Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. - Zachary A. King; Andreas Dräger; Ali Ebrahim; Nikolaus Sonnenschein; Nathan E. Lewis; Bernhard O. Palsson (PLoS Comput. Biol., 2015)

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)

Escher-FBA: a web application for interactive flux balance analysis. - Elliot Rowe; Bernhard O. Palsson; Zachary A. King (BMC Syst. Biol., 2018)

COBRAme: A computational framework for genome-scale models of metabolism and gene expression. - Colton J. Lloyd; Ali Ebrahim; Laurence Yang 001; Zachary A. King; Edward Catoiu; Edward J. O'Brien; Joanne K. Liu; Bernhard O. Palsson (PLoS Comput. Biol., 2018)

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. - Chuankai Cheng; Edward J. O'Brien; Douglas McCloskey; Jose Utrilla; Connor A. Olson; Ryan A. LaCroix; Troy E. Sandberg; Adam M. Feist; Bernhard O. Palsson; Zachary A. King (PLoS Comput. Biol., 2019)

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. - Jean-Christophe Lachance; Colton J. Lloyd; Jonathan M. Monk; Laurence Yang 001; Anand Sastry 002; Yara Seif; Bernhard O. Palsson; Sébastien Rodrigue; Adam M. Feist; Zachary A. King; Pierre-Étienne Jacques (PLoS Comput. Biol., 2019)

The genetic basis for adaptation of model-designed syntrophic co-cultures. - Colton J. Lloyd; Zachary A. King; Troy E. Sandberg; Ying Hefner; Connor A. Olson; Patrick V. Phaneuf; Edward J. O'Brien; Jon G. Sanders; Rodolfo A. Salido; Karenina Sanders; Caitriona Brennan; Gregory Humphrey; et al. (PLoS Comput. Biol., 2019)

Visualizing metabolic network dynamics through time-series metabolomic data. - Lea Buchweitz; James T. Yurkovich; Christoph Blessing; Veronika Kohler; Fabian Schwarzkopf; Zachary A. King; Laurence Yang 001; Freyr Jóhannsson; Ólafur E. Sigurjónsson; Ottar Rolfsson; Julian Heinrich; Andreas Dräger (BMC Bioinform., 2020)

Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data. - Avi Kumar; Jack Mitchener; Zachary A. King; Christian M. Metallo (BMC Bioinform., 2020)

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. - Charles J. Norsigian; Neha Pusarla; John Luke McConn; James T. Yurkovich; Andreas Dräger; Bernhard O. Palsson; Zachary A. King (Nucleic Acids Res., 2020)