Publications

Published Research Articles

• Brunner, James D., and Nicholas Chia. "Metabolic model-based ecological modeling for probiotic design." Elife 13 (2024): e83690. Preprint 

• Brunner, James D., Aaron J. Robinson, and Patrick SG Chain. "Combining compositional data sets introduces error in covariance network reconstruction." ISME communications 4.1 (2024): ycae057. Preprint 

• Brunner, James D., Laverne A. Gallegos-Graves, and Marie E. Kroeger. "Inferring microbial interactions with their environment from genomic and metagenomic data." PLOS Computational Biology 19.11 (2023): e1011661. Preprint 

• 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.

• Brunner, James Donald, Aaron Jon Robinson, and Chain Patrick Sam Guy. Is Transkingdom Network Analysis Possible?. No. LA-UR-23-32660. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2023. 

• 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 (Video Available)

• Developing a mathematical structure to reflect microbial community interactions. Banff International Research Station, 2020.

• Robust permanence of polynomial dynamical systems. Banff International Research Station, 2017.

Software Tools Available

• James D. Brunner. MetConSIN: https://github.com/lanl/metconsin 

• James D. Brunner. Synthetic Transkingdom Data: https://github.com/LANL-Bioinformatics/synthetic_transkingdom_data 

• James D. Brunner. FriendlyNets: https://github.com/lanl/friendlyNets 

• 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