General MOFA framework:

@article{Argelaguet2018,
    author = {Argelaguet, R. and Velten, B. and Arnol, D. and Dietrich, S. and Zenz, T. and Marioni, J. C. and Buettner, F. and Huber, W. and Stegle, O.},
    title = {Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets},
    journal = {Mol Syst Biol},
    year = {2018},
    volume = {14},
    number = {6},
    pages = {e8124}
}

Multi-group framework and single cell applications (MOFA+):

@article{Argelaguet2020,
    author = {Argelaguet, R. and Arnol, D. and Bredikhin, D. and Deloro, Y. and Velten, B. and Marioni, J.C. and Stegle, O.},
    title = {MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data},
    journal = {Genome Biology},
    year = {2020},
    volume = {21},
    number = {1},
    pages = {111}
} 

Integration of temporal and spatial omics data (MEFISTO):

@article{Velten2020,
    author = {Velten, B. and Braunger, J.M. and Arnol, D. and Argelaguet, R. and Stegle, O.},
    title = {Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO},
    journal = {bioRxiv},
    year = {2020},
    url = {https://www.biorxiv.org/content/10.1101/2020.11.03.366674v1}
}