |
| 2017 | Recent improvements of the BEL Information Extraction workFlow (BELIEF) for biomedical text mining and curation Szostak, Justyna; Madan, Sumit; Hayes, William; Doerpinghaus, Jens; Fluck, Juliane; Talikka, Marja; Peitsch, Manuel C.; Hoeng, Julia |
Poster |
| 2017 | Automatic extraction of BEL-statements based on neural networks Ali, Mehdi; Madan, Sumit; Fischer, Asja; Petzka, Henning; Fluck, Juliane |
Konferenzbeitrag Conference Paper |
| 2017 | Of mice and men: Comparative analysis of neuro-inflammatory mechanisms in human and mouse using cause-and-effect models Kodamullil, A.T.; Iyappan, A.; Karki, R.; Madan, S.; Younesi, E.; Hofmann-Apitius, M. |
Zeitschriftenaufsatz Journal Article |
| 2016 | BioCreative V track 4: A shared task for the extraction of causal network information using the Biological Expression Language Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; Lek, Adrian van der; Mevissen, Theo; Fluck, Juliane |
Zeitschriftenaufsatz Journal Article |
| 2016 | Overview of the interactive task in BioCreative V Wang, Q.; Abdul, S.S.; Almeida, L.; Ananiadou, S.; Balderas-Martínez, Y.I.; Batista-Navarro, R.; Campos, D.; Chilton, L.; Chou, H.-J.; Contreras, G.; Cooper, L.; Dai, H.-J.; Ferrell, B.; Fluck, J.; Gama-Castro, S.; George, N.; Gkoutos, G.; Irin, A.K.; Jensen, L.J.; Jimenez, S.; Jue, T.R.; Keseler, I.; Madan, S.; Matos, S.; McQuilton, P.; Milacic, M.; Mort, M.; Natarajan, J.; Pafilis, E.; Pereira, E.; Rao, S.; Rinaldi, F.; Rothfels, K.; Salgado, D.; Silva, R.M.; Singh, O.; Stefancsik, R.; Su, C.-H.; Subramani, S.; Tadepally, H.D.; Tsaprouni, L.; Vasilevsky, N.; Wang, X.; Chatr-Aryamontri, A.; Laulederkind, S.J.F.; Matis-Mitchell, S.; McEntyre, J.; Orchard, S.; Pundir, S.; Rodriguez-Esteban, R.; Auken, K. van; Lu, Z.; Schaeffer, M.; Wu, C.H.; Hirschman, L.; Arighi, C.N. |
Zeitschriftenaufsatz Journal Article |
| 2016 | Integration of UIMA text mining components into an event-based asynchronous microservice architecture Hodapp, Sven; Madan, Sumit; Fluck, Juliane; Zimmermann, Marc |
Konferenzbeitrag Conference Paper |
| 2016 | The BEL information extraction workflow (BELIEF): Evaluation in the BioCreative V BEL and IAT track Madan, Sumit; Hodapp, Sven; Senger, Philipp; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Peitsch, Manuel; Fluck, Juliane |
Zeitschriftenaufsatz Journal Article |
| 2016 | Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL) Fluck, Juliane; Madan, Sumit; Ansari, Sam; Kodamullil, Alpha T.; Karki, Reagon; Rastegar-Mojarad, Majid; Catelett, Natalie L.; Hayes, William; Szostak, Justyna; Hoeng, Julia; Peitsch, Manuel C. |
Zeitschriftenaufsatz Journal Article |
| 2015 | Construction of biological networks from unstructured information based on a semi-automated curation workflow Szostak, Justyna; Ansari, Sam; Madan, Sumit; Fluck, Juliane; Talikka, Marja; Iskandar, Anita; Leon, Hector de; Hofmann-Apitius, Martin; Peitsch, Manuel C.; Hoeng, Julia |
Zeitschriftenaufsatz Journal Article |
| 2015 | Overview of the interactive task in BioCreative V Wang, Qinghua; Abdul, Shabbir Syed; Almeida, Lara; Ananiadou, Sophia; Balderas-Martínez, Yalbi Itzel; BatistaNavarro, Riza; Campos, David; Chilton, Lucy; Chou, Hui-Jou; Contreras, Gabriela; Cooper, Laurel; Dai, Hong-Jie; Fluck, Juliane; Gama, Socorro; Gkoutos, Georgios; Irin, Afroza Khanam; Jensen, Lars Juhl; Jimenez, Silvia; Jue, Toni Rose; Keseler, Ingrid; Madan, Sumit; Matos, Sérgio; McQuilton, Peter; Mort, Matthew; Natarajan, Jeyakumar; Pafilis, Evangelos; Pereira, Emiliano; Rao, Shruti; Rinaldi, Fabio; Salgado, David; Singh, Onkar; Stefancsik, Raymund; Su, Chu-Hsien; Subramani, Suresh; Tadepally, Hamsa Dhwani; Tsaprouni, Loukia; Vasilevsky, Nicole; Wang, Xiaodong; Chatr-aryamontri, Andrew; Laulederkind, Stan; Matis-Mitchell, Sherri; McEntyre, Johanna; Orchard, Sandra; Pundir, Sangya; Rodriguez-Esteban, Raul; Auken, Kimberly Van; Lu, Zhiyong; Schaeffer, Mary; Hirschman, Lynette; Arighi, Cecilia |
Konferenzbeitrag Conference Paper |
| 2015 | Track 4 overview: Extraction of causal network information in biological expression language (BEL) Fluck, Juliane; Madan, Sumit; Ellendorf, Tilia; Mevissen, Heinz-Theodor; Clematide, Simon; Lek, Adrian van der; Rinaldi, Fabio |
Konferenzbeitrag Conference Paper |
| 2015 | BELIEF dashboard - a web-based curation interface to support generation of BEL networks Madan, Sumit; Hodapp, Sven; Fluck, Juliane |
Konferenzbeitrag Conference Paper |
| 2014 | BELIEF - a semiautomatic workflow for BEL network creation Fluck, Juliane; Madan, Sumit; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Zimmermann, Marc; Hofmann-Apitius, Martin; Peitsch, Manuel C |
Konferenzbeitrag Conference Paper |
| 2013 | BEL networks derived from qualitative translations of BioNLP shared task annotations Fluck, Juliane; Klenner, Alexander; Madan, Sumit; Ansari, Sam; Bobic, Tamara; Hoeng, Julia; Hofman-Apitius, Martin; Peitsch, Manuel |
Konferenzbeitrag Conference Paper |
| 2012 | Online communities support policy-making: The need for data analysis Klinger, R.; Senger, P.; Madan, S.; Jacovi, M. |
Konferenzbeitrag Conference Paper |