282 citations · 368 across the 10 of their papers we have counts for
10 papers
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…
Invariant Risk Minimisation for Cross-Organism Inference: Substituting Mouse Data for Human Data in Human Risk Factor Discovery
Odhran O'Donoghue, Paul Duckworth, Giuseppe Ughi +10
Human medical data can be challenging to obtain due to data privacy concerns, difficulties conducting certain types of experiments, or prohibitive associated costs. In many setting…
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…
Minimizing the number of optimizations for efficient community dynamic flux balance analysis
James D. Brunner, Nicholas Chia
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known tec…
Metabolite mediated modeling of microbial community dynamics captures emergent behavior more effectively than species-species modeling
James D. Brunner, Nicholas Chia
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community compositi…
Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis
Jaeyun Sung, Seunghyeon Kim, Josephine Jill T. Cabatbat +5
A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a…
Prediction and Inference with Missing Data in Patient Alert Systems
Curtis B. Storlie, Terry M. Therneau, Rickey E. Carter +4
We describe the Bedside Patient Rescue (BPR) project, the goal of which is risk prediction of adverse events for non-ICU patients using ~200 variables (vitals, lab results, assessm…
Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology
Nicholas Chia, Nigel Goldenfeld
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introducti…
The dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change
Nicholas Chia, Nigel Goldenfeld
A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transiti…
Lambda-prophage induction modeled as a cooperative failure mode of lytic repression
Nicholas Chia, Ido Golding, Nigel Goldenfeld
We analyze a system-level model for lytic repression of lambda-phage in E. coli using reliability theory, showing that the repressor circuit comprises 4 redundant components whose…