Deriving enzymatic and taxonomic signatures of metagenomes from short read data. - Uri Weingart; Erez Persi; Uri Gophna; David Horn 001 (BMC Bioinform., 2010)

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)

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. - Raphy Zarecki; Matthew A. Oberhardt; Leah Reshef; Uri Gophna; Eytan Ruppin (PLoS Comput. Biol., 2014)

Detecting Horizontal Gene Transfer between Closely Related Taxa. - Orit Adato; Noga Ninyo; Uri Gophna; Sagi Snir (PLoS Comput. Biol., 2015)

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli. - Matthew A. Oberhardt; Raphy Zarecki; Leah Reshef; Fangfang Xia; Miquel Duran-Frigola; Rachel Schreiber; Christopher S. Henry; Nir Ben-Tal; Daniel J. Dwyer; Uri Gophna; Eytan Ruppin (PLoS Comput. Biol., 2016)