Reframing gene essentiality in terms of adaptive flexibility. - Gabriela I. Guzmán; Connor A. Olson; Ying Hefner; Patrick V. Phaneuf; Edward Catoiu; Lais B. Crepaldi; Lucas Goldschmidt Micas; Bernhard O. Palsson; Adam M. Feist (BMC Syst. Biol., 2018)

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. - Patrick V. Phaneuf; Dennis Gosting; Bernhard O. Palsson; Adam M. Feist (Nucleic Acids Res., 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)

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. - Kevin Rychel; Katherine Decker; Anand V. Sastry; Patrick V. Phaneuf; Saugat Poudel; Bernhard O. Palsson (Nucleic Acids Res., 2021)