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EMAT Simulated 3D Nanoparticle Structures Dataset2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Advanced Electron Microscopy Techniques and Applications Open access
Alexander S. Skorikov, Wouter Heyvaert, Wiebke Albrecht, Daniël M. Pelt, Sara Bals
0citations -
3D fluorescence microscopy data synthesis for segmentation and benchmarking2021 PLoS ONE article Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access cited by 1 patent
Dennis Eschweiler, Malte Rethwisch, Mareike Jarchow, Simon Koppers, Johannes Stegmaier
23citations -
Mapping gene by early life stress interactions on child subcortical brain structures: A genome‐wide prospective study2022 JCPP Advances article Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Koen Bolhuis, Rosa H. Mulder, Casper L. de Mol, Serena Defina, Varun Warrier, Tonya J.H. White, +3 more
16citations -
Improving the Quality of Unstructured Cancer Data Using Large Language Models: A German Oncological Case Study2024 Studies in health technology and informatics book-chapter Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Yongli Mou, J. Lehmkuhl, Nicolas Sauerbrunn, Anja Köchel, Jens Panse, Daniel Truh, +3 more
3citations -
Polygenic risk scores and brain structures both contribute to externalizing behavior in childhood - A study in the Adolescent Brain and Cognitive Development (ABCD) cohort2023 Neuroscience Applied article Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Jalmar Teeuw, Nina Roth Mota, Marieke Klein, Neeltje E. Blankenstein, Jorim J. Tielbeek, Lucres M. C. Jansen, +2 more
16citations -
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology RNA and protein synthesis mechanisms Open access
Alan Zammit, Leon Helwerda, René C. L. Olsthoorn, Fons J. Verbeek, Alexander P. Gultyaev
10citations -
CDE-Mapper: Using retrieval-augmented language models for linking clinical data elements to controlled vocabularies2025 Computers in Biology and Medicine article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Komal Gilani, Marlo Verket, Michel J. Dumontier, Hans‐Peter Brunner‐La Rocca, Visara Urovi
4citations -
Large-Language Models for data extraction from written kidney biopsy reports2026 medRxiv preprint Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Leon Niggemeier, David Laurin Hölscher, Tim CJ Herkens, Philine Gilles, Peter Böör, Roman David Bülow
1citations -
CDE-Mapper: Using Retrieval-Augmented Language Models for Linking Clinical Data Elements to Controlled Vocabularies2025 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Komal Gilani, Marlo Verket, Michel J. Dumontier, Hans‐Peter Brunner‐La Rocca, Visara Urovi
0citations -
The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine2021 medRxiv preprint Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies Open access
Julius O.B. Jacobsen, Michael Baudis, Gareth S Baynam, J. Beckmann, Sergi Beltrán, Tiffany J. Callahan, +41 more
14citations -
When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases2024 Journal of Chemical Theory and Computation article Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics Open access
Jeroen Methorst, Niek van Hilten, Art Hoti, Kai Steffen Stroh, Herre Jelger Risselada
10citations -
Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology RNA and protein synthesis mechanisms Open access cited by 5 patents
Ilaria Manfredonia, Chandran Nithin, Almudena Ponce-Salvatierra, Pritha Ghosh, Tomasz K. Wirecki, Tycho Marinus, +5 more
22citations -
SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Tamim Abdelaal, Thomas Höllt, Boudewijn P. F. Lelieveldt
2citations -
Validation of a Text-Mining Tool for Extracting Routine Clinical Care Data in Early-Stage Resectable Non–Small Cell Lung Cancer2026 JCO Clinical Cancer Informatics article Biochemistry, Genetics and Molecular Biology Biomedical Text Mining and Ontologies
Hanieh Abedian Kalkhoran, Tobias Martinot, Lydia Henrike Nicole Schonewille, Melek Hüyük, Michiel H.J. Huigen, Henk‐Jan Guchelaar, +3 more
0citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Kirti Biharie, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
6citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
1citations -
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements2020 Nucleic Acids Research article Biochemistry, Genetics and Molecular Biology RNA and protein synthesis mechanisms Open access cited by 4 patents
Ilaria Manfredonia, Chandran Nithin, Almudena Ponce-Salvatierra, Pritha Ghosh, Tomasz K. Wirecki, Tycho Marinus, +5 more
323citations -
Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma2020 Metabolites article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Tom van der Laan, Isabelle Boom, Joshua C. L. Maliepaard, Anne-Charlotte Dubbelman, Amy C. Harms, Thomas Hankemeier
36citations -
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, Roman David Bülow, Christoph Kuppe, David Laurin Hölscher, Mingbo Cheng, +9 more
8citations -
GraphHDBSCAN*: Graph-based Hierarchical Clustering on High Dimensional Single-cell RNA Sequencing Data2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Seyed Ardalan Ghoreishi, Aleksandra Szmigiel, James Shiniti Nagai, Ivan G. Costa, Arthur Zimek, Ricardo J. G. B. Campello
0citations -
A Workflow for Missing Values Imputation of Untargeted Metabolomics Data2020 Metabolites article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Tariq O. Faquih, Maarten van Smeden, Jiao Min Luo, Saskia le Cessie, Gabi Kastenmüller, Jan Krumsiek, +6 more
53citations -
Normalization strategies for lipidome data in cell line panels2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Hanneke Leegwater, Zhengzheng Zhang, Xiaobing Zhang, Thomas Hankemeier, Amy C. Harms, Annelien J.M. Zweemer, +2 more
4citations