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XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models2025 Nature Protocols article Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
German Preciat, Agnieszka B. Wegrzyn, Xi Luo, Ines Thiele, Thomas Hankemeier, Ronan M. T. Fleming
15citations -
Multi-omic data fusion reveals the in vivo enzyme kinetics of Vibrio natriegens at the genome-scale2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
St. Elmo Wilken, Martin Beyß, Miroslav Kratochvíl, Alexa Grebel, Karen Methling, Anja Stefanski, +7 more
0citations -
Multimodal evidence for impaired glymphatic brain clearance as a mediator of “inflammaging” in schizophrenia – integrating insights from in vivo neuroimaging, omics, and post-mortem single nucleus-RNA-Seq data2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Cerebrospinal fluid and hydrocephalus Open access
Xiaolin Tan, Malte Simon, Daniel Rosebrock, Mariia M Firulyova, Doris Gruber-Schoffnegger, Marisa Fuerst, +7 more
0citations -
Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies2023 arXiv (Cornell University) preprint Computer Science Research Data Management Practices Open access
Yu-Ning Huang, Michael I. Love, Cynthia Ronkowski, Dhrithi Deshpande, Lynn M. Schriml, Annie Wong‐Beringer, +9 more
2citations -
Integrating multi-omics technologies to decipher microbiome functions2026 Nature Communications article Biochemistry, Genetics and Molecular Biology Gut microbiota and health Open access
Tim Van Den Bossche, Eunice Lazau, Velma T. E. Aho, J. Alfredo Blakeley‐Ruiz, Maximilian Wolf, Benoit Josef Kunath, +39 more
0citations -
Second funding phase proposal: NFDI4Microbiota – National Research Data Infrastructure for Microbiota Research2026 Research Ideas and Outcomes article Computer Science Research Data Management Practices Open access
Konrad U. Förstner, Sina V. Barysch, Anke Becker, Michael Beckstette, Sebastian Beyvers, Martin Bole, +32 more
0citations -
Semi-automated background removal limits loss of data and normalises the images for downstream analysis of imaging mass cytometry data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Marieke E. Ijsselsteijn, Antonios Somarakis, Boudewijn P. F. Lelieveldt, Thomas Höllt, Noel F.C.C. de Miranda
2citations -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
3citations -
The Cell Ontology in the age of single-cell omics2026 Scientific Data data-paper 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, +28 more
0citations -
pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources2026 Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Yojana Gadiya, Javier Millán Acosta, Ammar Ammar, Alejandro Adriaque Lozano, Delano Wetstede, Dominik Martinát, +4 more
2citations -
scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access cited by 1 patent
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
41citations -
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ping‐Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien‐Yu Chen, +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