Publications

Published Research Articles

James D. Brunner and Nicholas Chia. Minimizing the number of optimizations for efficient community dynamic flux balance analysis. PLOS Computational Biology, 16(9):1-20, 09 2020. doi: 10.1371/journal. pcbi.1007786. Preprint.
James D. Brunner and Nicholas Chia. Confidence in the dynamic spread of epidemics under biased sampling conditions. PeerJ, 8, 2020. doi: 10.7717/peerj.9758. Preprint.
David F. Anderson, James D. Brunner, Gheorghe Craciun, and Matthew D. Johnston. On classes of reaction networks and their associated polynomial dynamical systems. Journal of Mathematical Chemistry, 58(9):1895-1925, 2020. doi: 10.1007/s10910-020-01148-9. Preprint.
James D. Brunner and Nicholas Chia. Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species-species modelling. Journal of the Royal Society Interface, 16(159):2019 0423, 2019. doi: 10.1098/rsif.2019.0423. Preprint.
James D. Brunner and Gheorghe Craciun. Robust persistence and permanence of polynomial and power law dynamical systems. SIAM Journal on Applied Mathematics, 78:801-825, 2018. doi: 10.1137/17M1133762. Preprint.

James D. Brunner. EpidemicSampling: https://github.com/jdbrunner/EpidemicSampling
James D. Brunner, Jacob Kim, and Kord M. Kober. StochEpiLib: https://github.com/kordk/stoch_epi_lib
James D. Brunner and Nicholas Chia. SurfinFBA: https://github.com/jdbrunner/surfin_fba

James D. Brunner, Jacob Kim, Timothy Downing, Eric Mjolsness, and Kord M. Kober. A dynamical system model for predicting gene expression from the epigenome. 2021. Preprint. [Submitted to PLOS ONE]
James D. Brunner and Nicholas Chia. A topological framework for community metabolic modeling. 2021
James D. Brunner, Edison J. Cevallos, Gina Suh, and Nicholas Chia. Improving phage therapy for the treatment of antibiotic resistant bacterial infections. 2021
James D. Brunner and Nicholas Chia. Probiotic design using metabolic modeling. 2021