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Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data2020 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan G. Gleixner, Manu P. Kumar, Elisabetta Mereu, +6 more
367citations -
The Immunometabolic Atlas: A tool for design and interpretation of metabolomics studies in immunology2022 PLoS ONE article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Pascal Maas, Ilona den Hartog, Alida S. D. Kindt, Sonja Boman, Thomas Hankemeier, J. G. Coen van Hasselt
3citations -
Official Progress Report 2023-2025: NFDI Section (Meta)data, Terminologies, Provenance - Working Group Ontology Harmonization and Mapping2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Semantic Web and Ontologies Open access
Philip Strömert, A. Gerber, Ulrik Stervbo, Heike Fliegl, Damien Goutte-Gattat, Mark Doerr, +6 more
0citations -
Official Progress Report 2023-2025: NFDI Section (Meta)data, Terminologies, Provenance - Working Group Ontology Harmonization and Mapping2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Research Data Management Practices Open access
Philip Strömert, A. Gerber, Ulrik Stervbo, Heike Fliegl, Damien Goutte-Gattat, Mark Doerr, +6 more
0citations -
The Cell Ontology in the age of single-cell omics2026 eScholarship (California Digital Library) article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian D. Aevermann, Alida Avola, +29 more
6citations -
CMEO: a metadata-centric ontology for clinical studies exploration and harmonization assessment2025 BMC Medical Informatics and Decision Making article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Komal Gilani, Marlo Verket, Hans‐Peter Brunner‐La Rocca, Enrico Nicolis, Katharina Marx-Schütt, Visara Urovi, +1 more
1citations -
D5.2.2.1 Integrated NFDI4Energy simulation scenario ontology2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Modeling and Simulation Systems Open access
Jan Sören Schwarz, Laura Fuentes Grau, Nan Liu, Zhiyu Pan, Ramiz Qussous, Philipp Schmurr, +2 more
0citations -
D5.2.2.1 Integrated NFDI4Energy simulation scenario ontology2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Modeling and Simulation Systems Open access
Jan Sören Schwarz, Laura Fuentes Grau, Nan Liu, Zhiyu Pan, Ramiz Qussous, Philipp Schmurr, +2 more
0citations -
FAIR in practice: minimum metadata schema for bioinformatics analytics by machines2026 Journal of Biomedical Semantics article Computer Science Research Data Management Practices Open access
Daphne Wijnbergen, Núria Queralt-Rosiñach, Valérie Barbié, Emma Verkinderen, Nirupama Benis, Annika Jacobsen, +4 more
0citations -
FAIR survey : improving documentation and archiving practices in archaeological field survey through CIDOC CRM13citations
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Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data2022 Journal of Biomedical Semantics article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Rajaram Kaliyaperumal, Mark D. Wilkinson, Pablo Alarcón Moreno, Nirupama Benis, Ronald Cornet, Bruna dos Santos Vieira, +13 more
48citations -
A Platform Ecosystem Providing New Data For The Energy Transition2024 ACM SIGEnergy Energy Informatics Review article Engineering Integrated Energy Systems Optimization Open access
Markus Duchon, Jessy Matar, Mahsa Faraji Shoyari, Alexander Perzylo, Ingmar Kessler, Patrick Buchenberg, +17 more
6citations -
bio.tools: an expanded web service for research software in the life sciences2026 Nucleic Acids Research article Decision Sciences Scientific Computing and Data Management Open access
Ana Mendes, Hans Ienasescu, Christian A T Andersen, Erin Calhoun, Piotr Jaroslaw Chmura, Kathleen Collier, +17 more
0citations -
A Simple Standard for Sharing Ontological Mappings (SSSOM)2022 Database article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew Brush, Tiffany J. Callahan, +35 more
89citations -
Using Ontologies for the Formalization and Recognition of Criticality for Automated Driving2022 IEEE Open Journal of Intelligent Transportation Systems article Computer Science Semantic Web and Ontologies Open access
Lukas Westhofen, Christian Neurohr, Martin Butz, Maike Scholtes, Michael Schuldes
48citations