References

If you use CCC-RISE in your research, please cite the following papers:

CCC-RISE Paper

Integrative tensor-based analysis of cell-cell communication in single-cell RNA sequencing across experimental conditions. Andrew Ramirez, Aaron Meyer. In preparation, 2025.

RISE Paper

CCC-RISE is built upon the RISE framework for single-cell analysis across conditions.

Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE. Cell Systems, 2025. DOI: 10.1016/j.cels.2025.101294

Tensor Decomposition Methods

CCC-RISE combines CP (CANDECOMP/PARAFAC) decomposition with PARAFAC2 to analyze the four-dimensional structure of cell-cell communication data. PARAFAC2 allows factor matrices in one mode to change across slices while maintaining a constant cross-product constraint.

Roald, M., Schenker, C., Calhoun, V.D., Adali, T., Bro, R., Cohen, J.E., & Acar, E. (2022). An AO-ADMM approach to constraining PARAFAC2 on all modes. SIAM Journal on Mathematics of Data Science, 4(3), 1191-1222. DOI: 10.1137/21M1450033