27 citations · 76 across the 9 of their papers we have counts for
9 papers
Combining Compositional Data Sets Introduces Error in Covariance Network Reconstruction
James D. Brunner, Aaron J. Robinson, Patrick S. G. Chain
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant ro…
Inferring microbial interactions with their environment from genomic and metagenomic data
James D. Brunner, Laverne A. Gallegos-Graves, Marie E. Kroeger
Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profoun…
Metabolic Model-based Ecological Modeling for Probiotic Design
James D. Brunner, Nicholas Chia
The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-c…
A dynamical system model for predicting gene expression from the epigenome
James Brunner, Jacob Kim, Timothy Downing +2
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA…
Confidence in the dynamic spread of epidemics under biased sampling conditions
James D. Brunner, Nicholas Chia
The interpretation of sampling data plays a crucial role in policy response to the spread of a disease during an epidemic, such as the COVID-19 epidemic of 2020. However, this is a…
On classes of reaction networks and their associated polynomial dynamical systems
David F. Anderson, James D. Brunner, Gheorghe Craciun +1
In the study of reaction networks and the polynomial dynamical systems that they generate, special classes of networks with important properties have been identified. These include…