Many-Body Optimization Using an Ab Initio Monte Carlo Method. - Ned C. Haubein; Scott A. McMillan; Linda J. Broadbelt (J. Chem. Inf. Comput. Sci., 2003)

Ab Initio Stochastic Optimization of Conformational and Many-Body Degrees of Freedom. - Scott A. McMillan; Ned C. Haubein; Randall Q. Snurr; Linda J. Broadbelt (J. Chem. Inf. Comput. Sci., 2003)

Encoding of Polycyclic Si-Containing Molecules for Determining Species Uniqueness in Automated Mechanism Generation. - Hsi-Wu Wong; Xuegeng Li; Mark T. Swihart; Linda J. Broadbelt (J. Chem. Inf. Comput. Sci., 2003)

Exploring the diversity of complex metabolic networks. - Vassily Hatzimanikatis; Chunhui Li; Justin A. Ionita; Christopher S. Henry; Matthew D. Jankowski; Linda J. Broadbelt (Bioinform., 2005)

In silico feasibility of novel biodegradation pathways for 1, 2, 4-trichlorobenzene. - Stacey D. Finley; Linda J. Broadbelt; Vassily Hatzimanikatis (BMC Syst. Biol., 2010)

A Computational Approach To Design and Evaluate Enzymatic Reaction Pathways: Application to 1-Butanol Production from Pyruvate. - Di Wu; Qin Wang; Rajeev S. Assary; Linda J. Broadbelt; Goran Krilov (J. Chem. Inf. Model., 2011)

Efficient searching and annotation of metabolic networks using chemical similarity. - Dante A. Pertusi; Andrew E. Stine; Linda J. Broadbelt; Keith E. J. Tyo (Bioinform., 2015)

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. - James G. Jeffryes; Ricardo L. Colastani; Mona Elbadawi-Sidhu; Tobias Kind; Thomas D. Niehaus; Linda J. Broadbelt; Andrew D. Hanson; Oliver Fiehn; Keith E. J. Tyo; Christopher S. Henry (J. Cheminformatics, 2015)

Application and comparison of derivative-free optimization algorithms to control and optimize free radical polymerization simulated using the kinetic Monte Carlo method. - Hanyu Gao; Andreas Wächter; Ivan A. Konstantinov; Steven G. Arturo; Linda J. Broadbelt (Comput. Chem. Eng., 2018)

Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. - Beatriz Peñalver Bernabé; Ines Thiele; Eugene Galdones; Anaar Siletz; Sriram Chandrasekaran; Teresa K. Woodruff; Linda J. Broadbelt; Lonnie D. Shea (BMC Bioinform., 2019)

Bayesian inference of metabolic kinetics from genome-scale multiomics data. - Peter C. St. John; Jonathan Strutz; Linda J. Broadbelt; Keith E. J. Tyo; Yannick J. Bomble (PLoS Comput. Biol., 2019)

MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics. - Jonathan Strutz; Kevin M. Shebek; Linda J. Broadbelt; Keith E. J. Tyo (Bioinform., 2022)

Pickaxe: a Python library for the prediction of novel metabolic reactions. - Kevin M. Shebek; Jonathan Strutz; Linda J. Broadbelt; Keith E. J. Tyo (BMC Bioinform., 2023)