Automated inference of Boolean models from molecular interaction maps using CaSQ. - Sara Sadat Aghamiri; Vidisha Singh; Aurélien Naldi; Tomás Helikar; Sylvain Soliman; Anna Niarakis; Jinbo Xu (Bioinform., 2020)

TaBooN Boolean Network Synthesis Based on Tabu Search. - Sara Sadat Aghamiri; Franck Delaplace (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery. - Brandt Bessell; Josh Loecker; Zhongyuan Zhao; Sara Sadat Aghamiri; Sabyasachi Mohanty; Rada Amin; Tomás Helikar; Bhanwar Lal Puniya (Briefings Bioinform., 2023)