Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data. - Tom C. Freeman; Leon Goldovsky; Markus Brosch; Stijn van Dongen; Pierre Mazière; Russell J. Grocock; Shiri Freilich; Janet M. Thornton; Anton J. Enright (PLoS Comput. Biol., 2007)

Stratification of co-evolving genomic groups using ranked phylogenetic profiles. - Shiri Freilich; Leon Goldovsky; Assaf Gottlieb; Eric Blanc; Sophia Tsoka; Christos A. Ouzounis (BMC Bioinform., 2009)

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. - Shiri Freilich; Anat Kreimer; Elhanan Borenstein; Uri Gophna; Roded Sharan; Eytan Ruppin (PLoS Comput. Biol., 2010)

NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species. - Anat Kreimer; Adi Doron-Faigenboim; Elhanan Borenstein; Shiri Freilich (Bioinform., 2012)

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. - Roie Levy; Rogan Carr; Anat Kreimer; Shiri Freilich; Elhanan Borenstein (BMC Bioinform., 2015)