An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. - Pep Charusanti; Sadhana Chauhan; Kathleen McAteer; Joshua A. Lerman; Daniel R. Hyduke; Vladimir L. Motin; Charles Ansong; Joshua N. Adkins; Bernhard O. Palsson (BMC Syst. Biol., 2011)

COBRApy: COnstraints-Based Reconstruction and Analysis for Python. - Ali Ebrahim; Joshua A. Lerman; Bernhard Ø. Palsson; Daniel R. Hyduke (BMC Syst. Biol., 2013)

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. - Joanne K. Liu; Edward J. O'Brien; Joshua A. Lerman; Karsten Zengler; Bernhard O. Palsson; Adam M. Feist (BMC Syst. Biol., 2014)

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. - Zachary A. King; Justin Lu; Andreas Dräger; Philip Miller; Stephen Federowicz; Joshua A. Lerman; Ali Ebrahim; Bernhard O. Palsson; Nathan E. Lewis (Nucleic Acids Res., 2016)