Bibliography

ABGD13

Mochizuki A., Fiedler B., Kurosawa G., and Saito D. Dynamics and control at feedback vertex sets. ii: a faithful monitor to determine the diversity of molecular activities in regulatory networks. Journal of Theoretical Biology, 335:130–146, Oct 21 2013. doi:10.1016/j.jtbi.2013.06.009.

AO03

R. Albert and H. G. Othmer. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in drosophila melanogaster. Journal of Theoretical Biology, 223(1):1–18, 2003.

CAES+06

A. Chaos, M. Aldana, C. Espinosa-Soto, B. G. P. de Leon, A. G. Arroyo, and E. R. Alvarez-Buylla. From genes to flower patterns and evolution: dynamic models of gene regulatory networks. Journal of Plant Growth Regulation, 25(4):278–289, 2006.

CGWR18

Rion Brattig Correia, Alexander J. Gates, Xuan Wang, and Luis M. Rocha. Cana: a python package for quantifying control and canalization in boolean networks. Frontiers in Physiology, 9:1046, 8 2018. URL: http://www.informatics.indiana.edu/rocha/publications/FSB18.php, doi:10.3389/fphys.2018.01046.

DT11

E. Dubrova and M. Teslenko. A sat-based algorithm for finding attractors in synchronous boolean networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(5):1393–1399, 2011.

GMMPR16

A. Gates, S. Manicka, M. Marques-Pita, and L.M. Rocha. The effective structure of complex networks drives dynamics, criticality and control. In Complex Networks 2016: The 5th International Workshop on Complex Networks & Their Applications, 107–109. Milan, Nov. 30 - Dec. 02 2016.

GRBCR21

Alexander J. Gates, Xuan Wang Rion Brattig Correia, and Luis M. Rocha. The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling. Proceedings of the National Academy of Sciences (PNAS), 2021. doi:10.1073/pnas.2022598118.

GR14

Alexander J. Gates and Luis M. Rocha. Structure and dynamics affect the controllability of complex systems: a preliminary study. In Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems, 429–430. MIT Press., 2014.

GR16

Alexander J. Gates and Luis M. Rocha. Control of complex networks requires both structure and dynamics. Scientific Reports, 2016. URL: http://www.informatics.indiana.edu/rocha/publications/NSR16.php, doi:10.1038/srep24456.

HKM+12

Tomáš Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu, and Jim A Rogers. The cell collective: toward an open and collaborative approach to systems biology. BMC Systems Biology, 2012. doi:10.1186/1752-0509-6-96.

KKL17

Claus Kadelka, Jack Kuipers, and Reinhard Laubenbacher. The influence of canalization on the robustness of boolean networks. Physica D: Nonlinear Phenomena, 2017.

LLL+04

Fangting Li, Tao Long, Ying Lu, Qi Ouyang, and Chao Tang. The yeast cell-cycle network is robustly designed. PNAS, 101(14):4781–4786, April 6 2004.

MPR13

Manual Marques-Pita and Luis M. Rocha. Canalization and control in automata networks: body segmentation in drosophila melanogaster. PLoS ONE, 8(3):e55946, 2013. URL: http://www.informatics.indiana.edu/rocha/publications/plos2012.html, doi:10.1371/journal.pone.0055946.

MSOI+02

R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon. Network motifs: simple building blocks of complex networks. Science, 298(5594):824–827, Oct 25 2002.

PQR98

Panos M. Pardalos, Tianbing Qian, and Mauricio G.C. Resende. A greedy randomized adaptive search procedure for the feedback vertex set problem. Journal of Combinatorial Optimization, 2(4):339–412, Dec 1998.

Qui55

W V Quine. A Way to Simplify Truth Functions. American Mathematical Monthly, 62:627–631, 1955.

ZSA17

Jorge Gómez Tejeda Zañudo, Maurizio Scaltriti, and Réka Albert. A network modeling approach to elucidate drug resistance mechanisms and predict combinatorial drug treatments in breast cancer. Cancer Convergence, 1(1):5, 2017.

ZSY+08

Ranran Zhang, Mithun Vinod Shah, Jun Yang, Susan B Nyland, Xin Liu, Jong K Yun, Réka Albert, and Thomas P Loughran. Network model of survival signaling in large granular lymphocyte leukemia. Proceedings of the National Academy of Sciences, 105(42):16308–16313, 2008.