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

Pharmacokinetics and pharmacodynamics of VEGF-neutralizing antibodies. - Stacey D. Finley; Marianne O. Engel-Stefanini; Princess I. Imoukhuede; Aleksander S. Popel (BMC Syst. Biol., 2011)

Mechanistic modeling quantifies the influence of tumor growth kinetics on the response to anti-angiogenic treatment. - Thomas D. Gaddy; Qianhui Wu; Alyssa D. Arnheim; Stacey D. Finley (PLoS Comput. Biol., 2017)

Mechanistic insight into activation of MAPK signaling by pro-angiogenic factors. - Min Song; Stacey D. Finley (BMC Syst. Biol., 2018)

Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model. - Mahua Roy; Stacey D. Finley (PLoS Comput. Biol., 2019)

Multi-scale modeling of macrophage - T cell interactions within the tumor microenvironment. - Colin G. Cess; Stacey D. Finley (PLoS Comput. Biol., 2020)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

Siamese neural networks for a generalized, quantitative comparison of complex model outputs. - Colin G. Cess; Stacey D. Finley (CoRR, 2022)

Kinetic and data-driven modeling of pancreatic β-cell central carbon metabolism and insulin secretion. - Patrick E. Gelbach; Dongqing Zheng; Scott E. Fraser; Kate L. White; Nicholas A. Graham; Stacey D. Finley (PLoS Comput. Biol., 2022)

Calibrating agent-based models to tumor images using representation learning. - Colin G. Cess; Stacey D. Finley (PLoS Comput. Biol., 2023)

Flux sampling in genome-scale metabolic modeling of microbial communities. - Patrick E. Gelbach; Handan Cetin; Stacey D. Finley (BMC Bioinform., 2024)