solveME: fast and reliable solution of nonlinear ME models. - Laurence Yang 001; Ding Ma 003; Ali Ebrahim; Colton J. Lloyd; Michael A. Saunders; Bernhard O. Palsson (BMC Bioinform., 2016)

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)

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. - Laurence Yang 001; Ali Ebrahim; Colton J. Lloyd; Michael A. Saunders; Bernhard O. Palsson (BMC Syst. Biol., 2019)

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. - Bin Du; Laurence Yang 001; Colton J. Lloyd; Xin Fang; Bernhard O. Palsson (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)

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. - Joanne K. Liu; Colton J. Lloyd; Mahmoud M. Al-Bassam; Ali Ebrahim; Ji-Nu Kim; Connor A. Olson; Alexander Aksenov; Pieter C. Dorrestein; Karsten Zengler (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)

Expanding the Scope of Genome-scale Models of Metabolism and Gene Expression - Colton J. Lloyd (2019)

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. - Colton J. Lloyd; Jonathan Monk; Laurence Yang 001; Ali Ebrahim; Bernhard O. Palsson (PLoS Comput. Biol., 2021)