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iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments2025 Analytical Chemistry article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Damien Olivier‐Jimenez, Rico J. E. Derks, Oscar Harari, Carlos C Cruchaga, Muhammad Ali, Alessandro Ori, +5 more
10citations -
SpatialCOC: an integrative framework for spatial continuous mapping and cross-omics correction in spatial multi-omics data2026 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingxuan Li, Peisen Sun, Yisi Luo, Guancheng Zhou, Xiaofei Yang, Deyu Meng, +1 more
1citations -
A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object2022 Research Ideas and Outcomes article Decision Sciences Scientific Computing and Data Management Open access
Anna Niehues, Casper de Visser, Fiona A. Hagenbeek, Naama Karu, Alida S. D. Kindt, Purva Kulkarni, +5 more
1citations -
Bayesian network imputation methods applied to multi-omics data identify putative causal relationships in a type 2 diabetes dataset containing incomplete data: An IMI DIRECT Study
Richard A. J. Howey, Jonathan Adam, Jerzy Adamski, Natalie N. Atabaki, Søren Brunak, Piotr Jaroslaw Chmura, +32 more
1citations -
Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis2022 Environmental Microbiome article Computer Science Research Data Management Practices Open access
Tomislav Cernava, Daria Rybakova, François Buscot, Thomas Clavel, Alice Carolyn McHardy, Fernando Meyer, +45 more
59citations -
A comprehensive database for integrated analysis of omics data in autoimmune diseases2021 BMC Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Jordi Martorell‐Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro Dominguez, Juan Antonio Villatoro-García, Guillermo Barturen, +10 more
51citations -
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data2024 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Arno van Hilten, Jeroen van Rooij, Bastiaan T. Heijmans, Peter A.C. ’t Hoen, Joyce B. J. van Meurs, Rick Jansen, +46 more
22citations -
Integrative multi‐omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention‐Deficit /Hyperactivity Disorder2023 American Journal of Medical Genetics Part B Neuropsychiatric Genetics article Medicine Attention Deficit Hyperactivity Disorder Open access
Nikki Hubers, Fiona A. Hagenbeek, René Pool, Sébastien Dejean, Amy C. Harms, Peter J. Roetman, +8 more
23citations -
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses2021 Molecular Systems Biology article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Aurélien J. F. Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gábor, Kristina Bennet Emdal, +12 more
156citations -
Visual cohort comparison for spatial single-cell omics-data2020 IEEE Transactions on Visualization and Computer Graphics article Computer Science Data Visualization and Analytics Open access
Antonios Somarakis, Marieke E. Ijsselsteijn, Sietse J. Luk, Boyd Kenkhuis, Noel F.C.C. de Miranda, Boudewijn P. F. Lelieveldt, +1 more
20citations -
tRigon: an R package and Shiny App for integrative (path-)omics data analysis2024 BMC Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
David Laurin Hölscher, Michaël Goedertier, Barbara M. Klinkhammer, Patrick Droste, Ivan G. Costa, Peter Boor, +1 more
7citations -
Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT2024 Scientific Reports article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Jumamurat R. Bayjanov, Cenna Doornbos, Ozan Özışık, Woosub Shin, Núria Queralt-Rosiñach, Daphne Wijnbergen, +9 more
2citations -
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 -
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 -
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