redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. - Meriç Ataman; Daniel F. Hernandez Gardiol; Georgios Fengos; Vassily Hatzimanikatis (PLoS Comput. Biol., 2017)

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. - Meriç Ataman; Vassily Hatzimanikatis (PLoS Comput. Biol., 2017)

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks. - Anush Chiappino-Pepe; Stepan Tymoshenko; Meriç Ataman; Dominique Soldati-Favre; Vassily Hatzimanikatis (PLoS Comput. Biol., 2017)

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis. - Pierre Salvy; Georgios Fengos; Meriç Ataman; Thomas Pathier; Keng C. Soh; Vassily Hatzimanikatis (Bioinform., 2019)

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH). - Benedict Borer; Meriç Ataman; Vassily Hatzimanikatis; Dani Or (PLoS Comput. Biol., 2019)