References

Case studies: applying network controllability in cancer

Kanhaiya, K., Czeizler, E., Gratie, C., Ion, P.: Controlling directed protein interaction networks in cancer. Technical Report 1155, Turku Centre for Computer Science (2016)

Target structural network controllability method that is the core of this pipeline

Czeizler, E., Gratie, C., Chiu, W.K., Kanhaiya, K., Petre, I.: Target controllability of linear networks. In: Bartocci, E., Lio, P., Paoletti, N. (eds.) Computational Methods in Systems Biology. Lecture Notes in Bioinformatics, vol. 9859, pp. 67--81. Springer, (2016)

The original paper inspiring our research direction: method to identify the set of driver nodes with the time-dependent control that can guide the system's entire dynamics.

Liu, Y.-Y., Slotine, J.-J., Barabasi, A.-L.: Controllability of complex networks. Nature 473(7346), 167--173 (2011). doi:10.1038/nature10011

Anduril pipeline framework: the underlying framework for our backend analysis pipeline

Ovaska, K., Laakso, M., Haapa-Paananen, S., Louhimo, R., Chen, P., Aittoaki, V., Valo, E.: Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome medicine 2(9), 65 (2010). doi:10.1186/gm186

Moksiskaan - the tool to integrate pathway data from different sources into comprehensive biomolecular networks

Laakso, M., Hautaniemi, S.: Integrative platform to translate gene sets to networks. Bioinformatics 26, 1802--1803 (2010). doi:10.1093/bioinformatics/btq277