Independence among synthetic genetic devices in the bacterium Escherichia coli extends to the time-domain. - Meghdad Hajimorad; Jay D. Keasling (BioCAS, 2014)

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities. - Amit Ghosh; Jerome P. Nilmeier; Daniel Weaver; Paul D. Adams; Jay D. Keasling; Aindrila Mukhopadhyay; Christopher J. Petzold; Héctor García Martín (PLoS Comput. Biol., 2014)

A Method to Constrain Genome-Scale Models with 13C Labeling Data. - Héctor García Martín; Vinay Satish Kumar; Daniel Weaver; Amit Ghosh; Victor Chubukov; Aindrila Mukhopadhyay; Adam P. Arkin; Jay D. Keasling (PLoS Comput. Biol., 2015)

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. - Garrett W. Birkel; Amit Ghosh; Vinay Satish Kumar; Daniel Weaver; David Ando; Tyler W. H. Backman; Adam P. Arkin; Jay D. Keasling; Héctor García Martín (BMC Bioinform., 2017)

Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. - Garrett W. Birkel; Amit Ghosh; Vinay Satish Kumar; Daniel Weaver; David Ando; Tyler W. H. Backman; Adam P. Arkin; Jay D. Keasling; Héctor García Martín (BMC Bioinform., 2017)

ClusterCAD: a computational platform for type I modular polyketide synthase design. - Clara H. Eng; Tyler W. H. Backman; Constance B. Bailey; Christophe N. Magnan; Héctor García Martín; Leonard Katz; Pierre Baldi; Jay D. Keasling (Nucleic Acids Res., 2018)

ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design. - Xavier B. Tao; Sarah Lafrance; Yifei Xing 001; Alberto A Nava; Héctor García Martín; Jay D. Keasling; Tyler W. H. Backman (Nucleic Acids Res., 2023)

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale. - Tyler W. H. Backman; Christina Schenk; Tijana Radivojevic; David Ando; Jahnavi Singh; Jeffrey J. Czajka; Zak Costello; Jay D. Keasling; Yinjie Tang; Elena V. Akhmatskaya; Héctor García Martín (PLoS Comput. Biol., 2023)

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering. - Søren D. Petersen; Lucas Levassor; Christine M. Pedersen; Jan Madsen; Lea G. Hansen; Jie Zhang; Ahmad K. Haidar; Rasmus John Normand Frandsen; Jay D. Keasling; Tilmann Weber; Nikolaus Sonnenschein; Michael K. Jensen (PLoS Comput. Biol., 2024)

Foldy: An open-source web application for interactive protein structure analysis. - Jacob B. Roberts; Alberto A Nava; Allison N. Pearson; Matthew R. Incha; Luis E. Valencia; Melody Ma; Abhay Rao; Jay D. Keasling (PLoS Comput. Biol., 2024)