GapFind/GapFill (2007): Identifying and filling of genome-scale models

IPRO (2006): Iterative Protein Redesign and Optimization

iPS189 (2009): Genome-scale model for Mycoplasma genitalium

imPS1485 (2007): Isotope mapping model for E. coli (238 reactions and 184 metabolites)

FCF (2004): Flux Coupling Analysis

eShuffle (2001): Prediction of crossover distributions using DNA shuffling