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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 -
iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Damien Olivier‐Jimenez, Rico J. E. Derks, Oscar Harari, Carlos C Cruchaga, Muhammad Asri Mohd Ali, Alessandro Ori, +5 more
0citations -
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 Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Decision Sciences Scientific Computing and Data Management Open access
Anna Niehues, Casper de Visser, Fiona A. Hagenbeek, Purva Kulkarni, René Pool, Naama Karu, +7 more
1citations -
Integrative analysis of CAKUT multi-omics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint 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, +7 more
0citations -
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 -
A comprehensive and centralized database for exploring omics data in Autoimmune Diseases2020 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
1citations -
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 -
XomicsToModel: Omics data integration and generation of thermodynamically consistent metabolic models2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
German Preciat, Agnieszka B. Wegrzyn, Ines Thiele, Thomas Hankemeier, Ronan M. T. Fleming
10citations -
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 -
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Aurélien J. F. Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Kristina Bennet Emdal, Dorte B. Bekker‐Jensen, +7 more
16citations -
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 -
Editorial: Multi-omics data integration: key to thoroughly understanding the immune system2023 Frontiers in Cell and Developmental Biology editorial Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Cristina Jiménez, María Hernández‐Sánchez, Jacques J. M. van Dongen, Paula Díez
1citations