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.

Public Talks Available

Software Tools Available

Articles in Preparation

  • 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