isiKnock

Signaling pathways are complex and intertwined processes. The perturbation of biological systems can reveal the complicated interplay and dependencies of pathway components.

isiKnock is a software to automatically conduct and visualize in silico knockouts for signaling pathways (Hannig et al. 2019). isiKnock predicts the knockout behavior based on the calculation of signal flows at steady state. For an explanation of the concept of in silico knockouts, we refer to Scheidel et al. 2016 and Amstein et al. 2017.

Hannig et al. (2019) isiKnock: in silico knockouts in signaling pathways, Bioinformatics, 35(5), 892–894

Amstein et al. (2017) Manatee invariants reveal functional pathways in signaling networks. BMC systems biology, 11(1), 72.

Scheidel et al. (2016) In silico knockout studies of xenophagic capturing of Salmonella. PLoS computational biology, 12(12), e1005200.